Post on 24-Jan-2023
PART II: Lectures 39-40Kirsi Granberg
Introduction to molecular biologyand biochemistry (BIO2210/2220)
Cancer
Cancer
• Uncontrolled proliferation and invasion ofthe cells
• Our own cells become dangerous for us• Might be deadly (1/4 of us in Europe)• Highly studied
– Great input in research
Cancer progression• Benign• Malignant: ability to invade into the
surrounding tissue• Metastatic: ability to develop secondary
tumors
Cancer epidemiology
• Environmental factors that affect cancerdevelopment
• Certain viruses– Human papilloma virus and cervical cancer
• Tobacco• Obesity• Etc• Cannot explain all the forms of cancer
Figure 20-45 Essential Cell Biology (© Garland Science 2010)
Genetic instability• Different degrees• Accumulation of genetic changes• Mutations• Chromosomal alterations
Figure 20-46 Essential Cell Biology (© Garland Science 2010)
Cancer cells andevolution
• Selective advantage• Selection pressure
– Also in medication
Figure 20-47 Essential Cell Biology (© Garland Science 2010)
Alterations in oncogenes and tumor suppressors
Figure 20-48 Essential Cell Biology (© Garland Science 2010)
Activation mechanismsfor proto-oncogenes
Figure 20-49 Essential Cell Biology (© Garland Science 2010)
Different types of genes can be important
Cancer research – colorectal cancer• Cancer of epithelial cells in colon and
rectum
www.nlm.nih.gov,
Cancer research – colorectal cancer
• Increased susceptibility to colorectal cancerin certain families– Development of massive ammounts of
tumorous growths (polyps)
Cancer research – colorectal cancer
• Increased susceptibility to colorectal cancerin certain families– Development of massive ammounts of
tumorous growths (polyps)– -> Inactivation or deletion of Adenomatous
Polyposis Coli (APC) gene• This happens also in 60% of patients that
have both functional genes in their genome
Cancer research – colorectal cancer• When APC was discovered, its function was
not known– > Co-immunoprecipitation studies to find
interacting proteins• -catenin was found to interact with APC
– Known for its role in adherence junctions• -catenin was found to interact with LEF-
1/TCF– Which is a transcription regulator– > totally different role for -catenin
Cancer treatment
• Challenges– Genetic instability and rapid proliferation rate
allow resistance mechanisms to happen– Can we prevent it?– Cancers are generally detected only after they
have reached a certain size (diameter of 1 cm)-> already genetically diverse and maybe evenmetastasized
General cancer treatments
• Surgery• Therapies based on the intrinsic properties
of cancer cells– Cancer cells are more vulnerable to DNA
damage– > radiotherapy (ionization) and DNA-damaging
chemotherapy– Inherited Brca1 and Brca2 mutations
More recent treatment strategies• Blocking the formation of new blood vessel
(anti-angiogenic therapies)• Use of immune system to kill cancer cell• Drugs that target specific oncogenes
– Inhibitors and other modulators– E.g. Cleevec/Clivec (also called Imatinib)
targets BRC-Abl in Philadelphia chromosome-positive (Ph+) chronic myelogenous leukemia(CML) and KIT in gastrointestinal stromaltumors (GIST)
Figure 20-54 Essential Cell Biology (© Garland Science 2010)
Cleevec –targeted therapy against kinase
Cancer summary• Cancer progression• Genetic instability• Oncogenes and tumor suppressors• Cancer epidemiology• Hallmarks of cancer• Cancer treatment
– Surgery– DNA damage– Targeted therapies
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Massive parallel sequencing
• Also called next-generation sequencing(NGS)
• Is deep sequencing– Generating massive amount of reads (data)
from one sample• Happens via spatially separated, clonally
amplified DNA templates or single DNAmolecules in a flow cell
Refs: Wikipedia and illumina
Sequencing Approaches (1)
• Pyrosequencing– DNA polymerase is able to move only in the
presence of a correct base• Sequencing by reversible terminator
chemistry– fluorescently-labeled terminator bound dNTPs– the cycle of nucleotide incorporation,
fluorescence imaging and cleavage
• Sequencing-by-ligation mediated by ligaseenzymes– Binding of one-base-encoded probes or two-
base-encoded probes– Ligation– Fluorescent imaging
• Phospholinked Fluorescent Nucleotides orReal-time sequencing– imaging the continuous incorporation of dye-
labelled nucleotides during DNA synthesis
Sequencing Approaches (2)
Sample preparationTruSeq Stranded Total RNA
1. 0.1-1 ug Total RNA2. Depletion of ribosomal RNA3. RNA fragmentation4. First strand cDNA synthesis5. Second Strand cDNA synthesis -> DNA6. Adenylation of 3’ end7. Adapter ligation8. PCR amplification9. Library normalization10. Library pooling Video
Bioinformatics and science
• We should catch fishes that are still hidden• We should question current information
– Sometimes• Everything is relative and context-
dependent
Bioinformatic approaches
• Bioinformatics can add value to whicheverscientific questions we might have– When it has a connection to living entities
• How close connectionto biology world?– Depends on your preferences
danthecomputerguytips.blogspot.com
1. Sequence analysis2. Literature analysis3. Genome annotation4. Computational evolutionary biology5. Analysis of gene expression6. Analysis of regulation7. Analysis of protein expression8. Analysis of mutations in cancer9. Comparative genomics10. Network and systems biology11. High-throughput image analysis12. Structural bioinformatic approaches