THAI HUN TAITEIT UT LA IN TUTTA LATOARE
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THAI HUN TAITEIT UT LA IN TUTTA LATOARE US009970056B2 ( 12 ) United States Patent Potashkin et al . ( 10 ) Patent No .: US 9 , 970 , 056 B2 (45) Date of Patent : May 15 , 2018 ( 54 ) METHODS AND KITS FOR DIAGNOSING , PROGNOSING AND MONITORING PARKINSON ' S DISEASE 14 - 384 . ( 71 ) Applicant : Rosalind Franklin University of Medicine and Science , North Chicago , IL ( US ) ( 72 ) Inventors : Judith Ann Potashkin , North Chicago , IL ( US ); Jose Alfredo Santiago , North Chicago , IL ( US ) ( 73 ) Assignee : Rosalind Franklin University of Medicine and Science , North Chicago , IL ( US ) ( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 U . S .C . 154 ( b ) by 94 days . Aviles - Olmos , et al . “ Parkinson 's Disease , Insulin Resistance and Novel Agents of Neuroprotection ” , Brain , 2013 , vol . 136 ( Pt 2 ), pp . 374 - 384 . Bassil , et al , “ Insulin , IGF - 1 and GLP - 1 Signaling in Neurodegenerative Disorders : Targets for Disease Modification ?” , Prog Neurobiol , Jul . 2014 , vol . 118 , pp . 1 - 18 . ( Abstract only ) . Bonnefond , et al . , “ The Emerging Genetics of Type 2 Diabetes ” , Trends Mol Med , Sep . 2010 , vol . 16 (9 ), pp . 407 - 416 . ( Abstract only ) . Cereda , et al ., “ Diabetes and Risk of Parkinson 's Disease : A Systematic Review and Meta - Analysis ” , Diabetes Care , Dec . 2011 , vol . 34 , pp . 2614 - 2623 . Cereda , et al . , “ Diabetes and Risk of Parkinson 's Disease ” , Move ment Disorders , 2013 , vol . 28 , pp . 257 - 261 ( Abstract only ). Cereda , et al ., “ Clinical Features of Parkinson ' s Disease When Onset of Diabetes Came First : A Case - Control Study ” , Neurology , May 8, 2012 , vol . 78 ( 19 ) , pp . 1507 - 1511 , doi : 10 . 1212 / WNL . Ob013e3182553cc9 , Epub Apr . 25 , 2012 . ( Abstract only ). Chen - Plotkin , et al ., “ Plasma Epidermal Growth Factor Levels Predict Cognitive Decline in Parkinson 's Disease " , Ann Neurol , Apr . 2011 , vol . 69 ( 4 ) , pp . 655 - 663 , doi : 10 . 1002 / ana . 22271 , Epub Nov . 29 , 2010 . Deas , et al . , “ PINK1 Deficiency in Beta - Cells Increases Basal Insulin Secretion and Improves Glucose Tolerance in Mice ” , Open Biol , Apr . 7 , 2014 , vol . 4 , p . 140051 , http :// dx . doi . org / 10 . 1098 / rsob . 140051 . DiFonzo , et al ., “ A Frequent LRRK2 Gene Mutation Associated with Autosomal Dominant Parkinson 's Disease ” , Lancet , Jan . 29 , 2005 , vol . 365 ( 9457 ), pp . 412 - 415 . ( Abstract only ). Ding , et al . , “ Association of SNCA with Parkinson : Replication in the Harvard NeuroDiscovery Center Biomarker Study ” , Movement Disorders , 2011 , vol . 26 , pp . 2283 - 2286 . Ding , et al ., “ Unrecognized Vitamin D3 Deficiency is Common in Parkinson 's Disease : Harvard Biomarker Study ” , Neurology , Oct . 22 , 2013 , vol . 81 ( 17 ), pp . 1531 - 1537 . Dunn , et al ., “ Dysregulation of Glucose Metabolism is an Early Event in Sporadic Parkinson 's Disease ” , Neurobiology of Aging , May 2014 , vol . 35 ( 5 ), pp . 1111 - 1115 . Farrer , et al . , “ LRRK2 Mutations in Parkinson 's Disease ” , Neurol ogy , Sep . 13 , 2005 , vol . 65 (5 ) , pp . 738 - 740 . ( Abstract only ). ( Continued ) ( 21 ) Appl . No . : 14 / 870 , 960 ( 22 ) Filed : Sep . 30 , 2015 ( 65 ) Prior Publication Data US 2016 / 0244833 A1 Aug . 25 , 2016 Related U . S . Application Data ( 60 ) Provisional application No . 62 / 120 , 848 , filed on Feb . 25 , 2015 . ( 51 ) Int . Ci . C120 1 / 68 ( 2018 . 01 ) ( 52 ) U . S . CI . CPC . . . C12Q 1/ 6883 ( 2013 . 01 ); C12Q 2600 / 158 ( 2013 . 01 ) ( 58 ) Field of Classification Search None See application file for complete search history . ( 56 ) References Cited U .S . PATENT DOCUMENTS 8 , 772 , 468 B2 7 / 2014 Potashkin 8 , 841 , 436 B29 / 2014 Gorodeski et al . 2005 / 0026191 A1 * 2 / 2005 Carman .. . .. . ... .. .. .. .. CO7K 14 / 47 435 /6 . 16 2011 / 0021600 A1 * 1/ 2011 Yamada . .. . . . . . . .. . A61K 31 / 7088 514 / 44 A OTHER PUBLICATIONS Primary Examiner — James S Ketter ( 74 ) Attorney , Agent , or Firm — McDonnell Boehnen Hulbert & Berghoff LLP ( 57 ) ABSTRACT Network - based meta - analysis of four independent microar ray studies identified the hepatocyte nuclear factor ( HNF4A ), a transcription factor associated with gluconeo genesis and diabetes , as a central regulatory hub gene upregulated in blood of PD patients . In parallel , the poly pyrimidine tract binding protein 1 ( PTBP1 ), involved in the stabilization and mRNA translation of insulin , was identified as the most downregulated gene . Using both markers , PD patients were classified with 90 % sensitivity and 80 % speci ficity . Longitudinal performance analysis demonstrated that relative abundance of HNF4A and PTBP1 mRNAs signifi cantly decreased and increased , respectively , in PD patients during 3 years follow up period . The inverse regulation of HNF4A and PTBP1 provides a molecular rationale for the altered insulin signaling observed in PD patients . The lon gitudinally dynamic biomarkers identified in this study may be useful for monitoring disease - modifying therapies for PD . Adler , et al . , “ Low Clinical Diagnostic Accuracy of Early vs Advanced Parkinson 's Disease : Clinicopathologic Study ” , Neurol ogy , Jul . 29 , 2014 , vol . 83 , pp . 406 - 412 . Alieva , et al ., “ Involvement of Endocytosis and Alternative Splicing in the Formation of the Pathological Process in the Early Stages of Parkinson ' s Disease ” , Biomed Res Int , 2014 , vol . 2014 , Article ID 718732 , doi : 10 . 1155 / 2014 / 718732 , Epub Apr . 3 , 2014 . Aviles - Olmos , et al ., “ Exenatide and the Treatment of Patients with Parkinson 's Disease ” , The Journal of Clinical Investigation , 2013 , vol . 123 (6 ) , pp . 2730 - 2736 . Aviles - Olmos , et al . " Motor and Cognitive Advantages Persist 12 Months After Exenatide Exposure in Parkinson ' s Disease ” , Journal of Parkinson 's Disease , 2014 , vol . 4 , pp . 337 - 344 . 12 Claims , 8 Drawing Sheets
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Transcript of THAI HUN TAITEIT UT LA IN TUTTA LATOARE
THAI HUN TAITEIT UT LA IN TUTTA LATOARE US009970056B2
( 12 ) United States Patent Potashkin et al .
( 10 ) Patent No . : US 9 , 970 , 056 B2 ( 45 ) Date of Patent : May 15 , 2018
( 54 ) METHODS AND KITS FOR DIAGNOSING , PROGNOSING AND MONITORING PARKINSON ' S DISEASE 14 - 384 .
( 71 ) Applicant : Rosalind Franklin University of Medicine and Science , North Chicago , IL ( US )
( 72 ) Inventors : Judith Ann Potashkin , North Chicago , IL ( US ) ; Jose Alfredo Santiago , North Chicago , IL ( US )
( 73 ) Assignee : Rosalind Franklin University of Medicine and Science , North Chicago , IL ( US )
( * ) Notice : Subject to any disclaimer , the term of this patent is extended or adjusted under 35 U . S . C . 154 ( b ) by 94 days .
Aviles - Olmos , et al . “ Parkinson ' s Disease , Insulin Resistance and Novel Agents of Neuroprotection ” , Brain , 2013 , vol . 136 ( Pt 2 ) , pp . 374 - 384 . Bassil , et al , “ Insulin , IGF - 1 and GLP - 1 Signaling in Neurodegenerative Disorders : Targets for Disease Modification ? ” , Prog Neurobiol , Jul . 2014 , vol . 118 , pp . 1 - 18 . ( Abstract only ) . Bonnefond , et al . , “ The Emerging Genetics of Type 2 Diabetes ” , Trends Mol Med , Sep . 2010 , vol . 16 ( 9 ) , pp . 407 - 416 . ( Abstract only ) . Cereda , et al . , “ Diabetes and Risk of Parkinson ' s Disease : A Systematic Review and Meta - Analysis ” , Diabetes Care , Dec . 2011 , vol . 34 , pp . 2614 - 2623 . Cereda , et al . , “ Diabetes and Risk of Parkinson ' s Disease ” , Move ment Disorders , 2013 , vol . 28 , pp . 257 - 261 ( Abstract only ) . Cereda , et al . , “ Clinical Features of Parkinson ' s Disease When Onset of Diabetes Came First : A Case - Control Study ” , Neurology , May 8 , 2012 , vol . 78 ( 19 ) , pp . 1507 - 1511 , doi : 10 . 1212 / WNL . Ob013e3182553cc9 , Epub Apr . 25 , 2012 . ( Abstract only ) . Chen - Plotkin , et al . , “ Plasma Epidermal Growth Factor Levels Predict Cognitive Decline in Parkinson ' s Disease " , Ann Neurol , Apr . 2011 , vol . 69 ( 4 ) , pp . 655 - 663 , doi : 10 . 1002 / ana . 22271 , Epub Nov . 29 , 2010 . Deas , et al . , “ PINK1 Deficiency in Beta - Cells Increases Basal Insulin Secretion and Improves Glucose Tolerance in Mice ” , Open Biol , Apr . 7 , 2014 , vol . 4 , p . 140051 , http : / / dx . doi . org / 10 . 1098 / rsob . 140051 . DiFonzo , et al . , “ A Frequent LRRK2 Gene Mutation Associated with Autosomal Dominant Parkinson ' s Disease ” , Lancet , Jan . 29 , 2005 , vol . 365 ( 9457 ) , pp . 412 - 415 . ( Abstract only ) . Ding , et al . , “ Association of SNCA with Parkinson : Replication in the Harvard NeuroDiscovery Center Biomarker Study ” , Movement Disorders , 2011 , vol . 26 , pp . 2283 - 2286 . Ding , et al . , “ Unrecognized Vitamin D3 Deficiency is Common in Parkinson ' s Disease : Harvard Biomarker Study ” , Neurology , Oct . 22 , 2013 , vol . 81 ( 17 ) , pp . 1531 - 1537 . Dunn , et al . , “ Dysregulation of Glucose Metabolism is an Early Event in Sporadic Parkinson ' s Disease ” , Neurobiology of Aging , May 2014 , vol . 35 ( 5 ) , pp . 1111 - 1115 . Farrer , et al . , “ LRRK2 Mutations in Parkinson ' s Disease ” , Neurol ogy , Sep . 13 , 2005 , vol . 65 ( 5 ) , pp . 738 - 740 . ( Abstract only ) .
( Continued )
( 21 ) Appl . No . : 14 / 870 , 960 ( 22 ) Filed : Sep . 30 , 2015 ( 65 ) Prior Publication Data
US 2016 / 0244833 A1 Aug . 25 , 2016 Related U . S . Application Data
( 60 ) Provisional application No . 62 / 120 , 848 , filed on Feb . 25 , 2015 .
( 51 ) Int . Ci . C120 1 / 68 ( 2018 . 01 )
( 52 ) U . S . CI . CPC . . . C12Q 1 / 6883 ( 2013 . 01 ) ; C12Q 2600 / 158
( 2013 . 01 ) ( 58 ) Field of Classification Search
None See application file for complete search history .
( 56 ) References Cited U . S . PATENT DOCUMENTS
8 , 772 , 468 B2 7 / 2014 Potashkin 8 , 841 , 436 B29 / 2014 Gorodeski et al .
2005 / 0026191 A1 * 2 / 2005 Carman . . . . . . . . . . . . . . . . . CO7K 14 / 47 435 / 6 . 16
2011 / 0021600 A1 * 1 / 2011 Yamada . . . . . . . . . . . . A61K 31 / 7088 514 / 44 A
OTHER PUBLICATIONS
Primary Examiner — James S Ketter ( 74 ) Attorney , Agent , or Firm — McDonnell Boehnen Hulbert & Berghoff LLP
( 57 ) ABSTRACT Network - based meta - analysis of four independent microar ray studies identified the hepatocyte nuclear factor ( HNF4A ) , a transcription factor associated with gluconeo genesis and diabetes , as a central regulatory hub gene upregulated in blood of PD patients . In parallel , the poly pyrimidine tract binding protein 1 ( PTBP1 ) , involved in the stabilization and mRNA translation of insulin , was identified as the most downregulated gene . Using both markers , PD patients were classified with 90 % sensitivity and 80 % speci ficity . Longitudinal performance analysis demonstrated that relative abundance of HNF4A and PTBP1 mRNAs signifi cantly decreased and increased , respectively , in PD patients during 3 years follow up period . The inverse regulation of HNF4A and PTBP1 provides a molecular rationale for the altered insulin signaling observed in PD patients . The lon gitudinally dynamic biomarkers identified in this study may be useful for monitoring disease - modifying therapies for PD .
Adler , et al . , “ Low Clinical Diagnostic Accuracy of Early vs Advanced Parkinson ' s Disease : Clinicopathologic Study ” , Neurol ogy , Jul . 29 , 2014 , vol . 83 , pp . 406 - 412 . Alieva , et al . , “ Involvement of Endocytosis and Alternative Splicing in the Formation of the Pathological Process in the Early Stages of Parkinson ' s Disease ” , Biomed Res Int , 2014 , vol . 2014 , Article ID 718732 , doi : 10 . 1155 / 2014 / 718732 , Epub Apr . 3 , 2014 . Aviles - Olmos , et al . , “ Exenatide and the Treatment of Patients with Parkinson ' s Disease ” , The Journal of Clinical Investigation , 2013 , vol . 123 ( 6 ) , pp . 2730 - 2736 . Aviles - Olmos , et al . " Motor and Cognitive Advantages Persist 12 Months After Exenatide Exposure in Parkinson ' s Disease ” , Journal of Parkinson ' s Disease , 2014 , vol . 4 , pp . 337 - 344 . 12 Claims , 8 Drawing Sheets
US 9 , 970 , 056 B2 Page 2
( 56 ) References Cited
OTHER PUBLICATIONS Foltynie , et al . , “ Exenatide as a Potential Treatment for Patients with Parkinson ' s Disease : First Steps into the Clinic ” , Alzheimer & Dementia , Feb . 2014 , vol . 10 , pp . S38 - 46 , doi : 10 . 1016 / j . jalz . 2013 . 12 . 005 . Geng , et al . , “ Alpha - Synuclein Binds the K ( ATP ) Channel at Insulin - Secretory Granules and Inhibits Secretion ” , Am J Physiol Endocrinol Metab , Feb . 2011 , vol . 300 ( 2 ) , pp . E276 - 286 , doi : 10 . 1152 / ajpendo . 00262 . 2010 , Epub Sep . 21 , 2010 . Gilks , et al . , “ A Common LRRK2 Mutation in Idiopathic Parkin son ' s Disease ” , Lancet , Jan . 18 , 2005 , vol . 365 ( 9457 ) , pp . 415 - 416 . ( Abstract only ) . Han , et al . , “ Diagnosis of Parkinson ' s Disease Based on Disease Specific Autoantibody Profiles in Human Sera ” , PloS One , 2012 , vol . 7 ( 2 ) , Article ID e32383 , pp . 1 - 6 , doi : 10 . 1371 / journal . pone . 0032383 , Epub Feb . 22 , 2012 . Harries , et al . , “ The Diabetic Phenotype in HNF4A Mutation Carriers is Moderated by the Expression of HNF4A Isoforms from the P1 Promoter During Fetal Development ” , Diabetes , Jun . 2008 , vol . 57 ( 6 ) , pp . 1745 - 1752 , doi : 10 . 2337 / db07 - 1742 , Epub Mar . 20 , 2008 . Hegele , et al . , “ Dynamic Protein - Protein Interaction Wiring of the Human Spliceosome " , Mol Cell , Feb . 24 , 2012 , vol . 45 ( 4 ) , pp . 567 - 580 , doi : 10 . 1016 / j . molcel . 2011 . 12 . 034 . Hetz , et al . , “ Targeting the Unfolded Protein Response in Disease ” , Nat Rev Drug Discov , Sep . 2013 , vol . 12 ( 9 ) , pp . 703 - 719 , doi : 10 . 1038 / nrd3976 . ( Abstract only ) . Hu , et al . , “ Type 2 Diabetes and the Risk of Parkinson ' s Disease ” , Diabetes Care , Apr . 2007 , vol . 30 ( 4 ) , pp . 842 - 847 , Epub Jan . 24 , 2007 . Jain , et al , “ Age - and Diet - Dependent Requirement of DJ - 1 for Glucose Homeostasis in Mice with Implications for Human Type 2 Diabetes ” , J Mol Cell Biol , Aug . 2012 , vol . 4 ( 4 ) , pp . 221 - 230 , doi : 10 . 1093 / jmcb / mjs025 , Epub May 19 , 2012 . Knoch , et al , “ CAMP - Dependent Phosphorylation of PTB1 Pro motes the Expression of Insulin Secretory Granule Proteins in Beta Cells ” , Cell Metab , Feb . 2006 , vol . 3 ( 2 ) , pp . 123 - 134 . Konstandi , et al . , “ Role of PPARalpha and HNF4alpha in Stress Mediated Alterations in Lipid Homeostasis ” , Plos One , Aug . 14 , 2013 , vol . 8 ( 8 ) , Article ID e70675 , pp . 1 - 12 , doi : 10 . 1371 / journal . pone . 0070675 , eCollection 2013 . Li , et al , “ GLP - 1 Receptor Stimulation Preserves Primary Cortical and Dopaminergic Neurons in Cellular and Rodent Models of Stroke and Parkinsonism ” , Proc Natl Acad Sci USA , Jan . 27 , 2009 , vol . 106 ( 4 ) , pp . 1285 - 1290 , doi : 10 . 1073 / pnas . 0806720106 , Epub Jan . 21 , 2009 . Lu , et al . , “ Diabetes and Risk of Parkinson ' s Disease : An Updated Meta - Analysis of Case - Control Studies ” , PloS One , 2014 , vol . 9 ( 1 ) , Article ID e85781 , pp . 1 - 12 . Marcil , et al . , “ Modification in Oxidative Stress , Inflammation , and Lipoprotein Assembly in Response to Hepatocyte Nuclear Factor 4alpha Knockdown in Intestinal Epithelial Cells ” , The Journal of Biological Chemistry , 2010 , vol . 285 ( 52 ) , pp . 40448 - 40460 . Mehanna , et al . , “ Unrecognized Vitamin D3 Deficiency is Common in Parkinson ' s Disease : Harvard Biomarker Study ” , Neurology , May 6 , 2014 , vol . 82 ( 18 ) , p . 1666 , Discussion 1666 , doi : 10 . 1212 / 01 . wnl . 0000449750 . 81263 . 7d . Menon , et al . , “ Shared Molecular and Functional Frameworks Among Five Complex Human Disorders : A Comparative Study on Interactomes Linked to Susceptibility Genes ” , PloS One , 2011 , vol . 6 ( 4 ) , Article ID e18660 , pp . 1 - 9 , Epub Apr . 21 , 2011 . Mercado , et al . , “ An ERcentric View of Parkinson ' s Disease ” , Trends Mol Med , Mar . 2013 , vol . 19 ( 3 ) , pp . 165 - 175 , doi : 10 . 1016 / j . molmed . 2012 . 12 . 005 , Epub Jan . 24 , 2013 . ( Abstract only ) . Moher , et al . , " Preferred Reporting Items for Systematic Reviews and Meta - Analysis : the PRISMA Statement ” , PLOS Med , Jul . 21 , 2009 , vol . 6 ( 7 ) , Article ID e1000097 , pp . 1 - 6 , doi : 10 . 1371 / journal . pmed . 1000097 , Epub Jul . 21 , 2009 .
Molochnikov , et al . , “ A Molecular Signature in Blood Identifies Early Parkinson ' s Disease ” , Mol Neurodegener , May 31 , 2012 , vol . 7 , p . 26 , doi : 10 . 1186 / 1750 - 1326 - 7 - 26 . Moroo , et al . , “ Loss of Insulin Receptor Immunoreactivity from the Substantia Nigra Pars Compacta Neurons in Parkinson ' s Disease ” , Acta Neuropathol , 1994 , vol . 87 ( 4 ) , pp . 343 - 348 . ( Abstract only ) . Morris , et , al . , “ Neurodegeneration in an Animal Model of Parkin son ' s Disease is Exacerbated by a High - Fat Diet ” , Am J Physiol Regul Integr Comp Physiol , Oct . 2010 , vol . 299 ( 4 ) , pp . R1082 1090 , doi : 10 . 1152 / ajpregu . 00449 . 2010 , Epub Aug . 11 , 2010 . Morris , et al . , “ Insulin Resistance Impairs Nigrostriatal Dopamine Function ” , Exp Neurol , Sep . 2011 , vol . 231 ( 1 ) , pp . 171 - 180 , doi : 10 . 1016 / j . expneurol . 2011 . 06 . 005 . Mutez , et al . , “ Transcriptional Profile of Parkinson ' s Blood Mononuclear Cells with LRRK2 Mutation ” , Neurobiol Aging , Oct . 2011 , vol . 32 ( 10 ) , pp . 1839 - 1848 , doi : 10 . 1016 / j . neurobiolaging . 2009 . 10 . 016 , Epub Jan . 22 , 2010 . ( Abstract only ) . Nolan , et al . , “ Parkinson ' s Disease in the Nuclear Age of Neuroinflammation ” , Trends in Molecular Medicine , Mar . 2013 , vol . 19 , pp . 187 - 196 , Epub Jan . 11 , 2013 . ( Abstract only ) . Potashkin , et al . , “ Biosignatures for Parkinson ' s Disease and Atypi cal Parkinsonian Disorders Patients ” , PloS One , 2012 , vol . 7 ( 8 ) , Article ID 43595 , pp . 1 - 13 . Przedborski , “ Inflammation and Parkinson ' s Disease Pathogen esis ” , Movement Disorders : Official Journal of the Movement Disorder Society , 2010 , vol . 25 , Suppl 1 , pp . S55 - S57 . Puigserver , et al . , “ Insulin - Regulated Hepatic Gluconeogenesis Through FOXO 1 - PGC - 1alpha Interaction ” , Nature , May 29 , 2003 , vol . 423 ( 6939 ) , pp . 550 - 555 , Epub May 18 , 2003 . ( Abstract only ) . Rajput , et al . , “ Accuracy of Parkinson ' s Disease Diagnosis Unchanged in 2 Decades ” , Neurology , 2014 , vol . 85 ( 5 ) , pp . 386 387 , Epub Jun . 27 , 2014 . ( Abstract only ) . Rhee , et al . , “ Regulation of Hepatic Fasting Response by PPARgamma Coactivator - 1 alpha ( PGC - 1 ) : Requirement for Hepatocyte Nuclear Factor 4alpha in Gluconeogenesis ” , Proc Natl Acad Sci USA , Apr . 1 , 2003 , vol . 100 ( 7 ) , pp . 4012 - 4017 . Rhodes , et al . , “ Meta - Analysis of Microarrays : Interstudy Valida tion of Gene Expression Profiles Reveals Pathway Dysregulation in Prostate Cancer ” , Cancer Res , Aug . 1 , 2002 , vol . 62 ( 15 ) , pp . 4427 - 4433 . Rothman , et al , “ Metabolic Abnormalities and Hypoleptinemia in Alpha - Synuclein A53T Mutant Mice ” , Neurobiol Aging , May 2014 , vol . 35 ( 5 ) , pp . 1153 - 1161 , doi : 10 . 1016 / j . neurobiolaging . 2013 . 10 . 088 . Rotermund , et al . , “ Diet - Induced Obesity Accelerates the Onset of Terminal Phenotypes in Alpha - Synuclein Transgenic Mice ” , J Neurochem , Dec . 2014 , vol . 131 ( 6 ) , pp . 848 - 858 , doi : 10 . 1111 / jnc . 12813 , Epub Aug . 11 , 2014 . ( Abstract only ) . Santiago , et al . , “ Integrative Network Analysis Unveils Convergent Molecular Pathways in Parkinson ' s Disease and Diabetes ” , Plos One , Dec . 2013 , vol . 8 ( 12 ) , Article ID e83940 , pp . 1 - 8 . Santiago , et al . , " A Network Approach to Diagnostic Biomarkers in Progressive Supranuclear Palsy ” , Movement Disorders , 2014 , vol . 29 ( 4 ) , pp . 550 - 555 . Santiago , et al . , “ Shared Dysregulated Pathways Lead to Parkin son ' s Disease and Diabetes ” , Trends in Molecular Medicine , 2013 , vol . 19 ( 3 ) , pp . 176 - 186 . Santiago , et al . , “ System - Based Approaches to Decode the Molecu lar Links in Parkinson ' s Disease and Diabetes ” , Neurobiology of Disease , 2014 , http : / / dx . doi . org / 10 . 1016 / j . nbd . 2014 . 03 . 019 . Santiago , et al . , “ Specific Splice Variants are Associated with Parkinson ' s Disease ” , Movement Disorders , 2013 , vol . 28 ( 12 ) , pp . 1724 - 1727 . Santiago , et al . , “ Network Analysis Identifies SOD2 mRNA as a Potential Biomarker for Parkinson ' s Disease ” , PloS One , Oct . 2014 , vol . 9 ( 10 ) , Article ID e109042 , pp . 1 - 9 . Santiago , et al . , “ Network - Based Metaanalysis Identifies HNF4A and PTBP1 as Longitudinally Dynamic Biomarkers for Parkinson ' s Disease " , PNAS , Feb . 17 , 2015 , vol . 112 ( 7 ) , pp . 2257 - 2262 . Santiago , et al . , “ A Network Approach to Clinical Intervention in Neurodegenerative Diseases ” , Trends Mol Med , Dec . 2014 , vol . 20 ( 12 ) , pp . 694 - 703 , doi : 10 . 1016 / j . molmed . 2014 . 10 . 002 , Epub Oct . 30 , 2014 . ( Abstract only ) .
US 9 , 970 , 056 B2 Page 3
( 56 ) References Cited
OTHER PUBLICATIONS
Scheele , et al . , “ Altered Regulation of the PINK1 Locus : A Link Between Type 2 Diabetes and Neurodegeneration ” , FASEB Journal , 2007 , vol . 21 , pp . 3653 - 3665 . Scherzer , et al . , “ Molecular Markers of Early Parkinson ' s Disease Based on Gene Expression in Blood ” , Proceedings of the National Academy of Sciences of the United States of America , 2007 , vol . 104 ( 3 ) , pp . 955 - 960 . Scherzer , et al . , “ GATA Transcription Factors Directly Regulate the Parkinson ' s Disease - Linked Gene Alpha - Synuclein ” , Proc Natl Acad Sci USA , Aug . 5 , 2008 , vol . 105 ( 31 ) , pp . 10907 - 10912 . Shehadeh , et al . , “ SRRM2 , a Potential Blood Biomarker Revealing High Alternative Splicing in Parkinson ' s Disease ” , PLoS One , Feb . 8 , 2010 , vol . 5 ( 2 ) , Article ID e9104 , pp . 1 - 8 , doi : 10 . 1371 / journal . pone . 0009104 . Soreq , et al . , “ Exon Arrays Reveal Alternative Splicing Aberrations in Parkinson ' s Disease Leukocytes ” , Neurodegener Dis , 2012 , vol . 10 ( 1 - 4 ) , pp . 203 - 206 , doi : 10 . 1159 / 000332598 , Epub Dec . 9 , 2011 . Soreq , et al , “ Small RNA Sequencing - Microarray Analyses in Parkinson ' s Leukocytes Reveal Deep Brain Stimulation - Induced Splicing Changes that Classify Brain Region Transcriptomes ” , Front Mol Neurosci , May 13 , 2013 , vol . 6 , Article ID 10 , pp . 1 - 20 , doi : 10 . 3389 / fnmol . 2013 . 00010 , eCollection 2013 . Soreq , et al , “ Long Non - Coding RNA and Alternative Splicing Modulations in Parkinson ' s Leukocytes Identified by RNA Sequencing ” , PLOS Comput Biol , Mar . 20 , 2014 , vol . 10 ( 3 ) , Article ID e1003517 , pp . 1 - 22 , doi : 10 . 1371 / journal . pcbi . 1003517 , eCollec tion 2014 .
Tseng , et al , “ Comprehensive Literature Review and Statistical Considerations for Microarray Meta - Analysis ” , Nucleic Acids Res , 2012 , vol . 40 ( 9 ) , pp . 3785 - 3799 , doi : 10 . 1093 / nar / gkr1265 , Epub Jan . 19 , 2012 . Valdes , et al . , “ Control of Dopaminergic Neuron Survival by the Unfolded Protein Response Transcription Factor XBP1 ” , Proc Natl Acad Sci USA , May 6 , 2014 , vol . 111 ( 18 ) , pp . 6804 - 6809 . Wang , et al . , “ Metabolic Inflammation Exacerbates Dopaminergic Neuronal Degeneration in Response to Acute MPTP Challenge in Type 2 Diabetes Mice ” Experimental Neurology , 2014 , vol . 251 , pp . 22 - 29 , Epub Nov . 9 , 2013 . ( Abstract only ) . Xia , et al . , “ INMEX — A Web - based Tool for Integrative Meta Analysis of Expression Data ” , Nucleic Acids Res , 2013 , vol . 41 ( Web Server issue ) , pp . W63 - 70 , doi : 10 . 1093 / nar / gkt338 , Epub Jun . 12 , 2013 . Xia , et al . , “ Network Analyst Integrative Approaches for Pro tein — Protein Interaction Network Analysis and Visual Explora tion ” Nucleic Acids Res , Jul . 2014 , vol . 42 ( Web Server issue ) , pp . W167 - 174 , doi : 10 . 1093 / nar / gku443 , Epub May 26 , 2014 . Yin , et al . , “ Hepatic Hepatocyte Nuclear Factor 4alpha is Essential for Maintaining Triglyceride and Cholesterol Homeostasis ” , Arterioscler Throm Vasc Biol , Feb . 2011 , vol . 31 ( 2 ) , pp . 328 - 336 , doi : 10 . 1161 / ATVBAHA . 110 . 217828 . Zheng , et al . , “ PGC - 1alpha , a Potential Therapeutic Target for Early Intervention in Parkinson ' s Disease ” , Sci Transl Med , Oct . 6 , 2010 , vol . 2 ( 52 ) , pp . 52ra73 , doi : 10 . 1126 / scitranslmed . 3001059 . Zoubarev , et al . , “ Gemma : A Resource for the Reuse , Sharing and Meta - Analysis of Expression Profiling Data ” , Bioinformatics , 2012 , vol . 28 ( 17 ) , pp . 2272 - 2273 , doi : 10 . 1093 / bioinformatics / bts430 , Epub Jul . 10 , 2012 .
* cited by examiner
atent May 15 , 2018 Sheet 1 of 8 US 9 , 970 , 056 B2
FIG . 1A Microarrays FIG . 1B WWWW Wate - DE Individual - DE
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Networkina?yst Class XPD HC
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& GSE6613 Biomarker discovery 12 : 35 : 55 : 55 ,
FIG . 1C 0 2 4
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VRTN3
CACNATE CACNA11 SF3A2
CYP 1181 SEMA6B SPATA2L
A SYNGR $ EN2 TPSGI SPEF HNF4A THY
U . S . Patent May 15 , 2018 Sheet 2 of 8 US 9 , 970 , 056 B2
FIG . 2A NOUFB4
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U . S . Patent May 15 , 2018 Sheet 3 of 8 US 9 , 970 , 056 B2
FIG . 3A PROBE Cohort FIG . 3B HBS Cohort
Pm0 . 001 - 0 . 001
Relative abundance HNFAA MANA www . ws
HO HC HC ad FIG . 3C FIG . 3D
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U . S . Patent May 15 , 2018 Sheet 4 of 8 US 9 , 970 , 056 B2
FIG . 4A
porno 0 : 20 : p = 0 . 008
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U . S . Patent May 15 , 2018 Sheet 5 of 8 US 9 , 970 , 056 B2
FIG . 5A FIG . 5B - 0 . 002 OH
Od wat ons * * * * * * * * *
Steinsentir * *
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U . S . Patent May 15 , 2018 Sheet 6 of 8 US 9 , 970 , 056 B2
Figure 6
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U . S . Patent atent May 15 , 2018 Sheet 7 of 8 US 9 , 970 , 056 B2
FIG . 7A upregulated splicing factors
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U . S . Patent May 15 , 2018 Sheet 8 of 8 US 9 , 970 , 056 B2
FIG HNFAA
AUC - 0 . 72
Sensitivity ( % )
op 20 100 40 60 80 100 % - % Specificity
FIG . 8B PTBP1
Sensitivity ( % )
o pag AUC = 0 . 82
20 100 40 60 80 100 % - % Specificity
FIG . 8C 100 %
HNF4A - PTBP1 Sensitivity ( % ) AUC = 0 . 90
20 40 60 80 100 100 % - % Specificity
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METHODS AND KITS FOR DIAGNOSING , neurons to react as they would to dopamine . An antiviral PROGNOSING AND MONITORING drug , amantadine , also appears to reduce symptoms . In May
PARKINSON ' S DISEASE 2006 , the FDA approved rasagiline to be used along with levodopa for patients with advanced PD or as a single - drug
CROSS REFERENCE 5 treatment for early PD . In some cases , surgery may be appropriate if the disease
This application is related to U . S . provisional patent does not respond to drugs . A therapy called deep brain application No . 62 / 120 , 848 , filed Feb . 25 , 2015 , the disclo - stimulation ( DBS ) has now been approved by the U . S . Food sure of which is incorporated by reference herein in its and Drug Administration . In DBS , electrodes are implanted entirety . The sequence listing submitted herewith is incor - 10 into the brain and connected to a small electrical device porated by reference in its entirety . called a pulse generator that can be externally programmed .
