Gastroenterology 2015;149:1153–1162
Genetics and Molecular Pathogenesis of Gastric
Adenocarcinoma
Patrick Tan1,2,3,4,7 Khay-Guan Yeoh5,6,7
1
Cancer and Stem Cell Biology Program, Duke-National University of Singapore Graduate Medical School; 2Genome Institute
of Singapore, Agency for Science, Technology, and Research; 3Cancer Science Institute of Singapore, National University of
Singapore; 4Cellular and Molecular Research, National Cancer Centre Singapore; 5Department of Medicine, Yong Loo Lin
School of Medicine, National University of Singapore; 6Department of Gastroenterology and Hepatology, National University
Health System; and 7Singapore Gastric Cancer Consortium, Singapore
Gastric cancer (GC) is globally the fifth most common
cancer and third leading cause of cancer death. A complex
disease arising from the interaction of environmental and
host-associated factors, key contributors to GC’s high
mortality include its silent nature, late clinical presenta-
tion, and underlying biological and genetic heterogeneity.
Achieving a detailed molecular understanding of the
various genomic aberrations associated with GC will be
critical to improving patient outcomes. The recent years
has seen considerable progress in deciphering the genomic
landscape of GC, identifying new molecular components
such as ARID1A and RHOA, cellular pathways, and tissue
populations associated with gastric malignancy and pro-
gression. The Cancer Genome Atlas (TCGA) project is a
landmark in the molecular characterization of GC. Key
challenges for the future will involve the translation of
these molecular findings to clinical utility, by enabling
novel strategies for early GC detection, and precision
therapies for individual GC patients.
Keywords: Cancer Genetics; Cancer Genomics; Gastric Cancer.
G astric cancer (GC) is currently the third leading
cause of global cancer-related death, and particu-
larly prevalent in Asia. Despite a steadily declining inci-
dence, GC still causes more than 723,000 deaths a year.1
Achieving a detailed molecular understanding of GC patho-
genesis is pivotal to improving patient outcomes for this
complex disease. This is clearly exemplified by the TOGA
Phase III trial, where GC patients with HER2/neu receptor
tyrosine kinase (RTK)-positive tumors experienced clinical
benefit from chemotherapy plus trastuzumab (a HER2-
targeting antibody) relative to chemotherapy alone.2 In
this review, we have attempted to capture the latest ad-
vances in GC molecular genetics. Special attention is paid to
the recent landmark TCGA study, where almost 300 GCs
GENOMICS
were simultaneously profiled on multiple molecular plat-
forms to identify 4 genomic subtypes: CIN (chromosomal
instability), MSI (microsatellite instability), GS (genome
stable), and EBV (Epstein-Barr virus).3 The comprehensive
nature of the TCGA study provides an invaluable resource
upon which to interpret other related GC findings.
Gastric Premalignancy and the Critical
Role of Inflammation
The human stomach consists of the fundus, corpus or
body, and pyloric antrum. The gastric mucosa contains three
main types of glands: cardiac glands (containing mucus-
producing foveolar cells), oxyntic glands (parietal cells and
chief cells producing hydrochloric acid and pepsinogen
respectively), and pyloric glands with mucus–secreting cells
and endocrine G cells secreting gastrin. Chronic atrophic
gastritis and intestinal metaplasia (IM) involving the gastric
mucosa are considered important steps in GC pathogenesis
(Figure 1).4 Mucosal atrophy is characterized by loss of
glandular elements and replacement by metaplastic cells or
fibrosis, with concomitant hypochlorhydria. IM is a pre-
neoplastic lesion characterized by transformation of the
gastric mucosa into an intestinal-like phenotype, replete
with goblet cells and intestinal mucins. IM, associated with
Abbreviations used in this paper: CIMP, CpG island methylation pheno-
type; CIN, Chromosomal instability; EBV, Epstein-Barr virus; EMT,
epithelial-mesenchymal transition; GC, gastric cancer; GS, genome sta-
ble; Helicobacter pylori, H pylori; HDGC, hereditary diffuse gastric cancer;
IM, intestinal metaplasia; lincRNAs, long intergenic noncoding RNAs;
miRNAs, microRNAs; MSI, microsatellite instability; NGS, next-generation
sequencing; sCNAs, somatic copy number alterations; TFs, transcription
factors; TCGA, The Cancer Genome Atlas.
Most current article
© 2015 by the AGA Institute
0016-5085/$36.00
http://dx.doi.org/10.1053/j.gastro.2015.05.059
 1154 Tan and Yeoh
GENOMICS
Figure 1. Cause and pathogenesis of intestinal-type GC. A summary of current knowledge of the cause and pathogenesis of
intestinal type GC is shown, including host and environmental factors as well as acquired molecular events.52,143–145 GC,
gastric cancer.
over-expression of the homeobox transcription factor
CDX2,5 is currently classified into three subtypes: intestinal
type, gastric type, and mixed gastric-intestinal type. The
latter, also known as incomplete IM, is considered to confer
the highest risk for GC development. Injury to the gastric
mucosa has also been observed to cause metaplastic
changes with spasmolytic peptide expression. This phe-
nomena, termed spasmolytic peptide expressing metaplasia
(SPEM) or trefoil factor family 2 (TFF2) expressing meta-
plasia, is induced after Helicobacter pylori (H pylori) infec-
tion and chronic gastritis.6 Spasmolytic peptide expressing
metaplasia has also been implicated as a precursor event in
GC progression.7
In most patients, frank GC is often preceded by several
decades of chronic gastric mucosal inflammation. Chronic
inflammation activates the NF-kB transcription factor, a key
mediator of tumor promotion.8 Chronic inflammation also
causes increased oxidative stress, due to reactive oxygen
species and nitrosamines generated by leukocytes and mac-
rophages which can damage proliferating cells. Moreover, the
production of chemokines and cytokines may induce not only
leukocyte migration but also promote carcinogenesis. Exper-
imentally, mice with impaired immune systems such as severe
combined immune deficiency (SCID) or recombinase
activating gene (RAG2)-deficient mice are very susceptible to
H pylori infection, but do not develop significant gastric dis-
ease.9 Such data further supports an important functional role
of the host immune system in GC pathogenesis.
