Cancer Genetics I-III 2023 PDF

Cancer Genetics I-III_2023 Robin T. Varghese, Ph.D. E-mail: [email protected] Cancer is the 2nd leading cause of death in the US • 1 in 5 in US population will have cancer in their lifetime • accounts for about 20% of annual deaths • accounts for 10% of medical care costs (in developed countri...

Cancer Genetics I-III_2023 Robin T. Varghese, Ph.D. E-mail: [email protected] Cancer is the 2nd leading cause of death in the US • 1 in 5 in US population will have cancer in their lifetime • accounts for about 20% of annual deaths • accounts for 10% of medical care costs (in developed countries) • affects all ethnicities and both sexes regardless of age CA: A Cancer Journal for Clinicians, Volume: 71, Issue: 1, Pages: 7-33, 2021 Cancer involves abnormal cell growth • Cancer is a group of diseases involving abnormal cell growth with the potential to spread to other parts of the body • Not a single disease! Many different types and subtypes Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011 Mar 4;144(5):646-74. Genetics plays a critical role in cancer development, progression, and treatment • Gene dysfunction is implicated in initiating and driving cancerous changes in tissues • Inherited mutations in certain genes can predispose carriers to heritable cancer syndrome • Also, more commonly, these cancer initiating mutations are linked to sporadic cancer development • Analysis and documentation of common mutations in cancer tissue (signature or profile) • Personalized medicine---tumor’s gene signature---may provide prognosis • Candidate drugs to target specific cellular processes Cancer classes -Carcinomas, which originate in epithelial tissue, such as the cells lining the intestine, bronchi, or mammary ducts -Hematopoietic malignant neoplasms, such as leukemia, lymphoma, and myelomas which spread throughout the bone marrow, lymphatic system, and peripheral blood. -Sarcomas, in which the tumor has arisen in mesenchymal tissue, such as bone, muscle, vessels or connective tissue. -Central Nervous System (CNS) tumors arise from cells various components of the central and peripheral nervous system. Cancer staging TNM Staging System: most widely used (exception: brain & spinal cord tumors, blood cancers) Primary Tumor (T) = refers to the size and extent of the main tumor Regional Lymph Nodes (N) = refers to # of nearby lymph nodes w./ cancer Distant Metastasis (M) = presence & extent of metastasis or spread May also be grouped into five less-detailed stages: Stage 0: § Abnormal cells present but have NOT spread (may also be called “in-situ”) § Not “cancer”, but may become cancerous Stage I – III: § Cells are cancerous § The higher the classification, the larger the tumor and the more invasive Stage IV: § Cancer has metastasized to distant sites Cancer growth and evolution Non-lethal genetic damage lies at the heart of carcinogenesis May arise from: a. consequence of random replication errors (e.g., incorporation of incorrect nucleotide) b. exposure to environmental factors/carcinogens (e.g., UV radiation, polycyclic aromatic hydrocarbons (PAH)) c. faulty DNA maintenance/repair processes (e.g., inactivating mutations in genes involved in DNA repair) A tumor forms via the clonal expansion of a SINGLE precursor cell that has incurred genetic damage or mutation (change in DNA sequence) a. Somatic/acquired/sporadic mutation: occurs after conception b. Germline/inherited mutation: inherited from parents and incorporated into DNA of every cell of offspring. Cancer growth and evolution Neoplasm (“tumor”): disorder of cell growth triggered by a series of acquired mutations that affect a single cell and its progeny 1. Benign Tumors: gross & microscopic appearance relatively innocent, remains localized Ø Generally designated by tissue origin, microscopic or macroscopic pattern 2. Malignant Tumors (“cancers”): potential for rapid growth, invasion, and destruction of nearby tissue (=METASTASIS) Benign vs Malignant Tumors Characteristic Benign Malignant Differentiation Well differentiated – sometimes typical of origin tissue Some lack differentiation (“anaplastic”) – structure often atypical Growth Rate Progressive & slow – may come to standstill or regress Erratic – may be slow à rapid Local Invasion Cohesive, expansile, well-demarcated masses that do not invade or infiltrate surrounding tissues Locally invasive – infiltrate surrounding tissues Often encapsulated, non-fixed Metastases Absent Frequent – likely w./ larger, undifferentiated primary tumors Pathways: i) seeding of body cavities/surfaces, ii) lymphatic spread, iii) hematogenous Carcinogenesis Stage 0 Stage I-III Carcinogenesis: process by which ‘normal’ cells are transformed into cancerous cells Stage IV Multiple stages