DBS can reduce the need for levodopa and related drugs , STATEMENT REGARDING FEDERALLY which in turn decreases the involuntary movements called
SPONSORED RESEARCH dyskinesias that are a common side effect of levodopa . It 15 also helps to alleviate fluctuations of symptoms and to
This invention was made with U . S . government support reduce tremors , slowness of movements , and gait problems . by the US Army Medical Research and Materiel Command DBS requires careful programming of the stimulator device under awards number W81XWH - 09 - 0708 and in order to work correctly . W81XWH13 - 1 - 0025 . There is a need in the art for a better understanding of the
20 underlying disease mechanism and methods to facilitate the BACKGROUND OF THE DISCLOSURE discovery of accurate biomarkers and therapeutic targets for
Parkinson ' s disease . Parkinson ' s disease ( PD ; also known as idiopathic or
primary parkinsonism , hypokinetic rigid syndrome ( HRS ) , SUMMARY OF THE DISCLOSURE or paralysis agitans ) belongs to a group of conditions called 25 motor system disorders , which are the result of the loss of This disclosure demonstrates that network - based meta dopamine - producing brain cells . The four primary symp - analysis of four independent microarray studies provides a toms of PD are tremor , or trembling in hands , arms , legs , useful framework to identify candidate biomarkers , and that jaw , and face ; rigidity , or stiffness of the limbs and trunk ; expression of highly ranked genes identified can be used as bradykinesia , or slowness of movement ; and postural insta - 30 diagnostic and prognostic biomarkers for PD . bility , or impaired balance and coordination . As these symp - In one aspect , the disclosure provides a method for toms become more pronounced , patients may have difficulty diagnosing , prognosing or monitoring Parkinson ' s Disease walking , talking , or completing other simple tasks . PD ( PD ) in a human subject , comprising : ( a ) obtaining a blood usually affects people over the age of 60 . Early symptoms of sample from a human subject suspected of having PD ; ( b ) PD are subtle and occur gradually . In some people the 35 determining the expression level of at least one gene in the disease progresses more quickly than in others . As the blood sample from the human subject suspected of having disease progresses , the shaking , or tremor , which affects the PD , wherein the at least one gene is selected from : HNF4A , majority of people with PD may begin to interfere with daily THY1 , SPEF1 , SF3A2 , SEMA6B , EN2 , RTN3 , BCAM , activities . Other symptoms may include depression and SPATA2L and TPSG1 ; and ( c ) comparing the expression other emotional changes ; difficulty in swallowing , chewing , 40 level of the at least one gene expressed in the blood sample and speaking ; urinary problems or constipation ; skin prob - to the expression level of the at least one gene expressed in lems ; and sleep disruptions . There are currently no blood or a non - PD , healthy control sample , whereby the increased laboratory tests that have been proven to help in diagnosing expression level of the at least one gene expressed in the sporadic PD . Therefore the diagnosis is based on medical blood sample from the human subject suspected of having history and a neurological examination , but the disease can 45 PD as compared to the non - PD sample is indicative of PD , be difficult to diagnose accurately . Doctors may sometimes thereby diagnosing the human subject as having PD . request brain scans or laboratory tests in order to rule out In another aspect , the disclosure provides a method of other diseases . treating a human subject for Parkinson ' s Disease ( PD ) , the
At present , there is no cure for PD , but a variety of method comprising : ( a ) obtaining a diagnosis identifying a medications provide dramatic relief from the symptoms . 50 human subject as having PD , wherein the diagnosis was Usually , affected individuals are given levodopa ( L - DOPA ; obtained by : ( i ) obtaining a blood sample from a human SINEMETTM , PARCOPATM ATAMETTM , STALEVOTM subject suspected of having PD ; ( ii ) determining the expres MADOPARTM , and PROLOPATM ) combined with carbi - sion level of at least one gene selected from : HNF4A , dopa ( LODOSYNTM ) ( products containing a combination of THY1 , SPEF1 , SF3A2 , SEMA6B , EN2 , RTN3 , BCAM , levodopa and carbidopa include DUOPA? and 55 SPATA2L and TPSG1 ; and ( iii ) comparing the expression RYTARY® ) . Carbidopa delays the conversion of levodopa level of the at least one gene expressed in the blood sample into dopamine until it reaches the brain . Nerve cells can use to the expression level of the at least one gene expressed in levodopa to make dopamine and replenish the brain ' s dwin a non - PD , healthy control sample , whereby the increased dling supply . Although levodopa helps at least three - quarters expression level of the at least one gene expressed in the of PD cases , not all symptoms respond equally to the drug . 60 blood sample from the human subject suspected of having Bradykinesia and rigidity typically respond best , while PD as compared to the non - PD sample is indicative of PD , tremor may be only marginally reduced . Problems with thereby diagnosing the human subject as having PD ; and ( b ) balance and other symptoms may not be alleviated at all . administering to the subject a PD treatment regimen . Anticholinergics may help control tremor and rigidity . Dop - In yet another aspect , the disclosure provides a Parkin amine agonists , such as bromocriptine , pergolide , pramipex - 65 son ' s Disease ( PD ) diagnosis , prognosis or monitoring kit , ole , ropinirole , piribedil , cabergoline , apomorphine and lisu - consisting of a set of probes suitable for the detection and ride , mimic the role of dopamine in the brain , causing the quantification of the nucleic acid expression of at least one
US 9 , 970 , 056 B2 gene selected from : HNF4A , THY1 , SPEF1 , SF3A2 , representation of the top 50 differentially expressed genes SEMA6B , EN2 , RTN3 , BCAM , SPATA2L and TPSG1 . across different microarrays identified from the meta - analy
In a second aspect , the disclosure provides a method for sis ( row - wise comparison ) . The heat map was re - scaled to diagnosing , prognosing or monitoring Parkinson ' s Disease prevent domination by study - specific effects . PD denotes ( PD ) in a human subject , comprising : ( a ) obtaining a blood 5 Parkinson ' s disease and HC denotes healthy controls . sample from a human subject suspected of having PD ; ( b ) FIGS . 2A and 2B show the network analysis of differen determining the expression level of at least one gene in the tially expressed genes in blood of PD . FIG . 2A . Zero - order blood sample from the human subject suspected of having interaction network of genes upregulated in blood of PD PD , wherein the at least one gene is selected from : PTBP1 , ( Red ) . FIG . 2B . Zero - order interaction network of genes SLC4A1 , DAZAP2 , EPB42 , HELZ , SELENBP1 , NUDT4 , 10 downregulated in blood of PD ( Green ) . CA1 , AHSP and ALAS2 ; and ( c ) comparing the expression FIGS . 3A , 3B , 3C and 3D show the evaluation of HNF4A level of the at least one gene expressed in the blood sample and PTBP1 mRNAs as biomarkers for PD at baseline . FIG . to the expression level of the at least one gene expressed in 3A . Relative abundance of HNF4A mRNA in blood of PD a non - PD , healthy control sample , whereby the decreased expression level of the at least one gene expressed in the 15 patients ( black circles ) compared to HC ( white circles ) in blood sample from the human subject suspected of having samples from the PROBE cohort . FIG . 3B . Replication of PD as compared to the non - PD sample is indicative of PD , biomarker expression in an independent set of samples from thereby diagnosing the human subject as having PD . patients enrolled in the Harvard Biomarker Study ( HBS )
In another aspect , the disclosure provides a method of study . FIG . 3C . Relative abundance of PTBP1 mRNA in treating a human subject for Parkinson ' s Disease ( PD ) , the 20 blood of PD patients compared to HC in samples from the method comprising : ( a ) obtaining a diagnosis identifying a PROBE cohort . FIG . 3D . Replication of PTBP1 mRNA human subject diagnosed as having PD , wherein the diag - expression in an independent set of samples from patients nosis was obtained by : ( i ) obtaining a blood sample from a enrolled in the HBS study . Relative abundance of each human subject suspected of having PD ; ( ii ) determining the biomarker was calculated using GAPDH as a reference gene expression level of at least one gene in the blood sample 25 and HC as calibrator . A student t - test ( two - tailed ) was used from the human subject suspected of having PD selected to estimate the significance between PD cases and controls . from : PTBP1 , SLC4A1 , DAZAP2 , EPB42 , HELZ , Post - hoc pair - wise comparisons were performed using a SELENBP1 , NUDT4 , CA1 , AHSP and ALAS2 ; and ( iii ) Tukey test of significance . Error bars represent 95 % confi comparing the expression level of the at least one gene dence intervals . expressed in the blood sample to the expression level of the 30 FIGS . 4A and 4B show the biomarker correlation analy at least one gene expressed in a non - PD , healthy control sis . FIG . 4A . Pearson correlation analysis between HNF4A sample , whereby the decreased expression level of the at mRNA and PTBP1 mRNA in blood of PD patients ( black least one gene expressed in the blood sample from the circles ) and HC ( white circles ) in samples from PROBE and human subject suspected of having PD as compared to the HBS . FIG . 4B . Correlation analysis between HNF4A non - PD sample is indicative of PD , thereby diagnosing the 35 mRNA and Hoehn and Yahr scale in PD patients from both human subject as having PD ; and ( b ) administering to the cohorts . Error bars represent 95 % confidence intervals . subject a PD treatment regimen . FIGS . 5A , 5B , 5C and 5D show the longitudinal perfor
In yet another aspect , the disclosure provides a Parkin - mance of HNF4A and PTBP1 mRNAs in the HBS study . son ' s Disease ( PD ) diagnosis , prognosis or monitoring kit , FIG . 5A . Individual trajectories for the relative abundance of consisting of a set of probes suitable for the detection and 40 HNF4A mRNA over time for HC ( blue ) and PD patients quantification of the nucleic acid expression of at least one ( red ) in the HBS study . FIG . 5B . Average rate of HNF4A gene : PTBP1 , SLC4A1 , DAZAP2 , EPB42 , HELZ , mRNA in PD patients compared to HC calculated via linear SELENBP1 , NUDT4 , CA1 , AHSP and ALAS2 . mixed effects regression analysis adjusting for sex , age and
These and other features and advantages of the present BMI . FIG . 5C . Individual trajectories for the relative abun disclosure will be more fully understood from the following 45 dance of PTBP1 mRNA over time for HC and PD patients . detailed description of the invention taken together with the FIG . 5D . Average rate of PTBP1 mRNA expression in PD accompanying claims . It is noted that the scope of the claims patients compared to HC calculated via linear mixed effects is defined by the recitations therein and not by the specific regression analysis . Red and blue lines denote PD and HC , discussion of features and advantages set forth in the present respectively . TO and T2 indicate baseline and 3 years follow description . 50 up period , respectively . Post - hoc pair - wise comparisons
were performed using a Tukey test of significance BRIEF DESCRIPTION OF THE DRAWINGS ( * * p = 0 . 0001 , * p = 0 . 001 ) . Error bars represent standard error .
FIG . 6 shows the network - based meta - analysis of FIGS . 1A , 1B and 1C show the network - based and microarray studies in blood of PD . Network - based meta
transcriptomic meta - analysis . FIG . 1A . Four independent 55 analysis identified HNF4A and GATA1 as the most promi microarray datasets were downloaded from the Gene nent hub genes across the four microarrays datasets . Expression Ommibus ( GEO ) and preprocessed in INMEX FIGS . 7A and 7B show the dysregulated splicing factors where meta - analysis was undertaken using the Fisher ' s in blood of PD . FIG . 7A . Upregulated splicing factors in method . Datasets were subsequently uploaded into Networ - blood of PD identified across the four microarray datasets . kAnalyst to perform network and functional analysis and to 60 FIG . 7B . Downregulated splicing factors in blood of PD identify key regulatory hub genes across the multiple identified across the four microarray datasets . microarray studies . Finally , the most significant genes were FIGS . 8A , 8B and 8C show the ROC analysis of HNF4A evaluated as biomakers for PD in blood samples obtained and PTBP1 mRNAs . FIG . 8A . ROC analysis to evaluate the from two independent cohorts of patients . FIG . 1B . Venn performance of HNF4A mRNA as a diagnostic biomarker in diagram of differentially expressed genes identified from the 65 samples from PROBE and HBS studies . FIG . 8B . ROC meta - analysis ( Meta - DE ) and those from each individual analysis to evaluate the performance of PTBP1 mRNA as a microarray analysis ( Individual - DE ) . FIG . 1C . Heat map diagnostic biomarker in PROBE and HBS . FIG . 8C . ROC
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analysis combining HNF4A and PTBP1 mRNAs as diag diagnostic biomarkers . This is a powerful approach to inte nostic biomarkers in PROBE and HBS . AUC denotes area grate gene expression data and to gain insight into complex under the curve . diseases . The utility of network biology to identify biologi
cally relevant biomarkers for neurodegenerative diseases DETAILED DESCRIPTION OF THE 5 has been demonstrated recently ( Santiago & Potashkin
DISCLOSURE ( 2014 ) A network approach to clinical intervention in neu rodegenerative diseases . Trends Mol Med 20 ( 12 ) : 694 - 703 ;
The present disclosure demonstrates that network - based Santiago & Potashkin ( 2013 ) Integrative network analysis meta - analysis of four independent microarray studies pro - unveils convergent molecular pathways in Parkinson ' s dis vides a useful framework to identify candidate biomarkers , 10 ease and diabetes . PLoS One 8 ( 12 ) : e83940 ; Santiago & and that expression of highly ranked genes identified can be Potashkin ( 2014 ) A network approach to diagnostic bio used as diagnostic and prognostic biomarkers for PD . markers in progressive supranuclear palsy . Mov Disord
The development of therapeutic strategies for Parkinson ' s 29 ( 4 ) : 550 - 555 ) . disease ( PD ) is hampered by the lack of reliable biomarkers Network - based meta - analysis identified HNF4A and to identify patients at early stages of the disease and track the 15 PTBP1 , previously implicated in diabetes , as the most therapeutic effect of potential drugs and neuroprotective significant up and downregulated genes in blood of PD agents . Readily accessible biomarkers capable of providing patients . These results were confirmed in blood samples information about disease status are expected to accelerate from two independent clinical trials . Relative abundance of this progress . Network - based meta - analysis identified prom - HNF4A mRNA correlated with disease severity in PD ising blood biomarkers for recognizing early stage PD 20 patients . Moreover , longitudinal analysis of HNF4A and patients with high diagnostic accuracy . Longitudinal analy - PTBP1 revealed that their relative abundance changed over sis demonstrated that HNF4A and PTBP1 are longitudinally time indicating their potential use to track the clinical course dynamic biomarkers that provide insights into the molecular of PD patients . mechanisms underlying the altered insulin signaling in PD It should be understood that the embodiments described patients and may enable novel therapeutic strategies . Fur - 25 herein , are provided for explanatory purposes , and are not ther , HNF4A was identified as a potential biomarker to intended to be limiting . monitor disease severity . All publications , patents and patent applications cited
Substantial efforts have been devoted to the development herein are hereby expressly incorporated by reference for all of diagnostic strategies for PD . In particular , changes in purposes to the extent they are consistent with this disclo mRNA from cellular whole blood can facilitate the identi - 30 sure . fication of dysregulated processes and diagnostic biomark Methods well known to those skilled in the art can be used ers for PD . Several molecular signatures in blood have been to construct expression vectors and recombinant bacterial identified . For example , 22 unique genes were found differ - cells according to this disclosure . These methods include in entially expressed in blood of PD patients compared to vitro recombinant DNA techniques , synthetic techniques , in healthy controls ( Scherzer et al . , ( 2007 ) Molecular markers 35 vivo recombination techniques , and PCR techniques . See , of early Parkinson ' s disease based on gene expression in for example , techniques as described in Maniatis et al . , blood . Proc Natl Acad Sci U . S . A 104 ( 3 ) : 955 - 960 ) . Likewise , 1989 , MOLECULAR CLONING : A LABORATORY specific splice variants in blood were associated with PD in MANUAL , Cold Spring Harbor Laboratory , New York ; samples obtained from two independent clinical trials ( Pot - Ausubel et al . , 1989 , CURRENT PROTOCOLS IN ashkin et al . , ( 2012 ) Biosignatures for Parkinson ' s disease 40 MOLECULAR BIOLOGY , Greene Publishing Associates and atypical parkinsonian disorders patients . PLoS One and Wiley Interscience , New York , and PCR Protocols : A 7 ( 8 ) : e43595 , and Santiago et al . , ( 2013 ) Specific splice Guide to Methods and Applications ( Innis et al . , 1990 , variants are associated with Parkinson ' s disease . Mov Dis Academic Press , San Diego , Calif . ) . ord 28 ( 12 ) : 1724 - 1727 ) . In addition , altered expression of Before describing the present invention in detail , a num the vitamin D receptor ( VDR ) in blood and reduced plasma 45 ber of terms will be defined . As used herein , the singular levels of 25 - hydroxy vitamin D , have been associated with forms “ a ” , “ an ” , and “ the ” include plural referents unless the PD ( Ding et al . ( 2013 ) Unrecognized vitamin D3 deficiency context clearly dictates otherwise . For example , reference to is common in Parkinson disease : Harvard Biomarker Study . a “ nucleic acid ” means one or more nucleic acids . Neurology 81 ( 17 ) : 1531 - 1537 ) . Furthermore , plasma levels It is noted that terms like " preferably ” , “ commonly ” , and of the epidermal growth factor ( EGF ) have been associated 50 " typically ” are not utilized herein to limit the scope of the with cognitive decline in PD ( Chen - Plotkin et al . ( 2011 ) claimed invention or to imply that certain features are Plasma epidermal growth factor levels predict cognitive critical , essential , or even important to the structure or decline in Parkinson disease . Ann Neurol 69 ( 4 ) : 655 - 663 ) . function of the claimed invention . Rather , these terms are
Environmental stressors and genetic factors are most merely intended to highlight alternative or additional fea likely involved in the pathogenesis of PD . Among the 55 tures that can or cannot be utilized in a particular embodi genetic factors associated with PD , mutations in the gene ment of the present invention . encoding leucine - rich repeat kinase 2 ( LRRK2 ) are the most In one aspect , the disclosure provides a method for common cause of autosomal dominant PD and a consider - diagnosing , prognosing or monitoring Parkinson ' s Disease able risk factor in idiopathic forms of the disease . Given the ( PD ) in a human subject , comprising : ( a ) obtaining a blood complex interaction between environmental and genetic 60 sample from a human subject suspected of having PD ; ( b ) factors in sporadic PD , four independent microarray studies determining the expression level of at least one gene in the were integrated from patients harboring a mutation in the blood sample from the human subject suspected of having LRRK2 gene ( G2019S ; glycine to serine substitution at PD , wherein the at least one gene is selected from : HNF4A , amino acid 2019 ) , sporadic , and untreated PD patients in THY1 , SPEF1 , SF3A2 , SEMA6B , EN2 , RTN3 , BCAM , order to identify a universal signature in blood associated 65 SPATA2L and TPSG1 ; and ( c ) comparing the expression with PD . A transcriptomic and network - based meta - analysis level of the at least one gene expressed in the blood sample was performed to identify key regulators and potential to the expression level of the at least one gene expressed in
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a non - PD , healthy control sample , whereby the increased SLC4A1 , DAZAP2 , EPB42 , HELZ , SELENBP1 , NUDT4 , expression level of the at least one gene expressed in the CA1 , AHSP and ALAS2 ; and ( c ) comparing the expression blood sample from the human subject suspected of having level of the at least one gene expressed in the blood sample PD as compared to the non - PD sample is indicative of PD , to the expression level of the at least one gene expressed in thereby diagnosing the human subject as having PD . 5 a non - PD , healthy control sample , whereby the decreased
In another aspect , the disclosure provides a method of expression level of the at least one gene expressed in the treating a human subject for Parkinson ' s Disease ( PD ) , the blood sample from the human subject suspected of having method comprising : ( a ) obtaining a diagnosis identifying a PD as compared to the non - PD sample is indicative of PD , human subject as having PD , wherein the diagnosis was thereby diagnosing the human subject as having PD . obtained by : ( i ) obtaining a blood sample from a human 10 In another aspect , the disclosure provides a method of subject suspected of having PD ; ( ii ) determining the expres sion level of at least one gene selected from : HNF4A , treating a human subject for Parkinson ' s Disease ( PD ) , the THY1 , SPEF1 , SF3A2 , SEMA6B , EN2 , RTN3 , BCAM , method comprising : ( a ) obtaining a diagnosis identifying a SPATA2L and TPSG1 ; and ( iii ) comparing the expression human subject diagnosed as having PD , wherein the diag level of the at least one gene expressed in the blood sample 15 sed in the blood sample 15 nosis was obtained by : ( i ) obtaining a blood sample from a to the expression level of the at least one gene expressed in human subject suspected of having PD ; ( ii ) determining the a non - PD , healthy control sample , whereby the increased expression level of at least one gene in the blood sample expression level of the at least one gene expressed in the from the human subject suspected of having PD selected blood sample from the human subject suspected of having from : PTBP1 , SLC4A1 , DAZAP2 , EPB42 , HELZ , PD as compared to the non - PD sample is indicative of PD , 20 SELENBP1 , NUDT4 , CA1 , AHSP and ALAS2 ; and ( iii ) thereby diagnosing the human subject as having PD ; and ( b ) comparing the expression level of the at least one gene administering to the subject a PD treatment regimen . expressed in the blood sample to the expression level of the
In an embodiment , the methods disclosed herein typically at least one gene expressed in a non - PD , healthy control involve determining expression levels of at least one gene in sample , whereby the decreased expression level of the at a biological sample obtained from a human subject sus - 25 least one gene expressed in the blood sample from the pected of having PD . The methods may involve determining human subject suspected of having PD as compared to the expression levels of at least 2 , at least 3 , at least 4 , at least non - PD sample is indicative of PD , thereby diagnosing the 5 , at least 6 , at least 7 , at least 8 , at least 9 , at least 10 , at least human subject as having PD ; and ( b ) administering to the 20 , at least 30 , at least 40 , at least 50 , at least 60 , at least 70 , subject a PD treatment regimen . at least 80 , at least 100 , at least 200 or more genes in a 30 In an embodiment , the methods disclosed herein typically biological sample obtained from an individual , wherein the involve determining expression levels of at least one gene in genes are selected from : HNF4A , THY1 , SPEF1 , SF3A2 , a biological sample obtained from a human subject sus SEMA6B , EN2 , RTN3 , BCAM , SPATA2L and TPSG1 ; or pected of having PD . The methods may involve determining the genes listed in Table 2 or Table 3 . expression levels of at least 2 , at least 3 , at least 4 , at least
In one embodiment , the at least one gene is HNF4A 35 5 , at least 6 , at least 7 , at least 8 , at least 9 , at least 10 , at least hepatocyte nuclear factor 4 , alpha ( official symbol : HNF4A ; 20 , at least 30 , at least 40 , at least 50 , at least 60 , at least 70 , and official full name : hepatocyte nuclear factor 4 , alpha ; at least 80 , at least 100 , at least 200 or more genes in a provided by HGNC ) . HNF4A is also known as : TCF ; HNF4 ; biological sample obtained from an individual , wherein the MODY ; FRTS4 ; MODY1 ; NR2A1 ; TCF14 ; HNF4a7 ; genes are selected from : PTBP1 , SLC4A1 , DAZAP2 , HNF4a8 ; HNF4a9 ; NR2A21 ; HNF4alpha . Nucleic acid 40 EPB42 , HELZ , SELENBP1 , NUDT4 , CA1 , AHSP and accession number : > gi / 385298689 | ref | NM _ 000457 . 41 ALAS2 ; or the genes listed in Table 2 or Table 3 . Homo sapiens hepatocyte nuclear factor 4 , alpha ( HNF4A ) , In one embodiment , the at least one gene is PTBP1 transcript variant 2 , mRNA ( SEQ ID NO : 07 ) . Protein polypyrimidine tract binding protein 1 ( official symbol : accession number : > gi / 31077205 | ref | NP _ 000448 . 3 | Homo PTBP1 ; official full name : polypyrimidine tract binding sapiens hepatocyte nuclear factor 4 - alpha isoform 45 protein 1 ; provided by HGNC ) . PTBP1 is also known as : HNF4alpha2 ( SEQ ID NO : 08 ) . PTB ; PTB2 ; PTB3 ; PTB4 ; PPTB ; HNRPI ; PTB - 1 ; PTB - T ;
In another embodiment , the expression level is deter - HNRNPI ; HNRNP - I ) . Nucleic acid accession number : mined by detecting messenger RNA of the at least one gene . > gi 209870087 | ref | NM _ 002819 . 41 Homo sapiens polypy If mRNA is determined , then the method may further rimidine tract binding protein 1 ( PTBP1 ) , transcript variant comprise reverse transcription of the messenger RNA prior 50 1 , mRNA ( SEQ ID NO : 09 ) . Protein accession number : to detecting . In an embodiment , determining the expression > gi | 4506243 | ref / NP _ 002810 . 1 | Homo sapiens polypyrimi level of the at least one gene is by measuring a level of dine tract - binding protein 1 isoform a ( SEQ ID NO : 10 ) . fluorescence by a sequence detection system following a In another embodiment , the expression level is deter quantitative , real - time polymerase chain reaction ( PCR ) mined by detecting messenger RNA of the at least one gene . assay . 55 If mRNA is determined , then the method may further
In yet another embodiment , an increased HNF4A expres - comprise reverse transcription of the messenger RNA prior sion level of the human subject at a later time point com to detecting . In an embodiment , determining the expression pared to the HNF4A expression level at an initial time point level of the at least one gene is by measuring a level of or expression levels the same as a healthy control indicates fluorescence by a sequence detection system following a an improved or steady prognosis of PD in the subject . 60 quantitative , real - time polymerase chain reaction ( PCR )
In a second aspect , the disclosure provides a method for assay . diagnosing , prognosing or monitoring Parkinson ' s Disease In yet another embodiment , an increased PTBP1 expres ( PD ) in a human subject , comprising : ( a ) obtaining a blood sion level of the human subject at a later time point com sample from a human subject suspected of having PD ; ( b ) pared to the PTBP1 expression level at an initial time point determining the expression level of at least one gene in the 65 indicates a worse prognosis of PD in the subject . Further blood sample from the human subject suspected of having more , a decreased PTBP1 expression level of the human PD , wherein the at least one gene is selected from : PTBP1 , subject after treatment compared to the PTBP1 expression
level
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level prior to treatment or PTB1 expression levels similar to example , other target amplification methods ( e . g . , TMA , the healthy control sample indicates a better prognosis of PD SDA , NASBA ) , or signal amplification methods ( e . g . , in the subject . bDNA ) . Alternatively , northern hybridization analysis using
As used herein , a “ sample ” is a biological sample isolated probes which specifically recognize one or more of the from a subject and can include , but is not limited to , whole 5 sequences or each gene can be used to determine gene blood , serum , plasma , blood cells , endothelial cells , tissue expression . biopsies , lymphatic fluid , ascites fluid , interstitial fluid , bone The difference in the level of biomarker between normal marrow , cerebrospinal fluid ( CSF ) , saliva , mucous , sputum , and abnormal is preferably statistically significant and may sweat , urine , or any other secretion , excretion , or other be an increase in biomarker expression level or a decrease in bodily fluids . A " blood sample ” refers to whole blood or any 10 biomarker expression level , and without any limitation of fraction thereof , including blood cells , serum and plasma . the method , achieving statistical significance , and thus the As used herein , the terms “ diagnosis ” , “ diagnostic ” , preferred analytical and clinical accuracy , generally but not
“ diagnosing ” , refer to an identification of PD or to a pre always requires that combinations of several biomarkers be disposition of developing PD , based on a detection of at least used together in panels and combined with mathematical one gene . The terms " prognosis ” , " prognostic ” , “ prognos - 15 algorithms in order to achieve a statistically significant ing ” , refer to the ability of predicting , forecasting or corre - biomarker index . lating a given detection or measurement with a future As used herein , the term " primer set " or " primers ” refers outcome of PD in the patient ( e . g . , severity , likelihood of to a pair of PCR primers that include a forward primer and successfully treating , or survival ) . The disclosure also reverse primer used in a PCR reaction and allows the relates to monitoring the influence of agents , treatments or 20 generation of an amplicon . Numerous primers used in the therapies for PD ( e . g . , drugs , compounds ) . As used herein , context of the present disclosure can be readily determined " monitoring ” refers to determining the regression , progres - by a person of ordinary skill in the art to which the present sion , course and / or onset of , and / or prognoses of PD before invention pertains . Non - limiting examples of primers are any treatment or during treatment in order to assess the PD shown in SEQ ID NO : 3 - 6 . A person skilled in the art can patient ' s improvement or lack thereof over time . 25 design numerous other primers based on the teachings
As used herein , the term " control sample ” or “ healthy herein and the common general knowledge . As used herein , control ” refers to a sample from a subject that does not have the term “ probes ” refers to a nucleic acid molecule which PD or subject that does not have PD . In a particular typically ranges in size from about 8 nucleotides to several embodiment , the control sample or healthy control does not hundred nucleotides in length . Such a molecule is typically have PD or is indicative of the absence of PD . Control 30 used to identify a target nucleic acid sequence in a sample samples can be obtained from patients / individuals not by hybridizing to such target nucleic acid sequence under afflicted with PD . Other types of control samples may also stringent hybridization conditions . Generally , an oligonucle be used . In a related facet , a control reaction may be otide useful as a probe or primer that selectively hybridizes designed to control the method itself ( e . g . , cell extraction , to a selected nucleotide sequence is at least about 15 the capture , the amplification reaction or detection method , 35 nucleotides in length , usually at least about 18 nucleotides , number of cells present in the sample , a combination thereof and particularly about 21 nucleotides in length or more in or any step which could be monitored to positively validate length . Primer and probe design software programs are also that the absence of a signal ( e . g . , the expression level of a commercially available , including without limitation , gene ) is not the result of a defect in one or more of the steps ) . Primer Detective ( ClonTech , Palo Alto , Calif . ) , Lasergene , Once a cut - off value is determined , a control sample giving 40 ( DNASTAR , Inc . , Madison , Wis . ) ; and Oligo software ( Na a signal characteristic of the predetermined cut - off value can t ional Biosciences , Inc . , Plymouth , Minn . ) and iOligo ( Cae also be designed and used in the methods of the present sar Software , Portsmouth , N . H . ) . invention . Diagnosis / prognosis tests are commonly charac - As used herein , a " sequence detection system ” is any terized by the following 4 performance indicators : sensitiv computational method in the art that can be used to analyze ity ( Se ) , specificity ( Sp ) , positive predictive value ( PPV ) , 45 the results of a PCR reaction . One example is the Applied and negative predictive value ( NPV ) . Biosystems HT7900 fast Real - Time PCR system . In certain As used herein , the terms “ nucleic acid ” , “ polynucle embodiments , gene expression can be analyzed using , e . g . ,
otide ” , “ nucleotide ” , and “ oligonucleotide ” can be used direct DNA expression in microarray , Sanger sequencing interchangeably to refer to single stranded or double analysis , Northern blot , the Nanostring® technology , serial stranded , nucleic acid comprising DNA , RNA , derivatives 50 analysis of gene expression ( SAGE ) , RNA - seq , tissue thereof , or combinations thereof . microarray , or protein expression with immunohistochem
Expression of the genes disclosed herein can be measured istry or western blot technique . at the RNA level using any method known in the art . For I n an embodiment , the methods disclosed here further example , expression can be measured using Real - Time PCR comprise determining a treatment regimen for the human assays ( RT - PCR ) , e . g . , using primers specific for the differ - 55 subject . The methods could be used to generate a prescrip entially expressed sequences . As used herein , the term tion treatment to treat , delay development or prevent pro “ real - time PCR ” ( also called quantitative real - time poly - gression of PD in an individual identified by the methods merase chain reaction ) refers to a method for the detection disclose herein as having PD . Furthermore , the method and quantitation of an amplified PCR product based on disclosed herein to adapt the correct or most appropriate incorporation of a fluorescent reporter dye ; the fluorescent 60 treatment regimen and / or monitor the patient response to signal increases in direct proportion to the amount of PCR therapy . product produced and is monitored at each cycle , ‘ in real - In yet another aspect , the disclosure provides a Parkin time ' , such that the time point at which the first significant son ' s Disease ( PD ) diagnosis , prognosis or monitoring kit , increase in the amount of PCR product correlates with the consisting of a set of probes suitable for the detection and initial amount of target template . In one embodiment , real - 65 quantification of the nucleic acid expression of at least one time PCR can be preceded by reverse - transcription of the gene selected from : HNF4A , THY1 , SPEF1 , SF3A2 , messenger RNA . RNA can also be quantified using , for SEMA6B , EN2 , RTN3 , BCAM , SPATA2L and TPSG1 . In
US 9 , 970 , 056 B2 12
another aspect , the disclosure provides a Parkinson ' s Dis - probes to a common Entrez ID , all datasets were prepro ease ( PD ) diagnosis , prognosis or monitoring kit , consisting cessed using the log , - transformation and quantile normal of a set of probes suitable for the detection and quantification ization . Each individual dataset was visualized in box - plots of the nucleic acid expression of at least one gene : PTBP1 , to ensure identical distribution among the samples . Differ SLC4A1 , DAZAP2 , EPB42 , HELZ , SELENBP1 , NUDT4 , 5 ential expression analysis was performed with INMEX for CA1 , AHSP and ALAS2 . each dataset independently using a false discovery rate
In an embodiment , the present disclosure also relates to ( FDR ) of 0 . 05 , a significance of p < 0 . 05 and moderated t - test kits containing nucleic acid primers and kits containing based on the Limma algorithm . In INMEX , the results from nucleic acid primers and nucleic acid probes to diagnose and individual microarray dataset analyses are only for reference prognose PD in a sample of human thought to be afflicted 10 comparison and not required for meta - analysis in the sub with PD or known to be afflicted with PD . Such kit generally sequent steps . After microarray preprocessing steps , a data comprises a first container means having at least one oligo - integrity check was performed before proceeding to the nucleotide probe and / or primer that hybridizes to a target meta - analysis . For meta - analysis , the Fisher ' s method was nucleic acid ( e . g . , HNF4A or PTBP1 RNA ) and a second used with a significance level of p < 0 . 05 to combine p - values container means containing at least one other oligonucle - 15 from the multiple datasets . Fisher ' s method is a widely used otide primer and / or probe that hybridizes to the above - statistical approach in meta - analysis to combine p - values mentioned nucleic acid specific sequences . The kit may from different studies independently of the sample size ( Xia further include other containers comprising additional com - et al . ( 2013 ) INMEX — a web - based tool for integrative ponents such as an additional oligonucleotide or primer meta - analysis of expression data . Nucleic Acids Res 41 ( Web and / or one or more of the following : buffers , reagents to be 20 Server issue ) : W63 - 70 ; Tseng et al . , ( 2012 ) Comprehensive used in the assay ( e . g . , wash reagents , polymerases , internal literature review and statistical considerations for microar controls or else ) and reagents capable of detecting the ray meta - analysis . Nucleic Acids Res 40 ( 9 ) : 3785 - 3799 ) . presence of bound nucleic acid probe ( s ) / primer ( s ) . Numer - Gene ontology and functional analysis was performed using ous embodiments of the kits of the present invention are Network Analyst ( Xia et al . , ( 2014 ) NetworkAnalyst - inte possible . For example , the different container means can be 25 grative approaches for protein - protein interaction network divided in amplifying reagents and detection reagents . In analysis and visual exploration . Nucleic Acids Res 42 ( Web addition , the kits may further include instructions for prac Server issue ) : W167 - 74 . Epub May 26 , 2014 ) . ticing the diagnostic and / or prognostic methods of the present disclosure . Such instructions can concern details TABLE 1 relating to the experimental protocol as well as to the cut - off 30 Microarray studies in blood used for meta - analysis . values for the PD specific biomarker ratio that may be used .