Cause and Epidemiology of Gastric
Cancer
Environmental factors play critical roles in GC patho-
genesis, with major risk factors being H pylori infection, diet
Gastroenterology Vol. 149, No. 5
and smoking.10 High salt intake, often due to traditional
diets containing salted fish, is the best documented dietary
risk factor for atrophic gastritis.11 Recent data also suggests
that iron deficiency may be a GC risk factor, as iron deple-
tion can accelerate the progression of carcinogenesis by
augmenting H pylori virulence.12 EBV infection is recognized
as an etiological agent in 5%–10% of GCs.13,14
H pylori is the most significant environmental risk factor
for GC and is recognized as a class I carcinogen by the
World Health Organization. Although more than 50% of the
world population is infected with H pylori, only 1%–2% of
infected people will develop GC in their lifetime.15 A major
H pylori virulence factor is the cytotoxin-associated gene A
(CagA), within the bacterial cag pathogenicity island (cag-
PAI) which is injected into the cytoplasm of gastric
epithelial cells upon microbial colonization.16 In transgenic
mice, systemic expression of CagA has been shown to
induce gastric epithelial hyperplasia, gastric polyps, gastric
and intestinal adenocarcinomas.17 Genetic variations in
CagA, specifically present in Asian strains but not non-Asian
strains, are also associated with increased chronic gastritis,
gastric ulcer and gastric adenocarcinoma in human pa-
tients.18 In gastric epithelial cells, CagA undergoes tyrosine
phosphorylation by Src kinase and activates SHP-2 (Src
homology 2- containing tyrosine phosphatase). Activated
SHP-2 induces the Ras-ERK pathway, a key regulator of cell
growth, migration, and adhesion.19 CagA also disrupts tight
junctions20 and can target the PAR1/MARK kinase to alter
apical-basolateral cell polarity, ultimately causing disorga-
nization of the gastric mucosal architecture.21 CagA also has
tyrosine phosphorylation-independent functions, including
interactions with the Met tyrosine kinase and E-cadherin.
This latter interaction disrupts binding between E-cadherin
and b-catenin, leading to nuclear accumulation of b-catenin
October 2015
and subsequent activation of b-catenin-dependent
transcription.22
Several clinical studies have evaluated the utility of H
pylori eradication for GC prevention. Randomized trials in
high risk populations have suggested that H pylori eradica-
tion is most effective in patient subgroups where prema-
lignant lesions have not yet developed.23 For example, a H
pylori eradication program in Matsu Island, Taiwan showed
that eradication reduces the incidence of atrophic gastritis
and peptic ulcer but not intestinal metaplasia.24 In a meta-
analysis of 6 randomized controlled trials, H pylori eradi-
cation reduced the risk of developing GC by RR of 0.65 (95%
CI, 0.43–0.98).25 In Japan, which has high rates of GC
prevalence and H pylori infection, the national health in-
surance system approved eradication therapy for H pylori-
related chronic gastritis in 2013.26
Smoking has been associated with a 1.5–2.5 fold
increased risk of GC in both case-control and cohort studies,
and this risk increases with the frequency and duration of
smoking. Studies have reported that smokers have higher
hazard ratios (HR) of GC in the cardia (HR, 2.86–4.10)
compared to distal portions of the stomach (HR,
1.52–1.94).27 Carcinogens in tobacco smoke, notably nitro-
samines and other nitroso compounds, may exert mutagenic
effects, thereby increasing GC risk.28 Smoking also increases
the risk for precancerous lesions such as intestinal meta-
plasia and dysplasia.29
EBV has been detected in 5%–10% of GC.13,14 A meta-
analysis of 70 studies including 15,952 cases of GC
demonstrated that EBV-associated GC predominantly arises
in men and is found in cardia and body sites more often
than in the antrum.14 A major molecular feature of EBV-
associated GCs is CpG island promoter methylation of
cancer-related genes.30 Expression of EBV viral latent
membrane protein 2A (LMP2A) may be responsible for the
promotion of DNA methylation, by inducing STAT3 phos-
phorylation and subsequent transcription of DNA methyl-
transferase 1 (DNMT1). EBV also encodes a large number of
microRNAs (miRNAs),31 mostly encoded in the BHRF1 and
BART regions of the genome. EBV miRNAs can repress
cellular proteins, including p53 up-regulated modulator of
apoptosis (PUMA), DICER1, and BIM.32 A recent study
profiling 44 known EBV miRNAs in clinical samples from
EBV-associated GC patients found that EBV-miR-BART4-5p
plays an important role in gastric carcinogenesis through
regulation of apoptosis.33
Gastric Cancer Host Genetics
Besides environmental agents, GC pathogenesis also in-
volves host genetic factors. One of the first host genetic
factors identified in GC involved polymorphisms in the
proinflammatory gene interleukin 1-b (IL-1 b).34 A more
recent study reported that combinations of single nucleotide
polymorphisms (SNPs) in immune-related genes [inter-
leukin 1-b (IL-1 b), interleukin 1 receptor antagonist
(IL-1RN), tumor necrosis factor- a (TNF- a) and interleukin
