基因組大數(shù)據(jù)與分子診斷在精準(zhǔn)醫(yī)療中的風(fēng)險(xiǎn)評(píng)估

1、基因組大數(shù)據(jù)與分子診斷在精準(zhǔn)醫(yī)療中的風(fēng)險(xiǎn)評(píng)估健康科學(xué)與生物醫(yī)學(xué)技術(shù)發(fā)展的關(guān)鍵問(wèn)題1. Genomics(分子解剖圖譜)2. Cell and immuno therapy(扶正驅(qū)邪)3. Vaccine development (多價(jià)細(xì)菌疫苗)4. Gut microbion-omics (1000種,約1014 數(shù)量, 30萬(wàn)基因;胃100種, H pylori ?)5. Brain science (百病生于氣;認(rèn)知與精神相關(guān)疾患；情緒、焦慮、睡眠障礙與代謝異常)6. Big data to knowledge (BD2K,辯證施治)7. Regulatory science for bi

2、ologicalsBiobank, data and Q&C&A內(nèi)傷脾胃百病由生，肺與大腸相表里2015,奧巴馬:精準(zhǔn)醫(yī)學(xué)計(jì)劃(2.15億$)2004,克林頓 :人類基因組計(jì)劃(38億$)1971,尼克松:攻克癌癥計(jì)劃,(1億$) 保持國(guó)家創(chuàng)新實(shí)力和引領(lǐng)世界科學(xué)技術(shù)發(fā)展潮流的科學(xué)中心地位 以基因組為輔助技術(shù)認(rèn)識(shí)生命健康并診療疾病 簡(jiǎn)便如同量血壓,測(cè)體溫,治療如同輸血一樣精確健康診所專業(yè)診所名醫(yī)診所 把醫(yī)療衛(wèi)生工作的重點(diǎn)放到農(nóng)村去!毛澤東, 1965,6,26 看病難, 看病貴;過(guò)渡醫(yī)療和治療不足; 優(yōu)質(zhì)醫(yī)療裝備,技術(shù),藥品進(jìn)口依賴性過(guò)大; 醫(yī)療資源利用不當(dāng)和欠公平中國(guó)醫(yī)藥學(xué)是一個(gè)偉大的寶庫(kù),應(yīng)

3、當(dāng)努力發(fā)掘加以提高毛澤東梅奧醫(yī)學(xué)中心 (Mayo clinic)1863年創(chuàng)立NIH資助1.42億美元用于精準(zhǔn)醫(yī)學(xué)研究計(jì)劃理念: 以患者為中心(無(wú)論是技術(shù)、醫(yī)療、科研)發(fā)明創(chuàng)造:可地松,MDT10萬(wàn)人的小鎮(zhèn),3萬(wàn)多人為梅奧員工基礎(chǔ)醫(yī)療:70個(gè)標(biāo)準(zhǔn)化診所綜合醫(yī)院:17個(gè)城市,養(yǎng)老院:7個(gè)醫(yī)生:4200名,( 7% );信息學(xué)(IT/APP):7000名 ( 9% ),提供10億美元的多種服務(wù)研究中心50個(gè)/實(shí)驗(yàn)室158個(gè);專職科研193/3317收入:2015,103億美元醫(yī)療:86億捐贈(zèng):5億實(shí)驗(yàn)室檢測(cè)14億;每天3萬(wàn)多份標(biāo)本來(lái)自世界各地(124)全美前20位的醫(yī)院和4000家醫(yī)院或診所與梅奧

4、合作存有大約4000萬(wàn)人份各類疾病的生物樣本 我們面臨資源、人才、技術(shù)、運(yùn)行模式與監(jiān)管的風(fēng)險(xiǎn)與挑戰(zhàn)！基因組測(cè)序技術(shù)的成熟和價(jià)格的下降將推動(dòng)基因組醫(yī)學(xué)的發(fā)展與普及，但病例和樣本將成為瓶頸1000元?研究隊(duì)列、生物樣本的質(zhì)和量將成為瓶頸5病例和生物樣本與臨床及科學(xué)問(wèn)題的關(guān)系60-120$ -600-1200$20052015質(zhì)量與成本控制重要的科學(xué)問(wèn)題科學(xué)問(wèn)題臨床診療問(wèn)題診療新方法和技術(shù)科學(xué)發(fā)現(xiàn)和知識(shí)生物樣本臨床數(shù)據(jù)大數(shù)據(jù)是獲得新認(rèn)知和創(chuàng)造新價(jià)值的源泉 如何面對(duì)“數(shù)據(jù)鴻溝”的挑戰(zhàn)（四個(gè)特征） VOLUME數(shù)據(jù)量大,（預(yù)測(cè)和判斷能力） What生物標(biāo)志物的篩選與鑒定望聞問(wèn)切 VARIETY 類型繁多