GEO EXAMPLES accession No . of
number samples Description Platform Methods » GSE6613 PD = 50 ; Early stage sporadic Affymetrix Microarray Meta - Analysis HC = 22 PD patients ( mean Human Genome
Gene expression data from microarrays studies was Hoehn and Yahr = U133A downloaded from the Gene Expression Omnibus ( GEO ) and 2 . 3 )
GSE18838 PD = 18 ; Sporadic PD patients Affymetrix Exon 2 GEMMA database ( Zoubarev et al . ( 2012 ) Gemma : a HC = 12 ( treated ) Arrays resource for the reuse , sharing and meta - analysis of expres - 40 GSE22491 PD = 10 ; ( G2019S ) LRRK2 Agilent Whole sion profiling data . Bioinformatics 28 ( 17 ) : 2272 - 2273 ) by HC = 7 mutation carriers Human Genome using the terms “ Parkinson ' s disease " and " blood ” or “ tran with PD
GSE54536 PD = 5 ; Untreated sporadic PD Ilumina HT - 12 scriptional profiling ” as of May 31 , 2014 . Microarray studies HC = 5 Patients ( mean Hoehn V4 using RNA prepared from human blood with 10 samples or and Yahr stage = 1 ) more were included in the study . Only samples from PD 45 patients and healthy controls were analyzed . A total of four 1 - Scherzer et al . ( 2007 ) Molecular markers of early Parkinson ' s disease based on gene
expression in blood . Proc Natl Acad Sci U . S . A . 104 ( 3 ) : 955 - 960 . microarray studies met the inclusion criteria and were con 2 - Shehadeh et al . ( 2010 ) SRRM2 , a potential blood biomarker revealing high alternative
splicing in Parkinson ' s disease . PLoS One 5 ( 2 ) : e9104 . sidered for subsequent analysis . The microarray studies 3 - Mutez et al . ( 2011 ) Transcriptional profile of Parkinson blood mononuclear cells with analyzed in this study are listed in Table 1 . GSE6613 LRRK2 mutation . Neurobiol Aging 32 ( 10 ) : 1839 - 1848 . 4 - Alieva et al . ( 2014 ) Involvement of endocytosis and alternative splicing in the formation
50 of the pathological process in the early stages of Parkinson ' s disease . Biomed Res Int 2014 : 718732 . with a mean Hoehn and Yahr stage of 2 . 3 from which nine
were untreated patients and 22 age and sex matched healthy Network - Based Meta - Analysis controls . GSE8838 included 18 sporadic PD patients treated Network - based meta - analysis was performed using Net with different PD medications and 12 HC . GSE22491 workAnalyst ( Xia et al . , ( 2014 ) NetworkAnalyst - integra included 10 PD patients carrying a LRRK2 mutation from 55 tive approaches for protein - protein interaction network which one patient was untreated and seven HC . GSE54536 analysis and visual exploration . Nucleic Acids Res 42 ( Web included 5 untreated PD patients and 5 HC . A microarray Server issue ) : W167 - 74 . Epub May 26 , 2014 ) . Microarray meta - analysis was conducted using the Integrative Meta datasets were processed as described above . Briefly , Analysis of Expression Data ( INMEX ; Xia et al . ( 2013 ) microarray datasets were preprocessed by a log , transfor INMEX - a web - based tool for integrative meta - analysis of 60 mation followed by quantile normalization . Duplicate genes expression data . Nucleic Acids Res 41 ( Web Server issue ) : were replaced by their mean value . A significance value of W63 - 70 ) in accordance with the PRISMA guidelines for p < 0 . 05 and a log2 fold change of 1 were used as a cut - off meta - analysis ( Moher et al . , ( 2009 ) Preferred reporting value . Network construction was restricted to contain only items for systematic reviews and meta - analyses : the the original seed proteins . PRISMA statement . PLoS Med 6 ( 7 ) : e1000097 ) . All gene 65 Information about Study Participants probes were converted to a common Entrez ID using the The Institutional Review Boards of Rosalind Franklin gene / probe conversion tool in INMEX . After matching all University of Medicine and Science approved the study
Ref .
-
a
??
?
14
HNF4A reverse :
US 9 , 970 , 056 B2 13
protocol . Written informed consent was received from all - continued participants . Clinical characteristics of the participants used in this study have been reported elsewhere in ( Potashkin et ( SEO ID NO : 04 ) al . , ( 2012 ) Biosignatures for Parkinson ' s disease and atypi 5 ' - CAGCAGCTGCTCCTTCATGGAC - 3 ' , cal parkinsonian disorders patients . PLoS One 7 ( 8 ) : e43595 ; 5 Santiago et al . , ( 2013 ) Specific splice variants are associated PTBP1 forward :
( SEQ ID NO : 05 ) with Parkinson ' s disease . Mov Disord 28 ( 12 ) : 1724 - 1727 ; 5 ' - GCTCAGGATCATCGTGGAGAA - 3 ' ; and Santiago & Potashkin ( 2013 ) Integrative network analy sis unveils convergent molecular pathways in Parkinson ' s PTBP1 reverse : disease and diabetes . PLoS One 8 ( 12 ) : e83940 . Briefly , 51 10 ( SEO ID NO : 06 )
5 ' - ATCTTCAACACTGTGCCGAACTT - 3 ' . PD patients ( 29 men , 22 women ; mean age at enrollment 63 . 16 + 6 . 42 ; Hoehn and Yahr scale 2 : 0 . 28 ) and 45 healthy Quantitative PCR assays were carried using 25 ul reactions age - matched controls ( 24 male , 21 women ; mean age at containing Power SYBR Green master mix ( Life Technolo enrollment 65 . 12 + 8 . 60 ) enrolled in the Diagnostic and Prog gies , Carlsbad , Calif . , USA ) , primer at a concentration of 5 nostic Biomarkers for Parkinson ' s Disease ( PROBE ) 15 UM and nuclease free water . PCR reactions were amplified ( # NCT00653783 ) . Clinical diagnosis of PD was based on using a DNA engine Opticon 2 Analyzer ( Bio - Rad Life the United Kingdom Parkinson ' s Disease Society Brain Sciences , Hercules , Calif . , USA ) . Amplification conditions Bank criteria . Healthy individuals had no history of neuro and detailed description of qPCR experiments are reported logical disease and a Mini - Mental State Examination elsewhere in Potashkin et al . , ( 2012 ) Biosignatures for ( MMSE ) test score higher than 27 . Inclusion and exclusion 20 Parkinson ' s disease and atypical parkinsonian disorders criteria for patients enrolled in the PROBE study have been reported in Potashkin et al . , ( 2012 ) Biosignatures for Par patients . PLoS One 7 ( 8 ) : e43595 ; and Santiago et al . , ( 2013 ) kinson ' s disease and atypical parkinsonian disorders Specific splice variants are associated with Parkinson ' s patients . PLoS One 7 ( 8 ) : e43595 . As an independent repli disease . Mov Disord 28 ( 12 ) : 1724 - 1727 ) . cation cohort of patients 96 individuals were used , including 25 Statistical Analysis 50 PD patients ( 31 men , 19 women ; Hoehn and Yahr scale Network - based microarray meta - analysis was performed 1 . 97 + 0 . 62 ; mean age at enrollment 63 . 12 + 8 . 96 ; mean age at using INMEX and NetworkAnalyst . A student t - test ( two onset 58 . 75 - 10 . 17 ) and 46 healthy age - matched controls ( 26 tailed ) was used to estimate the significance between PD men , 20 women ; mean age at enrollment 64 . 28210 . 42 ) cases and controls for numerical variables . Post - hoc pair enrolled in the Harvard Biomarker Study ( HBS ) . Three 30 wise comparisons were performed using a Tukey test . Pear years follow - up samples from cases and controls enrolled in son correlation analysis was used to determine statistical the HBS were collected and analyzed in this study . Diag - significance for HNF4A and PTBP1 adjusting for sex , age , nosis of cases and controls was assessed at each visit to Hoehn and Yahr scale in both cohorts and BMI in the HBS ensure high diagnostic accuracy . Additional information study . A ROC curve analysis was used to evaluate the about the participants enrolled in the HBS clinical trial has 35 diagnostic accuracy . A step - wise linear discriminant analysis been published previously Ding et al . ( 2011 ) Association of was performed to determine the sensitivity and specificity SNCA with Parkinson : replication in the Harvard Neuro values for the linear combination of both biomarkers . Power Discovery Center Biomarker Study . Mov Disord 26 ( 12 ) : analyses of completed experiments were performed to dem 2283 - 2286 . onstrate that the sample size used in this study allowed the Quantitative Real Time Polymerase Chain Reactions 40 detection of a difference of 0 . 5 in fold change with a power
Blood was collected and prepared as described using the of 99 % and a significance of 0 . 05 . A p - value less than 0 . 05 PAXgene Blood RNA system ( Qiagen , Valencia , Calif . , was regarded statistically significant . For the longitudinal USA ) ( Scherzer et al . ( 2007 ) Molecular markers of early analysis we used a linear mixed effects regression model Parkinson ' s disease based on gene expression in blood . Proc including subjects as random effects and adjusting for sex , Natl Acad Sci U . S . A . 104 ( 3 ) : 955 - 960 ; and Potashkin et al . , 45 age and BMI . Longitudinal data was analyzed using Super ( 2012 ) Biosignatures for Parkinson ' s disease and atypical Mix ( Scientific Software International Inc . , IL , USA ) and parkinsonian disorders patients . PLoS One 7 ( 8 ) : e43595 ) . Statistica 12 ( StatSoft Inc . , OK , USA ) . All other statistical Samples with RNA integrity values > 7 . 0 and ratio of absor - analyses were undertaken using Prism4 . 0 ( GraphPad , CA , bances at 260 / 280 nm between 1 . 7 and 2 . 4 were used in the USA ) . current study . A total of 1 ug of RNA was reversed tran - 50 scribed using the High Capacity RNA transcription kit ( Life Example 1 Technologies , Carlsbad , Calif . , USA ) . Primers were designed using Primer Express software and ordered ( Life Meta - Analysis of Blood Microarrays in PD Technologies , Carlsbad , Calif . , USA ) . The primer sequences used in this study are as follows : 55 In order to identify a common transcriptional signature in
blood of PD patients , four microarray studies ( Table 1 ) were analyzed using INMEX , a web interface for the integrative
GAPDH forward : meta - analysis . The overall meta - analysis workflow used in ( SEQ ID NO : 01 ) ( SEQ ID NO : 01 ) this study is shown in FIG . 1A . Meta - analysis using a
5 ' - CAACGGATTTGGTCGTATTGG - 3 ' ; 60 Fisher ' s test identified a total of 2 , 781 genes differentially expressed consistently across four microarray studies .
( SEQ ID NO : 02 ) Among this group , 680 genes were upregulated and 2 , 101 5 ' - TGATGGCAACAATATCCACTTTACC - 3 ' , were downregulated in PD compared to healthy controls .
The thy - 1 cell surface antigen ( THY1 ) and HNF4A were the HNF4A forward : ( SEO ID NO : 03 ) 65 most significant upregulated genes across the four microar 5 ' - CAGAATGAGCGGGACCGGATC - 3 ' ; ray datasets . The top ten upregulated and downregulated
genes are listed in Table 2 . The complete list of differentially
GAPDH reverse :
US 9 , 970 , 056 B2 15 16
TABLE 3 - continued Complete list of differentially expressed genes .
expressed genes is provided in Table 3 . There were 921 gained genes uniquely identified in the meta - analysis that show relatively weak , but consistent expression across the four datasets . A total of 491 genes were classified as lost genes ( i . e . , genes identified as differentially expressed genes 5 in individual datasets but not in the meta - analysis ) . Venn diagram of meta - analysis results is shown in FIG . 1B and heat map visualization of the top 50 genes across the different studies is displayed in FIG . 1C .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
TABLE 2 Top 10 upregulated and downregulated genes
in PD identified by meta - analysis . 15
Entrez ID Gene Symbol Combined
Tstat Combined
P - value
Upregulated genes
20 7070 3172
25876 8175 10501 2020 10313 4059
124044 25823
THY1 74 . 145 HNF4A 66 . 421 SPEF1 65 . 538 SF3A2 65 . 127 SEMA6B 61 . 057 EN2 60 . 476 RTN3 60 . 224 BCAM 60 . 06 SPATA2L 59 . 655 TPSG1 59 . 018
Downregulated genes
5 . 46E - 09 8 . 49E - 08 8 . 49E - 08 8 . 49E - 08 4 . 23E - 07 4 . 23E - 07 4 . 23E - 07 4 . 23E - 07 4 . 51E - 07 5 . 41E - 07
115703 4654
64405 81693
354 150094 7356 51286 63940 6369
387509 9653 54345 5024 401
1628 2128
64321 80023 8433
23373 55653 1762 3837 4326 57030 1339 2696 920
51299 79729
399664 2786 1137
80758 1822
25
30 5725 6521 9802 2038 9931 8991 11163 759
51327 212
PTBP1 SLC4A1 DAZAP2 EPB42 HELZ SELENBP1 NUDT4 CA1 AHSP ALAS2
- 58 . 731 - 58 . 117 - 56 . 939 - 55 . 377 - 54 . 311 - 54 . 268 - 53 . 277 - 52 . 77 - 52 . 673 - 52 . 324
5 . 60E - 07 6 . 77E - 07 9 . 20E - 07 1 . 39E - 06 1 . 83E - 06 1 . 83E - 06 2 . 54E - 06 2 . 97E - 06 3 . 00E - 06 3 . 40E - 06
35 35 551
ARHGAP33 MYOD1 CDH22 AMN KLK3 SIK1 SCGB1A1 CEND1 GPSM3 CCL24 GPR153 HS2ST1 SOX18 P2RX3 PHOX2A DBP EVX1 SOX17 NRSN2 UTF1 CRTC1 BCAS4 DMWD KPNB1 MMP17 SLC17A7 COX6A2 GIPR CD4 NRN1 SH3D21 MEX3D GNG4 CHRNA4 PRR7 ATN1 AVP BBC3 CACNB3 FOXB1 WNT6 DEAF1 HCRT TRIM46 GLYR1 IRF2BP1 APC2 MINK1 HNF1A AQP2 CRHR2 TMEM158 CGGBP1 CREB3L1 GATA3 HOXA3 PORCN BAALC GALR3 MMRN2 CCDC86 ALDOA MLXIPL TAOK2 GTF2B SLC5A2 DCAF10 TBC1D10B CACNA1C TMEM132A PIN1P1 ELF1 ACBD4 HRK GTF3C3
50 . 931 50 . 909 50 . 434 49 . 975 49 . 809 49 . 518 49 . 43 48 . 614 48 . 45 48 . 292 48 . 183 47 . 727 47 . 623 47 . 149 46 . 83 46 . 744 46 . 565 46 . 262 46 . 259 46 . 034 46 . 008 45 . 925 45 . 88 45 . 792 45 . 133 45 . 124 44 . 443 44 . 103 43 . 975 43 . 693 43 . 542 43 . 392 43 . 049 43 . 02 42 . 981 42 . 113 42 . 078 41 . 902 41 . 779 41 . 622 41 . 387 41 . 373 41 . 197 41 . 131 40 . 668 40 . 603 40 . 544 40 . 283 39 . 781 39 . 487 39 . 292 39 . 288 39 . 045 38 . 752 38 . 423 38 . 296 38 . 05 38 . 048 38 . 04 37 . 868 37 . 806 36 . 95 36 . 696 36 . 556 36 . 481 36 . 481 36 . 384 36 . 285 36 . 244 36 . 216 35 . 991 35 . 979 35 . 938 35 . 915 35 . 746
5 . 09E - 06 5 . 09E - 06 6 . 13E - 06 7 . 16E - 06 7 . 37E - 06 8 . 20E - 06 8 . 34E - 06 1 . 09E - 05 1 . 14E - 05 1 . 20E - 05 1 . 24E - 05 1 . 46E - 05 1 . 47E - 05 1 . 73E - 05 1 . 96E - 05 2 . 00E - 05 2 . 07E - 05 2 . 23E - 05 2 . 23E - 05 2 . 42E - 05 2 . 42E - 05 2 . 47E - 05 2 . 49E - 05 2 . 55E - 05 3 . 21E - 05 3 . 21E - 05 4 . 12E - 05 4 . 61 E - 05 4 . 81 E - 05 5 . 17E - 05 5 . 39E - 05 5 . 70E - 05 6 . 11E - 05 6 . 13E - 05 6 . 17E - 05 8 . 32E - 05 8 . 33E - 05 8 . 71E - 05 9 . 04E - 05 9 . 46E - 05
0 . 0001018 0 . 0001018 0 . 00010816 0 . 00011046 0 . 00013086 0 . 00013319 0 . 00013508 0 . 00014694 0 . 00016912 0 . 00018366 0 . 00019407 0 . 00019407 0 . 0002117 0 . 00022835 0 . 00024799 0 . 00025907 0 . 00027866 0 . 00027866 0 . 00027866 0 . 00029769 0 . 00030175 0 . 00040211 0 . 00042987 0 . 00044836 0 . 00045294 0 . 00045294 0 . 00046395 0 . 00048023 0 . 00048419 0 . 00048779 0 . 00052147 0 . 00052201 0 . 00052703 0 . 00053013 0 . 0005604
TABLE 3 40
Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
Upregulated genes 45
50
27113 784
27023 7475 10522 3060 80128 84656 26145 10297 50488 6927 359
1395 25907 8545
90993 2625 3200
64840 79870 8484 79812 79080
226 51085 9344 2959 6524 79269 26000
775 54972 5301 1997
79777 8739 9330
7070 3172 25876 8175 10501 2020 10313 4059
124044 25823 1584 1152
23546 8911 777
4209 6601 5430 5586 2272 23038 168544 64067 23492 60506
55
THY1 HNF4A SPEF1 SF3A2 SEMAOB EN2 RTN3 BCAM SPATA2L TPSG1 CYP11B1 ??? SYNGR4 CACNAII CACNALE MEF2D SMARCC2 POLR2A PKN2 FHIT WDTC1 ZNF467 NPAS3 CBX7 NYX
74 . 145 66 . 421 65 . 538 65 . 127 61 . 057 60 . 476 60 . 224 60 . 06 59 . 655 59 . 018 57 . 882 57 . 629 56 . 785 56 . 141 56 . 031 55 . 754 54 . 901 54 . 861 54 . 471 53 . 787 53 . 556 53 . 135 52 . 247 51 . 876 51 . 846
5 . 46E - 09 8 . 49E - 08 8 . 49E - 08 8 . 49E - 08 4 . 23E - 07 4 . 23E - 07 4 . 23E - 07 4 . 23E - 07 4 . 51E - 07 5 . 41E - 07 6 . 95E - 07 7 . 23E - 07 9 . 24E - 07 1 . 15E - 06 1 . 15E - 06 1 . 24E - 06 1 . 59E - 06 1 . 59E - 06 1 . 81E - 06 2 . 18E - 06 2 . 32E - 06 2 . 61 E - 06 3 . 41 E - 06 3 . 63E - 06 3 . 63E - 06
60
65
US 9 , 970 , 056 B2 17
TABLE 3 - continued 18
TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
56156 1376 6490 55262 11155 11346 10861 54531
221037 64061 22976 10401 26088 10206 10935 56981 916
64130 83737 51380 9640
15
1727 4150 4037 56882 80004 5305
51230 11011 27344 7841 23295 10671 3891 392
10195 8546 11054 90864 51647 5020
10814 79882 51367
575 4342 6640 4762 3846
79173 55146 79575 1314 3716 79958 27076 3292
20
861
25
30
35 9780
CYB5R3 MAZ LRP3 CDC42SE1 ESRP2 PIP4K2A PHF20 TLK2 PCSKIN MOGS MGRN1 DCTN6 KRT85 ARHGAP1 ALG3 AP3B1 OGFR SPSB3 FAM96B OXT CPLX2 ZC3H14 POP5 BAI1 MOS SNTA1 NEUROG1 KRTAP5 - 9 C19orf57 ZDHHC4 ABHD8 ???? JAK1 DENNDIC LYPD3 HSD17B1 PIEZO1 SPI1 NDUFS7 PLA2G6 HIST1 H4D SOX3 C6orf106 ZNF548 METAP1 MT3 LARP4B SOX21 ????? SPPL2B NR2C2 PIP5K1C CHAC1 HEBP2 PSORS1C2 RARRES3 VGF DRD2 COPB1 XRCC3 GAS8 DVL3 FAM110D ARTN PRAF2 YME1L1 RAB11B DUSP7 MTA1 STAT4 TEAD3 CNTNAP1 FAM120C RPSÁKB2 CDC42EP4
35 . 48 35 . 433 35 . 344 35 . 241 35 . 153 35 . 048 35 . 045 35 . 02 34 . 974 34 . 946 34 . 874 34 . 871 34 . 644 34 . 633 34 . 452 34 . 446 34 . 422 34 . 396 34 . 252 34 . 231 34 . 223 34 . 141 34 . 138 34 . 084 34 . 084 34 . 076 34 . 068 34 . 039 34 . 001 33 . 857 33 . 794 33 . 65 33 . 646 33 . 569 33 . 267 33 . 21 33 . 199 33 . 135 33 . 105 33 . 071 33 . 055 32 . 965 32 . 899 32 . 824 32 . 797 32 . 733 32 . 726 32 . 577 32 . 483 32 . 475 32 . 438 32 . 389 32 . 193 31 . 923 31 . 726 31 . 651 31 . 626 31 . 617 31 . 521 31 . 486 31 . 484 31 . 43 31 . 389 31 . 38 31 . 264 31 . 242 30 . 921 30 . 857 30 . 812 30 . 75 30 . 708 30 . 595 30 . 575 30 . 556 30 . 531
0 . 0006149 0 . 00061837 0 . 00063441 0 . 00065511 0 . 00067249 0 . 00069365 0 . 00069365 0 . 00069861 0 . 00070972 0 . 00071307 0 . 00072598 0 . 00072598 0 . 00077757 0 . 00077767 0 . 00081204 0 . 00081204 0 . 0008139 0 . 00081501 0 . 00085147 0 . 00085147 0 . 00085168 0 . 00087342 0 . 00087342 0 . 00088085 0 . 00088085 0 . 0008812 0 . 0008812 0 . 00088679 0 . 0008962 0 . 00093452 0 . 00094852 0 . 00099726 0 . 00099726 0 . 0010154 0 . 0011188 0 . 0011406 0 . 0011427 0 . 0011671 0 . 0011787 0 . 0011922 0 . 0011939 0 . 0012244 0 . 0012372 0 . 0012651 0 . 0012678 0 . 0012794 0 . 0012797 0 . 0013308 0 . 0013672 0 . 0013688 0 . 0013746 0 . 001395 0 . 0014881 0 . 0016257 0 . 0017164 0 . 0017505 0 . 0017612 0 . 0017642 0 . 0018072 0 . 001813 0 . 001813 0 . 0018298 0 . 0018453 0 . 0018479 0 . 0019146 0 . 0019284 0 . 0021132 0 . 0021566 0 . 0021859 0 . 0022299 0 . 0022534 0 . 0023331 0 . 0023458 0 . 0023566 0 . 0023635
6688 374291
8398 8360 6658 64771 147694 23173 4504 23185 11166 1050
56928 7182 23396 79094 23593
170680 5920 7425 1813 1315 7517 2622 1857
79927 9048 11230 10730 9230 1849 9112 6775 7005 8506
54954 6199 23580
TEX13B CPT2 PMEL C7orf43 LDB3 SYNPO SLC26A1 MIER2 JMJD1C TSPYL2 PAXIP1 PIAS3 GGAL TRIM13 PRDX3 PRDM11 CD3E LIN7B ITCH CSAD ZNF592 RUNX1 NDRG3 LPHN1 ICOSLG HLA - DOA1 NFATC3 HCN2 NUP214 SLC22A18AS MADCAM1 TFR2 PHF1 HNRNPAO INHBC MUL1 CYB5A TRIM24 CASZ1 UPF1 SNX3 CYB5R4 ACAD10 RNF113A KLHDC2 CACNB1 NFE2L1 FGFR4 CHD3 ZFR SLC37A4 TNFRSF13B NDUFB1 PIK3R2 NXPH4 ENPP4 KRT9 GPR12 SIVA1 CHGA P2RY4 INOSOD HERPUD1 TNFAIPS SCARB1 SSSCA1 ACVR1B PEX10 TMEM43 INPP5F CIDEB SPATA6 CACNG5 PAK4 RSPHÓA
57446 22859 23308 3117 4775 610 8021 5003 8174 7036 5252 10949 3626
79594 1528 8805
54897 5976 8724
51167 80724 7737 23588
782 4779 2264 1107
51663 2542
23495 4707 5296 11247 22875 3857 2835 10572 1113 5030
54891 9709 25816
949 10534
30 . 513 30 . 49 30 . 446 30 . 356 30 . 319 30 . 176 30 . 064 29 . 945 29 . 753 29 . 545 29 . 51 29 . 489 29 . 478 29 . 465 29 . 41 29 . 278 29 . 264 29 . 142 29 . 098 29 . 075 29 . 05 29 . 047 29 . 027 29 . 023 29 . 012 28 . 994 28 . 969 28 . 934 28 . 802 28 . 757 28 . 732 28 . 516 28 . 508 28 . 387 28 . 361 28 . 143 28 . 104 27 . 861 27 . 831 27 . 8 27 . 773 27 . 763 27 . 715 27 . 704 27 . 582 27 . 58 27 . 556 27 . 509 27 . 457 27 . 452 27 . 416 27 . 397 27 . 337 27 . 291 27 . 287 27 . 254 27 . 127 27 . 094 27 . 064 27 . 047 26 . 995 26 . 987 26 . 963 26 . 897 26 . 891 26 . 874 26 . 859 26 . 818 26 . 814 26 . 787 26 . 783 26 . 772 26 . 675 26 . 652 26 . 646
40
0 . 0023769 0 . 0023901 0 . 0024202 0 . 0024695 0 . 002498 0 . 0026062 0 . 002703 0 . 0028074 0 . 0029788 0 . 003156 0 . 0031791 0 . 0031941 0 . 0031993 0 . 0032112 0 . 0032568 0 . 0034075 0 . 0034213 0 . 0035598 0 . 0036012 0 . 0036231 0 . 003638 0 . 003638 0 . 0036544 0 . 0036545 0 . 0036652 0 . 0036696 0 . 0036772 0 . 0037121 0 . 003874 0 . 0039071 0 . 0039196 0 . 0041571 0 . 0041612 0 . 0043054 0 . 0043396 0 . 0046115 0 . 0046774 0 . 0050111 0 . 0050468 0 . 0050946 0 . 0051295 0 . 0051429 0 . 005213 0 . 0052153 0 . 0053556 0 . 0053556 0 . 0053921 0 . 0054553 0 . 0055362 0 . 0055362 0 . 0055963 0 . 0056319 0 . 0057107 0 . 0057664 0 . 0057664 0 . 0057925 0 . 0060305 0 . 0060964 0 . 0061315 0 . 0061657 0 . 0062437 0 . 0062546 0 . 0062629 0 . 0063702 0 . 0063776 0 . 0064004 0 . 0064161 0 . 0064687 0 . 0064718 0 . 0065036 0 . 0065036 0 . 0065137 0 . 0067005 0 . 0067467 0 . 0067486
45
50
55
91 60 5192 79188 22876 27141 54558 27091 10298 81492
65
H
US 9 , 970 , 056 B2 19 20
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
Entrez 5
Gene symbol ( Name )
Combined Tstat
Combined Pval ID
10
15
20
25
30
6867 9683
54923 8364 3643
23367 1659 6618 55802 6305 7874 4913
81606 8767
54905 6284 55274 3881 8874 2829 6134 29883 6559 65057 1880
27079 51052 29123 9091 7016 7852 924
23368 54858 5170 3659 4282 2692
83955 196403 24146 23162 11009 51406 9146 1633
64410 9903
81853 27092 6928 54800 64180 54939 1212
51106 10075 56904 23639 54328 54946 23376 25948 4771 2303
51150 3094 5984 11260
140467 689
56650 1513 6497 5970
35
TACC1 N4BP1 LIME1 HIST1H4C INSR LARP1 DHX8 SNAPC2 DCP1A SBF1 USP7 NTHL1 LBH RIPK2 CYP2W1 S100A13 PHF10 KRT31 ARHGEF7 XCR1 RPL10 CNOT7 SLC12A3 ACD GPR183 RPUSD2 PRLH ANKRD11 PIGO TESK1 CXCR4 CD7 PPP1R13B PGPEP1 PDPK1 IRF1 MIF GHRHR NACAP1 DTX3 CLDN15 MAPKXIP3 IL24 NOL7 HGS DCK KLHL25 KLHL21 TMEM14B CACNG4 HNF1B KLHL24 DPEP3 COMMD4 CLTB TFB1M HUWE1 SH3GLB2 LRRC6 GPR173 SLC41A3 UFL1 KBTBD2 NF2 FOXC2 SDF4 HINT1 RFC4 XPOT ZNF358 BTF3 CLDND1 CTSK SKI RELA
79413 2810 894
79622 1198
55337 2843
65988 56994 5140 4487 1877 9516
57820 79414 6440 4841 11124 84124 2010
79034 54915 8483
93 3748 3957 2359 23383 8560
146542 54851 1543
79656 26232 23013 51596 8542
55178 6357 1739 1523 3954 8045
55339 57104 54344
26 . 541 26 . 293 26 . 264 26 . 23 26 . 061 26 . 006 25 . 903 25 . 857 25 . 851 25 . 783 25 . 763 25 . 755 25 . 734 25 . 692 25 . 677 25 . 676 25 . 675 25 . 664 25 . 645 25 . 639 25 . 621 25 . 614 25 . 6 25 . 506 25 . 457 25 . 445 25 . 381 25 . 34 25 . 321 25 . 3 25 . 226 25 . 216 25 . 163 25 . 151 25 . 118 25 . 114 25 . 036 25 . 009 24 . 966 24 . 95 24 . 909 24 . 903 24 . 875 24 . 861 24 . 791 24 . 723 24 . 709 24 . 625 24 . 612 24 . 598 24 . 568 24 . 551 24 . 504 24 . 491 24 . 472 24 . 467 24 . 429 24 . 387 24 . 37 24 . 344 24 . 299 24 . 287 24 . 268 24 . 202 24 . 155 24 . 054 24 . 049 24 . 039 23 . 906 23 . 898 23 . 887 23 . 846 23 . 716 23 . 681 23 . 676
0 . 0069817 0 . 0074202 0 . 0074915 0 . 0075366 0 . 0078736 0 . 0079814 0 . 0082443 0 . 0083523 0 . 0083555 0 . 0085214 0 . 0085612 0 . 0085644 0 . 0086266 0 . 0087353 0 . 0087499 0 . 0087499 0 . 0087499 0 . 0087705 0 . 0088009 0 . 0088127 0 . 0088596 0 . 0088768 0 . 0088825 0 . 0091595 0 . 0092841 0 . 0093124 0 . 0094767 0 . 009584 0 . 0096224 0 . 009661 0 . 0098413 0 . 0098552 0 . 010013 0 . 010042 0 . 010126 0 . 010126 0 . 010363 0 . 010427 0 . 010491 0 . 010533 0 . 010654 0 . 010673 0 . 010712 0 . 010751 0 . 010885 0 . 011098 0 . 011127 0 . 011396 0 . 011434 0 . 011478 0 . 011561 0 . 01161 0 . 011747 0 . 01179 0 . 011863 0 . 011875 0 . 011962 0 . 012095 0 . 01214 0 . 012204 0 . 012327 0 . 012372 0 . 012456 0 . 012703 0 . 012875 0 . 013206 0 . 013211 0 . 013233 0 . 013717 0 . 013737 0 . 013776 0 . 013909 0 . 014299 0 . 01443 0 . 014447
ZBED2 SFN CCND2 SNRNP25 CLK3 C19orf66 GPR20 ZNF747 CHPT1 PDE3B MSX1 E4F1 LITAF CCNB11P1 LRFN3 SFTPC NONO FAF1 ZNF394 EMD C7orf26 YTHDF1 CILP ACVR2B KCNC3 LGALS2 FPR3 MAU2 DEGS1 ZNF688 ANKRD49 CYP1A1 BEND5 FBXO2 SPEN CUTA APOL1 RNMTL1 CCL13 DLG1 CUX1 LETM1 RASSF7 WDR33 PNPLA2 DPM3 UCP3 PRPF4 RCN2 KLK2 CPNE6 SYT5 ARHGAP19 ???? GTPBP3 RPL22 MORF4L1 ARID5A MED13 TAF10 C22orf26 PCCB ADARB2 MAGEAS FNTA NKX3 - 1 AK1 ENOPH1 ZNF444 CRHR1 POMT1 PRSS8 OSBP SZT2 OSBPL10
23 . 595 23 . 519 23 . 517 23 . 506 23 . 503 23 . 476 23 . 426 23 . 423 23 . 406 23 . 382 23 . 376 23 . 348 23 . 321 23 . 291 23 . 253 23 . 166 23 . 148 23 . 129 23 . 108 23 . 091 22 . 998 22 . 951 22 . 892 22 . 888 22 . 86 22 . 855 22 . 829 22 . 822 22 . 82 22 . 808 22 . 807 22 . 803 22 . 799 22 . 79 22 . 783 22 . 776 22 . 766 22 . 759 22 . 753 22 . 746 22 . 732 22 . 727 22 . 726 22 . 724 22 . 683 22 . 681 22 . 673 22 . 645 22 . 62 22 . 62 22 . 604 22 . 596 22 . 592 22 . 574 22 . 566 22 . 541 22 . 502 22 . 498 22 . 492 22 . 485 22 . 473 22 . 46 22 . 448 22 . 435 22 . 419 22 . 419 22 . 417 22 . 387 22 . 38 22 . 333 22 . 302 22 . 286 22 . 273 22 . 27 22 . 238
0 . 014807 0 . 015173 0 . 015173 0 . 015173 0 . 015173 0 . 015302 0 . 015499 0 . 015508 0 . 015539 0 . 01564 0 . 01566 0 . 015743 0 . 015845 0 . 015959 0 . 016134 0 . 016517 0 . 016589 0 . 016673 0 . 016751 0 . 016801 0 . 017211 0 . 017421 0 . 017577 0 . 017583 0 . 017725 0 . 017742 0 . 017888 0 . 017909 0 . 017909 0 . 017935 0 . 017935 0 . 017943 0 . 017951 0 . 017971 0 . 017995 0 . 018002 0 . 018038 0 . 018063 0 . 018098 0 . 018132 0 . 018206 0 . 018207 0 . 018207 0 . 018214 0 . 018368 0 . 018368 0 . 018375 0 . 018481 0 . 018597 0 . 018597 0 . 018635 0 . 018658 0 . 018662 0 . 01872 0 . 01876 0 . 018847 0 . 019081 0 . 019099 0 . 019127 0 . 019161 0 . 019232 0 . 019289 0 . 019312 0 . 019337 0 . 019421 0 . 019421 0 . 019421 0 . 019522 0 . 019543 0 . 01975 0 . 019906 0 . 019989 0 . 020053 0 . 02006 0 . 020209
40
7352
45
50
55
9128 5955 3817 9362 6861 84986 3704 84705 6146 10933 10865 9969 6881 55267 5096 105
4107 2339 4824 203
58478 55311 1394 10585 5652 5007 23334 114884
60 staflentinsta 65
US 9 , 970 , 056 B2 21 22
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
15
20
25
30
35
5195 23043 253782 51611 7048 6794 25844 4204 9815 5435 5957 2539 2002 1355
51634 80011 63892 148066 79695 22837 10845 8366 4210 10107 9982 6865
246126 54733 5450 23468 54971 757
10608 4284 7260 5730
55323 114881 54149 4752 10519 7270 25873 55630 55508 3718
56731 1760
256949 8786
80183 10201 10456 7392
66035 3484 3664 3764 4255
58494 26959 60370 5148 51333
886 4332 1967 8934
55321 2644
55854 2962 1933 4826 29924
PEX14 TNIK CERS6 DPH5 TGFBR2 STK11 YIPF3 MECP2 GIT2 POLR2F RCVRN G6PD ELK1 COX15 RBMX2 FAM192A THADA ZNRF4 GALNT12 COBLL1 CLPX HIST1H4B MEFV TRIM10 FGFBP1 TACR2 TXLNG2P SLC35F2 POUZAF1 CBX5 BANP TMEM50B MXD4 MIP TSSC1 PTGDS LARP6 OSBPL7 C2lorf91 N??? CIB1 TTF1 RPL36 SLC39A4 SLC35E3 JAK3 SLC2A4RG DMPK KANK3 RGS11 KIAA0226L NME6 HAX1 USF2 SLC2A11 IGFBP1 IRF6 KCNJS MGMT JAM2 HBP1 AVPI1 PDEG ZNF771 CCKAR MNDA EIF2B1 RAB7L1 TMEM74B GCHFR ZC3H15 GTF2F1 EEF1B2 NNAT EPN1
22 . 232 22 . 231 22 . 227 22 . 223 22 . 192 22 . 173 22 . 173 22 . 151 22 . 15 22 . 138 22 . 11 22 . 101 22 . 037 22 . 029 21 . 98 21 . 973 21 . 96 21 . 927 21 . 906 21 . 888 21 . 876 21 . 871 21 . 867 21 . 825 21 . 803 21 . 779 21 . 766 21 . 751 21 . 746 21 . 725 21 . 719 21 . 702 21 . 678 21 . 636 21 . 598 21 . 582 21 . 577 21 . 564 21 . 556 21 . 556 21 . 551 21 . 526 21 . 52 21 . 5 21 . 49 21 . 482 21 . 44 21 . 394 21 . 384 21 . 339 21 . 338 21 . 311 21 . 272 21 . 261 21 . 224 21 . 179 21 . 176 21 . 156 21 . 151 21 . 148 21 . 133 21 . 073 21 . 055 21 . 047 21 . 042 21 . 037 21 . 028 21 . 023 21 . 017 21 . 011 20 . 988 20 . 984 20 . 98 20 . 98 20 . 908
0 . 020209 0 . 020209 0 . 02023 0 . 020246 0 . 020344 0 . 020465 0 . 020465 0 . 020574 0 . 020574 0 . 020588 0 . 020709 0 . 020767 0 . 021165 0 . 021176 0 . 021424 0 . 021454 0 . 021543 0 . 021729 0 . 021809 0 . 021909 0 . 021961 0 . 021972 0 . 021992 0 . 022222 0 . 022327 0 . 022475 0 . 02255 0 . 022629 0 . 022643 0 . 022763 0 . 022797 0 . 022811 0 . 022948 0 . 023167 0 . 023402 0 . 023496 0 . 023532 0 . 02359 0 . 02359 0 . 02359 0 . 023604 0 . 023725 0 . 023748 0 . 023814 0 . 023892 0 . 023947 0 . 024171 0 . 024467 0 . 024536 0 . 02482 0 . 02482 0 . 024953 0 . 025256 0 . 025317 0 . 025485 0 . 025795 0 . 025804 0 . 025961 0 . 025993 0 . 026009 0 . 026089 0 . 026486 0 . 026602 0 . 026639 0 . 026663 0 . 026697 0 . 026747 0 . 026776 0 . 026817 0 . 026844 0 . 027013 0 . 027034 0 . 027052 0 . 027052 0 . 027482
9482 10892 54681 2841 26136 4807
48 26156 7707 23386
973 5698
55794 6474 4629 5303 10202 81858 23332 79803 79600
581 127833 1233
23471 572
54861 135138
7693 8624
56245 3217 4192 2817
51295 6810 4176 3589 3739 7404 9296 9329 5583 11092 57827 1548
25999 10922 55009 9022
54961 64077 23451
867 54093 1419
28962 868
9778 11161 2245 80153 56548 10220 10174 4832 10291 29761 51151 2788
80774 25790 10262 23484 64793
STX8 MALT1 P4HTM GPR18 TES NHLH1 ACO1 RSL1D1 ZNF148 NUDCD3 CD79A PSMB9 DDX28 SHOX2 MYH11 PIN4 DHRS2 SHARPIN CLASP1 HPS6 TCTN1 BAX SYT2 CCR4 TRAM1 BAD SNRK PACRG ZNF134 PSMG1 C2lorf62 HOXB7 MDK GPC1 ECSIT STX4 MCM7 IL11 KCNA4 UTY ATP6V1F GTF3C4 PRKCH C9orfy C6orf47 CYP2A6 CLIP3 FASTK C19orf24 CLIC3 SSH3 LHPP SF3B1 CBL SETD4 CRYGB OSTM1 CBLB KIAA0232 C14orfi FGD1 EDC3 CHSTE GDF11 SORBS3 NME3 SF3A1 USP25 SLC45A2 GNG7 LIMD2 CCDC19 SF3B4 LEPROTL1 CEP85
20 . 901 20 . 891 20 . 891 20 . 883 20 . 88 20 . 879 20 . 87 20 . 864 20 . 849 20 . 83 20 . 802 20 . 79 20 . 786 20 . 782 20 . 763 20 . 762 20 . 74 20 . 737 20 . 733 20 . 725 20 . 718 20 . 716 20 . 684 20 . 681 20 . 676 20 . 649 20 . 621 20 . 588 20 . 584 20 . 573 20 . 553 20 . 539 20 . 529 20 . 528 20 . 52 20 . 496 20 . 494 20 . 489 20 . 484 20 . 462 20 . 441 20 . 44 20 . 435 20 . 411 20 . 406 20 . 373 20 . 369 20 . 367 20 . 336 20 . 324 20 . 291 20 . 253 20 . 252 20 . 25 20 . 226 20 . 225 20 . 218 20 . 194 20 . 173 20 . 149 20 . 146 20 . 134 20 . 133 20 . 088 20 . 08 20 . 068 20 . 067 20 . 03 20 . 03 20 . 014 20 . 014 20 . 014 19 . 992 19 . 985 19 . 985
0 . 027511 0 . 027567 0 . 027567 0 . 027621 0 . 027638 0 . 027638 0 . 027716 0 . 02775 0 . 02783 0 . 027968 0 . 028184 0 . 028263 0 . 028268 0 . 028293 0 . 028387 0 . 028387 0 . 02852 0 . 028539 0 . 028566 0 . 02859 0 . 02859 0 . 02859 0 . 028812 0 . 028812 0 . 028821 0 . 029002 0 . 029227 0 . 029452 0 . 029459 0 . 029504 0 . 029664 0 . 029774 0 . 029842 0 . 029846 0 . 02989 0 . 030035 0 . 030035 0 . 030051 0 . 03006 0 . 03023 0 . 030408 0 . 030408 0 . 030425 0 . 03064 0 . 030677 0 . 03093 0 . 030952 0 . 030952 0 . 031154 0 . 031262 0 . 031526 0 . 03186 0 . 03186 0 . 031871 0 . 032043 0 . 032043 0 . 032058 0 . 032276 0 . 032437 0 . 032652 0 . 032654 0 . 032764 0 . 032764 0 . 033259 0 . 033336 0 . 033427 0 . 033427 0 . 033716 0 . 033716 0 . 033807 0 . 033807 0 . 033807 0 . 033999 0 . 034038 0 . 034038
40
45
50
55
60
65
US 9 , 970 , 056 B2 23 24
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Entrez Combined Tstat
Combined Pval 5
Gene symbol ( Name )
Combined Tstat
Combined Pval ID
19 10
15 .