10 (IL-10)] conferred a manifold increased risk of devel-
oping GC, but only in H pylori infected patients.35
Pathogenesis of Gastric Adenocarcinoma 1155
Furthermore, a combination of high-risk host genotypes
and high-risk H pylori genotypes greatly increased the
probability of GC, up to 87-fold over baseline. These studies
highlight again the critical role of host immunity in deter-
mining GC outcomes following H pylori infection.36 Certain
high risk GC genotypes may differ in different populations,
for example, a meta-analysis showed Asian high risk SNPs
GENOMICS
differ from those identified in the non-Asian population.37
Another identified host genetic factor for GC is prostate
stem cell antgen (PSCA), which influences susceptibility to
diffuse-type GC and may play a role in gastric epithelial cell
proliferation.38 PSCA genetic variants have also been
recently confirmed as influencing GC in a wide variety of
populations.39
Hereditary GC syndromes are rare and account for 1-3%
of GC, comprising mainly three types: hereditary diffuse
gastric cancer (HDGC), gastric adenocarcinoma and prox-
imal polyposis of the stomach (GAPPS) and familial intesti-
nal gastric cancer (FIGC).40 HDGC is due to E-cadherin
(CDH1) germline mutations,41 and patients with this con-
dition are often managed with prophylactic gastrectomies.41
Besides CDH1, other recently identified candidate HDGC
genes include CTNNA1, BRCA2 and STK11.42 GAPPS, first
reported in 2012, is characterized by autosomal dominant
transmission of fundic gland polyposis (including dysplastic
lesions or adenocarcinoma or both) restricted to the prox-
imal stomach with no evidence of colorectal/duodenal pol-
yposis or other hereditary gastrointestinal cancer
syndromes.43 Its genetic cause is as yet unknown. GC has
also been associated with other hereditary cancer syn-
dromes such as Lynch syndrome, hereditary nonpolyposis
colorectal cancer syndrome, familial adenomatous polypo-
sis, and Li-Fraumeni syndrome.40
Gastric Cancer Pathology
GC is morphologically, biologically, and genetically het-
erogeneous. Most GCs are adenocarcinomas, with lym-
phoma, sarcomas, and carcinoids comprising less than 5%.
Adenocarcinomas are grouped by the Lauren classification
into intestinal and diffuse types.44,45 In intestinal type tu-
mors, the malignant cells form gland-like structures, unlike
those in diffuse type tumors. Intestinal type GC is more
common in high-risk regions while diffuse type GC is more
common in low-risk areas. Diffuse type GC is more common
in young patients, in whom there is a female preponder-
ance,45 and behaves more aggressively than the intestinal
type.46 Besides the Lauren classification, other histopatho-
logical classifications for GC have been proposed. For
example, the WHO classification groups GC into 4 main
types based on the predominant histological pattern:
tubular, papillary, mucinous and signet ring cell.47
Molecular Genetic Landscape of
Gastric Cancer
Studies from several groups over the past decade have
now produced a near-comprehensive catalogue of GC-
associated “driver” alterations, including gene mutations,
 1156 Tan and Yeoh
GENOMICS
somatic copy number alterations (sCNAs), structural vari-
ants, epigenetic changes, and transcriptional changes
involving mRNAs and noncoding RNAs (ncRNAs) (Figure 2).
Certain driver alterations can also be associated with spe-
cific GC subtypes. For example, MSI is a genetic hypermu-
tability phenomenon where microsatellite regions in tumor
genomes accumulate mutations due to defective DNA
mismatch repair. Next-generation sequencing (NGS) studies
have shown that 15%–20% of GCs are characterized by MSI.
For ease of presentation, our review has been structured to
summarize each molecular level independently.
Gene Mutations in Gastric Cancer
Like most solid epithelial cancers, GCs are often char-
acterized by somatically-acquired mutations in various
genes. Current estimates based on NGS indicate that in each
individual GC (excluding hypermutated cases), there are
approximately 50 to 70 nonsynonymous mutations, a mu-
tation level comparable to colon and esophageal cancer.48
Mutated genes in GC can be broadly classified into three
categories: a) high-frequency drivers displaying a high-rate
of recurrence (>5%–10%) across multiple GCs; b)
low-frequency drivers that are recurrently mutated in the
1%–10% range, but which still contribute to disease path-
ogenesis; and c) bystander/passenger mutations that arise
as a consequence of underlying mutational processes such
as CpG deamination,49 but which do not functionally
contribute to tumorigenesis.
Among high-frequency drivers, TP53 is the most
frequently mutated gene in GC, exhibiting aberrations in
w50% of cases.50 Reflecting TP53’s cellular function as a
guardian of genomic integrity, TP53 mutated GCs often
exhibit high levels of sCNAs3,51 involving both broad
Gastroenterology Vol. 149, No. 5
Figure 2. Genomic fea-
tures of GC, inspired by
the classic Hallmarks of
Cancer report by Hanahan
and Weinberg.146 Details
of each genomic feature
are provided in the text.
