PART II: Lectures 39-40 Kirsi Granberg

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 progression

thefutureofthings.com

Figure 20-44 Essential Cell Biology (© Garland Science 2010)

Cancermetastasis

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


Genetic instability• Different degrees• Accumulation of genetic changes• Mutations• Chromosomal alterations


Cancer cells andevolution

• Selective advantage• Selection pressure

– Also in medication


Alterations in oncogenes and tumor suppressors


Activation mechanismsfor proto-oncogenes


Different types of genes can be important

The hallmarks of cancer

www.onclive.com

Cancer research – colorectal cancer• Cancer of epithelial cells in colon and

rectum

www.nlm.nih.gov,

Cancer research – colorectal cancer

thedigestivesystemxd.pbworks.com

• Different stages


• Increased susceptibility to colorectal cancerin certain families– Development of massive ammounts of

tumorous growths (polyps)


Polyps


• 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


APC and -catenin regulate Wnt-pathway


Phases ofcolorectal

cancercevelopment

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


Latedetection

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)


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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DEEP SEQUENCINGMETHODS

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 platforms

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

PART II: Lectures 39-40 Kirsi Granberg

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