20
25
26015 7586
79668 29855 5143 27132 7471 10452 4124 81030 79929 5345
64063 4482 1482 1499
57835 1369 5695 839
83714 55063 10520 10897 171586 7375 696
5371 230
10469 3658 5037
55145 7423 9403 55090 22800 6750 4858 6282 8526 1488
222161 956 3669 23
78996 64097 55030 1298
29098 8824 734
23452 29775 28978 79068 7275 1381
22897 201254 9922
54476 5031 1059
23429 1174 4649 51283 55422 6992 921
23648 796
64284
RPAP1 ZKSCAN1 PARP8 UBN1 PDE4C CPNE7 WNT1 TOMM40 MAN2A1 ZBP1 MAP6D1 SERPINF2 PRSS22 MSRA NKX2 - 5 CTNNB1 SLC4A5 CPN1 PSMB7 CASP6 NRIP2 ZCWPW1 ZNF211 YIF1A ABHD3 USP4 BTN1A1 PML ALDOC TIMM44 IREB2 PEBP1 THAP1 VEGFB SEP15 MED9 RRAS2 SST NOVA2 S100A11 DGKE CTBP2 DKFZP58611420 ENTPD3 ISG20 ABCF1 C7orf49 EPB41L4A FBXO34 COLIA2 RANGRF CES2 OSGIN2 ANGPTL2 CARD10 TMEM14A FTO TUB CRABP1 CEP164 STRA13 IQSEC1 RNF216 P2RY6 CENPB RYBP AP1S1 MYO9A BFAR ZNF331 PPP1R11 CD5 SSBP3 CALCA RAB17
30
19 . 962 19 . 926 19 . 914 19 . 894 19 . 853 19 . 846 19 . 842 19 . 819 19 . 813 19 . 811 19 . 811 19 . 807 19 . 795 19 . 783 19 . 767 19 . 75 19 . 701 19 . 7 19 . 697 19 . 676 19 . 653 19 . 643 19 . 635 19 . 634 19 . 633 19 . 627 19 . 603 19 . 601 19 . 598 19 . 59 19 . 589 19 . 589 19 . 554 19 . 549 19 . 539 19 . 537 19 . 513 19 . 501 19 . 487 19 . 475 19 . 474 19 . 43 19 . 406 19 . 397 19 . 395 19 . 382 19 . 362 19 . 304 19 . 296 19 . 295 19 . 292 19 . 268 19 . 252 19 . 239 19 . 234 19 . 217 19 . 21 19 . 206 19 . 188 19 . 182 19 . 176 19 . 174 19 . 167 19 . 159 19 . 147 19 . 109 19 . 106 19 . 104 19 . 094 19 . 078 19 . 067 19 . 048 19 . 033 19 . 032 19 . 018
55222 57152 9779
51170 55223 8111
63931 5442 539
79778 5995 10432 6035 26001 79643 79029 10868 6314 3303 2877 11168 841
2806 10927 9616 8933 4776
399979 931
8929 56255 8737 25813 7494 161
7695 9908
54549 8237 1103
55252 3177 8776
60491 23528 3480 3489 9032
23394 5089
64121 23263 51154 65992 29992
35
0 . 03423 0 . 034511 0 . 034565 0 . 034744 0 . 035179 0 . 035197 0 . 035243 0 . 035478 0 . 035498 0 . 035498 0 . 035498 0 . 035506 0 . 035601 0 . 035682 0 . 035833 0 . 035954 0 . 036418 0 . 036418 0 . 036437 0 . 036655 0 . 036894 0 . 036966 0 . 037004 0 . 037004 0 . 037004 0 . 03701 0 . 037287 0 . 037301 0 . 037326 0 . 037376 0 . 037376 0 . 037376 0 . 037709 0 . 03776 0 . 037882 0 . 037896 0 . 038098 0 . 038185 0 . 038303 0 . 038387 0 . 038387 0 . 038804 0 . 039053 0 . 039139 0 . 039139 0 . 039243 0 . 039443 0 . 040077 0 . 040179 0 . 040179 0 . 040193 0 . 040446 0 . 040594 0 . 040738 0 . 040782 0 . 041012 0 . 041062 0 . 041082 0 . 041266 0 . 041302 0 . 041361 0 . 041361 0 . 04142 0 . 041491 0 . 041602 0 . 04202 0 . 04202 0 . 042027 0 . 04214 0 . 042326 0 . 042455 0 . 042703 0 . 042863 0 . 042869 0 . 042989
LRRC20 19 . 011 SLURP1 19 . 01 TBC1D5 19 . 007 HSD17B11 TRIM62 18 . 997 GPR68 18 . 997 MRPS14 18 . 97 POLRMT 18 . 964 ATP50 18 . 949 MICALL2 18 . 943 RGR 18 . 938 RBM14 18 . 915 RNASE1 18 . 911 RNF167 18 . 909 CHMP6 18 . 903 SPATA5L1 18 . 897 USP20 18 . 885 ATXN7 18 . 853 HSPAIA 18 . 842 GPX2 18 . 822 PSIP1 18 . 809 CASP8 18 . 804 GOT2 18 . 776 SPIN1 18 . 773 RNF7 18 . 735 FAM127A 18 . 73 NFATC4 18 . 722 SNX19 18 . 709 MS4A1 18 . 701 PHOX2B 18 . 695 TMX4 18 . 67 RIPK1 18 . 65 SAMM50 18 . 646 XBP1 18 . 645 AP2A2 18 . 629 ZNF136 18 . 614 G3BP2 18 . 61 SDK2 18 . 559 USP11 18 . 555 CHAT 18 . 55 ASXL2 18 . 544 SLC29A2 18 . 531 MTMR1 18 . 527 NIF3L1 18 . 512 ZNF281 18 . 498 IGF1R 18 . 488 IGFBP6 18 . 484 TM4SF5 18 . 471 ADNP 18 . 468 PBX2 18 . 461 RRAGC 18 . 452 MCF2L 18 . 401 MRTO4 18 . 401 DDRGK1 18 . 399 PILRA 18 . 399
Downregulated genes
0 . 043055 0 . 043059 0 . 043087 0 . 043171 0 . 04319 0 . 04319 0 . 043409 0 . 043467 0 . 043581 0 . 043651 0 . 043716 0 . 043919 0 . 043937 0 . 043937 0 . 043978 0 . 044044 0 . 044211 0 . 044485 0 . 044628 0 . 044791 0 . 044863 0 . 044922 0 . 045226 0 . 045246 0 . 045718 0 . 045791 0 . 045864 0 . 046058 0 . 046126 0 . 046215 0 . 046501 0 . 046691 0 . 046705 0 . 046705 0 . 046923 0 . 047119 0 . 047156 0 . 04775 0 . 047778 0 . 04778 0 . 047813 0 . 047998 0 . 048042 0 . 048219 0 . 048357 0 . 048432 0 . 04849 0 . 048662 0 . 048686 0 . 048761 0 . 04883 0 . 049564 0 . 049564 0 . 049564 0 . 049564
40
45
50
55
existiitataasin 5725 6521 9802 2038 9931 8991 11163 759
51327 212
29978 830
66008 23392 5538 9741 10523 4602
PTBP1 SLC4A1 DAZAP2 EPB42 HELZ SELENBP1 NUDT4 CA1 AHSP ALAS2 UBQLN2 CAPZA2 TRAK2 KIAA0368 PPT1 LAPTM4A CHERP MYB
- 58 . 731 - 58 . 117 - 56 . 939 - 55 . 377 - 54 . 311 - 54 . 268 - 53 . 277 - 52 . 77 - 52 . 673 - 52 . 324 - 52 . 105 - 51 . 962 - 51 . 502 - 50 . 109 - 49 . 825 - 48 . 994 - 48 . 748 - 48 . 593
5 . 60E - 07 6 . 77E - 07 9 . 20E - 07 1 . 39E - 06 1 . 83E - 06 1 . 83E - 06 2 . 54E - 06 2 . 97E - 06 3 . 00E - 06 3 . 40E - 06 3 . 52E - 06 3 . 63E - 06 4 . 12E - 06 6 . 91E - 06 7 . 37E - 06 9 . 90E - 06 1 . 08E - 05 1 . 09E - 05
60
65 ?
US 9 , 970 , 056 B2 25 26 26
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
20
25
30
35
3312 54518 374868
9320 23262 54432
533 5292
10550 23406 9131 1859
55421 204851 51385 7353 3045
55197 4677 3049 1465
220972 23256 4694 7411 6713 8761
155066 10908 408 1349 5810 1445 54832 11154 4726 6510 2235 3134 1154
23741 55589
892 56889 7045 2752
79415 2994
51582 9166 51552 25793 3421
81929 6502 9816 375
55907 64761 1874 8720
50999 6612 9528 7979 6434 669 7323 3689 94239 1084
29969 6135 79623 27034
HSPA8 APBB1IP ATP9B TRIP12 PPIP5K2 YIPF1 AT?6?0B PIM1 ARL6IP5 COTL1 AIFM1 DYRKIA C17orf85 HIPK1 ZNF589 UFDIL HBD RPRDIA NARS HBO1 CSRP1 MARCH8 SCFD1 NDUFA1 VBP1 SOLE PABPC4 AT?6?0?2 PNPLA6 ARRB1 COXZB RAD1 CSK VPS13C AP4S1 NDUFS6 SLC1A5 FECH HLA - F CISH EID1
BMP2K CCNC TMOSF3 TGFBI GLUL C17orf62 GYPB AZIN1 EBAG9 RAB14 FBX07 IDH3G SEHIL SKP2 URB2 ARF1 CMAS PARP12 E2F4 MBTPS1 TMED5 SUMO3 TMEM59 SHFM1 TRA2B BPGM UBE2D3 ITGB2 H2AFV ??????? MDFIC RPL11 GALNT14 ACADS
- 48 . 59 - 48 . 031 - 47 . 683 - 47 . 407 - 47 . 18 - 46 . 662 - 46 . 62 - 46 . 48 - 46 . 428 - 45 . 707 - 45 . 467 - 45 . 42 - 44 . 974 - 44 . 829 - 44 . 618 - 44 . 369 - 44 . 194 - 43 . 955 - 43 . 741 - 43 . 698 - 43 . 687 - 43 . 565 - 43 . 314 - 43 . 262 - 43 . 217 - 43 . 19 - 43 . 113 - 43 . 111 - 43 . 091 - 42 . 665 - 42 . 633 - 42 . 484 - 42 . 358 - 42 . 329 - 42 . 316 - 42 . 295 - 42 . 105 - 42 . 062 - 41 . 962 - 41 . 92 - 41 . 776 - 41 . 755 - 41 . 616 - 41 . 48 - 41 . 431 - 41 . 217 - 41 . 098 - 40 . 783 - 40 . 685 - 40 . 593 - 40 . 506 - 40 . 375 - 40 . 375 - 40 . 257 - 40 . 023 - 39 . 973 - 39 . 934 - 39 . 907 - 39 . 849 - 39 . 84 - 39 . 839 - 39 . 802 - 39 . 762 - 39 . 761 - 39 . 753 - 39 . 676 - 39 . 653 - 39 . 627 - 39 . 494 - 39 . 458 - 39 . 43 - 39 . 356 - 39 . 066 - 39 . 043 - 39 . 023
1 . 09E - 05 1 . 30E - 05 1 . 46E - 05 1 . 59E - 05 1 . 73E - 05 2 . 04E - 05 2 . 05E - 05 2 . 11E - 05 2 . 13E - 05 2 . 62E - 05 2 . 87E - 05 2 . 89E - 05 3 . 38E - 05 3 . 56E - 05 3 . 86E - 05 4 . 20E - 05 4 . 48E - 05 4 . 81 E - 05 5 . 17E - 05 5 . 17E - 05 5 . 17E - 05 5 . 39E - 05 5 . 83E - 05 5 . 90E - 05 5 . 96E - 05 5 . 97E - 05 6 . 05E - 05 6 . 05E - 05 6 . 05E - 05 7 . 01E - 05 7 . 04E - 05 7 . 45E - 05 7 . 79E - 05 7 . 80E - 05 7 . 80E - 05 7 . 80E - 05 8 . 32E - 05 8 . 33E - 05 8 . 62E - 05 8 . 71E - 05 9 . 04E - 05 9 . 05E - 05 9 . 46E - 05 9 . 95E - 05
0 . 00010085 0 . 00010807 0 . 00011121 0 . 00012641 0 . 00013086 0 . 00013319 0 . 00013633 0 . 00014221 0 . 00014221 0 . 00014756 0 . 00016201 0 . 0001644 0 . 00016605 0 . 00016684 0 . 00016842 0 . 00016842 0 . 00016842 0 . 00016912 0 . 00016912 0 . 00016912 0 . 00016912 0 . 00017373 0 . 00017432 0 . 0001752 0 . 00018366 0 . 00018486 0 . 00018592 0 . 00019079 0 . 0002117 0 . 0002117 0 . 00021223
6748 6500 8864 1738 5634 10923 6728 4893
84890 10492 2193 5423 5537 8850
51312 3646 5266
54964 6603 1785 2937 9491 3157 7384 8677 26019 23596 1939 1399
57380 9519 6782 824
55666 378
6950 10138 10180 58533 10539 51019 51185 1327
22820 83937 64083 23499 79892 23404 10096 23151 6745 9978 4670 8780 3692 2987
11345 5826
51109 55743 83440 9526
23166 55621 81550
832 4191 2353 4088 1185 875
9111 79026 65264
SSR4 SKP1 PER2 DLD PRPS2 SUB1 SRP19 NRAS ADO SYNCRIP FARSA POLB PPP6C KAT2B SLC25A37 EIF?? PI3 Clorf56 SMARCD2 DNM2 GSS PSMF1 HMGCS1 UQCRC1 STX10 UPF2 OPN3 EIF2D CRKL MRS2 TBPL1 HSPA13 CAPN2 NPLOC4 ARF4 TCP1 YAF2 RBM6 SNX6 GLRX3 CCDC53 CRBN COX411 COPG1 RASSF4 GOLPH3 MACF1 ????? EXOSC2 ACTR3 GRAMD4 SSR1 RBX1 HNRNPM RIOK3 EIF6 GUK1 GABARAPL2 ABCD4 RDH11 CHFR ADPGK MPDU1 STAB1 TRMT1 TDRD3 CAPZB MDH2 FOS SMAD3 CLCN6 CBS NMI AHNAK UBEZZ
- 38 . 976 - 38 . 922 - 38 . 914 - 38 . 864 - 38 . 845 - 38 . 752 - 38 . 744 - 38 . 676 - 38 . 671 - 38 . 65 - 38 . 588 - 38 . 554 - 38 . 552 - 38 . 519 - 38 . 511 - 38 . 497 - 38 . 403 - 38 . 262 - 38 . 248 - 38 . 148 - 38 . 094 - 37 . 861 - 37 . 818 - 37 . 752 - 37 . 678 - 37 . 625 - 37 . 6 - 37 . 432 - 37 . 405 - 37 . 353 - 37 . 35 - 37 . 317 - 37 . 196 - 37 . 178 - 37 . 151 - 37 . 108 - 37 . 091 - 37 . 065 - 36 . 925 - 36 . 924 - 36 . 834 - 36 . 82 - 36 . 785 - 36 . 76 - 36 . 733 - 36 . 733 - 36 . 66 - 36 . 557 - 36 . 555 - 36 . 537 - 36 . 506 - 36 . 497 - 36 . 454 - 36 . 441 - 36 . 413 - 36 . 275 - 36 . 273 - 36 . 142 - 36 . 121 - 36 . 106 - 36 . 098 - 36 . 019 - 36 . 01 - 35 . 945 - 35 . 905 - 35 . 896 - 35 . 786 - 35 . 647 - 35 . 579 - 35 . 578 - 35 . 49 - 35 . 471 - 35 . 46 - 35 . 431 - 35 . 421
0 . 00021524 0 . 00021851 0 . 00021851 0 . 00022192 0 . 00022253 0 . 00022835 0 . 00022835 0 . 00023303 0 . 00023303 0 . 00023384 0 . 00023875 0 . 0002398 0 . 0002398 0 . 00024147 0 . 00024147 0 . 00024164 0 . 0002488 0 . 00026149 0 . 00026171 0 . 00027163 0 . 00027653 0 . 00029769 0 . 00030172 0 . 00030731 0 . 00031552 0 . 00032107 0 . 00032298 0 . 00034518 0 . 00034751 0 . 00035232 0 . 00035232 0 . 00035549 0 . 00037248 0 . 00037355 0 . 00037616 0 . 00038126 0 . 00038232 0 . 00038462 0 . 00040279 0 . 00040279 0 . 00041648 0 . 00041719 0 . 00042138 0 . 00042412 0 . 00042518 0 . 00042518 0 . 00043453 0 . 00044836 0 . 00044836 0 . 00044995 0 . 00045294 0 . 00045294 0 . 00045612 0 . 00045672 0 . 00046024 0 . 00048023 0 . 00048023 0 . 00050121 0 . 00050362 0 . 00050445 0 . 00050445 0 . 00051939 0 . 00051939 0 . 00052703 0 . 00053013 0 . 00053013 0 . 00055314 0 . 00058202 0 . 00059467 0 . 00059467 0 . 00061464 0 . 0006149 0 . 0006154 0 . 00061837 0 . 00061882
40
45
50
55
60
65
US 9 , 970 , 056 B2 27
TABLE 3 - continued 28
TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
15
23223 2617
89910 5025 598
5127 1175 6683 27068 10489 3189 10948 80135 5515 25932 23315 5531
23201 5684 4891 3949 10049 23633 5716 303
3364 1725 9246 56995 1778
81622 124565 51112 5908 6418 79982
55759 8649 9604 51096 2802 240
6133 5734 8314 6117 28952 9854 80762 5479
51015 6619 23360 5045 8639
10159 116985 5036 25940 23157
254394
20
25
50
ET 30
35 52
RRP12 GARS UBEZB P2RX4 BCL2L1 CDK16 AP2S1 SPAST PPA2 LRRC41 HNRNPH3 STARD3 RPF1 PPP2CA CLIC4 SLC9A8 PPP4C FAM168A PSMA3 SLC11A2 LDLR DNAJB6 KPNA6 PSMD10 ANXA2P1 HUS1 DHPS UBE2L6 TULP4 DYNC1H1 UNC93B1 SLC38A10 TRAPPC12 RAP1B SET DNAJB14 ACP1 RPRD2 BCL11B GYS1 STAT2 HARS BNIPUL ABCAT UPP1 SLC20A1 PHKA2 FAM206A ATP2A2 CAB39 BAG4 HMG20B ANKFY1 DENR NFE2 TMEM127 PARK7 LGALS1 ARF5 BIRC2 NEK4 BSDC1 SERPINB6 SFPQ RAB33B C5orf15 ACTG1 CCTWA DAPP1 SRRM1 AGPAT5 TUBGCP2 GGCT EIF1 SON
- 35 . 411 - 35 . 293 - 35 . 281 - 35 . 177 - 35 . 157 - 35 . 088 - 35 . 051 - 34 . 952 - 34 . 882 - 34 . 87 - 34 . 839 - 34 . 762 - 34 . 758 - 34 . 729 - 34 . 697 - 34 . 682 - 34 . 641 - 34 . 597 - 34 . 567 - 34 . 563 - 34 . 528 - 34 . 514 - 34 . 506 - 34 . 49 - 34 . 46 - 34 . 438 - 34 . 435 - 34 . 413 - 34 . 404 - 34 . 345 - 34 . 282 - 34 . 282 - 34 . 253 - 34 . 244 - 34 . 233 - 34 . 211 - 34 . 134 - 34 . 113 - 34 . 096 - 34 . 062 - 34 - 33 . 969 - 33 . 967 - 33 . 923 - 33 . 905 - 33 . 868 - 33 . 85 - 33 . 839 - 33 . 804 - 33 . 779 - 33 . 71 - 33 . 635 - 33 . 613 - 33 . 604 - 33 . 57 - 33 . 477 - 33 . 466 - 33 . 464 - 33 . 443 - 33 . 417 - 33 . 375 - 33 . 348 - 33 . 34 - 33 . 312 - 33 . 263 - 33 . 138 - 33 . 055 - 32 . 98 - 32 . 973 - 32 . 973 - 32 . 962 - 32 . 938 - 32 . 922 - 32 . 913 - 32 . 903
0 . 00061918 0 . 00064581 0 . 00064653 0 . 0006705 0 . 00067249 0 . 00068853 0 . 00069365 0 . 00071307 0 . 00072598 0 . 00072598 0 . 00073301 0 . 00075303 0 . 00075303 0 . 00075963 0 . 00076745 0 . 00076941 0 . 00077757 0 . 00078687 0 . 00079266 0 . 00079266 0 . 00080186 0 . 00080383 0 . 00080389 0 . 00080682 0 . 00081204 0 . 00081204 0 . 00081204 0 . 00081451 0 . 00081501 0 . 00083006 0 . 00084692 0 . 00084692 0 . 00085147 0 . 00085147 0 . 00085147 0 . 00085336 0 . 00087342 0 . 00087824 0 . 00088085 0 . 0008812 0 . 0008962 0 . 0009032 0 . 0009032 0 . 0009174 0 . 00092165 0 . 0009332 0 . 00093469 0 . 00093616 0 . 00094727 0 . 00095167 0 . 00097654 0 . 00099902 0 . 0010054 0 . 0010065 0 . 0010154 0 . 0010521 0 . 0010521 0 . 0010521 0 . 0010584 0 . 0010669 0 . 0010825 0 . 0010916 0 . 0010926 0 . 0011023 0 . 0011188 0 . 0011671 0 . 0011939 0 . 0012244 0 . 0012244 0 . 0012244 0 . 0012244 0 . 0012333 0 . 0012372 0 . 0012372 0 . 0012372
E 23248 64919 2997 6773 3035 665
10347 7378 6574 5256
54942 488
51719 9530 10362 51479 8562 4778 55654 11315 3956 381 329
6787 55108 5269 6421 83452 56951
71 908
27071 10250 55326 10844 79017 10209 6651
WDR12 LAMTOR3 RNF14 UTP18 GOLGA3 ALOX5 RPLE PTGER4 BAP1 RPA1 CCDC22 C2CD2L NDFIP1 PPIB ISOC1 SNAPC3 FNBP4 FURIN ?0C3 ATP6AP2 ARAP1 PA2G4 FAM98A SEPT6 MCM9 ACO2 FAM76A RBM15 ARPCIA UGP2 XK BLCAP ATP8A1 ???? TAPBP FGR PDCD6IP TAP1 SLC46A3 TKT CACYBP CCDC25 GTDC1 DDX21 SACMIL ATG12 NDUFB5 PLEKHF2 ACP2 DUSP6 OCRL MED12 FAM175B TNFRSF14 CASP7 EDC4 TRIM44 ATP6V1H INPPL1 IKBKE MCOLN1 TFIP11 ARHGDIB EIF281 RFX5 PDHA1 EIF3H CBX3 RNF24 TNFAIP1 FLII GPN3 TOMM70A UCP2 GSPT1
- 32 . 901 - 32 . 884 - 32 . 833 - 32 . 82 - 32 . 811 - 32 . 808 - 32 . 776 - 32 . 77 - 32 . 764 - 32 . 738 - 32 . 738 - 32 . 733 - 32 . 703 - 32 . 682 - 32 . 66 - 32 . 635 - 32 . 626 - 32 . 626 - 32 . 62 - 32 . 582 - 32 . 572 - 32 . 538 - 32 . 531 - 32 . 513 - 32 . 446 - 32 . 441 - 32 . 438 - 32 . 436 - 32 . 396 - 32 . 351 - 32 . 337 - 32 . 329 - 32 . 255 - 32 . 221 - 32 . 208 - 32 . 117 - 32 . 101 - 32 . 087 - 32 . 032 - 31 . 998 - 31 . 994 - 31 . 989 - 31 . 968 - 31 . 964 - 31 . 902 - 31 . 901 - 31 . 868 - 31 . 862 - 31 . 854 - 31 . 844 - 31 . 824 - 31 . 79 - 31 . 771 - 31 . 752 - 31 . 732 - 31 . 714 - 31 . 71 - 31 . 666 - 31 . 664 - 31 . 636 - 31 . 607 - 31 . 594 - 31 . 591 - 31 . 571 - 31 . 566 - 31 . 529 - 31 . 494 - 31 . 487 - 31 . 485 - 31 . 478 - 31 . 474 - 31 . 472 - 31 . 452 - 31 . 446 - 31 . 443
199870 64783 10552 7360 7504 10904 10396 51727 6892 2268 10015 6890
283537 7086
27101 55246 79712 9188 22908 9140 4711 79666
53 1848 4952 9968 23172 8764 840
23644 54765 51606 3636 9641
57192 24144
397 1965 5993 5160 8667 11335 11237 7126 2314 51184 9868 7351 2935
40
0 . 0012372 0 . 0012419 0 . 001265 0 . 0012651 0 . 0012651 0 . 0012651 0 . 0012755 0 . 0012758 0 . 0012758 0 . 0012794 0 . 0012794 0 . 0012794 0 . 0012889 0 . 0012969 0 . 0013053 0 . 0013141 0 . 0013141 0 . 0013141 0 . 0013143 0 . 0013308 0 . 0013308 0 . 0013467 0 . 0013472 0 . 0013536 0 . 0013746 0 . 0013746 0 . 0013746 0 . 0013746 0 . 0013939 0 . 0014138 0 . 0014185 0 . 0014199 0 . 0014602 0 . 0014775 0 . 0014821 0 . 0015318 0 . 0015383 0 . 0015437 0 . 0015755 0 . 0015928 0 . 0015928 0 . 0015928 0 . 0016017 0 . 0016017 0 . 0016332 0 . 0016332 0 . 0016513 0 . 0016519 0 . 0016539 0 . 0016568 0 . 0016666 0 . 0016866 0 . 0016962 0 . 0017055 0 . 001716 0 . 0017201 0 . 0017201 0 . 0017454 0 . 0017454 0 . 0017579 0 . 0017671 0 . 0017713 0 . 0017713 0 . 0017823 0 . 0017823 0 . 0018051 0 . 001813 0 . 001813 0 . 001813 0 . 001813 0 . 001813 0 . 001813 0 . 0018237 0 . 0018237 0 . 0018237
45
50
55
60
?? ?? ?? ?? ?? ??