GC, gastric cancer.
chromosomal regions and focal gene regions. GCs have
also been shown to exhibit mutations in other canonical
oncogenes (KRAS, CTNNB1, PIK3CA) and tumor suppressor
genes (SMAD4, APC).52 Reflecting the importance of RTK/
RAS/MAPK signaling in GC, frequent mutations in the
ERBB3 RTK and the ligand/RTK NRG1/ERBB4 genes have
recently been reported.53,54 Some of these mutations
appear to be enriched in specific GC subtypes, for example,
EBV-positive GCs frequently exhibit PIK3CA mutations,3
while diffuse-type GCs have been observed to exhibit
frequent somatic mutations in CDH1.55
Recent NGS studies of GC have also highlighted two new
GC genes - ARID1A and RHOA. ARID1A, mutated in 10%–15%
of GCs,56,57 encodes a component of the SWI/SNF chromatin
remodeler complex. ARID1A mutations in GC are typically
inactivating (eg, frameshifts, nonsense mutations), consistent
with ARID1A acting as a tumor suppressor. Functional anal-
ysis suggests that ARID1A plays a role in GC cell proliferation,
through the control of cell-cycle regulators CCNE1 and
E2F1.57 RHOA was recently shown by multiple studies to
exhibit recurrent mutations in diffuse-type/genome-stable
GCs.3,55,58 Unlike ARID1A where mutations are dispersed
throughout the gene, the RHOA mutations are localized to an
N-terminal hot-spot region (Tyr42, Arg5 and Gly17), and are
predicted to modulate downstream Rho signaling. Functional
analysis of these RHOA mutations suggest that they may
impart resistance to anoikis, a form of programmed cell death
occurring after cellular detachment from a solid substrate.55
Clinically, the discovery of RHOA hot-spot mutations is
particularly exciting, as it provides an inroad for the devel-
opment of new approaches to target diffuse-type GCs, tradi-
tionally associated with extremely poor prognosis.
Besides high-frequency driver mutations, genomic
studies have also uncovered a “long tail” of low frequency
October 2015
driver mutations in GC, such as the gastric mucin MUC6,
BCOR (encoding a BCL6 corepressor), FAT4 (a proto-
cadherin), and RNF43, a Wnt pathway regulator.3,55,57
Despite their lower mutation frequencies, these genes also
likely contribute to the ability of GCs to manifest different
cancer hallmarks. For example, mutations in the antigen-
presenting genes HLA-B and B2M, observed in MSI-
positive GCs, may play a role in evading host anti-tumor
immune responses arising from the presentation of tumor
neo-antigens.3 A key challenge for the GC field will be to
develop systematic, high-throughput approaches to func-
tionally test the effects of these mutations, either singly or in
combination, on the GC cell.
NGS analyses of GCs, particularly at the whole-genome
level, are also providing insights into prominent pathways
and mutation signatures associated with GC develop-
ment.55,59,60 For example, when all mutated genes (regard-
less of driver status) are considered in a collective pathway
analysis, cell adhesion and chromatin remodeling are
consistently highlighted as the top major disrupted path-
ways.56,57 Emerging evidence suggests that these processes
are likely to be disrupted even in premalignant gastric tis-
sues and early GC.61,62 A survey of mutational “signatures”,
referring to mutations occurring in particular sequence
contexts, has highlighted specific carcinogenic and muta-
tional processes active in GC, including microsatellite
instability, CpG age-associated deamination, and the acti-
vation of cytidine deaminases such as AID and
APOBEC3B.63–65 Emerging studies are now being performed
to study patterns of GC tumor evolution and clonality,
occurring either within the primary tumor, or between
primary lesions and metastatic sites.54,66 Such results will
be crucial for identifying molecular events associated with
GC progression rather than initiation, and may suggest
improved strategies for managing patients with advanced
metastatic GC.
sCNAs and Structural Variation in
Gastric Cancer
sCNAs are another major mechanism by which onco-
genes and tumor suppressor genes are selectively activated
or inactivated in GC. Several studies have reported genome-
scale analyses to identify GC genes affected by sCNA,67,68
highlighting specific genes targeted by this mechanism.
The most predominant class of genes frequently amplified
in GC are those related to RTK/RAS/MAPK signaling,
including HER2, EGFR, MET, FGFR2, and RAS genes (KRAS,
and to a lesser extent NRAS).3,67 In total, about 30%–40% of
GCs are likely to harbor a RTK/RAS/MAPK-related amplifi-
cation, and therapies targeting these genes are in clinical
trials, including trastuzumab (HER2), nimotuzumab (EGFR),
AZD4547 (FGFR2), and onartuzumab (MET) (Table 1).
Another gene frequently amplified in GC that may intersect
with the canonical RTK/RAS/MAPK pathway is VEGFA, a
mediator of angiogenesis that is particularly noteworthy
given the role of anti-angiogenic therapy in GC.69 In the
TCGA study, EBV-positive GCs were also found to harbor
frequent amplifications in PD-L1 and L2, which are immune
Pathogenesis of Gastric Adenocarcinoma 1157
checkpoint inhibitor genes, and are of particular relevance
as targets of immunotherapy.3
Another class of genes targeted by gene amplification in
GC are related to cell cycle control, including CCND1, CCNE1,
and CDK6. These cell-cycle genes are clinically relevant in
two capacities. First, direct therapies are available for tar-
gets such as CDK6, while CCND1 and CCNE1, which encode
GENOMICS
cyclin subunits, may also be targetable through their
cognate CDK partners (CDK4/6 for CCND1, CDK1/2 for
CCNE1). Second, coamplification of these cell-cycle regula-
tors with other therapeutic targets, particularly those in the
RTK/RAS/MAPK pathway, may modulate responses to the
therapies targeting the latter. For example, CCNE1 amplifi-
cations frequently occur together with HER2 amplifica-
tions,67,70 a configuration that has been linked to acquired
trastuzumab resistance in breast cancer.71 HER2/CCNE1
coamplification has recently been validated as a mechanism
of primary resistance against lapatinib (a dual EGFR/HER2
inhibitor) in HER2-amplified GC.70 Knowledge of the
amplification status of these cell-cycle related genes in in-
dividual GCs may thus further improve our ability to stratify
patients in clinical trials employing targeted agents.
