unravelling the molecular taxonomies of gastroesophageal ... · syed muhammad . fahmy alkaff. tony...
TRANSCRIPT
Patrick Tan, MD PhDProfessor, Duke-NUS Medical School
Deputy Executive Director, Biomedical Research Council,Agency for Science, Technology and Research (A*STAR)
ESMO World Congress on Gastrointestinal CancerBarcelona, June 2018
Unravelling the Molecular Taxonomies of Gastroesophageal Cancers
Tay et al., Cancer Research (2003)
Molecular and Clinical Heterogeneity in Gastric Cancer
Tay et al., (2003) Cancer Research
TCGA Study (~3-4 Major GC Genomic Subtypes)
USA TCGA (2014) Nature
A) ChromosomalInstability (CIN)
B) Microsatellite Instability (MSI)
C) Genome Stable(GS)
D) Epstein-BarrVirus (EBV)
Today’s Topics
1) What are the most Frequent Genetic Events in Gastric Cancers?- Mutations in the *Non-Coding* Genome
2) What are the Key Determinants for Development of Gastric Cancer? - Pre-Malignant Condition (Intestinal Metaplasia)
Genetic Mutations in GC Have Largely Focused on Protein Coding Genes
Amaro Taylor-Weiner (USA TCGA)
Genetic Mutations in GC Have Largely Focused on Protein Coding Genes
Amaro Taylor-Weiner (USA TCGA)
Non-Coding Driver Mutations are Still Unknown for Many Cancer Types (Including GC)
“Driver Mutations” are MutatedMore Frequently than theBackground Mutation Rate
Whole-Genome Analysis of Gastric Cancer
Anders Skanderup, GIS
Uniform Mutation Callingon 212 GC WGS
Many Factors (Covariates) Affect Whole-Genome Mutation Rates
Single-Nucleotide Variants(SNVs)
Mut
atio
n C
ount
Indels
Mutation Count
Statistically Significant Non-Coding Mutation Hotspots are Enriched in CTCF-Binding Sites (CBSs)
** Significance Remains Even After Correcting for Elevated CBS Mutation Rates
CTCF: Regulator of 3D GenomeOrganization
Wikipedia
CBS Hotspot Mutations are enriched in GCs with copy-number instability (CIN)
Overall CBS Hotspot Mutation Frequency = 25% TP53 Mutations = 50%ARID1A Mutations = 14%
CBS hotspot mutations are associated with local chromosomal breaks
CBS hotspots Frequently and Specifically Mutated in Gastrointestinal Cancers
Top-4• Gastric• Colorectal• Liver• Pancreas
Clinical Use-Case : Use of Non-coding Hotspots in Liquid Biopsies
Gene Sensitivity (%) Size (bp) Sensitivity / bp Cumulative Sensitivity
KRAS 6 15 0.4 6.0%Hotspots 54 720 0.08 56.8%
TP53 50 750 0.07 78.4%RHOA 6 180 0.03 79.7%
• Cancer cfDNA fraction very low in blood• Non-coding hotspots represent densely mutated regions (=TP53)• Disease monitoring of gastrointestinal cancers
Summary SlideWhole-genome analysis of GC reveals frequent mutations at CTCF Binding Sites (CBSs)
CBS Hotspots are significantly mutated even after adjusting for covariates, consistent with positive selection
CBS Hotspot Mutations Occur at Frequencies Exceeded Only by TP53 Mutations, in GCs with Chromosomal Instability
CBS Hotspot Mutations are Associated with Local Chromosomal Breaks and Regional Changes in Gene Expression
CBS Hotspot Mutations are Specifically Observed in Gastrointestinal Malignancies
Guo et al., (2018) Nature Communications
Today’s Topics
1) What are the most Frequent Genetic Events in Gastric Cancers?- Mutations in the *Non-Coding* Genome
2) What are the Key Determinants for Development of Gastric Cancer? - Pre-Malignant Condition (Intestinal Metaplasia)
Gastric Cancer and Intra-Patient Heterogeneity
Sundar and Tan (2018) Cancer Discovery
