CancerGenetics

1、Cancer Genetics羅建沅羅建沅二二0 0一四年十一月一四年十一月preventive double mastectomyCancer is a genetic diseaseCancersSporadically occurredHereditary occurredMutations of genesGenes mutation cause cancer encoding Proteins in signaling pathways for cell proliferation. Cytoskeletal components involved in contact inhibi

2、tion. Regulators of the mitotic cycle. Components of programmed cell death machinery. Proteins responsible for detecting and repairing mutations.Types of mutations Activating gain-of-function mutations of one allele of a proto-oncogene. Loss of function of both allele or dominant negative mutation o

3、f one allele of a tumor-suppressor gene. Chromosome translocation that cause misexpression of genes or create chimeric genes encoding proteins that have gained novel functional properties.Types of cancers Sarcomas: arisen in mesenchymal tissue: bone, muscle, or connective tissue; Carcinomas: origina

4、te in epithelial tissue: the calls lining the intestine, bronchi, or mammary ducts; Hematopoietic and lymphoid malignancies: leukemias and lymphomas, in bone marrow, lymphatic system, and peripheral blood.Further classified by Site, tissue type, histological appearance, degree of malignancy. Types o

5、f cancersLungBreast (women)ColonBladderProstate (men)Some common sarcomas:FatBoneMuscleLymphomas:Lymph nodesLeukemias:BloodstreamSome common carcinomas:腫瘤的幾大生物學(xué)特征腫瘤的幾大生物學(xué)特征u不受控生長，局部占位，損壞器官功能不受控生長，局部占位，損壞器官功能u 轉(zhuǎn)移游走，多處占位，損壞多器官功能轉(zhuǎn)移游走，多處占位，損壞多器官功能u 物理和化學(xué)效應(yīng)，個體全面衰竭物理和化學(xué)效應(yīng)，個體全面衰竭腫瘤研究內(nèi)容腫瘤研究內(nèi)容 病因?qū)W研究（環(huán)境致癌因素的篩

6、查） 遺傳學(xué)研究（單基因遺傳性腫瘤、多基因遺傳性易感） 癌細胞的“還原性”研究（癌基因、癌蛋白的發(fā)現(xiàn)及功能研究） 新的診斷治療方法的發(fā)明（化學(xué)、藥物、靶向藥、免疫、技術(shù)、設(shè)備、材料） 治療效果的臨床驗證病因及機理病因及機理 80%是環(huán)境因素 遺傳因素分為三個層面 單基因遺傳 多基因易感，處于研究階段 是唯一的體細胞基因突變的疾病 機體免疫狀態(tài)與腫瘤發(fā)生有關(guān)What Causes Cancer?Some viruses or bacteriaHeredityDietHormonesRadiationSome chemicalsPopulation-Based StudiesCANADA:Leuk

7、emiaRegions of Highest IncidenceBRAZIL:CervicalcancerU.S.:ColoncancerAUSTRALIA:SkincancerCHINA:LivercancerU.K.:LungcancerJAPAN:StomachcancerHeredity? Behaviors? Other Factors?1005050Stomach Cancer(Number of new cases per 100,000 people)U.S.JapanJapanese familiesin U.S.1007070Colon Cancer(Number of n

8、ew cases per 100,000 people)U.S.JapanJapanese familiesin U.S.Three Patterns of Tumor Inheritance Heredity familial tumor syndrome (monogenic inheritance) Multigenic cancer genetic susceptibility (multigene involved) Somatic tumor cell gene rearrangement (acquired)Hereditary Familial Tumor Syndrome G

9、ermline gene defect Somatic cell, especially germ cells Vertical inheritance to descendents Mostly autosomal dominant inheritance Clinical characteristics (syndrome) More than 20 hereditary familial tumor gene clonedStudy strategy linkage analysis , positional cloning, whole genome sequencing Accoun

10、t for total tumor morbidity 1%Criteria of HFTS identification 1.Age of individual onset 2. Family aggregation 3. Clinical syndrome 4. Genes diagnosisExamples of HFTS involved Genes Transcriptional regulatory factor (regulate cell cycle) Rb、WTI、P53 DNA repair enzyme genes ERCC、FACC DNA ligase hmsH1、h

11、msH2 Cytoskeleton and cell adhesion genes APC、medlin綜合征綜合征 腫瘤腫瘤 相關(guān)特征相關(guān)特征/CA /CA 染色體定位染色體定位 克隆基因克隆基因 作用機理作用機理 家族性視網(wǎng)膜母細胞瘤 視網(wǎng)膜母細胞瘤骨肉瘤 發(fā)育遲緩 13q14 Rb Retinoblastoma調(diào)節(jié)細胞周期結(jié)合病毒癌基因轉(zhuǎn)錄調(diào)控E2F 家族性Wilms腫瘤 Wilms腫瘤 WAGRWilms腫瘤無虹膜泌尿生殖系統(tǒng)異常智力發(fā)育遲緩Deny-DrashBeckwith-Wiedemann綜合征Organomegaly腎上腺皮質(zhì)癌肝母細胞癌 11q13 11p15 WT1 鋅指