A third class of GC-amplified genes corresponds to those
involved in transcriptional regulation, such as GATA factors
(GATA4, GATA6), KLF5, and MYC. Amplifications of GATA
factors and KLF5 appear to be restricted to gastrointestinal,
and possibly related hepatobiliary malignancies.72,73 These
transcription factors (TFs) are expressed in the developing
and normal stomach,74 and may act as “lineage-survival”
factors functioning to reawaken early developmental pro-
grams to drive GC tumorigenesis. Interestingly, recent
chromatin immunoprecipitation (ChIP) sequencing studies
provide evidence that these amplified TFs, may in fact
collaborate with one another to regulate common down-
stream promoters in genes associated with GC develop-
ment.73 Another transcription factor amplified in GC is
OCT1, a regulator of ERK signaling.75 Although traditionally
considered to be “undruggable” by the pharmaceutical in-
dustry, novel chemical biology technologies for disrupting
such oncogenic TFs are in development.76
Besides amplifications, genomic deletions also
frequently occur in GC, involving tumor suppressor genes
such as WWOX, RB1, PARK2, FHIT, and CDKN2A/B.67 So-
matic deletions in CDH1 have been associated with poor
patient prognosis,77 and genomic deletions involving
nonprotein coding genes such as mir-101a have been re-
ported, which can cause upregulation of the oncogenic his-
tone methyltransferase EZH2.78 Interestingly, while most
genomic deletions are often interpreted as loss-of-function
events, a recent study has shown that the phosphodies-
terase PDE4D, frequently targeted by microdeletions in
several cancers including GC, is associated with a constitu-
tively active PDE4D isoform that promotes tumor growth.79
It is thus possible that, as sequencing technologies improve,
detailed fine mapping of genomic deletion break-points will
highlight similar unexpected examples, prompting the
revisiting of these “deleted” genes as tumor suppressors.
Genomic rearrangements, either balanced or associated
with copy number changes, can also result in fusion genes,
 1158 Tan and Yeoh Gastroenterology Vol. 149, No. 5

Table 1.GC Genomic Alterations as Therapeutic Targets

Gene Alteration Prevalence in GCa Representative Therapies Clinical Statusb

ERRB2 Amplification/overexpression 10%–20% Traztuzumab/trastuzumab Approved/Phase III

emtansine
VEGFR2 Overexpression w50% Ramucirumab Approved
VEGF Overexpression 40%–50% Bevacizumab/regorafenib Phase III (negative)/phase II
GENOMICS

EGFR Amplification/overexpression 6%–27% Cetuximab/nimotuzumab Phase II/III

MET Amplification/overexpression 5%–40% Onartuzumab/AMG337 Phase II/III
FGFR2 Amplification/overexpression 4%–12% AZD4547/dovitinib Phase II
ATM Loss (Protein) 60% Olaparib Phase III
PIK3CA Mutation 5%–10% Everolimus/GDC0068 Pre-clinical/early trials
CDK4/6 Amplification 6%–15% LEE001 Phase II
PD-L1/L2 Amplification/overexpression 15% of EBV-positive GC MPDL3280A Preclinical/phase I
MSI Mutation 15%–20% Pembrolizumab (anti-PD1) Phase II
ARID1A Mutation 8%–10% EZH2 inhibition Preclinical

GC, gastric cancer; EBV, Epstein-Barr virus; MSI, microsatellite Instability.

a
Prevalence rates incorporate data based on both genomic alterations and protein immunohistochemistry.
b
Most ongoing trials do not involve biomarker-selected GC patients.

creating new chimeric protein products (eg, BCR-ABL
in chronic myelogenous leukemia), or causing high expression
of one gene through hijacking of the partner’s promoter (eg,
TMPRRS2-ERG in prostate cancer). An RNA-sequencing study
in 2010 revealed for the first time the presence of rare RAF-
fusion genes in GC and prostate cancers (eg, AGTRAP-BRAF),
and preclinical models expressing these RAF fusions were
shown sensitive to treatment by sorafinib, originally designed
as a RAF inhibitor.80 The second fusion gene identified in GC
was CD44-SLC1A2, which juxtaposes the SLC1A2 glutamate
transporter against the CD44 promoter.81 Tumors expressing
this gene fusion expressed high levels of SLC1A2 which may
facilitate the acquisition of glutamate by the cancer cell to fuel
cancer metabolism. Subsequently, CD44-SLC1A2 and related
APIP-SLC1A2 fusions have been observed in colon cancer,
indicating that such fusions may be restricted to
gastrointestinal-type cancers.82,83 ROS1 rearrangements in GC
have been recently reported,84 and in the TCGA study,
CLDN18-ARHGAP26 fusions were observed in genome-stable/
diffuse type GC. Interestingly, ARHGAP26 is a member of the
Rho-effector pathway, and the CLN18-ARHGAP26 fusions are
mutually exclusive to RhoA mutations and CDH1 mutations, all
pointing to a common dependence on cell-adhesion related
Rho signaling in diffuse-type GC.3 Indeed, recent functional
data has confirmed that CLDN18-ARHGAP26 expression in
epithelial cells can reduce cell-cell and cell-extracellular ma-
trix-adhesion, while contributing to epithelial-mesenchymal
transition (EMT).85 Taken collectively, these examples attest
to the presence of gene fusions in GC, which due to their
cancer-specific nature, may be exploited for improved di-
agnostics or therapeutics.
