Cancer Genetics & Genomics: Mechanisms of Inherited Cancer SusceptibilityMing Qi, PhD, FACMGAdopted from Shirley HodgsonCancer terminologyClassification by tissue type:carcinomaepithelial cell90% of all tumoursderived from ectoderm (mostly) or endoderm (some)sarcomaconnective tissue2% of all tumoursderived from mesodermleukaemiacirculatory or lymphatic8% of all tumoursderived from mesodermClassification by the type of cells:Adenomatous cellsductal or glandular cellsSquamous cellsflat cellsMyeloidblood cellLymphoidlymphocytes or macrophagesCancer terminologyClassification by the site of origin of the tumour:Breast: carcinoma of ductal, medullary, papillary, etc. cells Lung: small cell, bronchioloalveolar, squamous, large cell carcinomasBone: osteosarcoma, Ewings sarcomaEye: retinoblastoma Lip, tongue, mouth, nasal cavity: squamous cell carcinoma Lymphocytes: acute lymphocytic leukaemia, chronic lymphocytic leukaemia, Hodgkins lymphomaOvary: adenocarcinoma, choriocarcinoma, teratoma, Brenner tumourTestis: seminoma, teratocarcinoma,Cancer terminologyBenign tumoursare generally slow growing and enclosed in a fibrous capsule are relatively innocuous, although their location can make them serious (such as a tumour located in the brain)are not considered cancerous (that is, they are not malignant) are given names that usually end in oma (although a melanoma is a malignant skin cancer)Malignant tumoursproliferate rapidly, invading neighbouring tissues can metastasise, or spread, to other sites of the body are named using the conventions of tissue, cell type, and origine.g. A tumour of the bone is an osteoma if benign and an osteosarcoma if malignantInternational Facts on CancerIn 2007 over 12 million new cases were diagnosed across the planet and approximately 7.6 million cancer deaths occurredIn 2050, these numbers will rise to an expected 27 million new cases and 17.5 million cancer deaths if our ability to prevent, diagnose and treat cancer does not improveGarcia et al, Global Cancer Facts & Figures 2007, Atlanta, GA, American Cancer Society 2007.The environment:Some environmental agents associated with cancer are: Viruses Tobacco smoke Food Radiation Chemicals Pollution VirusesVirusesmostly in the form of DNA viruseshave been causally linked to cancer.human papillomavirusesprimarily types 16 and 18, which are sexually transmittedhave been linked to cervical cancer; more than 25 other types of papillomaviruses have been linked to cancer as well hepatitis B and Clinked to cancer of the liver human immunodeficiency virus (HIV)linked to Kaposis sarcoma and lymphoma retroviruseslinked to cancers in animals other than humansTobacco smokeis associated with 50% to 60% of all cancer deathsis causally linked to cancers of the lung, upper respiratory tract, oesophagus, bladder, pancreas is probably a cause of cancer of the stomach, liver, kidneys, colon, and rectumFoodis connected to 50% to 60% of cancer deathsis causally linked to cancers of the lung, upper respiratory tract, oesophagus, bladder, pancreas is probably a cause of cancers of the stomach, liver, kidneys, colon, and rectumRadiationUVB from the sun can damage DNA and is associated with more than 90% of skin cancers, including melanomas radon has been associated with lung cancer among those who work in mines; general levels of radon have not posed a significant cancer threatelectric and magnetic fields from power lines and household appliances have not been demonstrated contributors to the incidence of cancer or leukaemia radio frequency electromagnetic radiation from mobile phones or microwave ovens has not been linked to cancer. nuclear radiation is of sufficient energy to ionise molecules and is therefore carcinogenic.Chemicalsbenzene (myelogenous leukaemia) arsenic containing pesticides (lung cancer) polychlorinated biphenyls (liver and skin cancers) mineral oils (skin cancer)mineral fibres (lung cancer and mesothelioma)Chemicals, many of which have been historically linked to the workplace, have been successfully limited through public health efforts, because they have been associated with a variety of cancers. Examples of common chemicals that fall in this category are: PollutionPollution has been difficult to document