12、轉(zhuǎn)錄因子調(diào)節(jié)細胞周期 多發(fā)性內(nèi)分泌瘤2型（Sipple綜合征） 髓樣甲狀腺癌 甲狀旁腺增生前垂體腺瘤2型A 嗜鉻細胞瘤 甲狀旁腺增生2型B 嗜鉻細胞瘤 粘膜神經(jīng)瘤 Marfanoid habitus 家族性髓樣甲狀腺癌 10cen-10q11.2 Ret 受體酪氨酸激酶 著色性干皮病 皮膚癌 著色異常 性腺機能減退 CNS缺陷 8個互補群 ERCCXPA-XPG 螺旋酶核酸外切修復(fù) Franconi貧血 AML 各種血細胞減少骨髓異常 4個互補群 FACC DNA修復(fù) 46BR 淋巴網(wǎng)狀內(nèi)皮增生癥 陽光過敏免疫缺陷生長遲緩 DNA連接酶1 DNA連接 家族性腫瘤綜合征家族性腫瘤綜合征 譯自譯自

13、 Abeloff MD, et al. Clinical Oncology.New York : Curchill Livingsto,1995.168家族性腫瘤綜合征家族性腫瘤綜合征綜合征綜合征 腫瘤腫瘤 相關(guān)特征相關(guān)特征/CA /CA 染色體定位染色體定位 克隆基因克隆基因 作用機理作用機理 Bloom 綜合征 實體瘤 毛細血管擴張免疫損傷 BloomDNA Helicase毛細血管擴張共濟失調(diào)Ataxia Telangiectasia 淋巴瘤 小腦共濟失調(diào)毛細血管擴張免疫缺陷 5個互補群11q22-q23 ATMDNA repair家族性腺瘤息肉病 結(jié)腸癌 結(jié)腸息肉先天性視網(wǎng)膜色素上皮肥

14、大Gardner綜合征 5q21 APC 結(jié)合catenin HNPCC（Lynch綜合征） 結(jié)腸癌結(jié)腸癌 HNPCC I型HNPCC II型子宮內(nèi)膜癌（其他） 3p212p16 hMLH1hMSH2 DNA錯配修復(fù)DNA錯配修復(fù) Li-Fraumeni綜合征 肉瘤 乳腺癌腎上腺皮質(zhì)癌腦瘤 17q p53 調(diào)節(jié)細胞周期及其他轉(zhuǎn)錄因子防UV損傷 神經(jīng)纖維瘤病1型（NF1）（von-Reckling- hausen病） 神經(jīng)纖維瘤 神經(jīng)纖維肉瘤 Caf-au-lait斑 Lisch小結(jié)視神經(jīng)膠質(zhì)瘤 17q11.2 NF1 GAP相關(guān)的p21-ras調(diào)控與微管有關(guān) 神經(jīng)纖維瘤病2型 聽神經(jīng)瘤 腦膜瘤

15、Schwann細胞瘤視神經(jīng)膠質(zhì)瘤 22q12 Merlin 連接細胞膜和細胞骨架 家族性乳腺癌 乳腺癌乳腺癌 卵巢癌 17q21.113q12-13 BRCAI BRCA2 轉(zhuǎn)錄因子 譯自譯自 Abeloff MD, et al. Clinical Oncology.New York : Curchill Livingsto,1995.168Genetic Susceptibility of Cancers (1) 1. Conception of susceptibility 2. Characteristics : a. Environmental dependent b. Multige

16、ne involved c. Genetic change is slight, both structurally and functionally (i.e. SNP) d. Slightly prone to familial aggregation、 high incident populationGenetic Susceptibility of Cancers (2)EnvironmentHeredityGenetic Susceptibility of Cancers (3)Features of Environmental Carcinogen1. Three types en

17、vironment carcinogen a chemical b physical c biological2. Common features a nonfatal injury b time、body site、way、duration、dose of exposure c strongly rely on individual susceptibility ( metabolism、compensation、repair、immunity)Genetic Susceptibility of Cancers (4) 1. SNP (Single Nucleotide Polymorphi

18、sm)point mutation2. Distribution frequency in human genome 1%, 1/1000bp 3. Some SNPs are related to disease susceptibility Sites of SNPs intron exon promoteraa changeno aa changeForms of SNPs influence on function Influence on responsible expression (response to special environment) Influence on sec

19、ondary structure alteration (protein binding , antigen presentation) Influence on gene activity (dominance recessive, gene dosage effect) Isogenetic combined effect (fatal) Influence on shearing (intron boundary) Genetic Susceptibility of Cancers (5) General Strategy of Study1. Has to be known gene2

20、. Candidate gene selection3. Scientific design of the experiment4. Main technologies : PCR-SSCP, DHPLC, sequencing et al 5. Functional relevance confirmation Genetic Susceptibility of Cancers (6) Category of candidate genesChemical metabolic enzymes systemDNA damage-repair systemImmunological recogn

21、ition-regulation-reaction systemBiological factors vs cellular interaction factorsApoptosis genes Genetic Susceptibility of Cancers (7) Procedures of defining Susceptible Gene1.Candidates selection2.SNP discovery and analysis3.Testing frequency of specific SNP in high-risk group4.Comparison of SNP f