Epigenetic Alterations involving DNA
Methylation and Chromatin
Epigenetic aberrations are also emerging as important
players in GC pathogenesis. These can occur at the level of
DNA methylation, where methyl groups are attached to
cytosine bases at CG motifs; or histone modifications where
specific residues in histones are methylated, acetylated, or
phosphorylated. There is great interest in studying how
environmental risk factors for GC may modulate the gastric
epigenome. For example, H pylori has been shown to infect
and induce widespread DNA methylation changes in stom-
ach epithelial cells.86 Such “epigenetic field defects” are
likely to contribute to an individual’s risk of developing GC.
The epigenetic field model has recently been supported by a
recent prospective clinical trial.87
There is a rich body of GC literature relating promoter
DNA methylation to the transcriptional silencing of tumor
suppressor genes (CDH1, RUNX3, p16, and hMLH1).88
Alterations in DNA methylation can also influence GC pro-
gression and treatment response. For example, methylation-
associated silencing of PLA2G2A, a secreted phospholipase,
may play a role in driving aggressive GC,89 and methylation
of SULF2 and BMP4 have been linked to chemotherapeutic
responses.90,91 Beyond individual genes, genome-wide
studies have also revealed large scale patterns of DNA
methylation in GC. Multiple studies have confirmed that
certain GCs can exhibit a CpG island methylation phenotype
(CIMP), characterized by genome-wide methylation of CpG
islands.92–94 Patients with CIMP type GCs tend to be
younger, with less-differentiated tumors. Pathway analysis
reveals that genes targeted by CIMP in GC are enriched in
genes corresponding to PRC2-targets in embryonic stem
cells, suggesting a reawakening in CIMP tumors of a nascent
stem cell program. Interestingly, in preclinical assays, CIMP-
positive GCs appear to exhibit heightened sensitivity to DNA
methyltransferase inhibitors such as 5’aza.93
As described by earlier studies and confirmed by TCGA,
EBV-positive GCs also exhibit exceptionally high DNA
methylation levels,3,30 Indeed, among all tumor types stud-
ied by TCGA to date, EBV-positive GCs appear to exhibit the
highest DNA methylation levels, surpassing even CIMP tu-
mors. It is possible that such hypermethylation may repre-
sent a cellular reaction to viral infection. Emphasizing
the importance of tumor immunity in this GC subtype,
EBV-positive GCs also typically exhibit a high lymphocytic
October 2015
infiltrate,95 and (as described above) also frequently exhibit
PD-L1 and PD-L2 amplification. Another recent study has
recently reported additional mutated genes in EBV-positive
GC, which may contribute to tumor neo-antigen formation in
this unique and intriguing cancer subtype.96
In contrast to DNA methylation, our understanding of
histone modifications in GC is still embryonic. An earlier
study assessing patterns of the H3K37me3 repressive mark
found over a hundred genes exhibiting H3k27me3 differ-
ences between GCs and matched normal tissues.97 More
recently, a study employing a nano-scale chromatin immu-
noprecipitation techniques to profile multiple histone marks
in GCs and matched normal tissues,98 found evidence of
widespread alternative promoter usage and deregulated
enhancer elements, including an alternative isoform of the
MET RTK that produces a MET protein variant lacking the
SEMA N-terminal regulatory domain. Future work will be
focused on understanding the mechanisms underlying such
regulated regulatory elements, and how they might be
harnessed for predictive or prognostic potential.
Gastric Cancer Transcriptome—Gene
Signatures and Alternative Splicing
Altered regulation of gene expression programs are
critical to the ability of tumors to express different cancer
hallmarks. In early 2000, early microarray studies already
revealed a staggering diversity of expression programs
operative in GC, associated with different histological sub-
types, tumor status, and clinical traits.99–101 In the past
decade, groups have deployed more mature transcriptomic
technologies, on larger patient cohorts, to identify robust
gene expression “signatures” that can subtype GC in a
clinically relevant fashion. Such GC transcriptome studies
have typically fallen into two categories: a) unsupervised,
where GC subtypes are discovered based on molecular data
in an unbiased fashion and then correlated to clinical data;
or b) supervised, where clinical data is directly correlated to
molecular data to identify highly associated expression
patterns. Among unsupervised studies, one report, starting
from a panel of GC cell lines, identified two “intrinsic”
subtypes of GC (G-INT/G-DIF), that when mapped to pri-
mary GCs correlated with Lauren’s classification, and was
both prognostic and predictive to 5-FU related chemother-
apies.102 This classification has recently been extended to
three subtypes - proliferative, mesenchymal, and metabolic,
where cell lines with mesenchymal features were found to
be more responsive to PIK3CA/mTOR inhibitor com-
pounds.51 Other unsupervised classifications have been
proposed, including a recent 4-subtype system by the Asian
Cancer Research Group (ACRG), a collaboration between
academia and industry.103 In complement to these, groups
performing supervised analyses have also reported specific
gene signatures for directly predicting GC patient prognosis.
