Wei Zhou, Ph.D. Winship Cancer Institute October 2, … · Winship Cancer Institute October 2, 2005...
Transcript of Wei Zhou, Ph.D. Winship Cancer Institute October 2, … · Winship Cancer Institute October 2, 2005...
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Chromosomal deletion as predictors Chromosomal deletion as predictors for recurrence of early stage CRCfor recurrence of early stage CRC
Wei Zhou, Ph.D.Wei Zhou, Ph.D.
Winship Cancer InstituteWinship Cancer InstituteOctober 2, 2005October 2, 2005
Falk Symposium 149: Highlights in GI Oncology
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Colorectal Carcinoma
Early Stage Colon CancerEarly Stage Colon CancerSurgerySurgery
Colonoscopy with Colonoscopy with polypectomypolypectomySurgical resectionSurgical resection
Adjuvant TherapyAdjuvant Therapy55--FU/Leucovorin FU/Leucovorin IrinotecanIrinotecan (CPT(CPT--11), 11), OxaliplatinOxaliplatin, , C225C225Radiation therapyRadiation therapy
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Adjuvant Therapy for Early Stage CRC?
Over 70Over 70--80% 580% 5--year survival with surgery alone year survival with surgery alone
Only benefit a small proportion of total Only benefit a small proportion of total populationpopulation
Risk, side effects and costs of adjuvant therapyRisk, side effects and costs of adjuvant therapy
Large number of Large number of noncancernoncancer related deathrelated death
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Treatment Benefit in Dukes’ B Patients
No. of 5-year 5-yearPatients DFSsurvival
Surgery 509 73% 80%
5-FU+LV 507 76% 82%
FU: fluorouracil, LV: leucovorinBased on four National Surgical Adjuvant Breast and Bowel Project (NSABP) Clinical Trials (C-01, C-02, C-03 and C-04)Buyse & Piedbois, Seminars in Oncology, Vol 28, No.1 Suppl (Feb) 2001, pp20-24
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How to Predict Patients at High Risk of Recurrence?
Colorectal Carcinoma
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MIN and CIN Colorectal Cancers
MIN: Microsatellite Instability (MSI)MIN: Microsatellite Instability (MSI)Diploid Tumors (Near diploid tumors)Diploid Tumors (Near diploid tumors)~13% in colorectal, endometrial and gastric ~13% in colorectal, endometrial and gastric cancerscancers<2% in other cancer types<2% in other cancer types
CIN: Chromosome instabilityCIN: Chromosome instabilityAneuploidAneuploid TumorsTumors~85% in colorectal cancer~85% in colorectal cancer
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Disease Prognosis in MIN CRC tumors
Better Overall survivalBetter Overall survivalHR=0.65; 95% CI, 0.59HR=0.65; 95% CI, 0.59--0.710.71
Tumors with MSI derived no benefit Tumors with MSI derived no benefit from adjuvant FUfrom adjuvant FU
HR=1.24; 95% CI 0.72 to 2.14HR=1.24; 95% CI 0.72 to 2.14
Journal of Clinical Oncology, 23,(3) 2005: pp. 609-618
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LOH Analysis vs Other Methods
Underestimate the true extent of allele Underestimate the true extent of allele loss byloss by
KaryotypicKaryotypic studiesstudiesCGHCGHFISHFISH
Loss of a maternal or paternal allele in Loss of a maternal or paternal allele in a tumor are often accompanied by a a tumor are often accompanied by a gain of the opposite allelegain of the opposite allele
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Early stage patients without 18q loss have better survival (I)
Jen. J et al, 1994, NEJM, 331: 213-221
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Early stage patients without 18q loss have better survival (II)
Jen. J et al, 1994, NEJM, 331: 213-221
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Follow-up studies are controversial
Study Overall survival Disease-free survivalSample size HR9 95% CI P -value HR 95% CI P -value