depending on cancer type • Local proliferation (benign) • Invasion across the lamina propria • Spread to local lymph nodes • Distant metastases General scheme for development of a carcinoma in an epithelial tissue such as colonic epithelium Metastasis Metastasis is responsible for the greatest number of cancer related deaths • Cancer cells adapt to a tissue microenvironment at a metastatic site distant from the primary tumor • This process involves the selection of traits that are advantageous to cancer cells What genes are mutated in cancer? ~140 ”driver” genes In common solid tumors (colon, breast, brain, pancreas etc.), an average of 33 to 66 genes display subtle somatic mutations ~95% of these mutations are single-base substitutions (such as C>G) • 90.7% result in missense changes, • 7.6% result in nonsense changes • 1.7% result in alterations of splice sites or untranslated regions adjacent to the start and stop codons The remainder are deletions or insertions of one or a few bases (such as CTT>CT). Of the base substitutions, • Driver Mutations • Passenger Mutations • Underlie oncogenesis • Mostly neutral • Provide growth advantage • Carried along for a ride • Occur in: Proto-Oncogenes (gain-offunction mutations) • huge increase in frequency with loss of genome repair mechanisms Tumor Suppressor Genes (lossof-function mutations) Two classes of driver-gene mutations: Oncogenes – dominant acting analogous to “accelerator/gas pedal” Tumor-Suppressor Genes – recessive acting analogous to “brake pedal” Oncogene vs. Tumor Suppressor Tumorigenesis Activating mutations in a single (“hit”) allele of an oncogene are sufficient to confer high risk of tumorigenesis Ø Bias towards missense mutations (likely amino acid) For (classical) tumor suppressor locus to be tumorigenic, both alleles (“two-hit”) need to lose their function Ø May occur through mutational in-activation, loss of allele, or epigenetic silencing Ø Note: not all tumor suppressor genes follow this model! Figure 10.9A. Strachan et al. Genetics & Genomics in Medicine (2015) Oncogenes Proto-oncogene: genes involved in NORMAL cell growth Ø Growth factors (e.g. PDGF, TGF-α) Ø Growth factor receptor activity (e.g. Tyrosine kinases, EGFR) Ø Signal transduction proteins (e.g. RAS à MAPK & PI3K/AKT) Ø Nuclear transcription factors (e.g. MYC, D-cyclins) Ø Apoptosis inhibitors (e.g. BCL-2) “Activated” Oncogene: mutated counterpart of proto-oncogene, protein products (oncoproteins) promote autonomous growth of cancer cells in absence of normal signals/stimuli à freed from normal “check-points” in cell cycle = excessive proliferation/activity Figure 7-25. Robbins & Cotran Pathologic Basis of Disease (9th Ed.), 2015. Proto-oncogene activation Conversion or activation of proto-oncogene à oncogene generally involves a “Gain-ofFunction” mutation (i.e., “foot on the gas pedal”) Ø Mutation in only 1 allele is sufficient for induction of cancer Activated Oncogenes Gain-of-Function Coding Mutations: Ø Activates oncogene by certain point mutations at any 1 of a few key codons à act in dominant manner, requires only single “hit” to induce carcinogenesis Ø Encodes oncoprotein that differs slightly from normal protein encoded by proto-oncogene = constitutively active protein product (i.e., “foot on the accelerator”)e.g., RAS mutations occur in ~1 in every 6 cancers Translocation-induced Activation: Ø Occur when DNA molecules receive double-strand breaks & are rejoined incorrectly Ø Encodes for a novel protein with abnormal function, or results in aneuploidy = Results in growthregulatory genes under control of a different promoter and inappropriate expression of the gene Ø >300 cancer-associated translocations are identified, e.g., Philadelphia chromosome in CML t(9;22)(q34;q11) -> BCR-ABL1 protein Activation by Gene Amplification (or Regulatory Mutations): Ø Generate oncogenes whose protein products are identical with the normal proteins; their oncogenic effect is due to their being expressed at higher-than-normal levels or in cells where they normally are not expressed e.g., HER2 amplification in breast cancer Oncogenes Oncogene Chrom. Function/Activation ABL 9 Promotes cell growth through tyrosine kinase activity ALK 2 Encodes a receptor tyrosine kinase, regulates cell growth Lymphomas BCL-1 11 Encodes a cyclin that regulates CDK kinases and cell cycle Lymphoma, Breast cancer, Lung progression cancer BCL-2, 3, 6 18,19,3 Block apoptosis (programmed cell death) B-cell lymphomas and leukemias Kinase signaling directing cell growth Non-Hodgkin lymphoma, colorectal cancer, melanoma BRAF (RAF family) 7 Cancer Chronic myelogenous leukemia (CML) EGFR 7 Cell surface receptor that triggers cell growth through tyrosine kinase activity Lung Cancer ERBB-2 (HER2, neu) 17 Cell surface receptor that triggers cell growth through tyrosine kinase activity Breast, salivary gland, and ovarian carcinomas Approximately 80 oncogenes identified but it is estimated that there are ~300 Oncogenes – cont. Oncogene MYC (c-Myc) Chrom. 