One study reported a 6-gene signature that could be used to
compute an individualized “risk-score” for predicting GC
prognosis.104 In another study from Korea, investigators
explored expression patterns of >1000 GCs to identify an 8-
gene signature capable of predicting the prognosis of Stage
Pathogenesis of Gastric Adenocarcinoma 1159
II GC patients.105 This is a highly clinically-relevant ques-
tion, as Stage II patients identified as “poor prognosis” by
the gene signature might be prescribed adjuvant chemo-
therapy, while “good prognosis” patients might be treated
with surgery alone.
Transcriptomic information can also be exploited as a
powerful discovery method to identify deregulated path-
GENOMICS
ways in GC. One study exploring this approach reported that
GCs exhibiting combinations of activated oncogenic path-
ways were associated with poor prognosis relative to GCs
with activation of single pathways.106 Investigators have
also used RNA-sequencing data of GCs from different
countries to identify the AMPK/HNF4a/Wnt5a pathway as
a targetable oncogenic pathway in early stage GC.107,108
However, it should be noted that while transcriptomes are
highly dynamic, almost all GC transcriptomic studies to date
have relied upon analyzing GCs obtained at a single time-
point, usually upon surgical resection. There is thus great
interest in understanding gene expression (and other mo-
lecular) changes in GCs during temporal progression or
treatment. Demonstrating the power of this temporal
approach, one highly notable study used paired endoscopic
biopsies to study gene expression changes in GC patients
prior to and after developing resistance to 5-FU/platinum
therapies.109 They identified an acquired-resistance signa-
ture comprising genes related to cell survival (mTOR
pathway), DNA repair, and embryonic stem cell biology.
Data from such efforts, while still scanty in the literature,
will prove vital in attempts to overcome chemotherapy
resistance in GC.
Transcriptomic analysis is also revealing new molecular
features of GC biology, above and beyond those provided
through the study of DNA. One especially exciting field of
exploration is alternative splicing, where different transcript
isoforms of the same gene may play distinct functional or
oncogenic roles. One of most famous examples of alternative
splicing in GC involves the CD44 gene, which encodes a cell-
surface glycoprotein that binds hyaluronic acid and medi-
ates a diversity of cell-cell interactions. Recent data has
revealed that GC stem cells express a specific CD44 tran-
script variant (CD44v8-10) that can be used to enrich for
tumor-initiating cells.110 Functional analysis of this variant
suggests that its role is to act as a copartner of the xCT
cysteine transporter, to regulate oxidative stress.111 Another
recent example of alternative splicing in GC, revealed
through integrated exome/transcriptome analysis, involves
the selective use of the ZAK kinase isoform TV1 in tumors,
which is required to maintain cell proliferation in experi-
mental systems.112 Alternative splicing events can also
cause production of fusion genes in the absence of genome
rearrangements, through the process of “read-through”
transcription. One example of this process is PPP1R1B-
STARD3, involving two genes adjacent to one another in the
human genome, which fuses exon 6 of PPP1R1B to exon 2 of
STARD3. Interestingly, functional analysis suggests that gene
products arising from such “read-through” fusions may be
enriched in gastric tumors related to matched normal con-
trols, and may contribute towards certain pro-oncogenic
features.113
 1160 Tan and Yeoh
Non-coding RNAs, miRNAs and Beyond
Non-coding RNAs represent yet another active player
in GC pathogenesis, involving different RNA classes such
as miRNAs and long intergenic noncoding RNAs (lincR-
NAs). miRNAs are small RNAs (w22 nucleotides) that can
bind to target gene transcripts to induce the latter’s
GENOMICS
transcript or protein downregulation. Studies from mul-
tiple groups have now produced a growing list of >200
miRNAs with potential roles in GC development, pro-
gression, and treatment response.114,115 Examples of
oncogenic miRNAs include miR-21, miR-27a, and mir-
130b; which are overexpressed in GC tumors and cell
lines relative to normal controls.116,117 Oncogenic miRNAs
typically function to target and downregulate tumor
suppressor genes, for example, mir-21 has been reported
to target the tumor suppressor genes PTEN and
PDCD4,116,118 while mir-130b has been shown to regulate
RUNX3.117 Reciprocally, tumor suppressor miRNAs such
as mir-375, mir-486, mir-29c, and mir-101 are down-
regulated in GC, typically by DNA methylation or genomic
loss, and are required to silence genes with oncogenic
potential such as PDK1, OLFM4, ITGB1, and EZH2
respectively.78,119,120,121 Some miRNAs may also
contribute to GC pathogenesis by functioning as key
components of oncogenic signaling pathways, as shown
by recent data implicating mir-365 in PTEN/Akt
signaling,122 or by responding to external carcinogens (H
pylori) to stimulate cellular proliferation (eg, mir-210).123
Work is also ongoing to characterize the role of miRNAs
in tumor progression and drug resistance, with numerous
studies reporting miRNA expression patterns associated
with patient outcome.124,125 For example, miRNAs in the
mir-200 family play a key role in regulating EMT via EMT
regulators such as ZEB1, and mir-200 downregulaton is
associated with poor prognosis.126
In contrast to miRNAs, our current knowledge of the role
of lincRNAs in GC is still immature, however recent studies
examining expression of lincRNAs such as HOTAIR and
GAPLINC in GC suggest an important role for this RNA class
in GC development and progression.127,128 Identifying the
most prevalent deregulated lincRNAs in GC, and deciphering
their functional and mechanistic roles in regulating gene
expression and cancer behavior, will clearly be highly fertile
area for future GC research.