as a contributor to human cancer.However, long-term exposure to high levels of air pollution may increase lung cancer risk by as much as 25%.The Genetics of CancerNewspapers, magazines, radio, and television are reporting discoveries and breakthroughs attributing one form of cancer or another to a specific gene.Cancer of the breast, colon, prostate, and many other sites in the body are being connected to specific genes. But the meaning of this isnt always clear.What does it mean for you if your mother has or had breast cancer. or an aunt and two cousins have colon cancer?What does it mean for your children if youve been diagnosed with cancer of the endocrine glands or some other organ? Cancer in the mediareadingURLs:http:/www.infobiogen.fr/services/chromcancer/Kprones/RbKprID10031.htmlhttp:/cgap.nci.nih.gov/http:/www.intouchlive.com/home/frames.htm?http:/www.intouchlive.com/cancergenetics/&3http:/bioinformatics.weizmann.ac.il/hotmolecbase/entries/p53.htmBooks:Concepts of Genetics, Klug and Cummings, chapter 23Molecular Biology of the CellGoals of Cancer Genetic & Genome ResearchIdentify changes in the genomes of tumors that drive cancer progressionIdentify new targets for therapySelect drugs based on the genomics of the tumorcancer is a disease of the cell cycleTypes of genes which may mutate to cause cancer:Tumour suppressor genesoncogenesDNA repair genestelomerasep53Tumour suppressor genesThe genes normal function is to regulate cell division. Both alleles need to be mutated or removed in order to lose the gene activity.The first mutation may be inherited or somatic.The second mutation will often be a gross event leading to loss of heterozygosity in the surrounding area.Knudsens “two hit” hypothesisAlfred G Knudson1971RetinoblastomaRetinoblastomaRetinoblastoma (RB) is a malignant tumor of the developing retina that occurs in children, usually before the age of five years.All forms of retinoblastoma represent a mutation in the gene RB1 located in in the region 13q14.1-q14.2. The gene is about 180 kb in length with 27 exons that code for a transcript of only 4.7 kb. individual mutations are heterogeneous: 20% are deletions larger than 1kb; 30% are small deletions or insertions; 45% are point mutations. mutations have been found in 25 of the 27 coding exons and in promoter elements. Genotype-phenotype correlation:most mutant RB1-alleles show premature termination codons and are associated with almost complete penetrance (95%) and high expressivity (more than 6 individual retinoblastoma foci per individual and, therefore, most often involvement of both eyes);some rare mutant alleles that code for proteins with retention of parts of the functions of the wild-type protein or that result in diminished amounts of wild-type transcript are associated with incomplete penetrance (75%) and low expressivity (mean of less than 2 tumor foci)RB1Is regulated by phosphorylation by Cdk2Hypophosphorylated form binds and sequesters E2F (and viral proteins such as E7 from human papilloma virus-16)It also interacts directly with the product of the ABL gene and participates in several regulatory and feed back loops even involving its own transcription.Breast Cancer“Why do so many of my relatives have breast cancer.is this just plain bad luck or what?”Breast cancerher age, family history, age at which she began menstruating, whether she has given birth and her age at the time of the first birth, and whether or not a breast biopsy was performed in the past.Within the general population, there is an 11% chance that any woman will develop breast cancer over her lifetime. For any one individual, this risk may be increased or decreased by a variety of factors:Breast cancerBut its more complicated than that!Cancer geneticsApproximately 5-30% of commoner cancers occur in individuals with a strong genetic susceptibility.Familial clusters of cancer can be due to: rare genes with high penetrance, or commoner genes with low penetrance, interacting with environmental factors.What genetic factors increase cancer susceptibility?Features of inherited cancersCancer developing at an early ageChildhood cancersSeveral cancers in one individualA family history of the same or related cancer on the same side