Most Gastric Cancers* Follow a Multi-step Carcinogenesis Sequence
Yeoh and Tan (2015) Gastroenterology
*Diffuse-type GC does not involve metaplasia
Gastric Cancer Epidemiology Program(GCEP)
Four Singapore Hospitals : NUH, SGH, TTSH, CGHFunded by National Medical Research Council
GCEP Translational Study (“TransGCEP”) Selection of High-Risk IM Patients (n=148)
56% moderate/marked IM
All Chinese
All positive for Hp serology(Previous Infection)
Normal Mucosa
Mild IM (<30%)
IM (≥30% cellularity)
p value (IM vs Normal)
n=43 n=22 n=83Age (year), mean ±SD 62±7 60±7 62±7 0.17
RaceChinese 43 (100) 22 (100) 83 (100) --
Gender (%)Male 22 (51) 12 (55) 42 (51) 1Female 21 (49) 10 (45) 41 (49)
Smoking (%) 0.048Current/ Ex-Smoker 9 (21) 4 (18) 32 (39)
Non-smoker 34 (79) 18 (82) 51 (61)Alcohol consumption (%) 5 (12) 5 (23) 20 (24) 0.1
Family history of GC in first-degree relative (%)
7 (16) 3 (14) 13 (16) 1
Hp serology positivity (%) 43 (100) 22 (100) 83 (100) --
Chronic gastritis (%) 38 (88) 22 (100) 83 (100) 0.004Atrophic gastritis (%) 0 (0) 0 (0) 67 (81) --Low Grade Dysplasia (%) 0 (0) 0 (0) 2 (2) --
EGN (%) 0 (0) 0 (0) 4 (5) --Endoscopy surveillance (months), mean ±SD
56±12 58±8 49±18 0.04
DNA Mutations – Point Mutations and Indels(MAF>4%)
TP53 and ARID1AClonal Mutations are Rare
(TP53 – 2%; ARID1A – 3%)
Laser Capture Microdissection Confirms Mutations in IM Cells
IMs Exhibit Low Mutation Burdens Compared to GC
NL
IM
GC
Copy Number Alterations and Telomere Erosion
MYC
NL IM10% of IMs have sCNAs
Most sCNAs target Chr 8q
IMs have significantly shorter Telomeres (Genome Instability)
Sequencing Detects More Hp-Infected IMs Compared to Histology
All 15 have Hp DNA(100%)
33 cases have Hp DNA(27%)
Genomic Sequencing Can Detect Active Low-Level Hp Infection
Histology-confirmed HP casesShow no Hp reads after eradication
(ie Hp DNA is transient)
Giemsa staining confirms Hp infection inSequencing positive cases
IMs Exhibit Global DNA Methylation Alterationsand a Subgroup is Hypermethylated
IMs Exhibit IncreasedDNA Methylation
Normal Intestinal Metaplasia
Integration with Clinical Outcome(Regression, Persistence, Progression)
TransGCEPSamples
LGD/HGD /EGC
Regression criteria based on Rugge et al (2003)Progression includes both LGD and HGD, as both have higher GC risk than IM
Factors influencing IM regression and progression
Mutation Burden Telomere Length
DNA Methylation Copy Number Alterations
Regression
Summary Slide: What our Data SupportsGenomic profiling reveals that IMs exhibit low mutational burdens compared with GCs
In general, TP53 and ARID1A mutations are rare in IM
Some IMs have FBXW7 mutations, chromosome 8qamplifications, or shortened telomeres
Sequencing detects more IM patients with active H. pylori infection than histology
(Epi)genomic alterations in IM predict subsequent GC progression or regression
Huang et al., 2018 Cancer Cell
AcknowledgementsChang XuAngie Lay Keng TanMinghui LeeSuting TayKakoli DasManjie XingAliya FatehullahSyed Muhammad
Fahmy AlkaffTony Kiat Hon LimJonathan LeeKhek Yu HoSteven George RozenBin Tean TehNick BarkerChung King Chia
Christopher KhorChoon-Jin OoiKwong Ming FockJimmy SoWee Chian LimKhoon Lin LingTiing Leong AngAndrew Wong
Khay Guan YeohMing Teh
Kie Kyon HuangKalpana RamnarayananFeng ZhuSupriya Srivastava
Amanda Yu GuoMei Mei ChangWeitai HuangWen Fong OoiManjie Xing
Anders Skanderup
Andrea RajnakovaLee Guan LimWai Ming YapSoh Ee LeeJia Wei Lee