5、, (提煉與排除能力） How生物標(biāo)志物的生物學(xué)意義確定 VALUE價(jià)值密度低 (集成驗(yàn)證能力） Where生物標(biāo)志物的臨床意義確定 VOLOCITY 速度快、時(shí)效高(分類與評(píng)價(jià)能力) Which疾病鑒別診斷:細(xì)胞病理、分子診斷DNA Damage & Gene Mutation?Expression alterationand tumor behavior mRNA or miRNALevelProtein Level &LocalizationTissueCellPlasma/SerumAnimal modelPopulationRediscovering Tumor Markers Ba

6、sed on GeneExpression Profiling of Gastric Cancer？Digital Northern Analysis of MMP11 in Different TumorsYang YH et al: Clin Cancer Res 2008,14(1) 74-81Detection of MMP11 Protein Overexpressed in Primary Tumorsand Precancerous Lesion of Stomach/Testing SetYang YH et al: Clin Cancer Res 2008,14(1) 74-

7、81Relationship between clinical-pathologic featuresand serum MMP11 level of gastric cancerMMP11 proteinClinical featuresTotal numberp valuesPositive NegativeGenderMaleFemaleAge6060TNM Stage16871834285290.1680.1790.0820.5290.009127111616366481275936339DifferentiationWell20701340730PoorMetastasisPosit

8、iveNegative1213483153819Yang YH et al: Clin Cancer Res 2008,14(1) 74-81Analysis of MMP11 correlated with biomarkersMMP11Tumor markersp valuesPositive NegativeCEAPositiveNegativeCA199PositiveNegativeCA72.4PositiveNegativeCA242206934720.0910.0170.0520.072861343522573855PositiveNegative11452142Yang YH

9、et al: Clin Cancer Res 2008,14(1) 74-81Comparison of Sensitivities between Serum MMP11and Traditional Tumor MarkersPositiveNegativeTotalSensitivity ()CEA55631441321149319919517512630527.632.334.926.245.2CA199CA72.4CA242MMP116133138167Yang YH et al: Clin Cancer Res 2008,14(1) 74-81腫瘤發(fā)病機(jī)理的基本假說(shuō)與科學(xué)問(wèn)題驅(qū)動(dòng)的

10、臨床診療策略 基因突變: 癌基因激活(1976-1985)，抑抗體與分子靶向治療信號(hào)調(diào)控網(wǎng)絡(luò)紊23/49CML靶向治療 染色體易位：DNA斷裂點(diǎn)(1960)，融合基因(1980s);靶向修飾治療 表觀遺傳改變：DNA甲基化(2002-)，組蛋白乙?；揎?，非編碼RNA（miRNA IncRNA)細(xì)胞免疫及抗血管治療 干細(xì)胞起源 (1937)：種子與土壤(1889)，EMT; 非可控慢性炎癥：炎性細(xì)胞與免疫調(diào)節(jié)(1909-1957)，靶向免疫:PD1/PDL1, CAR-T細(xì)胞外基質(zhì)，T-reg,巨噬細(xì)胞T細(xì)胞，NK，中性粒細(xì)胞微創(chuàng)、干細(xì)胞與中醫(yī)藥治療 ?Different Pathologic

11、al Features with Different Prognosis in Gastric CancerIntestinal typeLaurens classificationDiffuse typeShanghai Ruijin Hospital (N=526)Identification of Somatic Mutations and Candidate Genesin Subtype of Gastric CancerIntestinal type (5) and diffuse type (4) GC and matched normal tissuesExome captur

12、e sequencing716 mutant genesSmall size samplesBiochip including 2267genesMutant genes reported in other cancersRelated genes selected from Cancer Gene Census databaseIntestinal type (58) and diffuse type (63) GC and matched normal tissuesTarget region capture sequencing8890 in intestinal type GC1256