of the familyRare cancersOncogenesCellular oncogene c-oncViral oncogene v-oncProto-oncogene, activated by mutation to c-oncOncogenesInherited activated oncogene is an unusual cause of inherited cancer susceptibility?May just increase frequency of precursor lesion.Proto-oncogene activationTypes of proto-oncogeneGrowth factore.g. SIS oncogene (PDGF)Types of proto-oncogeneGrowth factor receptore.g. tyrosine kinase receptorsTypes of proto-oncogeneG proteinse.g. rasTypes of proto-oncogeneNuclear transcription factorse.g. MYCp53suppresses progression through the cell cycle in response to DNA damageinitiates apoptosis if the damage to the cell is severe acts as a tumour suppressoris a transcription factor and once activated, it represses transcription of one set of genes (several of which are involved in stimulating cell growth) while stimulating expression of other genes involved in cell cycle controlTransformation is a multistep processTransformation is a multistep processColorectal Cancer11% of cancer-related deathsTumor progression may take 10-35 yearsAdenomatous polyp develops into carcinomaChromosome changes in colorectal cancerCancer karyotypeStable karyotypeCancerA Disease of the GenomeChallenge in Treating Cancer: Every tumor is different Every cancer patient is differentMultiple Endocrine Neoplasia 2AMultiple Endocrine Neoplasia 2AMedullary Thyroid Cancer MTC (100%)Pheochromocytoma(adrenal gland tumor) (50%)parathyroid hyperplasia (20%) Due to inherited mutations in the RET oncogeneMultiple Endocrine Neoplasia 2BMultiple Endocrine Neoplasia 2BMarfanoid habitusMucosal neuromasGanglioneuromatosis of GI tractVery early onset Medullary Thyroid Cancer (MTC) PheochromocytomaParathyroid hyperplasia (rare) 95% have missense mutation in exon 16 an elongated face and protruding, blubbery lips. Benign tumors (neoplasms) develop in the mouth and eye.RET RET oncogeneoncogeneTyrosine kinase receptor10q11.2 mutated oncogene remains activatedresponsible for uncontrolled growth of c-cellssomatic RET mutations found in 40-60% of sporadic MTCInactivating mutations may cause Hirschsprungs (巨结肠) Childhood syndromes due to inherited activating oncogene mutationsCostello syndrome: FTT, devel. delay, short stature, CHD, palmar/plantar excess skin, warts.17% risk of cancer (age 6m-6y): rhabdomyosarcoma, bladder carcinoma, acoustic neuroma, epithelioma, neuroblastoma Germline HRAS gain-of-function mutations.SHP2GRBSOSRAS-GDPRAS-GTPGAPRAFCell survival & proliferationMEKERKReceptor tyrosine kinaseGrowth factorsCardio-Facio-Cutaneous (CFC), Noonan and LEOPARD syndromesShort stature, webbed neck, dysmorphic facial features, CHD (PS), cardiomyopathy (overlap)RAS-MAPK pathway, gain of function mutationsNoonan: PTPN11, SOS1, KRAS, RAF1LEOPARD: PTPN11 and RAF1CFC: BRAF, MEK1, MEK2 mutations.Noonan SyndromeLEOPARD SyndromeCFCCancer risksNoonan Syndrome: small risk of juvenile myelomonocytic leukaemiaSomatic PTPN11 mutations detected in 35% of sporadic juvenile myelomonocytic leukaemiaFrequency of PTPN11 mutations in other malignancies CHILDHOOD Myelodysplastic syndrome 10%Acute Myelogenous Leukemia 4% Acute B-cell Lymphatic Leukemia 6%ADULT Myelodysplastic syndrome 1%Acute Myelogenous Leukemia 1.6%Chronic Myelomonocytic Leukemia 1.2%LIGAND EGFR STAT grb2 TGF PDGF JAK gp130 TCRFGF IRS-1 C kit PECAM-1CARDIACBLOODGROWTHAUTO- ANTIBODYFACECNSAMMLPTPN11GRBSOSRAS-GDPRAS-GTPGAPRAFMEKERKGatekeepersTumour suppressor genes: Mutations are rate limiting for tumour initiationInhibit cell growthLoss of function occurs early in tumour developmentGatekeepersClassical Knudsen HypothesisOften have a role in developmentSyndromes due to inherited gatekeeper defects often include phenotypic abnormalitiesSyndromes caused by inherited faulty “Gatekeepers”Familial Adenomatous PolyposisRetinoblastomaNeurofibromatosis types 1 and 2Gorlin SyndromeNeurofibromatosisLi-Fraumeni SyndromeCowden Syndrome.and many moreLoss of function at second allele characteristic in tumours.but not the whole storyTP53Li-Fraumeni Syndrome (LFS)p53 protein involved in overlapping pathways that control cell proliferation/homeostasis, including cell-cycle, apoptosis, DNA repair. “Guardian of the Genome”CHEK2 protein phosphorylates p53 ATM protein