65
US 9 , 970 , 056 B2 29 30
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
55754 23549 6888 9788 26608 10 522
20
25
30
35
55379 4144 10399 56910 51614 2821
10678 8536 9610
23637 25939 6829 26528 5526
27163 22868 4784 10653 55544
835 23608 79036 4057
90273 6622 23081 10666 6940 9911
22985 58497 11116 873
91782 55193 1124
34 7410
167227 29015 10480 3106
55082 6256 919
23309 8029 6721 22827 2969 5184 822
56950 6902 3054 307
22870 51316 51566 55341 55810 5250 8683
25896 26499 79718 4287 4615 4860
TMEM30A DNPEP TALDO1 MTSS1 TBL2 ATP5J LRRC59 MAT2A GNB2L1 STARD ERGIC3 GPI BØGNT2 CAMK1 RIN1 RABGAP1 SAMHD1 SUPTSH DAZAP1 PPP2R5B NAAA FASTKD2 NFIX SPINT2 RBM38 CASP2 MKRN1 KXD1 LTF CEACAM21 SNCA KDM4C CD226 ZNF354A TMCC2 ACIN1 PRUNE FGFR1OP CBR1 CHMP7 PBRM1 CHN2 ACADM VAV2 DCP2 SLC43A3 EIF3M HLA - B ARGLU1 RXRA CD247 SINGB CUBN SREBF2 PUF60 GTF2? PEPD CAPG SMYD2 TBCA HCFC1 ANXA4 PPPOR1 PLAC8 ARMCX3 LSG1 FOXJ2 SLC25A3 SRSF9 INTS7 PLEK2 TBL1XR1 ATXN3 MYD88 PNP
- 31 . 394 - 31 . 393 - 31 . 389 - 31 . 34 - 31 . 295 - 31 . 294 - 31 . 271 - 31 . 264 - 31 . 233 - 31 . 166 - 31 . 166 - 31 . 14 - 31 . 138 - 31 . 138 - 31 . 126 - 31 . 112 - 31 . 075 - 31 . 06 - 31 . 049 - 31 . 037 - 31 . 034 - 31 . 032 - 31 . 025 - 31 . 023 - 31 . 014 - 30 . 976 - 30 . 942 - 30 . 905 - 30 . 878 - 30 . 828 - 30 . 81 - 30 . 762 - 30 . 747 - 30 . 731 - 30 . 713 - 30 . 686 - 30 . 682 - 30 . 655 - 30 . 639 - 30 . 621 - 30 . 572 - 30 . 544 - 30 . 538 - 30 . 535 - 30 . 5 - 30 . 477 - 30 . 474 - 30 . 439 - 30 . 427 - 30 . 424 - 30 . 395 - 30 . 393 - 30 . 384 - 30 . 382 - 30 . 356 - 30 . 327 - 30 . 275 - 30 . 246 - 30 . 238 - 30 . 235 - 30 . 232 - 30 . 231 - 30 . 219 - 30 . 201 - 30 . 137 - 30 . 128 - 30 . 11 - 30 . 099 - 30 . 058 - 30 . 047 - 30 . 018 - 30 . 003 - 29 . 953 - 29 . 926 - 29 . 886
0 . 0018453 0 . 0018453 0 . 0018453 0 . 0018746 0 . 0019032 0 . 0019032 0 . 0019146 0 . 0019146 0 . 0019314 0 . 0019775 0 . 0019775 0 . 0019877 0 . 0019877 0 . 0019877 0 . 0019938 0 . 0020013 0 . 0020273 0 . 002036 0 . 0020415 0 . 0020431 0 . 0020431 0 . 0020431 0 . 0020431 0 . 0020431 0 . 0020461 0 . 0020746 0 . 0020992 0 . 0021228 0 . 0021422 0 . 0021781 0 . 0021859 0 . 002225 0 . 0022299 0 . 0022409 0 . 0022524 0 . 0022681 0 . 0022681 0 . 0022891 0 . 0023003 0 . 0023125 0 . 0023458 0 . 0023635 0 . 0023635 0 . 0023635 0 . 0023849 0 . 0023967 0 . 0023967 0 . 0024222 0 . 0024286 0 . 0024286 0 . 0024504 0 . 0024504 0 . 0024524 0 . 0024524 0 . 0024695 0 . 0024948 0 . 0025387 0 . 0025613 0 . 0025613 0 . 0025613 0 . 0025613 0 . 0025613 0 . 0025694 0 . 0025836 0 . 0026427 0 . 0026481 0 . 0026621 0 . 0026701 0 . 0027048 0 . 002712 0 . 0027397 0 . 0027525 0 . 002804 0 . 0028249 0 . 0028665
261726 355
55291 162427
708 3184 3267
25771 1808 9208 10859 60684 27430 5261 4478
51084 51755 55207 2550
27069 2729 4772 3181 9341 645
5293 9589 3190
23335 5584 55689 5579 4141 89781 23064 6746 9402 6947 4967 578 5982 5310 10066 84726 28951 4061 10623 51368 29109 2879 5782 3566 7127
60468 1847
113251 55072 6904
399665 833
5447 3936 997
10963 80256 1385
64419 80169 30001 28511 1938
51098 7347 272
57610
TIPRL FAS PPP6R3 FAM134C C1QBP HNRNPD AGFG1 TBC1D22A DPYSL2 LRRFIP1 LILRB1 TRAPPC11 MAT2B PHKG2 MSN CRYL1 CDK12 ARLSB GABBR1 GHITM GCLC NFATC1 HNRNPA2B1 VAMP3 BLVRB PIK3CD WTAP HNRNPK WDR7 PRKCI YEATS2 PRKCB MARS HPS4 SETX SSR2 GRAP2 TCN1 OGDH BAK1 RFC2 PKD1 SCAMP2 PRRC2B TRIB2 LYCE POLR3C TEX264 FHOD1 GPX4 PTPN12 ILAR TNFAIP2 BACH2 DUSP5 LARP4 RNF31 TBCD FAM102A CARS POR LCP1 CDC34 STIP1 FAM214B CREB1 MTMR14 ???1 EROIL NKIRAS2 EEF2 IFT52 UCHL3 AMPD3 RANBP10
- 29 . 866 - 29 . 845 - 29 . 817 - 29 . 806 - 29 . 773 - 29 . 77 - 29 . 759 - 29 . 757 - 29 . 741 - 29 . 723 - 29 . 718 - 29 . 716 - 29 . 713 - 29 . 708 - 29 . 687 - 29 . 676 - 29 . 669 - 29 . 666 - 29 . 629 - 29 . 62 - 29 . 573 - 29 . 559 - 29 . 544 - 29 . 523 - 29 . 514 - 29 . 51 - 29 . 504 - 29 . 486 - 29 . 455 - 29 . 448 - 29 . 435 - 29 . 414 - 29 . 389 - 29 . 372 - 29 . 362 - 29 . 302 - 29 . 256 - 29 . 228 - 29 . 219 - 29 . 178 - 29 . 158 - 29 . 137 - 29 . 118 - 29 . 117 - 29 . 09 - 29 . 052 - 29 . 047 - 29 . 046 - 29 . 029 - 29 . 008 - 28 . 996 - 28 . 993 - 28 . 986 - 28 . 975 - 28 . 974 - 28 . 972 - 28 . 948 - 28 . 947 - 28 . 923 - 28 . 921 - 28 . 906 - 28 . 892 - 28 . 845 - 28 . 808 - 28 . 793 - 28 . 787 - 28 . 785 - 28 . 781 - 28 . 774 - 28 . 755 - 28 . 745 - 28 . 743 - 28 . 741 - 28 . 709 - 28 . 703
0 . 0028846 0 . 0029044 0 . 0029321 0 . 0029403 0 . 0029737 0 . 0029737 0 . 0029787 0 . 0029787 0 . 0029885 0 . 0030017 0 . 0030017 0 . 0030017 0 . 0030017 0 . 0030029 0 . 0030232 0 . 0030318 0 . 0030343 0 . 0030343 0 . 003075 0 . 0030804 0 . 0031352 0 . 003147 0 . 003156 0 . 0031782 0 . 0031791 0 . 0031791 0 . 0031813 0 . 0031941 0 . 0032189 0 . 0032229 0 . 0032342 0 . 0032563 0 . 0032796 0 . 0032968 0 . 0033043 0 . 0033804 0 . 0034268 0 . 0034603 0 . 0034673 0 . 0035202 0 . 0035432 0 . 0035617 0 . 0035789 0 . 0035789 0 . 0036074 0 . 003638 0 . 003638 0 . 003638 0 . 0036544 0 . 0036652 0 . 0036696 0 . 0036696 0 . 0036743 0 . 0036772 0 . 0036772 0 . 0036772 0 . 0036989 0 . 0036989 0 . 0037213 0 . 0037213 0 . 0037382 0 . 0037527 0 . 0038195 0 . 0038716 0 . 0038822 0 . 0038832 0 . 0038832 0 . 0038846 0 . 0038899 0 . 0039071 0 . 0039121 0 . 0039121 0 . 0039121 0 . 0039511 0 . 0039541
40
45
: 50
|
55
60
65
US 9 , 970 , 056 B2 32
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
20
25
30
35
9869 1974 6277 6279 6760 6132 57698 3087 2548 9775 4090 7317
92017 4363 3055
55623 4758 54440 51510 79752 7024 974
81603 10282 23603 22934 8674 1796
57194 5739 4066 8312
64343 6729 80301 10299 7316 7318
55039 29915 11040 4609 8774 6924
51329 4190 79065 6883 23299 3093
55293 79939 23244 5691 5777
29086 166
51008 3418
56983 8650 2120 23276 27230 3590 4173
51637 2773 3104 9467 2242 8243
81689 5886 10379
SETDB1 EIF4A2 S100A6 S100A8 SS18 RPL8 KIAA1598 HHEX GAA EIF4A3 SMAD5 UBA1 SNX29 ABCC1 ??? THUMPD1 NEU1 SASH3 CHMP5 ZFAND1 TFCP2 CD79B TRIM8 BET1 COROIC RPIA VAMP4 DOK1 ATP10A PTGIR LYL1 AXIN1 AZI2 SRP54 PLEKHO2 MARCH6 UBC UBAT TRMT12 HCFC2 PIM2 MYC NAPG TCEB3 ARL61P4 MDH1 ATG9A TAF12 BICD2 UBEZK UEVLD SLC35E1 PDS5A PSMB3 PTPN6 BABAM1 AES ASCC1 IDH2 POGLUT1 NUMB ETV6 KLHL18 SERP1 IL1IRA MCM4 C14orf166 GNAI3 ZBTB48 SH???5 FES SMC1A ISCA1 RAD23A IRF9
- 28 . 696 - 28 . 679 - 28 . 679 - 28 . 677 - 28 . 67 - 28 . 643 - 28 . 642 - 28 . 628 - 28 . 598 - 28 . 562 - 28 . 558 - 28 . 556 - 28 . 544 - 28 . 525 - 28 . 521 - 28 . 516 - 28 . 514 - 28 . 5 - 28 . 491 - 28 . 484 - 28 . 466 - 28 . 443 - 28 . 424 - 28 . 401 - 28 . 398 - 28 . 387 - 28 . 363 - 28 . 351 - 28 . 335 - 28 . 314 - 28 . 306 - 28 . 305 - 28 . 293 - 28 . 272 - 28 . 27 - 28 . 253 - 28 . 238 - 28 . 233 - 28 . 177 - 28 . 173 - 28 . 163 - 28 . 158 - 28 . 152 - 28 . 15 - 28 . 148 - 28 . 091 - 28 . 089 - 28 . 088 - 28 . 085 - 28 . 082 - 28 . 081 - 28 . 074 - 28 . 061 - 28 . 042 - 28 . 032 - 28 . 011 - 27 . 986 - 27 . 976 - 27 . 961 - 27 . 961 - 27 . 949 - 27 . 925 - 27 . 911 - 27 . 896 - 27 . 889 - 27 . 843 - 27 . 838 - 27 . 83 - 27 . 827 - 27 . 789 - 27 . 786 - 27 . 733 - 27 . 728 - 27 . 723 - 27 . 713
0 . 0039603 0 . 0039726 0 . 0039726 0 . 0039726 0 . 0039773 0 . 0040108 0 . 0040108 0 . 0040273 0 . 0040705 0 . 004122 0 . 004122 0 . 004122 0 . 0041367 0 . 0041571 0 . 0041571 0 . 0041571 0 . 0041571 0 . 0041684 0 . 0041762 0 . 0041825 0 . 0042074 0 . 0042402 0 . 0042671 0 . 0042996 0 . 0042996 0 . 0043054 0 . 0043396 0 . 0043495 0 . 0043724 0 . 0044036 0 . 0044061 0 . 0044061 0 . 0044211 0 . 0044492 0 . 0044492 0 . 0044742 0 . 0044951 0 . 0044985 0 . 0045934 0 . 0045943 0 . 0046059 0 . 0046084 0 . 0046084 0 . 0046084 0 . 0046084 0 . 004683 0 . 004683 0 . 004683 0 . 004683 0 . 004683 0 . 004683 0 . 004689 0 . 0047073 0 . 0047362 0 . 0047498 0 . 0047828 0 . 0048254 0 . 0048376 0 . 0048533 0 . 0048533 0 . 0048696 0 . 0049103 0 . 0049326 0 . 0049548 0 . 0049631 0 . 0050416 0 . 0050438 0 . 0050468 0 . 0050468 0 . 005109 0 . 005109 0 . 0051976 0 . 0052027 0 . 0052043 0 . 005213
2222 2764
55823 54902 4063 7818 5426 64768 5909 7100 5119 4601 3326 4296 79980 55156
301 29894 3394 6723 81611 9852 7433 22887 3661 6595 64897 284904
3015 10527 3429
55164 3934
26354 5613
64118 2181 6990 6636 8451 23762 4720 8462
51701 9203 1716
200081 1389 26034 3784 26119 10092 11336 11171 9184 3313 23457 1200 8295 1642
10947 9129 2208 10460 10627 10723 91860 4678 9600 10367 6237 8891 1408
23353 60488
FDFT1 GMFB VPS11 TTC19 LYO DAP3 POLE IPPK RAPIGAP TLR5 CHMP1A MXI1 HSP90AB1 MAP3K11 DSN1 ARMC1 ANXA1 CPSF1 IRF8 SRM ANP32E EPM2AIP1 VIPR1 FOXJ3 IRF3 SMARCA2 C12orf43 SEC14L4 H2AFZ IPO7 IF127 SHQ1 LCN2 GNL3 PRKX DUSIL ACSL3 DYNLT3 SNRPF CUL4A OSBP2 NDUFS2 KLF11 NLK ZMYM3 DGUOK TXLNA CREBL2 IPCEF1 KCNQ1 LDLRAP1 ARPC5 EXOC3 STRAP BUB3 HSPA9 ABCB9 TPP1 TRRAP DDB1 AP3M2 PRPF3 FCER2 TACC3 MYL12A SLC12A7 CALML4 NASP PITPNM1 MICU1 RRAS EIF2B3 CRY2 SUN1 MRPS35
- 27 . 707 - 27 . 702 - 27 . 696 - 27 . 693 - 27 . 692 - 27 . 685 - 27 . 681 - 27 . 68 - 27 . 671 - 27 . 663 - 27 . 662 - 27 . 638 - 27 . 607 - 27 . 596 - 27 . 596 - 27 . 587 - 27 . 583 - 27 . 557 - 27 . 552 - 27 . 549 - 27 . 544 - 27 . 544 - 27 . 535 - 27 . 502 - 27 . 492 - 27 . 455 - 27 . 453 - 27 . 45 - 27 . 443 - 27 . 389 - 27 . 385 - 27 . 375 - 27 . 371 - 27 . 369 - 27 . 361 - 27 . 358 - 27 . 331 - 27 . 324 - 27 . 301 - 27 . 296 - 27 . 295 - 27 . 291 - 27 . 285 - 27 . 272 - 27 . 266 - 27 . 264 - 27 . 254 - 27 . 253 - 27 . 253 - 27 . 245 - 27 . 244 - 27 . 236 - 27 . 221 - 27 . 212 - 27 . 176 - 27 . 127 - 27 . 103 - 27 . 085 - 27 . 072 - 27 . 071 - 27 . 067 - 27 . 044 - 27 . 039 - 27 . 035 - 27 . 034 - 27 . 027 - 27 . 01 - 26 . 979 - 26 . 977 - 26 . 975 - 26 . 972 - 26 . 971 - 26 . 968 - 26 . 952 - 26 . 946
0 . 0052153 0 . 0052153 0 . 0052153 0 . 0052153 0 . 0052153 0 . 0052199 0 . 0052199 0 . 0052199 0 . 005233 0 . 0052383 0 . 0052383 0 . 0052804 0 . 0053394 0 . 0053502 0 . 0053502 0 . 0053556 0 . 0053556 0 . 0053921 0 . 0053921 0 . 0053921 0 . 0053921 0 . 0053921 0 . 0054041 0 . 0054639 0 . 0054771 0 . 0055362 0 . 0055362 0 . 0055362 0 . 0055448 0 . 0056436 0 . 0056461 0 . 0056597 0 . 0056597 0 . 0056597 0 . 0056701 0 . 0056701 0 . 0057194 0 . 0057275 0 . 0057664 0 . 0057664 0 . 0057664 0 . 0057664 0 . 0057664 0 . 0057899 0 . 0057925 0 . 0057925 0 . 0057925 0 . 0057925 0 . 0057925 0 . 0057986 0 . 0057986 0 . 0058092 0 . 0058364 0 . 0058516 0 . 0059296 0 . 0060305 0 . 0060816 0 . 0061111 0 . 0061294 0 . 0061294 0 . 0061315 0 . 0061669 0 . 006169 0 . 006169 0 . 006169 0 . 0061798 0 . 0062129 0 . 006258 0 . 006258 0 . 006258 0 . 006258 0 . 006258 0 . 0062589 0 . 0062837 0 . 0062884
40
45
50
55
60
65
US 9 , 970 , 056 B2 33 34
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Gene symbol ( Name )
Combined Tstat
Combined Pval ID
10
20
25
30
35
10549 152006 80895 6293 900 9993 54606 6302 26190 1176 5685
10128 51074 55114 3702 10482 29102 3726 9044 517
1843 9150 8775 50807 3759 10900 10404 55738 8662 5524
51279 23171 29916 55884 6480 30844 8408 7453
53944 103
4123 23164 9451 10280 91137 60685 5610 5598 8664 7726 25941
261734 133
54622 63925 3431 6272 10954 55249 80152 80279 3460
54664 55101 1981 5747
11180 10221 6571
84164 84061 7297 1431 2108 2733
PRDX4 RNF38 ILKAP VPS52 CCNG1 DGCR2 DDX56 TSPAN31 FBXW2 AP3S1 PSMA4 LRPPRC APIP ARHGAP17 ITK NXF1 DROSHA JUNB BTAF1 ATP5G2 DUSP1 CTDP1 NAPA ASAP1 KCNJ2 RUNDC3A ??? ARFGAP1 EIF3B PPP2R4 CIRL GPDIL SNX11 WSB2 STOGAL1 EHD4 ULK1 WARS CSNK1G1 ADAR MAN2C1 MPRIP EIF2AK3 SIGMAR1 SLC25A46 ZFAND3 EIF2AK2 MAPK7 EIF3D TRIM26 TPGS2 NPHP4 ADM ARL15 ZNF335 SP110 SORT1 PDIA5 YY1AP1 CENPT CDKSRAP3 IFNGR2 TMEM106B ATP5SL EIF4G1 PTK2 WDR6 TRIB1 SLC18A2 ASCC2 MAGT1 TYK2 CS ETFA GLE1
- 26 . 944 - 26 . 931 - 26 . 928 - 26 . 922 - 26 . 902 - 26 . 888 - 26 . 876 - 26 . 869 - 26 . 863 - 26 . 851 - 26 . 845 - 26 . 845 - 26 . 839 - 26 . 827 - 26 . 818 - 26 . 808 - 26 . 806 - 26 . 803 - 26 . 786 - 26 . 78 - 26 . 779 - 26 . 752 - 26 . 73 - 26 . 728 - 26 . 726 - 26 . 723 - 26 . 705 - 26 . 693 - 26 . 69 - 26 . 668 - 26 . 647 - 26 . 586 - 26 . 582 - 26 . 57 - 26 . 565 - 26 . 553 - 26 . 544 - 26 . 535 - 26 . 534 - 26 . 531 - 26 . 525 - 26 . 521 - 26 . 518 - 26 . 513 - 26 . 51 - 26 . 502 - 26 . 5 - 26 . 496 - 26 . 474 - 26 . 47 - 26 . 467 - 26 . 466 - 26 . 457 - 26 . 455 - 26 . 434 - 26 . 43 - 26 . 416 - 26 . 411 - 26 . 392 - 26 . 384 - 26 . 38 - 26 . 371 - 26 . 358 - 26 . 357 - 26 . 355 - 26 . 345 - 26 . 329 - 26 . 328 - 26 . 312 - 26 . 304 - 26 . 273 - 26 . 257 - 26 . 256 - 26 . 246 - 26 . 24
0 . 0062884 0 . 0063147 0 . 0063157 0 . 0063222 0 . 0063665 0 . 0063776 0 . 0064004 0 . 0064043 0 . 0064129 0 . 0064279 0 . 0064303 0 . 0064303 0 . 0064357 0 . 0064605 0 . 0064687 0 . 0064771 0 . 0064771 0 . 0064771 0 . 0065036 0 . 0065036 0 . 0065036 0 . 0065592 0 . 0066028 0 . 0066028 0 . 0066028 0 . 0066038 0 . 0066447 0 . 0066679 0 . 0066687 0 . 0067123 0 . 0067486 0 . 006904 0 . 0069059 0 . 0069302 0 . 0069361 0 . 0069623 0 . 0069793 0 . 0069838 0 . 0069838 0 . 0069848 0 . 0069949 0 . 006996 0 . 0069969 0 . 007005 0 . 0070061 0 . 0070175 0 . 0070175 0 . 007022 0 . 0070729 0 . 0070729 0 . 0070729 0 . 0070729 0 . 0070902 0 . 0070902 0 . 0071398 0 . 0071448 0 . 0071764 0 . 0071837 0 . 0072284 0 . 0072429 0 . 0072475 0 . 0072649 0 . 0072876 0 . 0072876 0 . 0072876 0 . 00731 0 . 0073438 0 . 0073438 0 . 0073812 0 . 0073978 0 . 0074712 0 . 0075 0 . 0075 0 . 007521 0 . 0075299
27044 79621
203197 1536
78991 10270
30 10445 80218 54805 2004 7536 4354
124583 27332 1432 3148 9314 9654 8883 9181 22902 4659 7111 8260 483
27032 7071
55297 51006 11078 4713 6891 79573 8898
54436 199
9738 27183 5690 1232 6446 2581 5330 7690
55148 3932
55827 7443 3043
56965 6427 23214 8804
552889 10295 25839 65980 57050
955 9325 84516 26065 7342 7716 2643
51728 29959 51108 79134 6814
64210 3268
55681 10134
SND1 RNASEH2B C9orf91 CYBB PCYOX1L AKAP8 ACAA1 MCRS1 NAA50 CNNM2 ELK3 SF1 MPP1 CANT1 ZNF638 MAPK14 HMGB2 KLF4 TTLL4 NAE1 ARHGEF2 RUFY3 PPP1R12A TMOD1 NAA10 ATP1B3 ATP2C1 KLF10 CCDC91 SLC35C2 TRIOBP NDUFB7 TAP2 TTC13 MTMR2 SHATC1 AIF1 CCP110 VPS4A PSMB2 CCR3 SGK1 GALC PLCB2 ZNF131 UBR7 LCK DCAF6 VRK1 HBB PARP6 SRSF2 XPO6 CREG1 ATXN7L3B BCKDK COG4 BRDO UTP3 ENTPD6 TRIP4 DCTN5 LSM14A UBP1 VEZF1 GCH1 POLR3K NRBP1 METTL9 TMEM185B STXBP3 MMS19 AGFG2 SCYL2 BCAP31
- 26 . 236 - 26 . 232 - 26 . 204 - 26 . 192 - 26 . 189 - 26 . 188 - 26 . 185 - 26 . 173 - 26 . 169 - 26 . 167 - 26 . 158 - 26 . 153 - 26 . 149 - 26 . 147 - 26 . 114 - 26 . 097 - 26 . 086 - 26 . 081 - 26 . 077 - 26 . 076 - 26 . 076 - 26 . 073 - 26 . 062 - 26 . 049 - 26 . 049 - 26 . 047 - 26 . 042 - 26 . 019 - 26 . 011 - 26 . 008 - 26 . 001 - 25 . 999 - 25 . 982 - 25 . 981 - 25 . 975 - 25 . 968 - 25 . 943 - 25 . 885 - 25 . 874 - 25 . 868 - 25 . 863 - 25 . 852 - 25 . 834 - 25 . 826 - 25 . 818 - 25 . 816 - 25 . 813 - 25 . 789 - 25 . 78 - 25 . 769 - 25 . 76 - 25 . 758 - 25 . 712 - 25 . 711 - 25 . 71 - 25 . 689 - 25 . 685 - 25 . 667 - 25 . 654 - 25 . 654 - 25 . 652 - 25 . 628 - 25 . 611 - 25 . 603 - 25 . 601 - 25 . 601 - 25 . 586 - 25 . 583 - 25 . 569 - 25 . 518 - 25 . 517 - 25 . 489 - 25 . 476 - 25 . 475 - 25 . 468
0 . 0075329 0 . 0075366 0 . 0076073 0 . 0076297 0 . 0076297 0 . 0076297 0 . 0076297 0 . 0076586 0 . 0076626 0 . 0076626 0 . 0076809 0 . 0076864 0 . 0076905 0 . 0076905 0 . 0077815 0 . 0078275 0 . 0078509 0 . 0078509 0 . 0078509 0 . 0078509 0 . 0078509 0 . 0078535 0 . 0078736 0 . 007893 0 . 007893 0 . 007893 0 . 0078995 0 . 0079634 0 . 0079794 0 . 0079814 0 . 0079861 0 . 0079861 0 . 0080248 0 . 0080248 0 . 0080367 0 . 0080502 0 . 0081228 0 . 008295 0 . 0083224 0 . 0083316 0 . 0083415 0 . 0083555 0 . 008403 0 . 0084203 0 . 0084359 0 . 0084359 0 . 0084382 0 . 0085086 0 . 0085235 0 . 0085512 0 . 0085612 0 . 0085612 0 . 0086809 0 . 0086809 0 . 0086809 0 . 008737 0 . 0087405 0 . 0087683 0 . 0087859 0 . 0087859 0 . 0087859 0 . 008843 0 . 0088781 0 . 0088825 0 . 0088825 0 . 0088825 0 . 0089219 0 . 0089221 0 . 0089625 0 . 0091319 0 . 0091319 0 . 0092145 0 . 0092479 0 . 0092479 0 . 0092621
40
45
i 50
f
55
60
65
US 9 , 970 , 056 B2 36 36 35
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10 l
5606 9810 55000 115353 5550 5696 682
10691 10127 9862 7421
22916 6182 327 834
4076 55863 1236
51056 317662
5682 596
9217 6185 27247 26039 3185 210
55803 51564 81542 9531 9039 7095 5925 8209 8893 7385 9990 25966
829 55719 3836 9275
65220 6398
20
3257 6634 3101
26017 29926 1032
79096 27020 23191 80833 1606
25792 3162
25977 6901 8115 7009 27240
388 3684
55788 9474 9489 10312 22818 2739
81688 6934 54941 11157 9049 80740
256987 1089
51069 10019
HPS1 SNRPD3 HK3 FAM32A GMPPA CDKN2D Cilorf49 NPTN CYFIP1 APOL3 DGKA CIZI HMOX1 NECAP1 TAZ TCL1A TMBIM6 SIT1 RHOB ITGAM LMBRD1 ATG5 PGS1 TCIRG1 COPZ1 GLO1 C6orf62 TCF7L2 RNF125 LSM6
25
30 AIP
35 523
MAP2K3 RNF40 TUG1 LRRC42 PREP PSMBS BSG GMEB1 ZNF263 MED24 VDR NCBP2 MRPL12 APEH CASP1 CAPRIN1 TMEM126B CCR7 LAP3 FAM149B1 PSMA1 BCL2 VAPB RPN2 NFU1 SS18L1 HNRNPF ALAD ADAP2 HDAC7 TMX1 BAG3 UBA3 SEC62 RB1 C2lorf33 EIF2B5 UQCRC2 SLC12A6 C2CD2 CAPZA1 FAM178A KPNA1 BCL7B NADK SECTM1 ADCY7 MAN2B2 ELAVL1 NDUFA4L2 ALDH3B1 MARCH5 MSL2 HIST1 H4E FYB CLIP4 ???? CIC AP2B1 PAPD7 CA2 HMG20A OPA1 PIK3IP1 COPS3 SIAH2 DSTN USP21 SPAG7 MATR3 CHMP4A VAMP1 LAMP3 RPN1 HECTD3
- 25 . 461 - 25 . 445 - 25 . 441 - 25 . 411 - 25 . 409 - 25 . 394 - 25 . 387 - 25 . 382 - 25 . 381 - 25 . 376 - 25 . 361 - 25 . 349 - 25 . 346 - 25 . 332 - 25 . 32 - 25 . 32 - 25 . 31 - 25 . 309 - 25 . 305 - 25 . 29 - 25 . 28 - 25 . 266 - 25 . 264 - 25 . 259 - 25 . 247 - 25 . 234 - 25 . 231 - 25 . 227 - 25 . 226 - 25 . 224 - 25 . 222 - 25 . 209 - 25 . 189 - 25 . 186 - 25 . 176 - 25 . 161 - 25 . 144 - 25 . 133 - 25 . 128 - 25 . 127 - 25 . 114 - 25 . 091 - 25 . 083 - 25 . 07 - 25 . 066 - 25 . 053 - 25 . 052 - 25 . 044 - 25 . 032 - 25 . 028 - 25 . 023 - 25 . 008 - 24 . 999 - 24 . 998 - 24 . 995 - 24 . 994 - 24 . 985 - 24 . 984 - 24 . 981 - 24 . 979 - 24 . 976 - 24 . 971 - 24 . 965 - 24 . 951 - 24 . 946 - 24 . 934 - 24 . 923 - 24 . 913 - 24 . 898 - 24 . 895 - 24 . 891 - 24 . 89 - 24 . 888 - 24 . 876 - 24 . 875
0 . 0092784 0 . 0093124 0 . 0093152 0 . 0094161 0 . 0094161 0 . 0094626 0 . 0094767 0 . 0094767 0 . 0094767 0 . 0094843 0 . 009532 0 . 009566 0 . 0095713 0 . 0096029 0 . 0096224 0 . 0096224 0 . 0096442 0 . 0096442 0 . 0096499 0 . 0096913 0 . 0097201 0 . 0097619 0 . 0097619 0 . 0097714 0 . 0098104 0 . 0098413 0 . 0098413 0 . 0098413 0 . 0098413 0 . 0098413 0 . 0098413 0 . 0098719 0 . 009942 0 . 0099435 0 . 0099732 0 . 010013 0 . 01006 0 . 010094 0 . 010102 0 . 010102 0 . 010126 0 . 010206 0 . 010229 0 . 01027 0 . 010277 0 . 010318 0 . 010318 0 . 010338 0 . 010368 0 . 010377 0 . 010385 0 . 010427 0 . 010448 0 . 010448 0 . 010448 0 . 010448 0 . 01047 0 . 01047 0 . 010472 0 . 010472 0 . 010475 0 . 010487 0 . 010491 0 . 010533 0 . 010541 0 . 010582 0 . 010616 0 . 010648 0 . 010684 0 . 010685 0 . 010687 0 . 010687 0 . 010689 0 . 010712 0 . 010712
- 24 . 873 - 24 . 855 - 24 . 848 - 24 . 847 - 24 . 841 - 24 . 835 - 24 . 832 - 24 . 83 - 24 . 825 - 24 . 804 - 24 . 803 - 24 . 8 - 24 . 798 - 24 . 797 - 24 . 795 - 24 . 794 - 24 . 792 - 24 . 78 - 24 . 779 - 24 . 775 - 24 . 764 - 24 . 75 - 24 . 748 - 24 . 747 - 24 . 722 - 24 . 715 - 24 . 708 - 24 . 704 - 24 . 698 - 24 . 691 - 24 . 672 - 24 . 658 - 24 . 657 - 24 . 648 - 24 . 64 - 24 . 639 - 24 . 623 - 24 . 61 - 24 . 591 - 24 . 579 - 24 . 577 - 24 . 574 - 24 . 566 - 24 . 557 - 24 . 547 - 24 . 54 - 24 . 538 - 24 . 528 - 24 . 525 - 24 . 524 - 24 . 52 - 24 . 49 - 24 . 46 - 24 . 44 - 24 . 439 - 24 . 437 - 24 . 436 - 24 . 434 - 24 . 431 - 24 . 43 - 24 . 413 - 24 . 409 - 24 . 404 - 24 . 403 - 24 . 387 - 24 . 386 - 24 . 382 - 24 . 368 - 24 . 368 - 24 . 358 - 24 . 357 - 24 . 356 - 24 . 348 - 24 . 34 - 24 . 336
40
0 . 010713 0 . 010767 0 . 010785 0 . 010785 0 . 010798 0 . 010816 0 . 010817 0 . 010819 0 . 010829 0 . 010885 0 . 010885 0 . 010885 0 . 010885 0 . 010885 0 . 010885 0 . 010885 0 . 010885 0 . 010917 0 . 010917 0 . 010925 0 . 010962 0 . 01101 0 . 01101 0 . 01101 0 . 011098 0 . 011117 0 . 011127 0 . 011135 0 . 011153 0 . 011175 0 . 011248 0 . 011296 0 . 011296 0 . 011323 0 . 011345 0 . 011345 0 . 011396 0 . 011434 0 . 0115 0 . 01154 0 . 01154 0 . 011546 0 . 011561 0 . 011595 0 . 011618 0 . 011639 0 . 011639 0 . 011674 0 . 011674 0 . 011674 0 . 01168 0 . 01179 0 . 011899 0 . 011962 0 . 011962 0 . 011962 0 . 011962 0 . 011962 0 . 011962 0 . 011962 0 . 012028 0 . 012035 0 . 012045 0 . 012045 0 . 012095 0 . 012095 0 . 012103 0 . 01214 0 . 01214 0 . 012163 0 . 012163 0 . 012163 0 . 012194 0 . 012208 0 . 012216
113
45
LYG6C SERINC5 CEACAM4 MRPL2 SH2B3 AT?6?1A AICDA CLTA CD63 PTGES2 BRD3 TMEM51 UOCRFS1 LRIF1 YTHDC2 TNFRSF1B CLEC4A CCT5 THAP11 SCP2 EPOR MCL1 LTBR AHSA1 NCF4 DR1 GLOD4 MTHFD1 DCAF8 RFK SOAT1 LIG4 UBE2J1 POLDIP2 TPD52L2 RIN2 FAM111A TFAM SLC16A3 MAPRE1 NCOA3 NRD1 SHC1 SLC35D2
57379 1211 967
80142 8019
55092 7386
55791 64848 7133
50856 22948 57215 6342 2057 4170 4055 10598 4689 1810 51031 4522 50717 55312 6646 3981
51465 26073 7165 54453 63901 7019 9123 22919 8202 4898 6464 11046
23324 1994
56901 221
54708 55167 8367 2533 79745 58488 23152
163 11044
50
760 55
60
10363 4976
113791 8533 6478 11034 27005 9552 9782
29082 6843 27074 6184 79654
65
US 9 , 970 , 056 B2 37
TABLE 3 - continued 38
TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
- 23 . 8
10
20
25
30
35
2588 57205 54187 6767 27130 2015 5125 9466 1130 9218 5023 1017 2323 2734 57591 3611
57140 3108 4839 9191 3783
112869 51304 51218 7846 8890 8915 962 2624 5859 3064 6451 6541 10913
375035 3068
57130 4000 994
11108 7866 1178 178
27352 4953
154881 51571 51573 26051 79144 9159 9557
55626 10113 9169 4899 23478 81537 25804
286 528 321
29957 5912 9935 6734 7296 9019 6744
140459 1116
79228 4790 57062 60314
GALNS ATP10D NANS ST13 INVS EMR1 PCSK5 IL27RA LYST VAPA P2RX1 CDK2 FLT3LG GLG1 MKL1 ILK RNPEPL1 HLA - DMA NOP2 DEDD KCNN4 CCDC101 ZDHHC3 GLRX5 TUBAIA EIF2 B4 BCL10 CD48 GATA2 QARS HTT SH3BGRL SLC7A1 EDAR SFT2D2 HDGF ATP13A1 LMNA CDC25B PRDM4 IFRD2 CLC AGL SGSM3 ODC1 KCTD7 FAM49B GDE1 PPP1R16B PPDPF PCSK7 CHDIL AMBRA1 PREB SCAF11 NRF1 SEC11A SGPP1 LSM4 ANK1 ATP6V1C1 APBA2 SLC25A24 RAP2B MAFB SRPR TXNRD1 MPZL1 SSFA2 ASB6 CHI3L1 THOC6 NFKB1 DDX24 C12orflo
- 24 . 335 - 24 . 327 - 24 . 325 - 24 . 311 - 24 . 31 - 24 . 299 - 24 . 254 - 24 . 229 - 24 . 22 - 24 . 206 - 24 . 205 - 24 . 201 - 24 . 2 - 24 . 196 - 24 . 191 - 24 . 182 - 24 . 158 - 24 . 128 - 24 . 127 - 24 . 125 - 24 . 119 - 24 . 118 - 24 . 117 - 24 . 112 - 24 . 101 - 24 . 097 - 24 . 087 - 24 . 078 - 24 . 078 - 24 . 074 - 24 . 073 - 24 . 073 - 24 . 061 - 24 . 052 - 24 . 047 - 24 . 045 - 24 . 036 - 24 . 028 - 24 . 024 - 24 . 009 - 23 . 995 - 23 . 992 - 23 . 991 - 23 . 99 - 23 . 982 - 23 . 97 - 23 . 958 - 23 . 952 - 23 . 946 - 23 . 937 - 23 . 934 - 23 . 928 - 23 . 926 - 23 . 921 - 23 . 91 - 23 . 898 - 23 . 885 - 23 . 884 - 23 . 872 - 23 . 871 - 23 . 865 - 23 . 863 - 23 . 858 - 23 . 845 - 23 . 842 - 23 . 841 - 23 . 839 - 23 . 837 - 23 . 826 - 23 . 825 - 23 . 825 - 23 . 818 - 23 . 807 - 23 . 802 - 23 . 8
0 . 012216 0 . 012239 0 . 012239 0 . 012292 0 . 012292 0 . 012327 0 . 012514 0 . 012623 0 . 012657 0 . 012703 0 . 012703 0 . 012703 0 . 012703 0 . 012713 0 . 01273 0 . 012763 0 . 012872 0 . 012996 0 . 012996 0 . 012996 0 . 013005 0 . 013005 0 . 013005 0 . 013017 0 . 013066 0 . 013074 0 . 013112 0 . 013132 0 . 013132 0 . 013132 0 . 013132 0 . 013132 0 . 013182 0 . 013206 0 . 013212 0 . 013212 0 . 01324 0 . 013268 0 . 013277 0 . 013345 0 . 0134 0 . 0134 0 . 0134 0 . 0134 0 . 013433 0 . 013484 0 . 013535 0 . 013556 0 . 013578 0 . 013613 0 . 013619 0 . 01364 0 . 01364 0 . 013657 0 . 013703 0 . 013737 0 . 013776 0 . 013776 0 . 013824 0 . 013824 0 . 013846 0 . 013846 0 . 013864 0 . 013909 0 . 013909 0 . 013909 0 . 01391 0 . 01391 0 . 013944 0 . 013944 0 . 013944 0 . 01397 0 . 01402 0 . 014027 0 . 014027