Jen et al. [1994] 145 2.83 1.32-6.08 0.008Watanabe et al. [2001] 221 2.04 1.3-3.2 0.002Barratt et al. [2002] 108 0.86 0.57-1.28 0.45Aschele et al. [2004] 42 2.16 1.04-4.49 0.04Carethers et al. [1998] 70 1.22 0.32-4.72 0.84Diep et al. [2003] 184 2.7 1.33-5.48 0.006Halling et al. [1999] 386 1.2 0.81-1.76 0.37 1.25 0.81-1.91 0.32Lanza et al. [1998] 112 7.13 2.1-23.9 <0.001 5.76 2.2-15 <0.001Ogunbuyi et al. [1996] 126 2 1.26-3.86 0.003Zauber et al. [2004] 93 0.91 not reported 0.86
Popat & Houlston, Euro J. Cancer, 41, pp2060-2070
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Detection of LOH by Microsatellite Analysis
Jen. J et al, 1994, NEJM, 331: 213-221
N T
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LOH Analysis in Primary Tumors is NOT Reliable
Normal tissue contaminationNormal tissue contaminationDNA from nonDNA from non--neoplastic cells can easily mask neoplastic cells can easily mask LOHLOH
Tumor DNA degradationTumor DNA degradationLiu, J. Liu, J. et al.et al. Loss of heterozygosity in tumor cells Loss of heterozygosity in tumor cells requires rerequires re--evaluation: the data are biased by the sizeevaluation: the data are biased by the size--dependent differential sensitivity of allele detection. dependent differential sensitivity of allele detection. FEBS FEBS LettLett.. 462462, 121, 121--8 (1999).8 (1999).
Low DNA yield with microLow DNA yield with micro--dissection dissection techniquestechniques
Sampling errorsSampling errors
N T
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Counting Alleles: Fault-Tolerant LOH Analysis
ParaffinParaffin--embedded samplesembedded samplesNot affected by PCRNot affected by PCR--bias, DNA bias, DNA degradation and normal tissue degradation and normal tissue contaminationcontamination
SingleSingle--step reaction setupstep reaction setup
QuantitativeQuantitativeRigorous mathematical toolsRigorous mathematical toolsTolerate up to 50% normal tissue Tolerate up to 50% normal tissue contamination contamination
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Counting allelesC T
+A
G
AT
GC Single molecule
amplification
Molecular beacon detection
Statistical Analysis
Tolerate upto 50% contamination
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CRC Patient Information
4 cohorts, 196 cases4 cohorts, 196 casesScotland, Italy, New York and Scotland, Italy, New York and BaltimoreBaltimore
DukeDuke’’s Stage A or Bs Stage A or B
Exclude HNPCC and FAPExclude HNPCC and FAP
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Chromosome Markers
8p8pLost during late stage of CRC developmentLost during late stage of CRC development9 SNP markers9 SNP markers
1818Commonly lost during transition between Commonly lost during transition between early adenomas to late early adenomas to late adeonmasadeonmas11 SNP markers11 SNP markers
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Data Analysis
Ch. 8p (9) & Ch. 18 (11)Ch. 8p (9) & Ch. 18 (11)
L tumors:L tumors: lost both lost both R/L tumors:R/L tumors: lost eitherlost eitherR tumors:R tumors: retain bothretain both
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Allele Status and Recurrence
TypesTypes PrognosisPrognosis RecurrenceRecurrence
R tumorsR tumors ExcellentExcellent 0%0%
R/L tumorsR/L tumors intermediateintermediate 27%27%
L tumorsL tumors PoorPoor 46%46%
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Allele status and Prognosis
P<0.001
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L patients with Duke’s A have a worse prognosisthan R patients with Duke’s B disease
R R R/LR/L LL
DukesDukes’’ AA 0%0% 14%14% 38%38%
DukesDukes’’ BB 0%0% 30%30% 48%48%
Recurrence Rate
(P<0.002)
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Why are L type tumors more likely to recur
AneuploidyAneuploidyL types tumors lose both 8p and 18L types tumors lose both 8p and 18More advance disease stageMore advance disease stageA general feature for all solid tumors???A general feature for all solid tumors???