stabilises p53Mutated in many sporadic cancersLFS: early-onset sarcoma, leukaemia/lymphoma, adrenocortical, brain, breast cancers.Colon cancer susceptibilityCan be caused by germline mutations in tumour suppressor genes or DNA repair defects, influenced by metabolic variation Colorectal polyposesFamilial adenomatous polyposis APCAttenuated polyposis/muliple adenomas Peutz-Jeghers syndrome LKB1Juvenile polyposis syndromeSMAD4 BMPR1AHereditary mixed polyposis syndrome 15qHyperplastic polyposis?FAPPJSJPSJuvenile Polyposis20% SMAD4 (18q 21.1)38% BMPR1A(10q 22-23) CRAC1(15q 14 - q22) - 2 large Ashkenazi families with the same ancestral haplotype D1551360-D155118 TGF betasuperfamilyCowden Syndrome Clinical features(Eng, Human Mutation, 22, 2003)Mucocutaneous lesions 90-100%Macrocephaly 40%Thyroid abnormalities 50-67%Thyroid carcinoma 10%Breast lesionsfibroadenomas 80%adenocarcinoma 50%GI lesions 40%GU lesions endometrial carcinoma 8% and renal ca.PTEN Tumor Suppressor GenePTEN, 9-Exon Gene, Encoding a 402-Amino Acid PhosphatasePPPPPPTENPI3KCell Cycle ArrestApoptosisStambolic et al Cell 1998Weng et al Cancer Res 1999Familial Adenomatous PolyposisGene identified through a patient with a deletion in chromosome 5Classical Tumour Suppressor gene APC Contains repeats which bind beta-catenin for degradation, but also has other functions, such as binding and stabilising microtubules, regulating cytoskeleton, mitosis, apoptosis. Chromosome instability pathway (CIN), with APC loss, SMAD4 & KRAS mutations, 18q loss APC gene functional regionsAPC functions Genotype-phenotype associations in FAPDifferent mutations in APC gene cause different disease severitySevere disease, 3000+ adenomatous polypsAttenuated polyposis (15 and 90% develop pancytopenia caused by aplastic anaemiaFanconi anaemiaAutosomal recessive chromosome breakage syndrome13 subtypes, 12 known genes, one is BRCA2 (FA-D1). Other genes include PALB2 (FA-N) and BRIP1 (FA-J) (low penetrance breast cancer susceptibility genes)Sensitivity to cross-linking agents e.g. diepoxybutane and mitomycin C.BRCA1-Associated Cancers:Lifetime RiskPossible increased risk of other cancers (eg, Possible increased risk of other cancers (eg, prostate, colon)prostate, colon)Breast cancer 56%Breast cancer 56%- - - -87% (often early age at onset)87% (often early age at onset)Second primary breast cancer 64%Second primary breast cancer 64%Ovarian cancer 16%Ovarian cancer 16%- - - -44%44%BRCA2-Associated Cancers: Lifetime RiskIncreased risk of prostate (?10-20%) and Increased risk of prostate (?10-20%) and pancreatic cancers (?3%)pancreatic cancers (?3%)breast cancer breast cancer (50%(50%- - - -80%)80%)ovarian cancer ovarian cancer (16%(16%- - - -21%)21%)male breast cancer male breast cancer (6%)(6%)contralateral contralateral breastbreast (50%) (50%)BRCA2BRCA1General PopBREAST CANCER RISKS IN BRCA1/2 CARRIERSBreast Cancer Linkage ConsortiumBRCA2BRCA1General PopOVARIAN CANCER RISKS IN BRCA1/2 CARRIERSBreast Cancer Linkage ConsortiumBreast Cancer Linkage Consortium, 1999Cancer Risks in BRCA1 CarriersBCLC, 1999Cancer Risks in BRCA2 CarriersBoth BRCA1 and BRCA2 are Important for DNA Repair3418 aa70 aaDSS11863 aaHRDSBIonising radiationChemicalDNA-PK-csKu 70/80End alignmentLigation by DNA Ligase IVHomology-directedBRCA1-BARD1 dependentRad52Resection/annealingSSAStrand invasionGCResectionLoading of RAD51 onto ssDNA by BRCA2BRCA2RAD51NHEJTrimmingLigationDouble Strand Break Repair PathwaysBRCA1NORMAL CELLSDNA DAMAGERepair by HRAlternative repairGenomic stabilitySurvival-+-+BRCA 1 or 2 DEFICIENT CELLSGross genomic instability Cell death or survival with Chromosomal deletions or exchangesDNA DAMAGERepair by HRAlternative repair (NHEJ or SSA)Wild-typeBrca1 or Brca2 deficientRAD51 focus formation after DNA damageSensitivity to Carboplatin in-vitroBRCA2 null cells are sensitive to carboplatin Chemotherapy HypothesisDNA DAMAGEDNA DAMAGEnormalBRCA1 or BRCA2 deficientHR NHEJ SSA BER NER etcHR NHEJ SSA BER NER etcGenotype Selective (Synthetic) LethalitylethalityxxxPoly (ADP-ribose) polymerase (PARP)Involved in DNA base-excision repairBinds directly to DNA damageProduces large branched chains of poly(ADP-ribose)CHEK2 GeneCHEK2: involved in cell cycle control and DNA repair