10802 217
6240 8935 80347 51177 1519 3609 4660 79813 4938 11329 27090 11022 9961 7145 8818 102
23198 11186 11213 22794 64422 7090 6873 26118 10116 3071 9665 6830 5151 6894 7336
27440 55343 10857 7706 7059 550
79073 4200 25840 7292 7574 28973 4318 1053 7535
51176 55032 79961 92856 25799 9612 56913 2766 2230 5093
25915 55717 23310 26469 4064 4524 54811 55769 5799 51021 65125 51474 10077 10014 7052 7001 5335
SEC24A ALDH2 RRM1 SKAP2 COASY PLEKHO1 CTSO ILF3 PPP1R12B EHMT1 OAS1 STK38 STOGALNAC4 TDRKH MVP TNS1 DPM2 ADAM10 PSME4 RASSF1 IRAK3 CASC3 ATG3 TLE3 TAF2 WSB1 FEM1B NCKAPIL KIAA0430 SUPTOH PDESA TARBP1 UBE2V2 CECR5 SLC35C1 PGRMC1 TRIM25 THBS3 AUP1 TMEM109 ME2 METTLTA TNFSF4 ZNF26 MRPS18B MMP9 ????? ZAP70 LEF1 SLC35A5 DENND2D IMP4 ZNF324 NCOR2 CIGALT1 GMPR FDX1 PCBP1 NDUFAF3 WDR11 NCAPD3 PTPN18 CD180 MTHFR ZNF562 ZNF83 PTPRN2 MRPS16 WNK1 LIMA1 TSPAN32 HDAC5 TGM2 PRDX2 PLCG1
- 23 . 795 - 23 . 795 - 23 . 792 - 23 . 788 - 23 . 782 - 23 . 781 - 23 . 773 - 23 . 766 - 23 . 764 - 23 . 759 - 23 . 759 - 23 . 757 - 23 . 733 - 23 . 724 - 23 . 724 - 23 . 721 - 23 . 713 - 23 . 712 - 23 . 708 - 23 . 693 - 23 . 687 - 23 . 673 - 23 . 666 - 23 . 657 - 23 . 652 - 23 . 65 - 23 . 648 - 23 . 636 - 23 . 624 - 23 . 593 - 23 . 567 - 23 . 565 - 23 . 543 - 23 . 519 - 23 . 512 - 23 . 508 - 23 . 507 - 23 . 506 - 23 . 504 - 23 . 502 - 23 . 49 - 23 . 472 - 23 . 47 - 23 . 466 - 23 . 456 - 23 . 451 - 23 . 45 - 23 . 433 - 23 . 427 - 23 . 418 - 23 . 418 - 23 . 417 - 23 . 412 - 23 . 407 - 23 . 389 - 23 . 388 - 23 . 384 - 23 . 369 - 23 . 369 - 23 . 361 - 23 . 358 - 23 . 356 - 23 . 355 - 23 . 352 - 23 . 342 - 23 . 334 - 23 . 334 - 23 . 333 - 23 . 318 - 23 . 31 - 23 . 307 - 23 . 301 - 23 . 296 - 23 . 284
0 . 014027 0 . 014032 0 . 014032 0 . 014036 0 . 014049 0 . 014066 0 . 014066 0 . 0141 0 . 014123 0 . 014126 0 . 014129 0 . 014129 0 . 014129 0 . 014253 0 . 014282 0 . 014282 0 . 014287 0 . 0143 0 . 0143 0 . 014316 0 . 014384 0 . 014406 0 . 014454 0 . 014479 0 . 014521 0 . 014537 0 . 014537 0 . 014541 0 . 014594 0 . 014653 0 . 014807 0 . 014942 0 . 014942 0 . 01506 0 . 015173 0 . 015173 0 . 015173 0 . 015173 0 . 015173 0 . 015173 0 . 015173 0 . 015232 0 . 015315 0 . 015319 0 . 015332 0 . 01538 0 . 01539 0 . 01539 0 . 015479 0 . 015499 0 . 01551 0 . 01551 0 . 01551 0 . 015524 0 . 015539 0 . 015623 0 . 015623 0 . 015638 0 . 015685 0 . 015685 0 . 015718 0 . 015718 0 . 015718 0 . 015718 0 . 015729 0 . 015763 0 . 015784 0 . 015784 0 . 015784 0 . 015855 0 . 015894 0 . 015898 0 . 015921 0 . 015943 0 . 015993
40
45
50
55
60 Perlast 65
US 9 , 970 , 056 B2 39
TABLE 3 - continued 40
TABLE 3 - continued
Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
- 23 . 266 - 23 . 263 - 23 . 257
10
15
20
4303 56905 81892 9209 29927 8509 9138 9398 3707
81544 4277 3182 4292 2060 27075 79089 6428 6050 1540 4940 7030 1616 6687 9445 1072 4245 6715
283232 9050 26277 3281 6448 25782 6158 3577 6708 51360 27040 23193 53635 79091
25
30
23118 3916 4311 5717 9830 55611 60496 1608
10681 382
64689 5585 1639 5162 4691 1718 7743 7994
57178 1436
23469 4856 5771 9761 9744 157 902 3958
84861 8986
23524 10618 3587
55149 7709 5686 5880 23020 55486 91289 10155 6776 4077 7805
55317
JO
FOXO4 C15orf39 SLIRP LRRFIP2 SEC61A1 NDST2 ARHGEF1 CD101 ITPKB GDPD5 MICB HNRNPAB MLH1 EPS15 TSPAN13 TMUB2 SRSF3 RNH1 CYLD OAS3 TFE3 DAXX SPG7 ITM2B CFL1 MGAT1 SRD5A1 TMEM80 PSTPIP2 TINF2 HSBP1 SGSH RABGGAP2 RPL28 CXCR1 SPTA1 MBTPS2 LAT GANAB PTOV1 METTL22 ACACA CEP104 SNTB1 RAB11A FGF13 SLPI FLNA ADIPOR1 EIF1B TBC1D2B FBXO3 CTSA TNFRSF25 SDPR TYMS SRRD PIKFYVE MAVS MARK3 TBP ????? MCM3AP AZU1 BRAP GALT UTP6 LINIC NDUFA10 TOMM34 YIPF5 TRAPPC10 HYOU1 MBNL3 FARP2
35
- 23 . 25 - 23 . 25 - 23 . 23 - 23 . 212 - 23 . 206 - 23 . 205 - 23 . 202 - 23 . 198 - 23 . 187 - 23 . 185 - 23 . 179 - 23 . 174 - 23 . 174 - 23 . 165 - 23 . 153 - 23 . 151 - 23 . 135 - 23 . 133 - 23 . 121 - 23 . 118 - 23 . 117 - 23 . 116 - 23 . 105 - 23 . 104 - 23 . 095 - 23 . 094 - 23 . 088 - 23 . 077 - 23 . 072 - 23 . 058 - 23 . 055 - 23 . 049 - 23 . 043 - 23 . 04 - 23 . 037 - 23 . 037 - 23 . 032 - 23 . 026 - 23 . 015 - 23 . 009 - 23 . 006 - 22 . 997 - 22 . 995 - 22 . 977 - 22 . 971 - 22 . 965 - 22 . 954 - 22 . 953 - 22 . 951 - 22 . 946 - 22 . 938 - 22 . 934 - 22 . 933 - 22 . 932 - 22 . 927 - 22 . 926 - 22 . 923 - 22 . 922 - 22 . 921 - 22 . 916 - 22 . 913 - 22 . 906 - 22 . 904 - 22 . 904 - 22 . 9 - 22 . 897 - 22 . 893 - 22 . 892 - 22 . 889 - 22 . 884 - 22 . 882 - 22 . 875
0 . 01609 0 . 016097 0 . 016123 0 . 016134 0 . 016134 0 . 016246 0 . 016351 0 . 016369 0 . 016369 0 . 016374 0 . 016386 0 . 016444 0 . 016445 0 . 016471 0 . 016484 0 . 016484 0 . 016517 0 . 016579 0 . 016584 0 . 016657 0 . 016663 0 . 016711 0 . 016711 0 . 016711 0 . 016711 0 . 016751 0 . 016751 0 . 016795 0 . 016795 0 . 016808 0 . 016867 0 . 016888 0 . 016968 0 . 016977 0 . 017 0 . 017026 0 . 017033 0 . 017033 0 . 017033 0 . 017056 0 . 017084 0 . 01714 0 . 017168 0 . 017175 0 . 017211 0 . 017213 0 . 017321 0 . 017345 0 . 017377 0 . 017421 0 . 017421 0 . 017421 0 . 017444 0 . 017481 0 . 01749 0 . 01749 0 . 017491 0 . 017504 0 . 017504 0 . 017505 0 . 017505 0 . 017505 0 . 017522 0 . 01753 0 . 017558 0 . 017558 0 . 017558 0 . 017572 0 . 017577 0 . 017577 0 . 017577 0 . 017583 0 . 017594 0 . 017596 0 . 017632
TAB2 LAMP1 MME PSMD11 TRIM14 OTUB1 AASDHPPT DGKG GNB5 ARF6 GORASP1 PKN1 DCTN1 PDHB NCL DHCR24 ZNF189 KATOA ZMIZ1 CSF1R PHF3 NOV PTPN2 MLEC ACAP1 ADRBK2 CCNH LGALS3 KLHL22 RPSÓKA4 SRRM2 TGOLN2 IL1ORA MTPAP ZBTB17 PSMA5 RAC2 SNRNP200 PARL LMF2 TRIM28 STATSA NBR1 LAPTM5 AP5S1 ARNT PPP2R1A MBD1 CKAP4 ORC4 MYL4 NUCB2 PEX5 TORIA TBCB SMAD2 MAPRE2 ARFGAP2 GNA15 CD6 PCID2 BHLHE40 PAN2 CAMP TRAFD1 SLC25A44 NUP210 RPS25 AVPR1A NR1D2 NNT CRNKL1 DDB2 NT5DC3 RNF10
- 22 . 848 - 22 . 828 - 22 . 823 - 22 . 818 - 22 . 815 - 22 . 807 - 22 . 806 - 22 . 797 - 22 . 797 - 22 . 794 - 22 . 787 - 22 . 782 - 22 . 776 - 22 . 775 - 22 . 771 - 22 . 764 - 22 . 735 - 22 . 727 - 22 . 719 - 22 . 711 - 22 . 71 - 22 . 709 - 22 . 709 - 22 . 703 - 22 . 697 - 22 . 695 - 22 . 694 - 22 . 687 - 22 . 679 - 22 . 674 - 22 . 673 - 22 . 672 - 22 . 667 - 22 . 666 - 22 . 665 - 22 . 66 - 22 . 66 - 22 . 645 - 22 . 632 - 22 . 631 - 22 . 626 - 22 . 618 - 22 . 615 - 22 . 615 - 22 . 61 - 22 . 61 - 22 . 6 - 22 . 596 - 22 . 594 - 22 . 588 - 22 . 588 - 22 . 583 - 22 . 581 - 22 . 579 - 22 . 565 - 22 . 562 - 22 . 553 - 22 . 547 - 22 . 544 - 22 . 543 - 22 . 542 - 22 . 535 - 22 . 524 - 22 . 514 - 22 . 484 - 22 . 471 - 22 . 461 - 22 . 455 - 22 . 452 - 22 . 452 - 22 . 446 - 22 . 445 - 22 . 445 - 22 . 441 - 22 . 436
0 . 017777 0 . 017888 0 . 017909 0 . 017909 0 . 017921 0 . 017935 0 . 017935 0 . 017951 0 . 017951 0 . 017957 0 . 017982 0 . 017995 0 . 018002 0 . 018002 0 . 018023 0 . 018043 0 . 018195 0 . 018207 0 . 018237 0 . 018254 0 . 018254 0 . 018254 0 . 018254 0 . 01829 0 . 018316 0 . 018316 0 . 018316 0 . 018349 0 . 018372 0 . 018375 0 . 018375 0 . 018375 0 . 018387 0 . 018387 0 . 018387 0 . 018396 0 . 018396 0 . 018481 0 . 018549 0 . 018549 0 . 018579 0 . 018597 0 . 018597 0 . 018597 0 . 018607 0 . 018607 0 . 018653 0 . 018658 0 . 018662 0 . 018668 0 . 018668 0 . 018687 0 . 01869 0 . 018692 0 . 01876 0 . 018765 0 . 018819 0 . 018847 0 . 018847 0 . 018847 0 . 018847 0 . 018877 0 . 018942 0 . 019007 0 . 019161 0 . 019232 0 . 019289 0 . 019308 0 . 019308 0 . 019308 0 . 019312 0 . 019312 0 . 019312 0 . 019327 0 . 019337
31 40
405
45 45
50
9731 6641 8766 2258 6590 2316
51094 10289 23102 26273 5476 8718 8436 7298
402055 200576 57506 4140 6908 56257 8888 566
8315 2592 55813 55327 4705 10953 81555 7109 10525 55796 9855
5518 4152 10970 5000 4635 4925 5830 1861 1155 4087 10982 84364 2769 923
55795 8553 9924 820
10906 9673
23225 6230 552
9975 23530 51340 1643
51559 9921
55
60
65
US 9 , 970 , 056 B2 41
TABLE 3 - continued 42
TABLE 3 - continued
Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
Be 4089 1380
54877 6303
10 29
20
25
30
35
51070 51393 196441
7355 805
25988 4939 54433 1783 9812 79618 64429 64127 55332 8031
54850 55213 23352 4701 55251 5452 55723 8869 6388 2887 3727
64386 2535 10961 8793 10444 8140
54509 6597 3660 4717
32 2313 23197 8125 7321
11235 64784 51604 8527 3695 4026
10181 4242 51466 23195 5965
22878 11070 10109 1520 8565 8242 1870 8906
79890 1947 6311 9444 55683 57097 25865 3687 317 55
5265 55619 6786 3551 4836
NOSIP TRPV2 ZFC3H1 SLC35A2 CALM2 HINFP OAS2 GAR1 DYNCILI2 KIAA0141 HMBOX1 ZDHHC6 NOD2 DRAM1 NCOA4 FBXL12 RCBTB1 UBR4 NDUFAZ PCMTD2 POU2F2 ASF1B STUGAL5 SDF2 GRB10 JUND MMP25 FZD2 ERP29 TNFRSF10D ZER1 SLC7A5 RHOF SMARCA4 IRF2 NDUFC1 ACACB FLI1 FAF2 ANP32A UBE2D1 PDCD10 CRTC3 PIGT DGKD ITGB7 LPP RBM5 MFNG EVL MDN1 RECOL TRAPPC8 TMEM115 ARPC2 CTSS YARS KDM5C E2F2 AP1G2 RIN3 EFNB1 ATXN2 OKI KANSL3 PARP11 PRKD2 ITGAX APAF1 ???? SERPINA1 DOCK10 STIM1 IKBKB NMT1
- 22 . 435 - 22 . 434 - 22 . 408 - 22 . 404 - 22 . 403 - 22 . 397 - 22 . 396 - 22 . 393 - 22 . 393 - 22 . 393 - 22 . 391 - 22 . 385 - 22 . 382 - 22 . 377 - 22 . 375 - 22 . 374 - 22 . 369 - 22 . 366 - 22 . 36 - 22 . 347 - 22 . 346 - 22 . 344 - 22 . 341 - 22 . 332 - 22 . 326 - 22 . 318 - 22 . 317 - 22 . 312 - 22 . 308 - 22 . 295 - 22 . 293 - 22 . 275 - 22 . 273 - 22 . 266 - 22 . 257 - 22 . 25 - 22 . 243 - 22 . 242 - 22 . 241 - 22 . 238 - 22 . 235 - 22 . 234 - 22 . 219 - 22 . 213 - 22 . 213 - 22 . 212 - 22 . 212 - 22 . 212 - 22 . 207 - 22 . 205 - 22 . 2 - 22 . 199 - 22 . 194 - 22 . 167 - 22 . 155 - 22 . 151 - 22 . 148 - 22 . 144 - 22 . 143 - 22 . 142 - 22 . 142 - 22 . 141 - 22 . 135 - 22 . 135 - 22 . 133 - 22 . 127 - 22 . 124 - 22 . 122 - 22 . 111 - 22 . 097 - 22 . 096 - 22 . 09 - 22 . 087 - 22 . 083 - 22 . 068
0 . 019337 0 . 019337 0 . 019475 0 . 019486 0 . 019486 0 . 019503 0 . 019503 0 . 019503 0 . 019503 0 . 019503 0 . 019506 0 . 019523 0 . 019539 0 . 019548 0 . 019549 0 . 019551 0 . 019571 0 . 019582 0 . 019613 0 . 019693 0 . 019693 0 . 0197 0 . 019706 0 . 01975 0 . 019787 0 . 019825 0 . 019825 0 . 01985 0 . 019871 0 . 019945 0 . 019945 0 . 020053 0 . 020053 0 . 020079 0 . 020139 0 . 020177 0 . 020208 0 . 020208 0 . 020208 0 . 020209 0 . 020209 0 . 020209 0 . 020261 0 . 020261 0 . 020261 0 . 020261 0 . 020261 0 . 020261 0 . 020287 0 . 020287 0 . 02031 0 . 02031 0 . 020335 0 . 020499 0 . 020574 0 . 020574 0 . 020574 0 . 020574 0 . 020574 0 . 020574 0 . 020574 0 . 020574 0 . 020589 0 . 020589 0 . 020591 0 . 020627 0 . 020638 0 . 020639 0 . 020709 0 . 020785 0 . 020785 0 . 020819 0 . 020828 0 . 020848 0 . 02095
23095 54918 55038 7786
57147 6643 23212 51079 23126
790 11273 55707 2961
79903 3903
64844 169611 5110 1836 4300 1147 5501
65083 27175 10607 5829
29914 79717 9904 5702 688
55841 53347 80146 2537 3632 1737 6280 26036 55833 9725 6742 9453 2188
27314 55303 1524 968 2873 8454
55690 64760 80742 5577 7189
81618 9410 10352 23365 5514 11160 23761 64581 9031 6812 26994
476 28977 60559
306
SMAD4 CR2 ZCCHC2 SAT1 ABR KIF1B CMTM6 CDCA4 MAP3K12 SCYL3 SNX2 RRS1 NDUFA13 POGZ CAD ATXN2L NECAP2 GTF2E2 NAA60 LAIR1 MARCH7 OLFML2A PCMT1 SLC26A2 MLLT3 CHUK PPP1CC NOL6 TUBG2 TBL3 PXN UBIAD1 PPCS RBM19 PSMC3 KLF5 WWC3 UBASHGA UXS1 IF16 INPP5A DLAT S100A9 ZNF451 UBAP2 TMEM63A SSBP1 GGPS1 FANCF RAB30 GIMAP4 CX3CR1 CD68 GPS1 CUL1 PACS1 FAM160B2 PRR3 PRKAR2B TRAF6 ITM2C SNRNP40 WARS2 ARHGEF12 PPP1R10 ERLIN2 PISD CLEC7A BAZ1B STXBP1 RNF11 ATP1A1 MRPL42 SPCS3 ANXA3
- 22 . 046 - 22 . 044 - 22 . 035 - 22 . 033 - 22 . 032 - 22 . 026 - 22 . 014 - 22 . 009 - 22 . 008 - 22 . 005 - 22 . 005 - 21 . 993 - 21 . 988 - 21 . 986 - 21 . 985 - 21 . 982 - 21 . 973 - 21 . 955 - 21 . 954 - 21 . 939 - 21 . 938 - 21 . 935 - 21 . 93 - 21 . 922 - 21 . 919 - 21 . 911 - 21 . 91 - 21 . 91 - 21 . 907 - 21 . 904 - 21 . 894 - 21 . 889 - 21 . 88 - 21 . 879 - 21 . 879 - 21 . 874 - 21 . 865 - 21 . 853 - 21 . 85 - 21 . 849 - 21 . 849 - 21 . 848 - 21 . 846 - 21 . 836 - 21 . 829 - 21 . 822 - 21 . 819 - 21 . 814 - 21 . 809 - 21 . 808 - 21 . 801 - 21 . 8 - 21 . 783 - 21 . 773 - 21 . 771 - 21 . 764 - 21 . 756 - 21 . 751 - 21 . 749 - 21 . 744 - 21 . 734 - 21 . 727 - 21 . 725 - 21 . 718 - 21 . 714 - 21 . 711 - 21 . 711 - 21 . 71 - 21 . 71 - 21 . 709 - 21 . 706 - 21 . 705 - 21 . 699 - 21 . 697 - 21 . 69
0 . 021114 0 . 021115 0 . 021165 0 . 021165 0 . 021165 0 . 021191 0 . 021272 0 . 021295 0 . 021295 0 . 021298 0 . 021298 0 . 021375 0 . 021405 0 . 021408 0 . 021408 0 . 021414 0 . 021454 0 . 021571 0 . 021571 0 . 021672 0 . 021672 0 . 021685 0 . 021717 0 . 021756 0 . 02177 0 . 021807 0 . 021807 0 . 021807 0 . 021809 0 . 021816 0 . 021886 0 . 021909 0 . 021945 0 . 021945 0 . 021945 0 . 021962 0 . 021997 0 . 022079 0 . 022079 0 . 022079 0 . 022079 0 . 022079 0 . 022079 0 . 022155 0 . 022199 0 . 022234 0 . 022239 0 . 02227 0 . 022294 0 . 022294 0 . 022327 0 . 022327 0 . 022457 0 . 022514 0 . 022523 0 . 022553 0 . 022613 0 . 022629 0 . 022633 0 . 022644 0 . 022722 0 . 022763 0 . 022763 0 . 022797 0 . 022797 0 . 022797 0 . 022797 0 . 022797 0 . 022797 0 . 022797 0 . 022802 0 . 022802 0 . 022833 0 . 022835 0 . 022881
40
45
50
55
60
65
US 9 , 970 , 056 B2 43
TABLE 3 - continued 44
TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
20
6563 3735
10261 310
22828 56940 51191 1192
23533 6598 9219 50650 5428 9997 92579 23240 9962 28960 57515 5510 2934 9764 10533 50853 63875 7064 22907 23659 27109 25849 83442 29099 11334 7056 23082 9592
84669 2185 10423 10943 7073 1487 4817 9097 373
3376
25
30
SLC14A1 KARS IGSF6 ANXAT SCAF8 DUSP22 HERC5 CLIC1 PIK3R5 SMARCB1 MTA2 ARHGEF3 POLG SCO2 G6PC3 KIAA0922 SLC23A2 DCPS SERINC1 PPP1R7 GSN KIAA0513 ATG7 VILL MRPL17 THOP1 DHX30 PLA2G15 ATP5S PARM1 SH3BGRL3 COMMD9 TUSC2 THBD PPRC1 IER2 USP32 PTK2B CDIPT MSL3 TIAL1 CTBP1 NIT1 USP14 TRIM23 IARS BTK CD27 REC8 BDH1 ITPR3 ZMYM2 NUSAP1 FAM89B GSTP1 CTNS SDF2L1 DIEXF EXOC7 FAM117A ACADVL SLC25A11 RBCK1 GTPBP2 SULT1B1 YTHDC1 TCN2 SLC11A1 IKBKAP AKR7A2 EIF4H CYP27A1 POP4 SOCS2 PGD
35
- 21 . 681 - 21 . 676 - 21 . 675 - 21 . 674 - 21 . 672 - 21 . 672 - 21 . 664 - 21 . 655 - 21 . 652 - 21 . 648 - 21 . 647 - 21 . 644 - 21 . 63 - 21 . 628 - 21 . 62 - 21 . 613 - 21 . 612 - 21 . 607 - 21 . 598 - 21 . 588 - 21 . 588 - 21 . 569 - 21 . 563 - 21 . 563 - 21 . 562 - 21 . 558 - 21 . 557 - 21 . 556 - 21 . 552 - 21 . 548 - 21 . 545 - 21 . 544 - 21 . 543 - 21 . 542 - 21 . 539 - 21 . 527 - 21 . 521 - 21 . 517 - 21 . 516 - 21 . 516 - 21 . 51 - 21 . 509 - 21 . 503 - 21 . 503 - 21 . 501 - 21 . 481 - 21 . 475 - 21 . 472 - 21 . 47 - 21 . 468 - 21 . 461 - 21 . 459 - 21 . 45 - 21 . 446 - 21 . 445 - 21 . 441 - 21 . 436 - 21 . 425 - 21 . 424 - 21 . 42 - 21 . 412 - 21 . 411 - 21 . 411 - 21 . 396 - 21 . 393 - 21 . 378 - 21 . 372 - 21 . 37 - 21 . 368 - 21 . 364 - 21 . 356 - 21 . 355 - 21 . 347 - 21 . 343 - 21 . 336
79991 22913 27099 6430 10428 55624 7867
51744 84065
940 334
54973 5591 2026
64218 57472 23179 1188 6449 57862 80219 57020 22898 54583 8216 2356 51107 54704 347902 79184 10951
801 5825 57148
948 6472 3995 3732 7203 1991 9887 51397
215 23339 7390 3978 5333 9459 27229
0 . 022942 0 . 022948 0 . 022948 0 . 022948 0 . 022948 0 . 022948 0 . 023006 0 . 023069 0 . 023081 0 . 023095 0 . 023095 0 . 023114 0 . 023211 0 . 023215 0 . 023269 0 . 023315 0 . 023315 0 . 023345 0 . 023402 0 . 023464 0 . 023464 0 . 02359 0 . 02359 0 . 02359 0 . 02359 0 . 02359 0 . 02359 0 . 02359 0 . 023604 0 . 023615 0 . 023622 0 . 023622 0 . 023622 0 . 023622 0 . 023632 0 . 023725 0 . 023748 0 . 023748 0 . 023748 0 . 023748 0 . 023786 0 . 02379 0 . 023814 0 . 023814 0 . 023814 0 . 023947 0 . 023985 0 . 023999 0 . 024003 0 . 024013 0 . 024062 0 . 024069 0 . 024136 0 . 024153 0 . 024153 0 . 024171 0 . 024197 0 . 024282 0 . 024282 0 . 024304 0 . 024346 0 . 024346 0 . 024346 0 . 024467 0 . 024467 0 . 024579 0 . 02462 0 . 02463 0 . 024631 0 . 024661 0 . 024713 0 . 024713 0 . 024781 0 . 024801 0 . 024822
OBFC1 RALY SND1 - IT1 SRSF5 CFDP1 POMGNT1 MAPKAPK3 CD244 TMEM222 CD28 APLP2 CPSF3L PRKDC ENO2 SEMALA CNOT6 RGL1 CLCNKB SGTA ZNF410 COQ10B C16orf62 DENND3 EGLN1 LZTR1 FPGS APHIA PDP1 AMIGO2 BRCC3 CBX1 CALM1 ABCD3 RALGAPB CD36 SHMT2 FADS3 CD82 CCT3 ELANE SMG7 COMMD10 ABCD1 VPS39 UROS LIG1 PLCD1 ARHGEF6 TUBGCP4 RCAN1 BST2 NIPSNAP1 APEX1 TMEM204 CEBPB CDC14A TSC22D1 KDMIA MYO1F SDCBP PTPRCAP ZNF143 PPM1F SUN2 ITPR1 STK10 ABL1 SYK PHF11 ZWINT HEBP1 NBN PDK2 PARG QRSL1
- 21 . 335 - 21 . 332 - 21 . 33 - 21 . 328 - 21 . 312 - 21 . 311 - 21 . 311 - 21 . 306 - 21 . 296 - 21 . 295 - 21 . 274 - 21 . 264 - 21 . 263 - 21 . 252 - 21 . 251 - 21 . 249 - 21 . 247 - 21 . 245 - 21 . 243 - 21 . 243 - 21 . 24 - 21 . 234 - 21 . 229 - 21 . 228 - 21 . 227 - 21 . 226 - 21 . 207 - 21 . 207 - 21 . 202 - 21 . 2 - 21 . 192 - 21 . 191 - 21 . 186 - 21 . 18 - 21 . 173 - 21 . 158 - 21 . 146 - 21 . 142 - 21 . 134 - 21 . 133 - 21 . 129 - 21 . 111 - 21 . 107 - 21 . 098 - 21 . 098 - 21 . 094 - 21 . 09 - 21 . 086 - 21 . 084 - 21 . 081 - 21 . 076 - 21 . 076 - 21 . 075 - 21 . 066 - 21 . 065 - 21 . 055 - 21 . 055 - 21 . 053 - 21 . 049 - 21 . 042 - 21 . 035 - 21 . 034 - 21 . 02 - 21 . 011 - 21 . 01 - 20 . 992 - 20 . 992 - 20 . 987 - 20 . 973 - 20 . 967 - 20 . 966 - 20 . 963 - 20 . 959 - 20 . 959 - 20 . 956
0 . 024822 0 . 024834 0 . 02484 0 . 024846 0 . 024953 0 . 024953 0 . 024953 0 . 024989 0 . 025059 0 . 025059 0 . 025245 0 . 025308 0 . 025308 0 . 025382 0 . 025382 0 . 025387 0 . 025395 0 . 025395 0 . 025395 0 . 025395 0 . 025407 0 . 025451 0 . 02548 0 . 02548 0 . 02548 0 . 02548 0 . 025617 0 . 025617 0 . 02565 0 . 025659 0 . 025716 0 . 025716 0 . 025755 0 . 025795 0 . 025827 0 . 025958 0 . 026018 0 . 026039 0 . 026089 0 . 026089 0 . 026117 0 . 026277 0 . 026306 0 . 026363 0 . 026363 0 . 02639 0 . 02642 0 . 026441 0 . 026449 0 . 026461 0 . 026483 0 . 026483 0 . 026486 0 . 026542 0 . 026542 0 . 026602 0 . 026602 0 . 026602 0 . 026627 0 . 026663 0 . 026698 0 . 026698 0 . 026797 0 . 026844 0 . 026844 0 . 027 0 . 027 0 . 027013 0 . 027106 0 . 027144 0 . 027144 0 . 027162 0 . 027176 0 . 027176 0 . 027187
40
695
45
1827
50
939 9985 622 3710 7750 51203 23625 2950 1497 23753 27042 23265 81558
37 8402 10616 54676 27284 91746 6948 6556 8518 8574 7458 1593 10775 8835 5226
55
684 8508 328
79652 1051 8556 8848 23028 4542 6386 5790 7702 9647 25777 3708 6793
25 6850 51131 11130 50865 4683 5164 8505 55278
60
65
US 9 , 970 , 056 B2 45 46
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
15
Bellotaszetaritzani izid 20
25
30
35
5128 8673 5111
55153 11072 10437 11322 56980 11142
710 11339 2317 6774 51102 84864 2132 8682 23450 23175 23673
140609 373156 55819 140885
5519 5411
23569 1386
11183 4074 1235
54855 79443 8030 4800
22881 5362
51816 10463 55832 3133
55697 47
7264 4643 998
57185 29890
468 9917 81571 59307 3676 9781 249
55020 10238 2665
80005 2869
10724 9698 80342 51144 10144 50615 30000 7307 4926 10211 3848 3840 54901 10346 6119
CDK17 VAMP8 PCNA SDAD1 DUSP14 IFI30 TMC6 PRDM10 PKIG SERPING1 OIP5 FLNB STAT3 MECR MINA EXT2 PEA15 SF3B3 LPIN1 STX12 NEK7 GSTK1 RNF130 SIRPA PPP2R1B PNN PADI4 ATF2 MAP4K5 MOPR CCR6 FAM46C FYCO1 CCDC6 NFYA ANKRDO PLXNA2 CECR1 SLC30A9 CAND1 HLA - E VAC14 ACLY TSTA3 MYO1E CDC42 NIPAL3 RBM15B ATF4 FAM20B MIR600HG SIGIRR ITGA4 RNF144A ALPL TTC38 DCAF7 GDI2 DOCK5 GRK5 MGEA5 PUM1 TRAF31P3 HSD17B12 FAM13A IL21R TNPO2 U2AF1 NUMA1 FLOT1 KRT1 KPNA4 CDKAL1 TRIM22 RPA3
- 20 . 955 - 20 . 952 - 20 . 949 - 20 . 949 - 20 . 948 - 20 . 943 - 20 . 94 - 20 . 938 - 20 . 933 - 20 . 927 - 20 . 911 - 20 . 91 - 20 . 909 - 20 . 907 - 20 . 906 - 20 . 9 - 20 . 892 - 20 . 888 - 20 . 865 - 20 . 862 - 20 . 861 - 20 . 86 - 20 . 857 - 20 . 842 - 20 . 842 - 20 . 839 - 20 . 829 - 20 . 82 - 20 . 82 - 20 . 818 - 20 . 805 - 20 . 796 - 20 . 795 - 20 . 789 - 20 . 786 - 20 . 779 - 20 . 774 - 20 . 772 - 20 . 769 - 20 . 766 - 20 . 764 - 20 . 762 - 20 . 758 - 20 . 757 - 20 . 75 - 20 . 744 - 20 . 742 - 20 . 741 - 20 . 73 - 20 . 729 - 20 . 727 - 20 . 722 - 20 . 719 - 20 . 717 - 20 . 716 - 20 . 716 - 20 . 706 - 20 . 704 - 20 . 702 - 20 . 7 - 20 . 694 - 20 . 692 - 20 . 692 - 20 . 681 - 20 . 68 - 20 . 679 - 20 . 678 - 20 . 674 - 20 . 672 - 20 . 671 - 20 . 667 - 20 . 663 - 20 . 662 - 20 . 655 - 20 . 646
0 . 027187 0 . 027202 0 . 027202 0 . 027202 0 . 027202 0 . 027245 0 . 027263 0 . 027263 0 . 027301 0 . 027349 0 . 027482 0 . 027482 0 . 027482 0 . 027482 0 . 027486 0 . 027511 0 . 027567 0 . 027582 0 . 02775 0 . 027751 0 . 027751 0 . 027751 0 . 027768 0 . 027882 0 . 027882 0 . 0279 0 . 027968 0 . 028041 0 . 028041 0 . 028041 0 . 028167 0 . 028232 0 . 028232 0 . 028264 0 . 028268 0 . 028311 0 . 028353 0 . 028355 0 . 028375 0 . 028387 0 . 028387 0 . 028387 0 . 028408 0 . 028408 0 . 028467 0 . 028514 0 . 02852 0 . 02852 0 . 028576 0 . 028577 0 . 028582 0 . 02859 0 . 02859 0 . 02859 0 . 02859 0 . 02859 0 . 028678 0 . 02869 0 . 028697 0 . 028701 0 . 028749 0 . 028749 0 . 028749 0 . 028812 0 . 028812 0 . 028812 0 . 028812 0 . 028827 0 . 02883 0 . 02883 0 . 028863 0 . 028888 0 . 028891 0 . 028954 0 . 029022
6499 10272 2650
79624 10147 9477 54505 10384 3122 3419
58477 3560 9110
65123 991
6722 953
10605 23312 1173
79879 9867
139322 958
5828 26009
115207 3561
23344 1509 8395 27128 55288 5571
55002 89845 10745 26152 8645
55024 1742 5230 22893 4253 8897 10589 55662 9913 10801 4708 104
10629 1371 9770 952
5033 10964 4122 9730 5862 10475 432
5983 8602 11222 25984 2124 9282 10921 55603 7555 27339 55726 51366 55324
SKIVAL FSTL3 GCNT1 C6orf211 SUGP2 MED20 DHX29 BTN3A3 HLA - DRA ID??? SRPRB IL2RB MTMR4 INTS3 CDC20 SRF ENTPD1 PAIP1 DMXL2 AP2M1 CCDC134 PJA2 APOOL CD40 PEX2 ZZZ3 KCTD12 IL2RG ESYT1 CTSD PIP5K1B CYTH4 RHOT1 PRKAG1 TMCO3 ABCC10 PHTF1 ZNF337 KCNK5 BANK1 DLG4 PGK1 BAHD1 CTAGES MTMR3 DRAP1 HIF1AN SUPTIL SEPT9 NDUFB2 ADARB1 TAFOL CPOX RASSF2 CD38 P4HA1 IF144L MAN2A2 VPRBP RAB2A TRIM38 ASGR1 RFC3 NOP14 MRPL3 KRT23 EVI2B MED14 RNPS1 FAM46A CNBP PRPF19 ASUN UBR5 ABCF3
- 20 . 644 - 20 . 637 - 20 . 631 - 20 . 62 - 20 . 619 - 20 . 618 - 20 . 615 - 20 . 599 - 20 . 599 - 20 . 595 - 20 . 591 - 20 . 59 - 20 . 583 - 20 . 583 - 20 . 582 - 20 . 576 - 20 . 573 - 20 . 573 - 20 . 563 - 20 . 563 - 20 . 56 - 20 . 545 - 20 . 542 - 20 . 533 - 20 . 531 - 20 . 526 - 20 . 52 - 20 . 517 - 20 . 515 - 20 . 507 - 20 . 505 - 20 . 503 - 20 . 502 - 20 . 5 - 20 . 494 - 20 . 491 - 20 . 49 - 20 . 487 - 20 . 485 - 20 . 48 - 20 . 479 - 20 . 466 - 20 . 466 - 20 . 45 - 20 . 446 - 20 . 445 - 20 . 435 - 20 . 435 - 20 . 434 - 20 . 418 - 20 . 415 - 20 . 405 - 20 . 404 - 20 . 394 - 20 . 391 - 20 . 388 - 20 . 388 - 20 . 384 - 20 . 384 - 20 . 366 - 20 . 366 - 20 . 364 - 20 . 361 - 20 . 361 - 20 . 358 - 20 . 357 - 20 . 355 - 20 . 34 - 20 . 339 - 20 . 336 - 20 . 334 - 20 . 318 - 20 . 314 - 20 . 314 - 20 . 312
0 . 029029 0 . 029091 0 . 029141 0 . 029227 0 . 029227 0 . 029227 0 . 029245 0 . 029391 0 . 029391 0 . 029417 0 . 029445 0 . 029445 0 . 029459 0 . 029459 0 . 029459 0 . 029504 0 . 029504 0 . 029504 0 . 029582 0 . 029582 0 . 0296 0 . 029737 0 . 029757 0 . 029823 0 . 029837 0 . 029849 0 . 02989 0 . 029906 0 . 029917 0 . 029991 0 . 029991 0 . 030001 0 . 030004 0 . 030013 0 . 030035 0 . 030051 0 . 030051 0 . 030058 0 . 030058 0 . 030089 0 . 030089 0 . 030208 0 . 030208 0 . 030359 0 . 03038 0 . 030384 0 . 030425 0 . 030425 0 . 030425 0 . 03059 0 . 03061 0 . 030677 0 . 030677 0 . 030774 0 . 030792 0 . 030804 0 . 030804 0 . 030818 0 . 030818 0 . 030952 0 . 030952 0 . 030961 0 . 030964 0 . 030964 0 . 030978 0 . 030978 0 . 030986 0 . 031141 0 . 031147 0 . 031154 0 . 031161 0 . 031316 0 . 031323 0 . 031323 0 . 031323
40
45
ein 50
55
60
65
US 9 , 970 , 056 B2 47
TABLE 3 - continued 48
TABLE 3 - continued
Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval | bau
10
halter 20
25
30
8993 80308 9819 55898 56172 64219 6429 5719 10288 8418 55233 2395
57658 83480 2130
10106 79815 6396
64418 4680 6821 9277 84243 171023
5879 3384 4052 5631
10054 2907 9632 8733 6856 2800 79137 23417 9734 3705 9354 55037 51371 9973 6160 2219 8473
51776 8626
54963 10554 23230 3927
64781 1655 4353
116138 3665 4627 10329 10235
553115 5199 7290 2648
11016 7462
51164 55558 4125 8669
63893 23169 8086
35
PGLYRP1 FLAD1 TSC22D2 UNC45A ANKH PJA1 SRSF4 PSMD13 LILRB2 ????? MOB1A FXN CALCOCO1 PUS3 EWSR1 CTDSP2 NIPAL2 SEC13 TMEM168 CEACAM6 SUOX WDR46 ZDHHC18 ASXL1 RAC1 ICAM2 LTBP1 PRPS1 UBA2 GRINA SEC24C GPAAL SYPL1 GOLGA1 FAM134A MLYCD HDACI ITPK1 UBE4A PTCD3 POMP CCS RPL31 FCN1 0?? ZAK TP63 UCKL1 AGPAT1 VPS13A LASP1 CERK DDX5 MPO KLHDC3 IRF7 MYH9 TMEM5 RASGRP2 PEF1 CFP HIRA ????? ATF7 LAT2 DCTN4 PLXNA3 MAN2B1 EIF3J UBE20 SLC35D1 AAAS HSD17B4 SELP PACSIN2
- 20 . 311 - 20 . 311 - 20 . 294 - 20 . 283 - 20 . 281 - 20 . 275 - 20 . 264 - 20 . 257 - 20 . 254 - 20 . 244 - 20 . 234 - 20 . 234 - 20 . 233 - 20 . 23 - 20 . 225 - 20 . 225 - 20 . 221 - 20 . 219 - 20 . 219 - 20 . 209 - 20 . 204 - 20 . 196 - 20 . 194 - 20 . 191 - 20 . 187 - 20 . 186 - 20 . 179 - 20 . 173 - 20 . 169 - 20 . 162 - 20 . 157 - 20 . 153 - 20 . 146 - 20 . 134 - 20 . 12 - 20 . 111 - 20 . 099 - 20 . 07 - 20 . 07 - 20 . 066 - 20 . 065 - 20 . 058 - 20 . 052 - 20 . 046 - 20 . 045 - 20 . 042 - 20 . 039 - 20 . 039 - 20 . 032 - 20 . 027 - 20 . 022 - 20 . 021 - 20 . 014 - 20 . 008 - 20 . 005 - 19 . 992 - 19 . 992 - 19 . 991 - 19 . 984 - 19 . 973 - 19 . 972 - 19 . 966 - 19 . 963 - 19 . 963 - 19 . 961 - 19 . 957 - 19 . 955 - 19 . 948 - 19 . 948 - 19 . 944 - 19 . 944 - 19 . 943 - 19 . 942 - 19 . 932 - 19 . 925
0 . 031323 0 . 031323 0 . 031503 0 . 031602 0 . 031617 0 . 031667 0 . 031784 0 . 031855 0 . 03186 0 . 031932 0 . 032017 0 . 032017 0 . 032017 0 . 032033 0 . 032043 0 . 032043 0 . 032058 0 . 032058 0 . 032058 0 . 032148 0 . 032201 0 . 032276 0 . 032276 0 . 0323 0 . 03232 0 . 03232 0 . 032395 0 . 032437 0 . 032466 0 . 032542 0 . 032585 0 . 032611 0 . 032654 0 . 032764 0 . 032913 0 . 032999 0 . 033137 0 . 033427 0 . 033427 0 . 033427 0 . 033427 0 . 033507 0 . 033555 0 . 033618 0 . 033618 0 . 033634 0 . 033647 0 . 033647 0 . 033716 0 . 03373 0 . 033778 0 . 03378 0 . 033807 0 . 03387 0 . 033884 0 . 033999 0 . 033999 0 . 033999 0 . 034038 0 . 034168 0 . 034168 0 . 034227 0 . 03423 0 . 03423 0 . 03423 0 . 034267 0 . 034275 0 . 034335 0 . 034335 0 . 034341 0 . 034341 0 . 034341 0 . 034341 0 . 034455 0 . 034518
7249 22880 54520 11337 9860 55640 7185 79571 64087 5286 25978 8558 547
8884 6749 60492 3984 1964
63899 9710
51706 79156 60626 8642 2815 9934 5905 10301 9603 4582
127703 4350 55128 10957 80777 1656 10365 89941 9674
55852 9416 26031 3662
79731 6932 58516 22863 9057 10257 5890 5660 9747 6573 8837 1677
114049 51181 51427 10233 10084 11188 54682 29893 4047 79947 4261 23271 10097 51282 9655 23550 55187 2975 389
10632
TSC2 MORC2 CCDC93 GABARAP LRIG2 FLVCR2 TRAF1 GCC1 ????2 PIK3C2A CHMP2B CDK10 KIF1A SLC5A6 SSRP1 CCDC90B LIMK1 EIF1AX NSUN3 KIAA0355 CYB5R1 PLEKHF1 RICIA DCHS1 GP9 P2RY14 RANGAP1 DLEU1 NFE2L3 MUC1 Clorf216 MPG TRIM68 PNRC1 CYB5B DDX6 KLF2 RHOT2 KIAA0040 TEX2 DDX23 OSBPL3 IRF4 NARS2 TCF7 FAM60A ATG14 SLC7A6 ABCC4 RAD51B PSAP FAM115A SLC19A1 CFLAR DFFB WBSCR22 DCXR ZNF107 LRRC23 POBP1 NISCH MANSC1 PS????? LSS DHDDS CIITA CAMSAP2 ACTR2 SCAND1 SOCS5 PSD4 VPS13D GTF3C1 RHOC ATP5L
- 19 . 923 - 19 . 921 - 19 . 919 - 19 . 916 - 19 . 916 - 19 . 912 - 19 . 902 - 19 . 899 - 19 . 898 - 19 . 885 - 19 . 88 - 19 . 878 - 19 . 868 - 19 . 857 - 19 . 851 - 19 . 849 - 19 . 848 - 19 . 831 - 19 . 821 - 19 . 82 - 19 . 813 - 19 . 81 - 19 . 81 - 19 . 807 - 19 . 805 - 19 . 804 - 19 . 8 - 19 . 793 - 19 . 792 - 19 . 788 - 19 . 783 - 19 . 778 - 19 . 773 - 19 . 772 - 19 . 765 - 19 . 76 - 19 . 758 - 19 . 755 - 19 . 751 - 19 . 747 - 19 . 736 - 19 . 729 - 19 . 728 - 19 . 725 - 19 . 718 - 19 . 715 - 19 . 713 - 19 . 713 - 19 . 711 - 19 . 71 - 19 . 696 - 19 . 685 - 19 . 685 - 19 . 674 - 19 . 673 - 19 . 672 - 19 . 667 - 19 . 652 - 19 . 645 - 19 . 644 - 19 . 636 - 19 . 634 - 19 . 634 - 19 . 629 - 19 . 629 - 19 . 628 - 19 . 628 - 19 . 622 - 19 . 618 - 19 . 589 - 19 . 588 - 19 . 582 - 19 . 581 - 19 . 576 - 19 . 572
0 . 034525 0 . 03453 0 . 034548 0 . 034557 0 . 034557 0 . 034576 0 . 034685 0 . 034701 0 . 034701 0 . 034838 0 . 034888 0 . 034902 0 . 035013 0 . 035132 0 . 035184 0 . 035191 0 . 035191 0 . 03537 0 . 035475 0 . 035477 0 . 035498 0 . 035498 0 . 035498 0 . 035506 0 . 035516 0 . 035516 0 . 035559 0 . 035605 0 . 035605 0 . 035649 0 . 035682 0 . 035737 0 . 035778 0 . 035778 0 . 035838 0 . 035897 0 . 035901 0 . 035928 0 . 035954 0 . 035983 0 . 036112 0 . 036187 0 . 036187 0 . 036214 0 . 036295 0 . 036309 0 . 036309 0 . 036309 0 . 036314 0 . 036317 0 . 036437 0 . 036563 0 . 036563 0 . 03667 0 . 03667 0 . 036672 0 . 036714 0 . 036894 0 . 036965 0 . 036966 0 . 037004 0 . 037004 0 . 037004 0 . 03701 0 . 03701 0 . 03701 0 . 03701 0 . 037061 0 . 037095 0 . 037376 0 . 037376 0 . 037444 0 . 037445 0 . 037492 0 . 037528
40
45
50 Entitativiteetitadelesitusten 55
60
3295 65 6403
11252
US 9 , 970 , 056 B2 49
TABLE 3 - continued 50 50
TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
27315 3959 8407
79719 79567 10973 2054 6010 6626 1743
10
399
20
4650 7107 1434
10020 10285
960 1387
10540 57466 2799 8079
51780 3683
64777 23122
705 9716
27335 81576 26003 55071 4811
25
30
7832
35 35
PGAP2 LGALS3BP TAGLN2 AAGAB FAM65A ASCC3 STX2 RHO SNRPA DLST RHOH MYo9B GPR137B CSEIL GNE SMNDC1 CD44 CREBBP DCTN2 SCAF4 GNS MLF2 KDM3B ITGAL RMNDSB CLASP2 BYSL AQR EIF3K CCDC130 GORASP2 C9orf40 NID1 BTG2 CDS2 COPS7A DLGAP4 DEF8 PSMB6 MKL2 PDIA4 CHD1 AKAPSL EIF4ENIF1 SMURF1 POLR2E MAP2K4 IFIT1 RREB1 LETMD1 TUBA4A SLC35A1 COL19A1 NARFL NOL10 ARAP3 VASP PDZK1IP1 HDAC4 DSCR3 DNAJA2 SPTAN1 ANKMY2 STUGAL EHD3 DEFA4 MED28 THOC5 TRPV4 IL23A DYNC112 KATNB1 VPS26A GATA1 GLTSCR1
- 19 . 571 - 19 . 569 - 19 . 556 - 19 . 554 - 19 . 531 - 19 . 528 - 19 . 528 - 19 . 522 - 19 . 517 - 19 . 515 - 19 . 515 - 19 . 51 - 19 . 508 - 19 . 507 - 19 . 502 - 19 . 495 - 19 . 495 - 19 . 491 - 19 . 487 - 19 . 484 - 19 . 483 - 19 . 483 - 19 . 474 - 19 . 471 - 19 . 464 - 19 . 462 - 19 . 461 - 19 . 456 - 19 . 452 - 19 . 451 - 19 . 444 - 19 . 443 - 19 . 438 - 19 . 433 - 19 . 429 - 19 . 42 - 19 . 418 - 19 . 416 - 19 . 413 - 19 . 405 - 19 . 395 - 19 . 394 - 19 . 389 - 19 . 382 - 19 . 382 - 19 . 381 - 19 . 377 - 19 . 377 - 19 . 364 - 19 . 363 - 19 . 35 - 19 . 345 - 19 . 344 - 19 . 342 - 19 . 331 - 19 . 327 - 19 . 326 - 19 . 32 - 19 . 318 - 19 . 314 - 19 . 312 - 19 . 292 - 19 . 287 - 19 . 284 - 19 . 283 - 19 . 275 - 19 . 268 - 19 . 266 - 19 . 263 - 19 . 262 - 19 . 259 - 19 . 244 - 19 . 242 - 19 . 236 - 19 . 216
8760 50813 22839 54849 5694
57496 9601 1105
26993 56478 57154 5434 6416 3434 6239 25875 7277 10559 1310
64428 79954 64411 7408 10158 9759 10311 10294 6709 57037 6483 30845 1669
80306 8563 59341 51561 1781
10300 9559 2623
29998
0 . 037528 0 . 037546 0 . 037709 0 . 037709 0 . 037957 0 . 037966 0 . 037966 0 . 038033 0 . 038087 0 . 038087 0 . 038087 0 . 038124 0 . 038132 0 . 038132 0 . 038183 0 . 038238 0 . 038238 0 . 038276 0 . 038303 0 . 03831 0 . 03831 0 . 03831 0 . 038387 0 . 038409 0 . 03849 0 . 038504 0 . 038504 0 . 038555 0 . 038598 0 . 038598 0 . 038674 0 . 038682 0 . 038723 0 . 038779 0 . 038804 0 . 038916 0 . 038932 0 . 03895 0 . 038971 0 . 039053 0 . 039139 0 . 039139 0 . 0392 0 . 039243 0 . 039243 0 . 039243 0 . 039278 0 . 039278 0 . 039441 0 . 039443 0 . 0396 0 . 039645 0 . 039645 0 . 039663 0 . 039799 0 . 039848 0 . 039848 0 . 039915 0 . 039934 0 . 03997 0 . 039979 0 . 040193 0 . 040251 0 . 040268 0 . 040268 0 . 040377 0 . 040446 0 . 040459 0 . 04048 0 . 04048 0 . 040509 0 . 040692 0 . 040714 0 . 04077 0 . 041015
5860 23093 29796 9663 4048 10129 8813 54948 2079
29960 55139 2220 54934 5875
79877 9948 55041 1820
11212 55739 26100 1088
84722 79840 79647 2040 3635
10781 5087 5817 5412 9274 2760 9923 489
57128 2932
146691 55016 51099 23133 92140 29888 57175 8703 3631 7916 2631 643 3835 706
23390 5900 25801 7248 521
55007 55968 64131 10130 7334
10797 58517 9695
157567 10484 7037
18 9885 3300 4179 51301 54555 9235 158
QDPR TTLL5 UQCR10 LPIN2 LTA4H FRY DPM1 MRPL16 ERH FTSJ2 ANKZF1 FCN2 KANSL2 RABGGTA DCAKD WDR1 PLEKHB2 ARIDA PROSC CARKD WIPI2 CEACAM8 PSRC1 NHEJ1 AKIRIN1 STOM INPP5D ZNF266 PBX1 PVR UBL3 BCL7C GM2A ZBTB40 ATP2A3 LYRM4 GSK?? TOMIL2 MARCH1 ABHD5 PHF8 MTDH STRN4 CORO1B B4GALT3 INPP4A PRRC2A GBAS CXCR5 KIF22 TSPO ZDHHC17 RALGDS GCA TSC1 ATP51 FAM118A NSFLIC XYLT1 PDIA6 UBE2N MTHFD2 RBM25 EDEM1 ANKRD46 SEC23A TFRC ABAT OSBPL2 DNAJB2 CD46 GCNT4 DDX49 IL32 ADSL
- 19 . 214 - 19 . 208 - 19 . 207 - 19 . 2 - 19 . 199 - 19 . 196 - 19 . 194 - 19 . 185 - 19 . 182 - 19 . 178 - 19 . 174 - 19 . 172 - 19 . 17 - 19 . 165 - 19 . 161 - 19 . 154 - 19 . 153 - 19 . 15 - 19 . 145 - 19 . 137 - 19 . 135 - 19 . 121 - 19 . 119 - 19 . 113 - 19 . 112 - 19 . 109 - 19 . 108 - 19 . 106 - 19 . 095 - 19 . 093 - 19 . 093 - 19 . 084 - 19 . 071 - 19 . 06 - 19 . 051 - 19 . 044 - 19 . 037 - 19 . 036 - 19 . 03 - 19 . 026 - 19 . 024 - 19 . 021 - 19 . 021 - 19 . 014 - 18 . 993 - 18 . 993 - 18 . 992 - 18 . 989 - 18 . 982 - 18 . 981 - 18 . 98 - 18 . 98 - 18 . 979 - 18 . 978 - 18 . 973 - 18 . 967 - 18 . 961 - 18 . 96 - 18 . 959 - 18 . 958 - 18 . 957 - 18 . 95 - 18 . 945 - 18 . 932 - 18 . 927 - 18 . 92 - 18 . 92 - 18 . 919 - 18 . 919 - 18 . 916 - 18 . 915 - 18 . 911 - 18 . 911 - 18 . 909 - 18 . 905
0 . 041023 0 . 041077 0 . 041082 0 . 041149 0 . 041158 0 . 041173 0 . 041188 0 . 041296 0 . 041302 0 . 041351 0 . 041361 0 . 041367 0 . 041381 0 . 041434 0 . 041468 0 . 04154 0 . 041541 0 . 041564 0 . 041609 0 . 041709 0 . 041726 0 . 041917 0 . 041943 0 . 042004 0 . 042004 0 . 04202 0 . 04202 0 . 04202 0 . 04214 0 . 04214 0 . 04214 0 . 042247 0 . 042424 0 . 042559 0 . 042678 0 . 042748 0 . 042839 0 . 042841 0 . 042881 0 . 042918 0 . 042933 0 . 042955 0 . 042955 0 . 043029 0 . 043214 0 . 043214 0 . 043214 0 . 04324 0 . 043314 0 . 043314 0 . 043314 0 . 043314 0 . 043314 0 . 043314 0 . 043383 0 . 043436 0 . 04349 0 . 04349 0 . 04349 0 . 043498 0 . 043498 0 . 043581 0 . 043639 0 . 043791 0 . 043852 0 . 043908 0 . 043908 0 . 043908 0 . 043908 0 . 043919 0 . 043919 0 . 043937 0 . 043937 0 . 043937 0 . 043967
40
45
50
55
60 ???
65
US 9 , 970 , 056 B2 51 52
TABLE 3 - continued TABLE 3 - continued Complete list of differentially expressed genes . Complete list of differentially expressed genes .
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval 5 5
Entrez ID
Gene symbol ( Name )
Combined Tstat
Combined Pval
10
20
25
9693 50485 3557 4035 9820 10227 79009 6738 7803 3479
58986 29780 6768 6241 10916 8870
51512 475 322
7099 9056 1029
51092 11325 51005 116496
3099 55638 57134 51307 7407 10959 8539 23016 3004 537
79754 1182
10611 10866 23424
373863 54332 55748 23590 7424
51669 5711 11282 8078 1025
55718 951
9806 9249 4863 5166 81619 7798 80344 79078 1486 7084 120
4668 23325 3052
57212 6631 54884 90634 8698 1508
57826 3988
RAPGEF2 SMARCAL ILIRN LRP1 CULT MFSD10 DDX50 TROVE2 PTP4A1 IGF1 TMEMSA PARVB ST14 RRM2 MAGED2 IER3 GTSE1 ATOX1 APBB1 TLR4 SLC7A7 CDKN2A SIDT2 DDX42 AMDHD2 FAM129A HK2 SYBU MAN1C1 FAM53C VARS TMED2 API5 EXOSC7 GZMM ATP6AP1 ASB13 CLCN3 PDLIM5 HCP5 TDRD7 DND1 GDAP1 CNDP2 PDSS1 VEGFC TMEM66 PSMD5 MGAT4B USP5 CDKO POLR3E CD37 SPOCK2 DHRS3 NPAT PDK4 TSPAN14 LUZP1 DCAF11 Clorf50 CTBS TK2 ADD3 NAGA KIAA1033 HCCS TP73 - AS1 SNRPC RETSAT N4BP2L1 S1PR4 CTSB RAP2C LIPA
- 18 . 904 - 18 . 895 - 18 . 882 - 18 . 882 - 18 . 881 - 18 . 88 - 18 . 879 - 18 . 878 - 18 . 877 - 18 . 876 - 18 . 875 - 18 . 873 - 18 . 864 - 18 . 86 - 18 . 858 - 18 . 843 - 18 . 839 - 18 . 839 - 18 . 837 - 18 . 834 - 18 . 833 - 18 . 832 - 18 . 824 - 18 . 822 - 18 . 82 - 18 . 82 - 18 . 817 - 18 . 813 - 18 . 812 - 18 . 811 - 18 . 809 - 18 . 802 - 18 . 796 - 18 . 795 - 18 . 794 - 18 . 792 - 18 . 787 - 18 . 784 - 18 . 777 - 18 . 774 - 18 . 764 - 18 . 76 - 18 . 759 - 18 . 75 - 18 . 749 - 18 . 743 - 18 . 74 - 18 . 723 - 18 . 722 - 18 . 708 - 18 . 705 - 18 . 701 - 18 . 692 - 18 . 692 - 18 . 688 - 18 . 681 - 18 . 68 - 18 . 673 - 18 . 667 - 18 . 665 - 18 . 657 - 18 . 656 - 18 . 655 - 18 . 654 - 18 . 652 - 18 . 649 - 18 . 648 - 18 . 639 - 18 . 632 - 18 . 628 - 18 . 616 - 18 . 609 - 18 . 609 - 18 . 608 - 18 . 604
9013 811
6811 23786 1119
10131 3796
27436 26509 51063 79845 6352 5424 23564 25814
387 2783
81552 23378 55012 10810 1615 9946 1803 9645
57146 10474 2534 5709 9258 5705 3779
80198 54809 3140 5473
53615 5552 26060
686 53346 57408 3265 663 9070 57634 50840 11275 23369 1108 3437 7533 79971 9746 23313 55862 54665 80778
30
0 . 043967 0 . 044072 0 . 044211 0 . 044211 0 . 044211 0 . 044211 0 . 044212 0 . 044212 0 . 044212 0 . 044212 0 . 044212 0 . 04423 0 . 044362 0 . 044409 0 . 044416 0 . 044627 0 . 044641 0 . 044641 0 . 044653 0 . 044679 0 . 044679 0 . 044679 0 . 044791 0 . 044791 0 . 044791 0 . 044791 0 . 04482 0 . 044863 0 . 044863 0 . 044863 0 . 044863 0 . 04494 0 . 045015 0 . 045015 0 . 045015 0 . 045031 0 . 045106 0 . 045123 0 . 04522 0 . 045246 0 . 045365 0 . 045422 0 . 045422 0 . 045541 0 . 045552 0 . 045622 0 . 045652 0 . 045864 0 . 045864 0 . 046063 0 . 046098 0 . 046126 0 . 04623 0 . 04623 0 . 046274 0 . 046368 0 . 046375 0 . 046475 0 . 046541 0 . 046557 0 . 046659 0 . 046659 0 . 046659 0 . 046659 0 . 046687 0 . 046691 0 . 046691 0 . 046793 0 . 046893 0 . 046923 0 . 047107 0 . 047156 0 . 047156 0 . 047156 0 . 047213
TAF1C CALR STX5 BCL2L13 CHKA TRAP1 KIF2A EML4 MYOF CALHM2 RNF122 CCL5 POLD1 DDAH2 ATXN10 RHOA GNB2 VOPP1 RRP8 PPP2R3C WASF3 DARS CRYZL1 DPP4 MICAL TMEM159 TADA3 FYN PSMD3 MFHAS1 PSMC5 KCNMB1 MUS81 SAMD9 MR1 PPBP MBD3 SRGN APPL1 BTD TMOSF1 LRTM1 HRAS BNIP2 ASH2L EP400 TAS2R14 KLHL2 PUM2 CHD4 IFIT3 YWHAH WLS CLSTN3 KIAA0930 ECHDC1 RSBN1 ZNF34
35
- 18 . 596 - 18 . 594 - 18 . 59 - 18 . 59 - 18 . 59 - 18 . 588 - 18 . 588 - 18 . 584 - 18 . 58 - 18 . 568 - 18 . 567 - 18 . 566 - 18 . 558 - 18 . 552 - 18 . 552 - 18 . 552 - 18 . 55 - 18 . 548 - 18 . 547 - 18 . 545 - 18 . 532 - 18 . 523 - 18 . 52 - 18 . 514 - 18 . 512 - 18 . 511 - 18 . 507 - 18 . 502 - 18 . 498 - 18 . 498 - 18 . 495 - 18 . 493 - 18 . 491 - 18 . 488 - 18 . 475 - 18 . 473 - 18 . 467 - 18 . 464 - 18 . 458 - 18 . 458 - 18 . 458 - 18 . 454 - 18 . 451 - 18 . 444 - 18 . 442 - 18 . 44 - 18 . 407 - 18 . 404 - 18 . 4 - 18 . 398 - 18 . 397 - 18 . 385 - 18 . 383 - 18 . 382 - 18 . 381 - 18 . 376 - 18 . 373 - 18 . 369
0 . 047325 0 . 047338 0 . 047364 0 . 047364 0 . 047364 0 . 047364 0 . 047364 0 . 047402 0 . 047462 0 . 047639 0 . 047639 0 . 047646 0 . 04775 0 . 047778 0 . 047778 0 . 047778 0 . 04778 0 . 047796 0 . 047796 0 . 047809 0 . 047987 0 . 048102 0 . 048132 0 . 048219 0 . 048219 0 . 048221 0 . 048266 0 . 048334 0 . 048357 0 . 048357 0 . 048382 0 . 048402 0 . 04841 0 . 048432 0 . 048622 0 . 04864 0 . 048686 0 . 048728 0 . 048761 0 . 048761 0 . 048761 0 . 04882 0 . 04883 0 . 048925 0 . 048944 0 . 048973 0 . 049521 0 . 049555 0 . 049564 0 . 049564 0 . 049564 0 . 049753 0 . 049772 0 . 049772 0 . 049776 0 . 049843 0 . 049885 0 . 049935
40
45
50
55 Biological and Functional Analysis In order to identify the overrepresented biological pro
cesses dysregulated in blood of PD patients , we performed a gene pathway analysis using NetworkAnalyst . Pathway analysis was performed using the set of up and downregu
60 lated genes separately . Upregulated genes in blood of PD were associated with the Kyoto Encyclopedia of Genes ( KEGG ) pathways ( p < 0 . 05 ) including bacterial invasion of epithelial cells , mitogen - activated protein kinase ( MAPK ) signaling pathway , fructose and mannose metabolism , T - cell
65 receptor signaling pathway , mammalian target of rapamycin ( mTOR ) signaling pathway , type 2 diabetes mellitus and colorectal cancer . The most important hub gene in terms of
53 US 9 , 970 , 056 B2
54 network topology measures , betweeness ( BC ) and degree of Longitudinal Performance of HNF4A and PTBP1 centrality ( DC ) , was HNF4A ( BC = 2213 ; DC = 84 ) ( FIG . 2A ) . In order to determine the longitudinal performance of
In parallel , downregulated genes in blood of PD patients HNF4A and PTBP1 , the relative abundance of each bio were associated with the KEGG pathways including protein marker in HBS samples collected was measured at two time processing in the endoplasmic reticulum ( ER ) , Epstein - Barr 5 points . The estimated rate of change for each biomarker was virus infection , and several types of cancer including pros determined via a linear mixed - effects model using the two tate , endometrial and lung cancer . The most prominent hub time points ( baseline and 3 years follow - up ) collected gene in terms of network topology measures was ubiquitin repeatedly between the same subjects adjusting for age , sex , C ( UBC ) ( BC = 495 ; DC = 1630 ) and PTBP1 was the most and BMI . Relative abundance of HNF4A mRNA signifi downregulated gene across the four microarray datasets 10 cantly decreased over time in PD patients compared to HC ( FIG . 2B , Table 2 ) . ( B = - 0 . 93 , p = 0 . 002 ) whereas PTBP1 mRNA increased in PD Network - Based Meta - Analysis patients ( B = 0 . 33 , p = 0 . 004 ) . Relative abundance of HNF4A HNF4A was confirmed as potential key hub gene in blood of PD by network - based meta - analysis implemented in and PTBP1 mRNAs was significantly upregulated in PD Network Analyst . The most highly ranked node across the 15 patients compared to HC in the follow up period ( FIGS . 5B four datasets based on network topology measures was and D ) . Correlation between the relative abundance of each HNF4A ( BC = 329 : DC = 35 ) followed by GATA1 ( BC = 10 . 5 ; biomarker and HY stage did not reach statistical significance DC = 8 ) . The resulting zero - order interaction network con - in the longitudinal analysis . tained 76 nodes and 81 edges ( FIG . 6 ) . In addition , network - Discussion based meta - analysis identified the aberrant expression of 20 Biomarker discovery and validation is a crucial step several splicing factors in PD patients ( FIGS . 7A and 7B ) . towards the improvement of clinical management of PD . Among the splicing factors , PTBP1 was the most signifi - Specifically , biomarkers that are useful to track the clinical cantly downregulated gene in PD patients identified in the course of PD are essential to the development of effective meta - analysis ( Table 2 , FIG . 2B , FIG . 7B ) . therapeutics . Network analysis offers an unbiased approach
In order to confirm the dysregulation of HNF4A and 25 to identify and prioritize biologically meaningful biomark PTBP1 at the protein level , a protein microarray study was ers for several neurodegenerative diseases . Here , a network analyzed in human serum samples of PD ( GSE29654 ) using based meta - analysis was performed integrating gene expres NetworkAnalyst . PTBP1 was significantly downregulated in sion profiles of untreated , sporadic and PD patients PD samples compared to healthy controls ( p = 0 . 002 ) . Altered harboring a LRRK2 ( G2019S ) mutation in order to identify expression of HNF4A was not confirmed in this protein 30 convergence among the different studies in blood of PD . microarray . Transcriptomic meta - analysis identified 2 , 781 genes consis Evaluation of HNF4A and PTBP1 mRNAs in Blood of PD tently differentially expressed in blood of PD across four
In order to validate the results obtained from the network - microarray studies . based meta - analysis , the most significant hub gene in the Network - based meta - analysis identified HNF4A as the upregulated network , HNF4A , and the most downregulated 35 most significant hub gene across the four microarrray data gene , PTBP1 , were analyzed as potential biomarkers for PD . sets , and PTBP1 was identified as the most significant Relative abundance of HNF4A and PTBP1 mRNAs was downregulated gene across the four microarrays datasets . measured in whole blood of PD patients compared to HNF4A and PTBP1 mRNAs were further evaluated as blood healthy controls ( HC ) from samples obtained from two biomarkers for PD . Relative abundance of HNF4A mRNA independent clinical trials , PROBE and HBS . Quantitative 40 was upregulated whereas PTBP1 mRNA was downregulated PCR assays revealed that HNF4A and PTBP1 mRNAs were in blood of PD patients compared to healthy individuals in significantly up - and downregulated , respectively , in blood samples obtained from two independent clinical trials ( FIG . of PD patients compared to HC in both cohorts of study 3A - D ) . Evaluation of biomarker performance showed that participants at baseline ( FIG . 3A - D ) . Analysis of receiver HNF4A and PTBP1 can distinguish PD patients from HC operating characteristic ( ROC ) was performed to evaluate 45 with a 90 % sensitivity and 80 % specificity ( FIG . 8C ) . The the diagnostic accuracy of both biomarkers . ROC analysis diagnostic performance of these two biomarkers is superior for HNF4A and PTBP1 resulted in an area under the curve than the one afforded by previously identified risk markers ( AUC ) of 0 . 72 and 0 . 82 , respectively ( FIG . 8 A - B ) . Com - in blood of PD and current clinical assessment ( Santiago et bination of both biomarkers resulted in an AUC value of al . , ( 2013 ) Specific splice variants are associated with Par 0 . 90 ( FIG . 8C ) . A step - wise linear discriminant analysis 50 kinson ' s disease . Mov Disord 28 ( 12 ) : 1724 - 1727 ; and showed that PD patients can be classified with 90 % sensi - Molochnikov et al . ( 2012 ) A molecular signature in blood tivity and 80 % specificity according to the following canoni - identifies early Parkinson ' s disease . Mol Neurodegener cal function : DPD = 0 . 10 + 0 . 56 * XPTRA - 0 . 20 % yNf4d , where 7 : 26 ) . The sensitivity of the two markers alone is also greater Dpp is the discriminant score value and X is the mRNA than the splice variant - specific RNA blood biosignature that expression level for each biomarker multiplied by its respec - 55 included 13 risk markers ( Potashkin et al . , ( 2012 ) Biosig tive canonical coefficient . natures for Parkinson ' s disease and atypical parkinsonian
Pearson correlation analysis demonstrated that relative disorders patients . PLoS One 7 ( 8 ) : e43595 ) . abundance of HNF4A and PTBP1 was independent of other HNF4A mRNA relative abundance significantly corre covariates including age ( HNF4A : r = - 0 . 25 , p = 0 . 9 ; PTBP1 : lated with PTBP1 mRNA . A significant negative correlation r = 0 . 09 , p = 0 . 59 ) and sex ( HNF4A : r = - 0 . 004 , p = 0 . 97 ; 60 was found between HNF4A mRNA expression and the HY PTBP1 : r = 0 . 05 , p = 0 . 76 ) in both cohorts of patients and body staging . Early PD patients with a low HY scale rating mass index ( BMI ) ( HNF4A : r = - 0 . 005 , p = 0 . 96 ; PTBP1 : ( HY = 1 ) showed a significantly higher upregulation of r = 014 , p = 0 . 37 ) in the HBS cohort . Correlation analysis HNF4A mRNA compared to patients with a higher HY scale revealed a significant negative correlation between HNF4A ( HY = 3 ) ( FIG . 4B ) . This finding suggests that HNF4A mRNA expression and PTBP1 mRNA ( r = - 0 . 20 , p = 0 . 008 , 65 mRNA may be useful to identify patients at very early stages FIG . 4A ) and Hoehn and Yahr stage ( HY ) at baseline of PD when therapeutic intervention may be most beneficial ( r = - 0 . 32 , p = 0 . 002 , FIG . 4B ) . and to monitor disease severity .