13、4 mutant sites in coding sequence3674 in diffuse type GC6682 in intestinal type GC2357 in diffuse type GC2208 in intestinal type GC959 in diffuse type GC9420 non-synonymousLarger size samples3167synonymous1905 genes272 potential related with well prognosisAssociation of gene mutation with clinic out

14、comeIsolation of candidate genes50 potential related with poor prognosis742 specific in intestinal type GC166 specific in diffuse type GC28 specific in intestinal type GCIsolation of specific pathway4 specific in diffuse type GCIdentification of driver gene and core pathway in intestinal and diffuse

15、 type GCCharacterization of mutation patterns between intestinal and diffuse type GCTable X: Categorization of core pathways and genes with non-synonymous mutation in GC(mutant gene isolated from 716 mutant genes)CaseinvolvedGeneinvolvedPathwayp-Valueq-ValueInput SymbolClassificationInflammationCyto

16、kine-cytokine receptorinteraction33550.0226780.0016220.0319690.004992IFNA13;IFNGR1;PPBP;TSLPNatural killer cell mediatedcytotoxicityKIR3DL1;IFNA13;IFNGR1;SOS2Cell cycleApoptosis33330.0365240.0172810.0426110.026377MCM7;PRB1;TP53Cell cycle andapoptosisCFLAR;IRAK3;TP53ECM-receptor interactionFocal adhe

17、sion34671.32E-052.82E-042.55E-040.001734LAMA1;COL1A2;ITGA6;ITGA8;LAMA3LAMA1;COL1A2;ITGA6;ITGA8;LAMA3;SOS2ECM andstructureCell adhesion molecules44333555340.0014250.0110980.002690.0048630.0195060.0075830.0256070.03539CD226;ITGA6;ITGA8;NLGN4X;VCANIQGAP1;ITGA6;ITGA8;NCKAP1L;SOS2IFNA13;IFNGR;SOS2;TSLPAR

18、;ERBB4;SOS2Regulation of actin cytoskeletonJak-STAT signaling pathwayErbB signaling pathwayTranscriptionfactor0.0162730.026574CalciumCalcium signaling pathwayADCY2;BST1;CACNA1F;ERBB4OR1I1;OR10G8;OR10G9;OR51Q1;OR2L3;OR2T4;OR51I1;OR5D14;OR6C70;OR2T34;OR10G2;OR10G3;OR10G7;OR10K1;OR13C3;OR14I1;OR2M5;OR2

19、T1;OR2T3;OR4A15;OR4C16;OR4K15;OR4Q3;OR4X2;OR51E1;OR51L1;OR52H1;OR5AR1;OR5B17;OR5L2;OR6K2;OR6T1;OR8H3;OR8J3Olfactory transduction8346.28E-291.28E-26MetabolishAdipocytokine signaling pathwaySmall cell lung cancerChronic myeloid leukemiaAxon guidance333335530.0080361.88E-040.0109320.0454850.0159150.001

20、2330.0194660.047109ADIPOQ;G6PC;PRKAG1LAMA1;ITGA6;LAMA3;TP53GAB2;SOS2;TP53Related cancerNervusDPYSL2;NTN4;SEMA6DHeterogeneity Correlated with Accumulation of Low FrequencyMutant Genes in Gastric CancerAIntestinal typeDiffuse typeBa b c Cluster1 n=9 (100% IT) Cluster2 n=16 (50.0% IT) Cluster3 n=84 (43

21、.6% IT)800600400200cbN=1105CN=717aN=83500%000053-1-332121Gene mutation frequencyDetection of Gene Mutation Profile Differences BetweenIntestinal and Diffuse Type of Gastric CancerXing R et ,unpublished data,2016Characterization of differential gene mutations correlatedwith different prognosis in gas

22、tric cancerSMARA4COL14A1PoorWellNID2ERBB4常規(guī)治療或微創(chuàng)消融治療TP53KRASXing R et al, unpublished, 2016Mutant ERBB4 Inhibits Proliferation and Invasion in Gastric CancerXing R et al: Unpublished data, 2016Schematic representation of ERBB4 as a molecular signaturefor subtypes in intestinal- and diffuse-type GCIn