22、requencies between disease group and control 5. Interaction analysis of SNPs, haplotype construction6. Functional testGenetic Susceptibility of Cancers (8) Significance of defining Susceptible Gene1. High-risk population identifying2. Intervention and prevention of cancers3. Early diagnosis and trea

23、tment4. Molecular mechanisms of carcinogenesis 5. Supplement to HGPGenetic variation of individualsWe are all 99.99% identical in our genomes BUTAdapted from Third Wave2012201420082010200620022007From $2B to $1K Human Genome 2,000,000 x dropDramatic Decrease of Cost in Sequencing a Human Genome!Fast

24、er & Cheaper NGSers $10/Gb one human genome/dayMiSeqHiSeq 2500NextSeqHiSeq X TenDecreasing Price Per GbIncreasing System Price & OutputFor ExamplesNGS SequencersRoche 454GS FLX TitaniumLife TechnologiesSOLiD 5500 xlPacific BiosciencesSMART PacBioRSIon TorrentIon Proton SequencerHelicos Biosc

25、iences HeliscopeMinIONIon Torrent PGMMiSeq DXHiSeq 2500HiSeq X TenOncogenes and Tumor Suppressor Genes in Tumor Cell Features of Oncogenes and Tumor Suppressor Genes Genes in charge of proliferation、 differentiation、apoptosisOncogene A mutant gene altered function or expression abnormal stimulation

26、of cell division and proliferation. The activating mutation can be: itself; regulatory elements; or genomic copy number unregulated function or overexpression of the oncogene. Dominant effect. OncogenesMutated/damaged oncogeneOncogenes accelerate cell growth and divisionCancer cellNormal cellNormal

27、genes regulate cell growthProto-Oncogenes and Normal Cell GrowthReceptorNormal Growth-Control PathwayDNACell proliferationCell nucleusTranscriptionfactorsSignaling enzymesGrowth factorOncogenes areMutant Forms of Proto-OncogenesCell proliferation driven by internal oncogene signalingTranscriptionAct

28、ivated gene regulatory proteinInactive intracellular signaling proteinSignaling protein from active oncogeneInactive growth factor receptorTumor Suppressor GenesNormal genes prevent cancerRemove or inactivate tumor suppressor genesMutated/inactivated tumor suppressor genesDamage to both genes leads

29、to cancerCancer cellNormal cellTumor Suppressor GenesAct Like a Brake PedalTumor Suppressor Gene ProteinsDNACell nucleusSignalingenzymesGrowth factorReceptorTranscriptionfactorsCell proliferationTumor suppressor Gate-keepers: directly involved in regulation of the cell cycle or growth inhibition. eg

30、, p53. Caretakers: involved in repairing DNA damage and maintaining genomic integrity, eg, WRN. The Structure of p531393IIIIIIIVVTransactivation DomainDNA Binding DomainTetramerization DomainNLSINLSII NLSIIINC* * DNA-Binding Regulatory RegionTumor suppression Transcriptional activator and repressor

31、Mutations in almost every kind of tumors Stress Response of p53StressDNA damagep53ActivateTargetsCell growth arrestApoptosisSenescenceActivation Phosphorylation AcetylationStabilizationMajor Post-translational Modification of p53Mdm2p531. Ubiquitination2. Phosphorylation3. Acetylationp53Pp53AATM/ATR

32、CBP/p300Mdm2DNA DamageMDM2APPhosphorylationAcetylationp53CBP/p300PCAFTFsTFsTFsp53p53PCAFTFsCBP/p300RNAPolymerase IIAAAAPPMDM2p53Growth ArrestCellular SenescenceApoptosisWRN is a member of RecQ familyWRN physically and functionally interacts with many proteinsWRN Telomere maintenanceTRF1TRF2POT1 DNA

33、replicationpol RPAPCNAFEN1TopoI DNA DSB repair HRNHEJp53MRNRad51Rad52BLMBRCA1Ku70/Ku80DNA- PKcsX4L4 DNA BERpol PPAR-1Werner syndrome Autosomal recessive disorders. Werners syndrome is named after Otto Werner, a German scientist, described the syndrome as part of his doctoral thesis in 1904.Werner sy

34、ndrome patients typically develop normally until they reach puberty. Following puberty they age rapidly, by age 40 they often appear several decades older. Numerous features of premature ageing: graying and loss of hair, wrinkling and ulceration of skin, atherosclerosis, osteoporosis, and cataracts.

35、 Short stature due to lack of usual growth spurt during puberty. Predisposition for cancerMostly associated with soft tissue sarcomas, osteosarcoma.Werner syndrome patientWilliam and Wilkens Publishing Inc.Chromosome translocation cause misexpression of genes or create chimeric genes encoding proteins that have gained novel functional properties. Philadelphia chromosome translocation, t(9;22)(q34;q11). Form BCR-ABL causes Chronic myelogenous leukemia (CML). Imatinib treat CML by inhibiting tyrosine kinase activity.Ph1 translocat