55 US 9 , 970 , 056 B2
56 Longitudinal performance analysis showed that relative whereas SF3B3 was downregulated ( FIG . 2 and FIG . 7 ) .
abundance of each biomarker significantly changed over These results suggest that assembly of the U2 snRNP that time in PD patients . For instance , HNF4A mRNA signifi binds to the 3 ' splice site may be facilitated in PD , but the cantly decreased whereas PTBP1 mRNA increased in PD efficient formation of an active splicing complex in PD is patients during 3 years follow up ( FIG . 5 ) . The correlation 5 119 lation 5 highly unlikely . The results from the meta - analysis also between the relative abundance of both biomarkers with HY revealed that many of the regulatory splicing factors , core
factors of the U1 , U4 , U5 and U6 snRNPs , and helicases are stage did not reach statistical significance in follow - up downregulated in PD further supporting the idea that splic samples , however . One possible explanation is that the HY ing may be both inefficient and dysregulated in PD ( FIG . stage did not change in most of the PD patients during the 7B ) . In this regard , aberrant alternative splicing in blood of 3 years period , whereas the relative abundance of the genes PD has been highlighted in numerous studies ( Potashkin et did change during this time period . These results suggest al . , ( 2012 ) Biosignatures for Parkinson ' s disease and atypi that the abundance of HNF4A and PTBP1 mRNAs in blood cal parkinsonian disorders patients . PLoS One 7 ( 8 ) : e43595 ; may be more sensitive than assessment of motor symptoms Santiago et al . , ( 2013 ) Specific splice variants are associated for monitoring disease progression . The dynamic change in with Parkinson ' s disease . Mov Disord 28 ( 12 ) : 1724 - 1727 ; expression over time of both biomarkers suggests that they Soreq et al . , ( 2012 ) Exon arrays reveal alternative splicing may be useful biomarkers to track the clinical course of PD aberrations in Parkinson ' s disease leukocytes . Neurode patients . gener Dis 10 ( 1 - 4 ) : 203 - 206 ; Soreq et al . ( 2013 ) Small RNA
One potential caveat is that most of the PD patients were sequencing - microarray analyses in Parkinson leukocytes medicated in this study , therefore , a potential confounding reveal deep brain stimulation - induced splicing changes that factor introduced by PD medications cannot be ruled out . - " classify brain region transcriptomes . Front Mol Neurosci Nevertheless , this finding is interesting in light of the 6 : 10 ; and Soreq et al . ( 2014 ) Long non - coding RNA and evidence that indicates that more than 50 % of the PD alternative splicing modulations in Parkinson ' s leukocytes patients are glucose intolerant and patients with diabetes that identified by RNA sequencing . PLoS Comput Biol 10 ( 3 ) : develop PD usually have a higher HY staging . Moreover , e1003517 ) . In addition , heterogeneous nuclear ribonucleo impaired glucose metabolism is suggested to be an early proteins ( hnRNPs ) , cap - binding proteins and proteins of the event in sporadic PD . Given that HNF4A plays a pivotal role exon junction complex were downregulated in PD suggest in hepatic gluconeogenesis and PTBP1 regulates and stabi ing that other post - transcriptional events such as cap - binding lize mRNA translation of insulin in the pancreas , the inverse protein complex formation , localization , maturation , non regulation of both genes provide a molecular rationale for sense - mediated mRNA decay and translation may be inef the impairment of insulin signaling in PD patients and thus - ficient or dysregulated in PD ( FIG . 2 and FIG . 7 ) . may be potential therapeutic targets . The vitamin D receptor ( VDR ) was also present in the
Analysis of a previous protein microarray study in human network of downregulated genes thus confirming previous serum samples with PD ( Han et al . , ( 2012 ) Diagnosis of findings reporting lower levels of VDR in blood and plasma Parkinson ' s disease based on disease - specific autoantibody as of PD patients . In addition , a subset of highly co - expressed profiles in human sera . PLoS One 7 ( 2 ) : e32383 ) revealed that genes associated with heme metabolism previously identi PTBP1 was significantly downregulated in PD patients fied in blood of two independent populations ALAS2 , compared to controls ( p = 0 . 02 ) , but expression of HNF4A FECH , and BLVRB were also found to be downregulated in was not identified . Thus , protein levels of PTBP1 may be the meta - analysis ( FIG . 2B ) . Further , other PD blood bio also a potential diagnostic biomarker for PD . markers HSPA8 and SKP1 were identified in the meta
The network of downregulated genes was centered in the to analysis . Collectively , these results confirm the presence of polyubiquitin precursor UBC and associated with protein a common molecular signature in human blood of PD processing in the ER ( FIG . 2B ) . In this regard , growing patients . evidence indicates that ER dysfunction is an early event in In summary , this study highlights the prominent conver the PD pathogenesis and targeting components of the gence among blood microarray studies from sporadic , de unfolded protein response may be a potential therapeutic - novo and the most common hereditary cause of PD and strategy . confirms the utility of blood as a useful source of biomarkers
The results from this meta - analysis also highlight the for PD . In addition , these results strengthen the association dysregulation of several splicing factors in blood of PD between PD and diabetes and provide insights into the patients . As the spliceosome assembles , protein - protein m olecular mechanisms underlying the impairment of insulin interactions are highly dynamic . One of the essential steps in signaling observed in PD patients . Further , this study under the assembly of the spliceosome is the formation of new scores the potential of network analysis as a powerful protein interactions that change the inactive B splicing framework to gain insight into the mechanisms underlying complex to an active complex in which SF3B2 , SF3B3 and PD and to identify potential therapeutic targets and biomark SF3B5 form new interactions with proteins of the U5 small ers of disease severity . Evaluation of HNF4A and PTBP1 nuclear ribonucleic particles ( snRNP ) . In this context , sev - > mRNAs in a larger prospective study including patients at eral of the core factors of the U2 snRNP were upregulated risk will be important to assess its clinical utility as a in PD including SF3A1 , SF3A2 , SF3B1 and SF3B4 , diagnostic tool for PD .
SEQUENCE LISTING
< 160 > NUMBER OF SEO ID NOS : 10
< 210 > SEQ ID NO 1 < 211 > LENGTH : 21 < 212 > TYPE : DNA
US 9 , 970 , 056 B2 57 58
- continued < 213 > ORGANISM : Artificial Sequence < 220 > FEATURE : < 223 > OTHER INFORMATION : Synthetic oligonucleotide
< 400 > SEQUENCE : 1
caacggattt ggtcgtattg g 21
< 210 > SEQ ID NO 2 < 211 > LENGTH : 25 < 212 > TYPE : DNA < 213 > ORGANISM : Artificial Sequence < 220 > FEATURE : < 223 > OTHER INFORMATION : Synthetic oligonucleotide
< 400 > SEQUENCE : 2 tgatgacaaca atatocact ttaco
? .
< 210 > SEQ ID NO 3 < 211 > LENGTH : 21 < 212 > TYPE : DNA < 213 > ORGANISM : Artificial Sequence < 220 > FEATURE : < 223 > OTHER INFORMATION : Synthetic oliognucleotide
?
?
< 400 > SEQUENCE : 3 cagaatgagc gggaccggat c 21
< 210 > SEQ ID NO 4 < 211 > LENGTH : 22 < 212 > TYPE : DNA < 213 > ORGANISM : Artificial Sequence < 220 > FEATURE : < 223 > OTHER INFORMATION : Synthetic oligonucleotide
< 400 > SEQUENCE : 4
cagcagctgc tccttcatgg ac 22
? .
< 210 > SEQ ID NO 5 < 211 > LENGTH : 21 < 212 > TYPE : DNA < 213 > ORGANISM : Artificial Sequence < 220 > FEATURE : < 223 > OTHER INFORMATION : Synthetic oligonucleotide
?
?
?
< 400 > SEQUENCE : 5
gctcaggatc atcgtggaga a 21
? .
< 210 > SEQ ID NO 6 < 211 > LENGTH : 23 < 212 > TYPE : DNA < 213 > ORGANISM : Artificial Sequence < 220 > FEATURE : < 223 > OTHER INFORMATION : Synthetic oligonucleotide
?
?
?
< 400 > SEQUENCE : 6
atcttcaaca ctgtgccgaa ctt 23
< 210 > SEQ ID NO 7 < 211 > LENGTH : 4737 < 212 > TYPE : DNA < 213 > ORGANISM : Homo sapiens
< 400 > SEQUENCE : 7
ggtttgaaag gaaggcagag agggcactgg gaggaggcag tgggagggcg gagggcgggg 60
gccttcgggg tgggcgccca gggtagggca ggtggccgcg gcgtggaggc agggagaatg 120
US 9 , 970 , 056 B2 59
- continued
cgactctcca aaaccctcgt cgacatggac atggccgact acagtgctgc actggaccca 180 gcctacacca ccctggaatt tgagaatgtg caggtgttga cgatgggcaa tgacacgtcc 240
ccatcagaag gcaccaacct caacgcgccc aacagcctgg gtgtcagcgc cctgtgtgcc 300 atctgcgggg accgggccac gggcaaacac tacggtgcct cgagctgtga cggctgcaag 360 ggcttcttcc ggaggagcgt gcggaagaac cacatgtact cctgcagatt tagccggcag 420
tgcgtggtgg acaaagacaa gaggaaccag tgccgctact gcaggctcaa gaaatgcttc 480
cgggctggca tgaagaagga agccgtccag aatgagcggg accggatcag cactcgaagg 540
tcaagctatg aggacagcag cctgccctcc atcaatgcgc tcctgcaggc ggaggtcctg 600
tcccgacaga tcacctcccc cgtctccggg atcaacggcg acattcgggc gaagaagatt 660
gccagcatcg cagatgtgtg tgagtccatg aaggagcagc tgctggttct cgttgagtgg 720
gccaagtaca toccagcttt ctgcgagctc cccctggacg accaggtggc cctgctcaga 780
gcccatgctg gcgagcacct gctgctcgga gccaccaaga gatccatggt gttcaaggac 840
gtgctgctcc taggcaatga ctacattgtc cctcggcact gcccggagct ggcggagatg 900
agccgggtgt ccatacgcat ccttgacgag ctggtgctgc ccttccagga gctgcagatc 960
gatgacaatg agtatgccta cctcaaagcc atcatcttct ttgacccaga tgccaagggg 1020
ctgagcgatc cagggaagat caagcggctg cgttcccagg tgcaggtgag cttggaggac 1080 tacatcaacg accgccagta tgactcgcgt ggccgctttg gagagctgct gctgctgctg 1140 cccaccttgc agagcatcac ctggcagatg atcgagcaga tccagttcat caagctcttc 1200
ggcatggcca agattgacaa cctgttgcag gagatgctgc tgggagggtc ccccagcgat 1260
gcaccccatg cccaccaccc cctgcaccct cacctgatgc aggaacatat gggaaccaac 1320
gtcatcgttg ccaacacaat gcccactcac ctcagcaacg gacagatgtg tgagtggccc 1380 cgacccaggg gacaggcagc cacccctgag accccacagc cctcaccgcc aggtggctca 1440
gggtctgage cctataagct cctgccggga gccgtcgcca caatcgtcaa gcccctctct 1500 gccatccccc agccgaccat caccaagcag gaagttatct agcaagccgc tggggcttgg 1560 gggctccact ggctcccccc agccccctaa gagagcacct ggtgatcacg tggtcacggo 1620 aaaggaagac gtgatgccag gaccagtccc agagcaggaa tgggaaggat gaagggcccg 1680 agaacatggc ctaagggcca catcccactg ccacccttga cgccctgctc tggataacaa 1740 gactttgact tggggagacc tctactgcct tggacaactt ttctcatgtt gaagccactg 1800
ccttcacctt caccttcatc catgtccaac ccccgacttc atcccaaagg acagccgcct 1860
ggagatgact tgaggcctta cttaaaccca gctcccttct tccctagcct ggtgcttctc 1920
ctctcctagc ccctgtcatg gtgtccagac agagccctgt gaggctgggt ccaattgtgg 1980 cacttggggc accttgctcc tccttctgct gctgccccca cctctgctgc ctccctctgc 2040 tgtcaccttg ctcagccatc ccgtcttctc caacaccacc tctccagagg ccaaggaggc 2100 cttggaaacg attcccccag tcattctggg aacatgttgt aagcactgac tgggaccagg 2160
caccaggcag ggtctagaag gctgtggtga gggaagacgc ctttctcctc caacccaacc 2220 tcatcctcct tcttcaggga cttgggtggg tacttgggtg aggatccctg aaggccttca 2280 acccgagaaa acaaacccag gttggcgact gcaacaggaa cttggagtgg agaggaaaag 2340 catcagaaag aggcagacca tccaccaggc ctttgagaaa gggtagaatt ctggctggta 2400 gagcaggtga gatgggacat tocaaagaac agcctgagcc aaggcctagt ggtagtaaga 2460
US 9 , 970 , 056 B2
- continued atctagcaag aattgaggaa gaatggtgtg ggagagggat gatgaagaga gagagggcct 2520 gctggagagc atagggtctg gaacaccagg ctgaggtcct gatcagcttc aaggagtatg 2580 cagggagctg ggcttccaga aaatgaacac agcagttctg cagaggacgg gaggctggaa 2640
gctgggaggt caggtggggt ggatgatata atgcgggtga gagtaatgag gottggggct 2700 ggagaggaca agatgggtaa accctcacat cagagtgaca tccaggagga ataagctccc 2760 agggcctgtc tcaagctctt ccttactccc aggcactgtc ttaaggcatc tgacatgcat 2820
catctcattt aatcctccct tcctccctat taacctagag attgtttttg ttttttattc 2880 tcctcctccc tccccgccct cacccgcccc actccctcct aacctagaga ttgttacaga 2940
agctgaaatt gcgttctaag aggtgaagtg attttttttc tgaaactcac acaactagga 3000 agtggctgag tcaggacttg aacccaggtc tccctggatc agaacaggag ctcttaacta 3060 cagtggctga atagcttctc caaaggctcc ctgtgttctc accgtgatca agttgagggg 3120 cttccggctc ccttctacag cctcagaaac cagactcgtt cttctgggaa ccctgcccac 3180
toccaggacc aagattggcc tgaggctgca ctaaaattca cttagggtcg agcatcctgt 3240 ttgctgataa atattaagga gaattcatga ctcttgacag cttttctctc ttcactcccc 3300 aagtcaaggg gaggggtggc aggggtctgt ttcctggaag tcaggctcat ctggcctgtt 3360 ggcatggggg tgggacagtg tgcacagtgt gggggcaggg gagggctaag caggcctggg 3420 tttgagggct gctccggaga ccgtcactcc aggtgcattc tggaagcatt agaccccagg 3480 atggagcgac cagcatgtca tocatgtgga atcttggtgg ctttgaggac attctggaaa 3540
atgccactga ccagtgtgaa caaaagggat gtgttatggg gctggaggtg tgattaggta 3600 ggagggaaac tgttggaccg actcctgccc cctgctcaac actgacccct ctgagtggtt 3660 ggaggcagtg ccccagtgcc cagaaatccc accattagtg attgtttttt atgagaaaga 3720
ggcgtggaga agtattgggg caatgtgtca gggaggaatc accacatccc tacggcagtc 3780 ccagccaagc ccccaatccc agcggagact gtgccctgct cagagctccc aagccttccc 3840 ccaccacctc actcaagtgc ccctgaaatc cctgccagac ggctcagcct ggtctgcggt 3900 aaggcaggga ggctggaacc atttctgggc attgtggtca ttcccactgt gttcctccac 3960 ctcctccctc cagcgttgct cagacctctg tcttgggaga aaggttgaga taagaatgtc 4020
ccatggagtg ccgtgggcaa cagtggccct tcatgggaac aatctgttgg agcagggggt 4080 cagttctctg ctgggaatct acccctttct ggaggagaaacccattocac cttaataact 4140
ttattgtaat gtgagaaaca caaaacaaag tttacttttt tgactctaag ctgacatgat 4200
attagaaaat ctctcgctct cttttttttt tttttttttt tttttggcta cttgagttgt 4260 ggtcctaaaa cataaaatct gatggacaaa cagagggttg ctggggggac aagcgtgggc 4320
acaatttccc caccaagaca ccctgatctt caggcgggtc tcaggagctt ctaaaaatco 4380
gcatggctct cotgagagtg gacagaggag aggagagggt cagaaatgaa cgctcttcta 4440
tttcttgtca ttaccaagcc aattactttt gccaaatttt tctgtgatct gccctgatta 4500 agatgaattg tgaaatttac atcaagcaat tatcaaagcg ggctgggtcc catcagaacg 4560 acccacatct ttctgtgggt gtgaatgtca ttaggtcttg cgctgacccc tgagccccca 4620
tcactgccgc ctgatggggc aaagaaacaa aaaacatttc ttactcttct gtgttttaac 4680
aaaagittat aaaacaaaat aaatgqcaca tatatttttt ????????????????? 4737
< 210 > SEQ ID NO 8 < 211 > LENGTH : 474
US 9 , 970 , 056 B2 64
- continued < 212 > TYPE : PRT < 213 > ORGANISM : Homo sapiens
< 400 > SEQUENCE : 8 Met Arq Leu Ser Lys Thr Leu Val Asp Met Asp Met Ala Asp Tyr Ser
Ala Ala Leu Asp Pro Ala Tyr Thr Thr Leu Glu Phe Glu Asn Val Gin 30
Val Leu Thr Met Gly Asn Asp Thr Ser Pro Ser Glu Gly Thr Asn Leu 40
Asn Ala Pro Asn Ser Leu Gly Val Ser Ala Leu Cys Ala Ile Cys Gly 55
Asp Arg Ala Thr Gly Lys His Tyr Gly Ala Ser Ser Cys Asp Gly Cys 65
? 70
Lys Gly Phe Phe Arg Arg Ser Val Arg Lys Asn His Met Tyr Ser Cys
Arg Phe Ser Arg Gin Cys Val Val Asp Lys Asp Lys Arg Asn Gin Cys 110
Arg Tyr cys Arg Leu Lys Lys Cys Phe Arg Ala Gly Met Lys Lys Glu 120
Ala Val Gin Asn Glu Arg Asp Arg Ile Ser Thr Arg Arg Ser Ser Tyr 135
Glu Asp Ser Ser Leu Pro Ser Ile Asn Ala Leu Leu Gln Ala Glu Val 145 150 mmmmmm mmmmm Leu Ser Arg Gin Ile Thr Ser Pro Val Ser Gly Ile Asn Gly Asp Ile
sms mmmmmm mmmmmmmmmm mmmmmmm mmmmmmm mmmmmmm Arg Ala Lys Lys Ile Ala Ser Ile Ala Asp Val Cys Glu Ser Met Lys 190
sms
mmmmmmm mmmmmm Glu Gin Leu Leu Val Leu Val Glu Trp Ala Lys Tyr Ile Pro Ala Phe 200
& Cys Glu Leu Pro Leu Asp Asp Gin Val Ala Leu Leu Arg Ala His Ala 215
Gly Glu His Leu Leu Leu Gly Ala Thr Lys Arg Ser Met Val Phe Lys 225 230
Asp Val Leu Leu Leu Gly Asn Asp Tyr Ile Val Pro Arg His Cys Pro
Glu Leu Ala Glu Met Ser Arg Val Ser Ile Arq Ile Leu Asp Glu Leu 270
Val Leu Pro Phe Gin Glu Leu Gin Ile Asp Asp Asn Glu Tyr Ala Tyr 280
Leu Lys Ala Ile Ile Phe Phe Asp Pro Asp Ala Lys Gly Leu Ser Asp 295
Pro Gly Lys Ile Lys Arg Leu Arg Ser Gin Val Gin Val Ser Leu Glu 305 310
Asp Tyr Ile Asn Asp Arg Gin Tyr Asp Ser Arg Gly Arg Phe Gly Glu
Leu Leu Leu Leu Leu Pro Thr Leu Gin Ser Ile Thr Trp Gln Met Ile 350
Glu Gin Ile Gin Phe Ile Lys Leu Phe Gly Met Ala Lys Ile Asp Asn 360
Leu Leu Gin Glu Met Leu Leu Gly Gly Ser Pro Ser Asp Ala Pro His 375
Ala His His Pro Leu His Pro His Leu Met Gln Glu His Met Gly Thr 385 390 400
US 9 , 970 , 056 B2 65
- continued
Asn Val Ile Val Ala Asn Thr Met Pro Thr His Leu Ser Asn Gly Gln 405 415 Thy His Leu ser Asn Glycin legate heç Met Cys Glu Trp Pro Arg Pro Arg Gly Gin Ala Ala Thr Pro Glu Thr
425 430
Pro Gin Pro Ser Pro Pro Gly Gly Ser Gly Ser Glu Pro Tyr Lys Leu 435 440 445
3
Leu Pro Gly Ala Val Ala Thr Ile Val Lys Pro Leu Ser Ala Ile Pro 450 455 460 ?
Gin Pro Thr Ile Thr Lys Gin Glu Val Ile 465 470
< 210 > SEQ ID NO 9 < 211 > LENGTH : 3340 < 212 > TYPE : DNA < 213 > ORGANISM : Homo sapiens
< 400 > SEQUENCE : 9
tgcgggcgtc tccgccattt tgtgagtcta taactcggag ccgttgggtc ggttcctgct 60 attccggcgc ctccactccg tcccccgcgg gtctgctctg tgtgccatgg acggcattgt 120
cccagatata gccgttggta caaagcgggg atctgacgag cttttctcta cttgtgtcac 180
taacggaccg tttatcatga gcagcaactc ggcttctgca gcaaacggaa atgacagcaa 240
gaagttcaaa ggtgacagcc gaagtgcagg cgtcccctct agagtgatec acatccggaa 300 gctccccatc gacgtcacgg agggggaagt catctccctg gggctgccct ttgggaaggt 360
caccaacctc ctgatgctga aggggaaaaa ccaggccttc atcgagatga acacggagga 420
ggctgccaac accatggtga actactacac ctcggtgacc cctgtgctgc gcggccagcc 480
catctacatc cagttctcca accacaagga gctgaagacc gacagctctc ccaaccaggc 540
gcgggcccag goggccctgc aggcggtgaa ctcggtccag tcggggaacc tggccttggc 600 tgcctcggcg goggccgtgg acgcagggat ggcgatggcc gggcagagcc ccgtgctcag 660
gatcatcgtg gagaacctct tctaccctgt gaccctggat gtgctgcacc agattttctc 720
caagttcggc acagtgttga agatcatcac cttcaccaag aacaaccagt tccaggccct 780 gctgcagtat goggaccccg tgagcgccca gcacgccaag ctgtcgctgg acgggcagaa 840
catctacaac gcctgctgca cgctgcgcat cgacttttcc aagctcacca gcctcaacgt 900 caagtacaac aatgacaaga gccgtgacta cacacgccca gacctgcctt ccggggacag 960
ccagccctcg ctggaccaga ccatggccgc ggccttcggt gcacctggta taatctcagc 1020 ctctccgtat gcaggagctg gtttccctcc cacctttgcc attcctcaag ctgcaggcct 1080 ttccgttccg aacgtccacg gcgccctggc ccccctggcc atcccctcgg cggcggcggc 1140
agctgcggcg gcaggtcgga tcgccatccc gggcctggcg ggggcaggaa attctgtatt 1200 gctggtcago aacctcaacc cagagagagt cacaccccaa agcctcttta ttcttttcgg 1260
cgtctacggt gacgtgcago gcgtgaagat cctgttcaat aagaaggaga acgccctagt 1320 gcagatggcg gacggcaacc aggcccagct ggccatgage cacctgaacg ggcacaagct 1380
gcacgggaag cccatccgca tcacgctctc gaagcaccag aacgtgcagc tgccccgcga 1440
gggccaggag gaccagggcc tgaccaagga ctacggcaac tcacccctgc accgcttcaa 1500
gaagccgggc tccaagaact tccagaacat attcccgccc tcggccacgc tgcacctctc 1560 caacatcccg ccctcagtct ccgaggagga tctcaaggtc ctgttttcca gcaatggggg 1620 cgtcgtcaaa ggattcaagt tcttccagaa ggaccgcaag atggcactga tocagatggg 1680
US 9 , 970 , 056 B2 67
- continued
ctccgtggag gaggcggtcc aggccctcat tgacctgcac aaccacgacc tcggggagaa 1740
ccaccacctg cgggtctcct tctccaagtc caccatctag gggcacaggc ccccacggcc 1800
gggccccctg gcgacaactt ccatcattcc agagaaaagc cactttaaaa acagctgaag 1860 tgaccttagc agaccagaga ttttattttt ttaaagagaa atcagtttac ctgtttttaa 1920 aaaaattaaa tctagttcac cttgctcacc ctgcggtgac agggacagct caggctcttg 1980 gtgactgtgg cagcgggagt tcccggccct ccacacccgg ggccagaccc tcggggccat 2040 gccttggtgg ggcctgtgtc gggcgtgggg cctgcaggtg ggcgccccga ccacgacttg 2100 gcttccttgt gccttaaaaa acctgccttc ctgcagecac acacccaccc ggggtgtcct 2160 ggggacccaa ggggtggggg ggtcacacca gagagaggca gggggcctgg ccggctcctg 2220
caggatcatg cagctggggc gcggcggccg cggctgcgac accccaaccc cagccctcta 2280 atcaagtcac gtgattctcc cttcaccccg cccccagggc cttcccttct gcccccaggc 2340 gggctccccg ctgctccagc tgcggagctg gtcgacataa tctctgtatt atatactttg 2400 cagttgcaga cgtctgtgcc tagcaatatt tccagttgac caaatattct aatctttttt 2460
catttatatg caaaagaaat agttttaagt aactttttat agcaagatga tacaatggta 2520
tgagtgtaat ctaaacttcc ttgtggtatt accttgtatg ctgttacttt tattttattc 2580 cttgtaatta agtcacaggc aggacccagt ttccagagag caggcggggc cgcccagtgg 2640 gtcaggcaca gggagccccg gtcctatctt agagcccctg agcttcaggg aaggggcggg 2700 cgtgtcgccg cctctggcat cgcctccggt tgccttacac cacgccttca cctgcagtcg 2760 cctagaaaac ttgctctcaa acttcagggt tttttcttcc ttcaaatttt ggaccaaagt 2820 ctcatttctg tgttttgcct gcctctgatg ctgggacccg gaaggcgggc gctcctcctg 2880 tcttctctgt gotctttcta ccgcccccgc gtcctgtccc gggggctctc ctaggatccc 2940 ctttccgtaa aagcgtgtaa caagggtgta aatatttata attttttata cctgttgtga 3000 gacccgag99 gcggcggcgc ggttttttat ggtgacacaa atgtatattt tgctaacago 3060
aattccaggc tcagtattgt gaccgcggag ccacagggga ccccacgcac attccgttgc 3120 cttacccgat ggcttgtgac gcggagagaa ccgattaaaa ccgtttgaga aactcctccc 3180
ttgtctagcc ctgtgttcgc tgtggacgct gtagaggcag gttggccagt ctgtacctgg 3240
acttcgaata aatcttctgt atcctcgctc cgttccgcct taaaaaaaaa aaaaaaaaaa 3300
???????????????????????????????????????? 3340
< 210 > SEQ ID NO 10 < 211 > LENGTH : 557 < 212 > TYPE : PRT < 213 > ORGANISM : Homo sapiens
< 400 > SEQUENCE : 10
Met Asp Gly Ile Val Pro Asp Ile Ala Val Gly Thr Lys Arg Gly Ser 15
Asp Glu Leu Phe Ser Thr Cys Val Thr Asn Gly Pro Phe Ile Met Ser 20 25 30
Ser Asn Ser Ala Ser Ala Ala Asn Gly Asn Asp Ser Lys Lys Phe Lys 45
che non
legate alla abb i amo
Gly Asp Ser Arg Ser Ala Gly Val Pro Ser Arg Val Ile His Ile Arg
Lys Leu Pro Ile Asp Val Thr Glu Gly Glu Val Ile Ser Leu Gly Leu 75
US 9 , 970 , 056 B2 69 | 70
- continued
J Pro Phe Gly Lys Val Thr Asn Leu Leu Met Leu Lys Gly Lys Asn Gln 85 95
Ala Phe Ile Glu Met Asn Thr Glu Glu Ala Ala Asn Thr Met Val Asn 100 105 110
Tyr Tyr Thr Ser Val Thr Pro Val Leu Arg Gly Gin Pro Ile Tyr Ile 120 125
Gin Phe Ser Asn His Lys Glu Leu Lys Thr Asp Ser Ser Pro Asn Gin
Ala Arq Ala Gln Ala Ala Leu Gln Ala Val Asn Ser Val Gln Ser Gly 145 155 160
Asn Leu Ala Leu Ala Ala Ser Ala Ala Ala Val Asp Ala Gly Met Ala 165 175
Met Ala Gly Gin Ser Pro Val Leu Arg Ile Ile Val Glu Asn Leu Phe 180 185 190 gg g? g ?
Tyr Pro Val Thr Leu Asp Val Leu His Gin Ile Phe Ser Lys Phe Gly 2000 205
Thr Val Leu Lys Ile Ile Thr Phe Thr Lys Asn Asn Gln Phe Gln Ala
Leu Leu Gin Tyr Ala Asp Pro Val Ser Ala Gln His Ala Lys Leu Ser 225 235 240
Leu Asp Gly Gin Asn Ile Tyr Asn Ala Cys Cys Thr Leu Arg Ile Asp 245 255
8 m
mm mmmm mmmmmmm mmmmm ? mam mmmmmmmm mmmmmm mmmmmm mmmm *
SEE Phe Ser Lys Leu Thr Ser Leu Asn Val Lys Tyr Asn Asn Asp Lys Ser 260 265 270
Ser Gin Pro Ser Arg Asp Tyr Thr Arg Pro Asp Leu Pro Ser Gly Asp 280 22 5
Leu Asp Gin Thr Met Ala Ala Ala Phe Gly Ala Pro G ] y Ile Ile Ser
Ala Ser Pro Tyr Ala Gly Ala Gly Phe Pro Pro Thr Phe Ala Ile Pro 305 315 320
Gln Ala Ala Gly Leu Ser Val Pro Asn Val His Gly Ala Leu Ala Pro 325 335
Leu Ala Ile Pro Ser Ala Ala Ala Ala Ala Ala Ala Ala Gly Arg Ile 340 345 350 |
Ala Ile Pro Gly Leu Ala Gly Ala Gly Asn Ser Val Leu Leu Val Ser 360 365
Asn Leu Agn Pro Glu Arg Val Thr Pro Gln Ser Leu Phe Ile Leu Phe
Gly Val Tyr Gly Asp Val Gin Arg Val Lys Ile Leu Phe Asn Lys Lys 385 395 400
Glu Asn Ala Leu Val Gln Met Ala Asp Gly Asn Gln Ala Gln Leu Ala 405 415
ggg D E E Met Ser His Leu Asn Gly His Lys Leu His Gly Lys Pro Ile Arg Ile
420 425 430
Thr Leu Ser Lys His Gin Asn Val Gin Leu Pro Arg Glu Gly Gin Glu 440 445
Asp Gin Gly Leu Thr Lys Asp Tyr Gly Asn Ser Pro Leu His Arg Phe
Lys Lys Pro Gly Ser Lys Asn Phe Gin Asn Ile Phe Pro Pro Ser Ala 465 475 480 32 ? ? Thr Leu His Leu Ser Asn Ile Pro Pro Ser Val Ser Glu Glu Asp Leu
485 490 495
US 9 , 970 , 056 B2 72
- continued Lys Val Leu Phe Ser Ser Asn Gly Gly Val Val Lys Gly Phe Lys Phe
500 505 510
Phe Gin Lys Asp Arg Lys Met Ala Leu Ile Gin Met Gly Ser Val Glu 515 520 525 si e non sabes
Glu Ala Val Gin Ala Leu Ile Asp Leu His Asn His Asp Leu Gly Glu 530 535 540
Asn His His Leu Arq Val Ser Phe Ser Lys Ser Thr Ile 545 550 555
The invention claimed is : ( b ) an increased PTBP1 expression level of the human 1 . A method for diagnosing , prognosing or monitoring 15 subject at a later time point compared to the PTBP1
Parkinson ' s Disease ( PD ) in a human subject , comprising : expression level at an initial time point indicates dis ( a ) obtaining a blood sample from a human subject ease progression of PD in the subject and no change of
suspected of having PD ; PTBP1 expression levels of the human subject at a later ( b ) determining the expression level of HNF4A and time point compared to the PTBP1 expression level at PTBP1 in the blood sample from the human subject an initial time point indicates no disease progression . suspected of having PD ; wherein the expression level 7 . A method of treating a human subject for Parkinson ' s of HNF4A is determined using a set of primer pairs Disease ( PD ) , the method comprising : suitable for the detection and quantification of the ( a ) obtaining a diagnosis identifying a human subject as nucleic acid expression of HNF4A , and wherein the 25 having PD , wherein the diagnosis was obtained by : expression level of PTBP1is determined using a set of ( i ) obtaining a blood sample from a human subject primer pairs suitable for the detection and quantifica suspected of having PD ; tion of the nucleic acid expression of PTBP1 ; and ( ii ) determining the expression level of HNF4A and wherein HNF4A is encoded by SEQ ID NO : 07 , and PTBP1 ; wherein the expression level of HNF4A is PTBP1 is encoded by SEQ ID NO : 09 ; wherein the set 30 determined using a set of primer pairs suitable for the of primers suitable for the detection and quantification detection and quantification of the nucleic acid of the nucleic acid expression of HNF4A comprise expression of HNF4A , and wherein the expression SEQ ID NO : 03 and SEQ ID NO : 04 , and wherein the level of PTBP1 is determined using a set of primer set of primers suitable for the detection and quantifi pairs suitable for the detection and quantification of cation of the nucleic acid expression of PTBP1 com - 35 the nucleic acid expression of PTBP1 ; and wherein prise SEQ ID NO : 05 and SEQ ID NO : 06 ; and HNF4A is encoded by SEQ ID NO : 07 , and PTBP1
( c ) comparing the expression level of HNF4A and PTBP1 is encoded by SEQ ID NO : 09 ; wherein the set of in the blood sample to the expression level of HNF4A primers suitable for the detection and quantification and PTBP1 in a non - PD , healthy control sample , of the nucleic acid expression of HNF4A comprise whereby an increased expression level of HNF4A in the 40 SEQ ID NO : 03 and SEQ ID NO : 04 , and wherein the blood sample from the human subject suspected of set of primers suitable for the detection and quanti having PD as compared to the non - PD sample is fication of the nucleic acid expression of PTBP1 indicative of PD and a decreased expression level of comprise SEQ ID NO : 05 and SEQ ID NO : 06 , and PTBP1 in the blood sample from the human subject ( iii ) comparing the expression level of HNF4A and suspected of having PD as compared to the non - PD 45 PTBP1 in the blood sample to the expression level of sample is indicative of PD , thereby diagnosing the HNF4A and PTBP1 in a non - PD , healthy control human subject as having PD . sample , whereby the increased expression level of
2 . The method of claim 1 , wherein the expression level is HNF4A in the blood sample from the human subject determined by detecting messenger RNA . suspected of having PD as compared to the non - PD
3 . The method of claim 1 , further comprising reverse 50 sample is indicative of PD , and a decreased expres transcription of the messenger RNA prior to detecting . sion level of PTBP1 in the blood sample from the
4 . The method of claim 1 , wherein determining the human subject suspected of having PD as compared expression level of the at least one gene is by measuring a to the non - PD sample is indicative of PD , thereby level of fluorescence by a sequence detection system fol diagnosing the human subject as having PD ; and lowing a quantitative , real - time polymerase chain reaction 55 ( b ) administering to the subject a PD treatment regimen . ( PCR ) assay . 8 . The method of claim 7 , wherein the expression level is
5 . The method of claim 1 , further comprising determining determined by detecting messenger RNA of HNFA4A and a treatment regimen for the human subject . PTBP1 .
6 . The method of claim 1 , wherein : 9 . The method of claim 7 , further comprising reverse ( a ) a decreased HNF4A expression level of the human 60 transcription of the messenger RNA prior to detecting .
subject at a later time point compared to the HNF4A 10 . The method of claim 7 , wherein determining the expression level at an initial time point indicates dis - expression level of the at least one gene is by measuring a ease progression and no change of HNF4A expression level of fluorescence by a sequence detection system fol levels of the human subject at a later time point lowing a quantitative , real - time polymerase chain reaction compared to the HNF4A expression level at an initial 65 ( PCR ) assay . time point indicates no disease progression of PD in the 11 . A Parkinson ' s Disease ( PD ) diagnosis , prognosis or subject ; and monitoring kit , consisting of a set of primer pairs suitable for
74 US 9 , 970 , 056 B2
73 the detection and quantification of the nucleic acid expres sion of HNF4A and a set of primer pairs suitable for the detection and quantification of the nucleic acid expression of PTBP1 , wherein HNF4A is encoded by SEO ID NO : 07 , and PTBP1 is encoded by SEQ ID NO : 09 , and the set of primers 5 suitable for the detection and quantification of the nucleic acid expression of HNF4A comprise SEQ ID NO : 03 and SEQ ID NO : 04 , and wherein the set of primers suitable for the detection and quantification of the nucleic acid expres sion of PTBP1 comprise SEQ ID NO : 05 and SEQ ID 10 NO : 06 .
12 . The kit of claim 11 , wherein the kit further comprises one or more of buffers , wash reagents , polymerases , internal controls , or reagents capable of detecting the presence of a bound nucleic acid primer . 15
* * * *