23、testinal typeDiffuse typeTP53MAPKSignalingTP53 & MAPK SignalingN=7N=38N=21N=51N=65P=0.909HR=1.0595%CI=0.4-2.6P=0.168HR=0.38N=34P=0.046HR=0.0095%CI=0.1-1.5Time since operation (months)Xing R and Lu YY et al unpublished data, 2016Copy number variations of HLA-I and activation ofNKp30 pathway determine

24、 the sensitivity of gastric cancercells to the cytotoxicity of natural-killer cellsRui Xing, Lin Li, Longyun Chen, Zhibo Gao, Hongyi Wang, Wenmei Li, Jiantao Cui,Geng Tian, Qiaoyi Liang, Jun Yu , Joseph JY Sung, Guangbin Luo, Hengjun Gao,Xun Xu, Huanming Yang, Jian Wang, Xiuqing Zhang, Jimin Wang,Ju

25、n Wang and Youyong LuPeking University Cancer Hospital & Institute,Beijing Genomics Institute at Shenzhen,The Chinese University of Hong Kong,Case Western Reserve University,Beijing University of Chinese Medicine,Shanghai Engineering Center for Molecular Medicine,NCI/NIHNPG,Oncogene, 2016, 35: 2584-

26、91Scientific Question Why Turmorigenecity difference of humantumor cell lines in nude mice ?The references related to animal model and cancer cell linesReferencesHuman tumor cell line398,471Human tumor cell line and nude miceHuman tumor cell line and nod scid miceHuman tumor cell line and tumorigeni

27、city24,9131,2743,369Athymic mice, 1974, Stutman OBGC823 cellsAGS cells5125,776Hela cell line, 1950sAnalysis of Tumorigenecity of Two Gastric Cancer Cell LinesCell line0.25x1060.3x1060.5x1061x1065x1061x1074/4(11d)63/66(10d)18/19(7d)4/4(3d)BGC823-0/3(90d)0/11(120d)0/10(120d)AGS-Landscape of BGC823 and

28、 AGS Cell Lines byWhole Genome Sequencing AnalysisBGC823AGSCell linesAGSCategoriesBGC823%NO. of chromosome58-62347519508647-503223593544SNP25160 ( 3.7%)1542 (17.9%)31160 ( 7.8%)CNVINDEL214549183389SVFusion gene115082010172121336 ( 6.2%)8（ 40 % ）Different sensitivity of BGC823 and AGS cells to NK cel

29、l cytotoxicityXing R et al Oncogene, 2016, 35: 2584-91Cytotoxicitic Ability Analysis of Natural Killer Cell toBGC823 and AGS CellsBGC823AGSXing R and Lu Y Y, Unpublished dataCNVs of HLA based on WGS profiling of BGC823 and AGS cellsXing R et al Oncogene, 2016, 35: 2584-91Active NKp30/VAV2/MAPK3/IL-1

30、2 pathway promotes thecytotoxicity of NK cells to AGS cellsXing R et al Oncogene, 2016, 35: 2584-91Combination of classic HLA-I and NKp30/MAPK3/IL-12 predictsprogression and metastatic potential in GC cells andXing R et al Oncogene, 2015, 35: 2584-91Schematic representation of the proposed mechanism

31、 of NKcell lysis for cancer cells.Xing R et al Oncogene, 2016, 35: 2584-91適應(yīng)性突變與疾病控制 有序、無(wú)序 與熵，遺傳度、負(fù)熵與生命和健康維護(hù)的關(guān)系 如何對(duì)應(yīng)癌癥發(fā)生的隨機(jī)性、異質(zhì)性和動(dòng)態(tài)演化的階段性？完留下最年輕最健康的細(xì)胞The point of no retuneEntropyMutation&整采集生命過(guò)程的信息RepairM M M M M M M MM M M M MM MMMM M M M M M WMWM M M MMMMMM M M M M MWM WW M M MMMMWM M M M M WWMWWW M M MMMWM M M MMWWWMWWWM MMMMWM M M MWWWWMWWWWMMMMWM M M WWWWWMWWWWMMMM WM M M WWWWWMWWWWWMMMWM M WWWWWW M WWWWWWMMWM WWWWWWM WWWWWWWW MWM WWWWWWMWW WWWWWW MWWWWWWWWWMMWWWWWW WWWAge&DamageWWWWWWWWMMWWWWWW WWWNegentropySNVs