Protein kinase and forkhead associated domain Phosphorylates p53, Cdc25c, and BRCA1.This function is lost in 1100delC mutation carriers, who have increased breast cancer risk. Genes causing a moderate increase in risk of breast cancerMutations in ATMCHEK2 MutationsMutations in some FA genes: PALB2 , BRIP1PALB2 interacts with BRCA2, and homozygous individuals have a severe form of FA, with high risk of Wilms tumour and medulloblastoma, rare in other FA subtypesBARD1 (BRCA1-interacting)NBS1Rahman, Nature Genetics 2007Interactions of Proteins Associated with Inherited Breast Cancer and Fanconi Anemia Other mechanisms for inherited cancer susceptibility?Von Hippel-Lindau DiseaseInherited paragangliomataVon-Hippel Lindau DiseaseAutosomal DomainantPhaeochromocytoma neuroendocrine tumor of the medulla of the adrenal glands (7-20%)Renal Clear Cell Carcinoma (approx. 70%)Retinal Angiomas (60%)Haemangioblastoma: cerebellar (60%), spinal (13-44%), brainstem (18%)Mean age at diagnosis 26y, penetrance complete by 60yFunction of VHL gene productNo significant homologyIdentification of interacting proteinsVascular nature of VHL tumours recognised Mechanism of tumourigenesis in VHL: Role of hypoxia inducible genesVHL tumours characterised by marked vascularityOverexpression of HIF target genes e.g. VEGF and carbonic anhydrase 9 Presence of “early lesions” in normal tissueMandriota et al 2002HIF-1 and hypoxic response genesHypoxia?Transcriptiona a HREVEGF, Glut1 etcVHLNucleus a aa aUbiquitylationProteolysisNormoxiaO2a a a a VHLHypoxiaa a a a a a O2VHLVHLnullGenotype-Phenotype, pVHL Function HIF dysregulation closely linked to haemangioblastoma risk Loss of fibronectin regulation linked to RCC, HAB and phaeo risk HIF dysregulation associated with but insufficient for RCC developmentHereditary Paragangliomas Rare tumours of extra-adrenal autonomic nervous system, commonest site in carotid body. 1 in 30,000 of general population 10%-50% are familial, AD SDHB, SDHDMitochondrial enzymes involved in oxygen sensing and Hif1 regulationSDHD/B deficiency causes susceptibility to paragangliomas and phaeochromocytomas; Complex II of respiratory chain SDHD deficiency causes accumulation of HIF1a aSDHD knock-down increases succinateIncreased succinate inhibits HIF prolyl hydroxylasesHIF accumulates, stimulates pro-angiogenic proteins such as VEGFHypoxic drivesuccinatefumarateSDHPHDHIF-1a apVHLGlucose metabolismGlucose metabolismAngiogenesisAngiogenesisECM modificationECM modificationMotilityMotilitySurvivalSurvivalmitochondriacytosolHIF-1a aOHHIF1a asuccinatea-ketoglutaratenucleusHIF-1a aHIF-1 transcriptionOHElongin C Elongin BCul 2UbUbUbExpression of HIF-1a and VEGF in HPGL paragangliomas H&E HIF-1a a CD34 VEGF (Light) VEGF (dark) -actinWilms tumour susceptibilityWAGR (Wilms-aniridia-genital malformations-mental retardation)Beckwith-Wiedemann syndromeMosaic variegated aneuploidy (BUB1B mutations)Simpson-Golabi-Behmel (GPC3 on X Chromosome)PerlmanHemihypertrophyFrasier and Denys-Drash Syndromes (WT1 mutations)Biallelic BRCA2 mutations-FALi Fraumeni Syndrome (TP53 splicing mutations)Wilms Tumour-WAGRCaused by a microdeletion of 11p13, WT1Wilms tumourAniridiaGenital abnormalitieshypospadiusambiguous genitaliaLearning disabilitiesBeckwith-Wiedemann syndromeAbnormalities of imprinting at 11p15, (WT2), maternally imprinted TSGovergrowthmacroglossiaabdominal wall defectsAdditional featureshemihypertrophyneonatal hypoglycaemiaurogenital abnormalitiesBeckwith-Wiedemann syndromeMultiple different mechanisms for inherited cancer susceptibilityFaulty tumour suppressor genes: common causeFaulty oncogenes: rarer causeFaulty DNA repair mechanisms: common causeRespiratory chain defects occasional causeMetabolic variation probably alters gene penetranceImprinting and promotor methylaton can alter gene expressionTherapeutic implicationsHNPCCtumours resistant to 5FU methylating agentsT(9,22) BCR-ABL translocation in CML: GleevecERBB2, HER2+ breast tumours respond to Herceptin (Trastuzumab)VEGF antibody, Avastin (Bevacizumab) in CRCEGF monoclonal antibody (Cetuximab) in CRCNon small cell lung cancer treatment with EGFR mutation responds to Iressa (Gefitinib)Analysing cancer genomesFrom Ding et al, Hum Mol Gen, 2010