Part 2 Flashcards
Earliest studies of cancer done in… lead to…
sea urchins, the theory that chromosomal aberrations lead to cancer
Categories of genetic alterations in cancer
Mutations (point, deletions, translocation), and chromosomal changes (increased copy number)
Categories of epigenetic alterations in cancer
DNA methylation, histone modifications, and MicroRNA/NonCoding RNA, deregulation of transcription/translation
Hotspot mutations
Common in the activation of oncogenes. Example: V600E in BRAF in Thyroid Carcinoma.
Truncating mutation
Common in inactivating a tumor suppressor. Introduction of an early stop codon. Example: Truncating mutations to tp53 in colorectal cancer
Can also activate an oncogene: cycD in Lymphoma. mutation removes PEST sequence, which is an important degratory signal.
Loss of heterozygosity
Can be induced by other mutations. RHEB and 4E can induce p53 LOH
Gene amplification
Can occur by double minute or intra-chromosomal amplification
Chromosomal translocations
Induce oncogenic protein fusions or overexpression: Philadelphia chromosome
Frequent in hematological malignancies:
- Bcl2 deregulated in follicular lymphoma
- MYC deregulated in Burkitt’s Lymphoma
Detecting chromosomal changes
FISH with different fluorescent markers -> Can see amplifications (more color), deletions (less color), or rearrangements (distance change)
DNA methylation
Methyltransferases methylate C
CpG islands are CG rich regions of DNA that can be highly methylated to suppress transcription
Measuring DNA methylation
Sodium bisulphite modification will change unmethylated C to U, which will be read as T by Taq polymerase. Sequencing original strand will reveal differences.
Histone modifications
Methylation regulated by polycomb complexes:
Have readers, writers, and erasers.
Activators: H3 acetylation, H3 K4 trimethylation
Repressors: H3 K9/27 trimethylation, DNA methylation
Regulators of histone methylation (Like EZH2, which is part of a writer complex) are frequently mutated in Cancer. GoF mutation -> repression of transcription
ChIP
Selection of antibodies allows you to choose which histone modification to screen for.
Types of sequencing
- Targeted: Most manageable in a hospital setting. Applicable to screens.
- Whole exome sequencing: All coding DNA, most available type of data.
- Whole genome sequencing: Allows investigation of ncRNA, ncDNA, challenging to interpret, expensive.
Comparative genomic hybridization
A method to simultaneously detect chromosomal aberrations across the whole genome
Role of IDH1 in cancer
Cancer-associated mutations produce 2-hydroxyglutarate. Can be used to id patients with IDH1-dependent brain tumor, slowing production of IDH1 can be life-extending for patients.
Accumulation of 2-HG in cells alters DNA methylation, impair TET2.
IDH1/2
IDH1 is mutated in gliomas, but either can be mutated in Acute myeloid leukemia AML. Both convert α-ketoglutarate to 2HG.
Major signaling pathways in cancer
- Ras
- Akt
- Notch
- Hedgehog
- TGFB
- Wnt
- Cell Death
Receptor Tyrosine Kinases
- Epidermal growth factor r (EGFR)
- Fibroblast growth factor r (FGFR)
- Platelet-derived growth factor
- Vascular endothelial growth factor
- Insulin-like growth factor
Downstream:
- Ras (activated bySOS, activates Raf and PI3K, Ral-GEF)
- PI3K
Ras
Oncogene.
Activated by SOS (Guanine exchange factor), having GTP makes it active. inactivated by a GTPase Activating Protein
Hotspot mutation keeps it in a constitutively active form
Downstream of Raf
MEK, Erk1/2, ( Mnk1 -> elF4E, Ets, Elk-1, SAP-1)
Involved in transcriptional regulation, proliferation, differentiation.
Erk1/2 aka Mitogen-activated protein (MAP) kinase, MEK = MAPKK, Raf = MAPKKK.
PI3K pathway
- PI3K phophorylates Inositol-phospholipid -> PIP3
- PI3K is regulated by PTEN.
- PIP3 activates AKT
- PTEN deleted in several cancers.
- PI3K pathway implicated in protein synthesis and survival
Myc
myc is a helix-loop-helix leucine zipper protein, frequently overexpressed.
Forms a dimer with max - activates the expression of several genes.
Is translated in burkitt’s lymphoma.
Rb pathway
CDKN2A/B –| (MDM2 –|tp53, CDK –| RB1)
mTOR
reactivates AKT
How to analyze pathway activity?
- Reporter constructs
- protein-protein interactions
- Mass cytometry (Cytof)
- Y2H, spectroscopy
- FRET (+ inhibitor: abolishes signal)