8 Function/Activation Transcription factor that promotes cell proliferation and DNA synthesis Cancer leukemias and lymphomas, including Burkitt lymphoma Neuroblastomas, retinoblastomas, and lung carcinomas N-MYC 2 RAS-H (HRAS) 11 G-protein. Signal transduction. Bladder carcinoma RAS-K (KRAS, KRAS) 12 G-protein, Signal transduction, activating kinases, GLUT1 glucose transporter and propagates growth factors Pancreatic, Lung, ovarian, and bladder carcinoma PIK3CA (PI3K) 3 Kinase with phosphorylation activity Breast and cervical cancer RET TERT (hTERT) Cell proliferation and DNA synthesis 10 Receptor tyrosine activation Medullary thyroid cancer, Hirschsprung's disease 5 Telomerase that maintains chromosome ends Central nervous system, bladder, thyroid, and skin cancers Ex. Mutant KRAS (oncogene) Gly12Asp mutation locks KRAS in active state Mutations Mutant KRAS is continuously in a GTP-bound, active state(ON). KRAS acts as a molecular on/off switch. Once it is Mutant KRAS initiates the propagation of growth factors, cell activated (ON), it recruits and activates growth signaling receptors like c-Raf and PI 3-kinase, and upregulates the factors as well as other cell signaling receptors. It GLUT1 glucose transporter. exists largely in an inactive state in non-dividing cells. Buscail, L., Bournet, B., & Cordelier, P. (2020). Role of oncogenic KRAS in the diagnosis, prognosis and treatment of pancreatic cancer. Nature Reviews Gastroenterology & Hepatology, 17(3), 153-168. Tumor Suppressor Genes (TSGs) Tumor suppressor gene directs the production of proteins that regulate/restrain cell division & growth Ø Gate-keepers: products directly regulate cell division by inhibiting cell proliferation and/or promoting apoptosis of cells w./ DNA damage Ø Care-takers: work indirectly to maintain integrity of genome by repairing DNA Mechanism/classification of tumor suppressor action Ø Ø Ø Ø Ø Proteins that regulate/inhibit progression through a specific stage of the cell cycle Receptors for secreted hormones that function to inhibit cell proliferation Check-point control proteins that arrest cell cycle if DNA/chromosomal damage is sensed Proteins that promote apoptosis Enzymes that participate in DNA repair Mutations (Loss-of-Function = “foot off the brake”) in these genes lead to failure of growth inhibition of suppressor action & promotion of aberrant proliferation Ø Usually, recessive mechanism à requires both alleles to be inactivated Tumor Suppressor Genes Gene Gene functions related to carcinogenesis Sporadic cancer RB1 Tumor suppression via apoptosis Retinoblastoma, small cell carcinoma, breast cancer TP53 Tumor suppression via cell cycle regulation, DNA repair, apoptosis Sarcoma, Lung cancer, breast cancer, many others APC Tumor suppression via cell cycle regulation Colorectal cancer VHL Tumor suppression via regulation of angiogenesis Clear cell renal carcinoma, lymphoma BRCA1, BRCA2 Tumor suppression via DNA repair Breast cancer, ovarian cancer MLH1, MSH2, PMS2 Tumor suppressor via DNA repair Colon cancer TP53, the Guardian of the Genome • p53 stops replication in cells that have DNA damage and targets the unrepaired cells for apoptosis. • DNA damage stimulates production of p53 protein. • p53 stimulates production of p21, which inhibits cyclin/CDK complexes and stops cell cycle progression and cell proliferation. • p53 stimulates production of DNA repair enzymes to fix the DNA problem. • If DNA is not repaired, p53 stimulates/activates genes for apoptosis P53 mutations implicated in >50% of cancers (Example of TSG) Caretakers: DNA Repair Genes DNA repair genes code for proteins that correct DNA defects: • prior to cell division • active throughout cell cycle after DNA replication and before chromosome segregation Failure to repair DNA mutations allows the cell to accumulate error -> Mutator Phenotype • Examples of DNA Repair Genes: BRCA1 and BRCA2à breast cancer MLH1 and MSH2à colon cancer Epigenetic Contributions to Cancer by Chromatin Modification Ref: IJMS 12: 983, 2011; Kwon and Shin How is cancer treated? Every cancer cell harbors numerous alterations in DNA sequence & copy number that affect genes and/or regulatory sequences Collectively, these changes perturb the expression and function of 1000’s of genes that control the characteristics of cancer and determine prognosis and response to treatment Difficult to predict prognosis of cancer patients based on traditional phenotypic information A diagram showing the major cancer genes for some