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Cancer Genomes
02-‐223 Personalized Medicine:
Understanding Your Own Genome Fall 2014
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The Economic Burden of Cancer
• The economic cost of cancer exceeds that of any other disease – Only accounts for disability and premature death, no direct medical costs
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Overview
• What is cancer and how does it develop?
• GeneKcs of cancer
• Finding cancer mutaKons
• Personalized medicine in cancer (next class)
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Development of Cancer Cells
• Types of cancers – Carcinomas: cancers arising from epithelial cells
– Sarcomas: cancers arising from connecKve Kssue or muscle cells – Leukemias and lymphomas: cancers derived from white blood cells
and their precursors
• Agents that trigger carcinogenesis – Chemical carcinogens (causes local DNA alteraKons)
– RadiaKon such as x-‐rays (causes chromosome breaks and translocaKons), UV light (causes DNA base alteraKons)
– Viruses: HepaKKs-‐B, HepaKKs-‐C virus for liver cancer
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Tumors
• Cancer cells – Reproduce in defiance of the normal restraints on cell growth and division
– Invade and colonize territories normally reserved for other cells
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Defective Control of Cell Death and Differentiation in Cancer Cells
• Both increased cell division and decreased apoptosis (cell death) can contribute to tumorigenesis
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Cancer Progression
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Cancer Progression
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Pathways of Tumorigenesis
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Overview
• What is cancer how does it develop?
• GeneKcs of cancer
• Finding cancer mutaKons
• Personalized medicine in cancer (next class)
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Germline Mutations
• Any detectable and heritable variaKon in the lineage of germ cells
• MutaKons in these cells are transmi[ed to offspring • So far, we focused on germline mutaKons for complex
diseases
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Somatic Mutations
• MutaKons in non germline cells
• These mutaKons are not transmi[ed to offsprings
• Cancer can be caused by both germline and somaKc mutaKons
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Cancer Progression
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Cancer Progression
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Cancer Progression
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Cancer Progression
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Cancer Mutations
• MutaKons in genome
• MutaKons in epigenome
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Epigenome
• Two-‐meter long DNA sequences are packaged into each cell
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Epigenetics: Histone Modification
Nucleosome consists of eight histone proteins
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Epigenetics: Histone Modification
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Histone Modification
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Epigenetics
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Epigenetics: Histone Modification
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Methylation
• MethylaKon of cytosine (C) nucleoKdes in DNA
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Methylation
• Associated with repressing gene expression – X-‐chromosome silencing
– Promoter regions of expressed genes in a Kssue are usually unmethylated
– Different methylaKon pa[erns have been observed in IdenKcal twins – environmental effects
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Cancer-Causing Genes
• Oncogenes – MutaKons that confer gain of funcKons to oncogenes can promote cancer
– MutaKons with growth-‐promoKng effects on the cell – O`en heterozygous mutaKon is enough to make cells cancerous. Why?
• Tumor suppressor genes – MutaKons that confer loss of funcKon can contribute to cancer – Typically homozygous mutaKon is required to make cells cancerous. Why?
• DNA maintenance genes – Indirect effects on cancer development
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Mutations in Tumor Suppressor Genes
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Mutations in Oncogenes
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Replication of DNA Damages
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Overview
• What is cancer how does it develop?
• GeneKcs of cancer
• Finding cancer mutaKons
• Personalized medicine in cancer (next class)
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How to Find Cancer Causing Mutations
• Germline cancer mutaKons?
• SomaKc cancer mutaKons?
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How to Find Cancer Causing Mutations
• Germline cancer mutaKons? – Genotype data are collected for a large number of normals and cancer
paKents (case/control studies)
• SomaKc cancer mutaKons? – Genotype data are collected for blood (normal) and cancer cells for
each cancer paKent, for a large number of cancer paKents.
– What is the challenge?
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Driver and Passenger Mutations
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Driver and Passenger Mutations
• Driver mutaKons – Causally implicated in oncogenesis – Gives growth advantage to cancer cells
• E.g., mutaKons that de-‐acKvate tumor suppressor genes – posiKvely selected in the microenvironment of the Kssue
• Passenger mutaKons – SomaKc mutaKons with no funcKonal consequences – Does not give growth advantage to cancer cells – However, the passenger mutaKons are propagated to daughter cells just
because they co-‐exist with the driver mutaKon in the same cell
• Key ScienKfic QuesKon: How can we disKnguish between driver and passenger mutaKons?
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Identifying Driver Mutations
• Compare the tumor genome with the normal genome of the same individual
• Compare the tumor genome with reference genome
• Other known DNA polymorphisms
• Signatures of driver mutaKons – Frequently observed mutaKons across tumors.
– MutaKons that cluster in subset of genes. Passenger mutaKons are more randomly distributed across genomes
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Challenges
• Challenges unique to cancer genome analysis – Sequence alignment and assembly can be significantly more challenging
because of highly rearranged chromosomes and high variaKon across cancer genomes
– SomaKc mutaKon calling is more challenging • the impurity of the sample
– Normal genomes have allele copies of 0, 1, or 2 – Cancer genomes can have allele copies of fracKons of 0, 1, or 2
• Most somaKc mutaKons are rare
• Different cancer types have different rates of mutaKons. Mutator phenotype may or may not present.
• Infrequently occurring driver mutaKons are hard to idenKfy.
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Methods for Detecting Driver Mutations
• SIFT – A tool that predicts whether an amino acid subsKtuKon affects protein
funcKon
– Classifies a subsKtuKon into tolerated or deleterious ones
• PolyPhen – So`ware for predicKng damaging effects of nonsynonymous mutaKons
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PolyPhen Features • Black: candidates, blue: selected
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h[p://cancergenome.nih.gov/
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The Cancer Genome Atlas
• Other types of data are also collected along with genome data – Tumor gene expressions
– Tumor microRNA expression – epigeneKc data – clinical data
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Summary
• The geneKc causes of cancer include both heritable germline mutaKons and somaKc mutaKons
• In cancer genome study, genome data are collected for both normal and cancer cells for the same individual
• The key challenge in studying the geneKc causes of cancer is to idenKfy driver mutaKons from background passenger mutaKons