Inactivation of TSG on 8p and 18qInactivation of TSG on 8p and 18q8p: ???8p: ???18q: DCC or DPC4/SMAD418q: DCC or DPC4/SMAD4
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Disease Progression of L types tumors in other organ sites (I)
Allelic statuses of 8p and 18 does not Allelic statuses of 8p and 18 does not predict disease recurrence in stage II predict disease recurrence in stage II and III prostate tumorsand III prostate tumors
Zhou et al, The Prostate, 2004, 15 (61), 81-91
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Disease Progression of L types tumors in other organ sites (II)
Morikawa et al 2005, in review
VariableNumber of
patients OR p Value 95% CI
Allelic typesR 8pR&18qR 0R/L 8pR&18qL 11 referentR/L 8pL&18qR 19 9.0 0.049* (1.17, 69.47)L type 8pL&18qL 24 6.0 0.12* (0.76, 47.22)
Based on chi-square test and Fisher's exact test* , approximate 95% confidence intervalsAI = allelic imbalance, R = retention/ no allelic imbalance, OR = odds ratio, CI = confidence intervals
No Distant Relapse Distant Relapse
n/a n/a
9
101015
19
Allelic status distribution in relation to distant relpase in IDC
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Why are L type tumors more likely to recur
AneuploidyAneuploidyL types tumors lose both 8p and 18L types tumors lose both 8p and 18More advance disease stageMore advance disease stageA general feature for all solid tumors???A general feature for all solid tumors???
Inactivation of TSG on 8p and 18qInactivation of TSG on 8p and 18q8p: ???8p: ???18q: DCC or DPC4/SMAD418q: DCC or DPC4/SMAD4
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Counting alleles in CRC
18q loss associates with vascular 18q loss associates with vascular invasion in early stage colorectal cancerinvasion in early stage colorectal cancer
Zhou W, et al. Nat Zhou W, et al. Nat BiotechnolBiotechnol 2001;19(1):782001;19(1):78--81.81.
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Conclusions
Counting alleles provides a sensitive and Counting alleles provides a sensitive and reliable approach for assessing LOH in clinical reliable approach for assessing LOH in clinical samples.samples.
Quantified assessment of AI of 8p and 18 can Quantified assessment of AI of 8p and 18 can identify subgroups of patients in whom tumors identify subgroups of patients in whom tumors are likely or not likely to recurare likely or not likely to recur
AI of 8p and 18 are probably associated with AI of 8p and 18 are probably associated with inactivation of tumor suppressor genes not a inactivation of tumor suppressor genes not a simple reflection of simple reflection of aneuploidyaneuploidy
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Improving the “counting alleles” method
Emulsion PCREmulsion PCR
Dressman, et al, PNAS, 100 (15): 8817-8822
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High Density SNP arraysThe The GeneChipGeneChip®® Human Mapping 100K SetHuman Mapping 100K Set
Two arraysTwo arraysExtensive genomic coverage (26 Kb/marker)Extensive genomic coverage (26 Kb/marker)One primer setOne primer set
ApplicationsApplicationsLOH analysisLOH analysisCopy number analysisCopy number analysis
ChallengeChallengeTissue DegradationTissue DegradationTissue contaminationTissue contamination
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School of Public HealthRobert LylesMichael GoodmanJack Mandel
Johns HopkinsBert VogelsteinKenneth W. KinzlerSteven N. GoodmanElizabeth A. MontgomeryIeMing ShihKatharine E. RomansMichael A. Choti
Second University of Naples, School of Medicine, ItalyGennaro GaliziaEva LietoFrancesca Ferraraccio
University of EdinburghMedical School, UKColin A. PurdieJuan PirisRobert MorrisDavid J. Harrison
Memorial Sloan-KetteringPhilip B. PatyAl Culliford
University Hospital AntwerpCecile Colpaert
Funding SupportACS, DoD, Georgia Cancer Coalition
AcknowledgementsZhou LabDiansheng ZhongAki MorikawaMichael GuoXiuju LiuTanisha Williams
PathologyMahul AminMilton DattaSharon Lim
UrologyJohn PetrosKyle RusthovenKathy Lachenmyer
Atlanta VAVijay VarmaTheresa Gillespie