cancers. The larger the gene name, the more frequently that gene is defective in that cancer type Genetic profiles of driver mutations for independent tumors Heterogeneity in Cancer Targeted cancer therapies Tumor Type Driver Gene and Mutation Breast cancer Amplified HER2 Non–small cell lung Activated EGFR cancer Chronic myelogenous Activated receptor leukemia and tyrosine kinases Abl, gastrointestinal stromal KIT, and PDGF tumor Non–small cell lung Translocated ALK cancer Melanoma Activated MEK Melanoma Representative FDAApproved Targeted Therapeutic Trastuzumab Mechanism of Action Anti-HER2 monoclonal antibody Gefitinib Tyrosine kinase inhibitor Imatinib, nilotinib, and Tyrosine kinase dasatinib inhibitor Crizotinib Trametinib Activated BRAF kinase Vemurafenib Tyrosine kinase inhibitor Serine-threonine kinase inhibitor Serine-threonine kinase inhibitor Chronic myeloid leukemia (CML), Philadelphia chromosome https://en.wikipedia.org/wiki/Imatinib#/media/File:Mechanism_imatinib.svg Imatinib is a competitive inhibitor of the Philadelphia chromosome fusion oncogene product. Hereditary cancers (inherited cancer syndromes) are germ line mutations that are inherited which predispose individuals to cancer. Inherited Cancer Syndromes Inherited cancer syndromes: Knudson two-hit hypothesis Tumor suppressor genes contribute to oncogenesis through loss of function >> must lose both alleles in a cell. Two-hit hypothesis Sporadic/Non-inherited Group • Neither parent is affected, no additional risk to other progeny • Both alleles are inactivated as a result of TWO SOMATIC events occurring within the same cell Ø often occurs during embryonic development • Tumor characteristics: Ø single tumors Ø unilateral occurrence Ø later onset Two-hit hypothesis Inherited Group • Affected individual often has affected parent, 50% chance of genetic transmission to EACH offspring • 1st “hit” is mutant allele present in GERMLINE (i.e., ALL cells affected) • 2nd “hit” is a SOMATIC alteration • Tumor characteristics: Ø multiple/bilateral tumors Ø multiple cancer types Ø early onset Inherited/ 40% of cases Retinoblastoma RB1 Gene https://en.wikipedia.org/wiki/Retinoblastoma 60% of cases Li-Fraumeni Syndrome • Mutations in the Tumor Suppressor gene p53 occur is 70% of LFS cases • TP53 is often called the guardian of the genome as it prevents propagation of genetically damaged cells in multiple ways. p53 is the most mutated gene in human cancer LFS cancers often include: • osteosarcoma (bone cancer), • soft-tissue sarcoma, • acute leukemia, • pre-menopausal breast cancer, • brain cancer, • leukemia, • lung cancer, • adrenal cortical tumors VHL- Hereditary Cancer Lynch Syndrome, or Hereditary Nonpolyposis Colon cancer (HNPCC) • DNA repair insufficiency in mismatch repair pathway (MMR) • Genes that may be involved: (mutations in) MSH1, MSH2, MSH6, PMS2, EPCAM (MMR Genes) *The most common form of hereditary colon cancer Mismatch repair mechanisms When DNA is replicated, MMR proteins act as “spell checkers” for erroneous base pairings or deletions correct defects occurring during synthesis Microsatellite Instability? Hereditary Breast-Ovarian Cancer Syndrome • BRCA1 and BRCA2 account for 3-5% of all breast cancer cases, but 70-80% of familial breast cancers Increased lifetime risk of Ovarian Cancer: ~15% (BRCA2 mutation) ~35% (BRCA1 mutation) Hereditary Cancer Syndromes ~5-10% • Represent <5% of all patients with cancer: • So, why is recognizing these patients/cases important? • When do you think about syndromes clinically? • • • • • • Hereditary cancer Syndromes Uncommon types of cancer Cancers in young people Multiple types of cancer in a single person Double hits (both eyes, both kidneys, both breasts) Young siblings with cancers Cancer occurring in uncommon setting (breast Ca in male) • Inheritance of a single mutant gene with high penetrance • Roughly 100 genes which are known to have deleterious mutations FYI: Hallmarks of Cancer Tumor cells typically demonstrate uncontrolled growth which is exacerbated by the following: Self-sufficiency in growth signals – capacity to proliferate w./o external stimuli Insensitivity to growth-inhibitory signals – unresponsive to components of pathway Altered cellular metabolism – metabolic switch favors anaerobic Evasion of apoptosis – resistance to programmed cell death Limitless replicative potential – unrestrictive proliferative capacity, immortality Sustained angiogenesis – induce pathologic angiogenesis Ability to invade & metastasize – intrinsic processes signal & promote invasion Ability to evade host immune response – alterations & adaptations contribute to tumor microenvironment Cumulative effect = IMMORTALITY!!! Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell 2011; 144:646-674