Beyond the Cancer Cell: Contributions
From the Tumor Microenvironment
Gastric tumors are composed not just of cancer cells
but also other cell populations including stromal cells,
immune cells, and blood vessels. Far from being innocent
bystanders, studies are now demonstrating that these
“noncancer” compartments are also likely to play impor-
tant roles in GC disease progression and aggressiveness.
Several studies have now confirmed that GCs with a high
stromal content, determined either by gene expression
analysis or histopathological evaluation, are associated
with poor prognosis.129,130 Similar findings have also been
Gastroenterology Vol. 149, No. 5
reported in other tumor types, such as breast, lung and
esophageal cancers.131,132 The mechanisms underlying the
role of the tumor stroma in supporting GC growth are
likely multifactorial, ranging from providing a suitable
extracellular matrix to maintain cancer cell growth, active
cell-cell interactions via cancer-associated fibroblasts
which can secrete growth-stimulatory molecules such as
IL-6, and providing a physical barrier inhibiting chemo-
therapy from reaching target malignant cells.133 Major
pathways implicated in the tumor stroma include TGFb
signaling and EMT-related signaling events, pointing to
complex interactions between cancer cells and their
nonmalignant neighboring cellular populations.130,133
Studies are now emerging at attempting to target the tu-
mor stroma for therapy.134
Another intra-tumor cellular population vitally
important to GC development are cells regulating tumor
vasculature and immunity. GCs have been shown to
secrete pro-angiogenic compounds such as VEGF, CXCL1,
and Ang-2 to stimulate blood vessel formation.133 In GC,
multiple clinical trials targeting various aspects of the
tumor angiogenesis axis have been conducted. In the
AVAGAST trial, the combination of bevacizumab (an
antibody targeting VEGFA) and chemotherapy did not
extend overall survival compared to patients treated
with chemotherapy alone.69 Recently however, the
RAINBOW and REGARD trials evaluating ramucirumab, a
VEGFR2-targeting antibody, reported an improvement in
overall survival in patients with advanced GC.135,136
Interestingly, for at least two of these studies (AVA-
GAST and RAINBOW), subsequent subset and biomarker
analysis revealed that GC patients from non-Asian
countries tended to receive clinical benefit from the
addition of bevacizumab, compared to patients from
Asian countries. It is thus possible that GC populations in
different countries (specifically Asian and non-Asian
countries) may respond differently to anti-angiogenic
and potentially other therapies.
Finally, immune cells of many different types are also
frequently observed in primary GCs, and certain subtypes
of GC (eg, EBV-positive GC and MSI-positive GC) are well-
known to be associated with a high lymphocytic infil-
trate. Depending on their specific identities and immune
functions, such tumor-infiltrating immune cells may play
pro- or anti-tumorigenic roles. For example, GCs with high
levels of regulatory T cells (FOXP3-positive) have been
reported to exhibit good prognosis,137 while those with
high levels of IL-17 producing CD8-positive T cells (cyto-
toxic T cells) are associated with poor prognosis.138 The
role of tumor immunity in cancer progression is extremely
broad, and readers are directed to other excellent reviews
dedicated to this subject.139 Interestingly, two recent
studies have also reported that Asian and non-Asian GC
populations may differ in their regulation of tumor im-
munity factors at the genetic and gene expression level,
which may impact region-specific effects on therapy
outcome and prognosis.140,141 Given the intimate rela-
tionship between immune cells and tumor vasculature, it
will be interesting to test if such differences might
October 2015
contribute to the above-mentioned geography-specific
clinical trial outcomes, or if they may impact patient se-
lection in future trials evaluating different types of immune
checkpoint inhibitors.
Conclusions and Challenges
Our knowledge of GC molecular pathogenesis has
considerably evolved over the years, but much remains
unknown. In terms of basic understanding, the role of novel
molecular entities such as lincRNAs and chromatin alter-
ations in GC remains to be unraveled. DNA sequencing
studies have also revealed a complex community of non-
cultivatable microbiota in the human stomach beyond H
pylori and EBV, and it will be critical to understand how the
gastric “microbiome” may interact with both H pylori and
the host immune response to influence gastric carcinogen-
esis.142 In the early detection field, molecular findings may
facilitate new approaches for diagnosing GC early, by iden-
tifying high-risk individuals through the molecular charac-
terization of preneoplastic lesions or even blood-based
biomarker assays. Finally, therapeutic strategies remain to
be developed to target specific GC subtypes (particularly
diffuse type GC), based upon their somatic driver alterations
or tumor-associated cell compartments (eg, stromal cells
and tumor-infiltrating immune cells). The next five years
will undoubtedly see a further explosion of findings in the
GC field, which will be essential to combat this deadly
disease.
Supplementary Material
NOTE: The first 50 references associated with this article
are available below in print. The remaining references
accompanying this article are available online only with the
electronic version of this article. To access the supplemen-
tary material accompanying this article, visit the online
version of Gastroenterology at www.gastrojournal.org, and
at http://dx.doi.org/10.1053/j.gastro.2015.05.059.
References
1. Ferlay JSI, Ervik M, Dikshit R, et al. International Agency
for Research on Cancer, Cancer Incidence, and Mortality
Worldwide. Lyon, France: IARC CancerBase no. 11,
2013.
2. Bang YJ, Van Cutsem E, Feyereislova A, et al. Trastu-
zumab in combination with chemotherapy versus
chemotherapy alone for treatment of HER2-positive
advanced gastric or gastro-oesophageal junction can-
cer (ToGA): a phase 3, open-label, randomised controlled
trial. Lancet 2010;376:687–697.
3. Cancer Genome Atlas Research N. Comprehensive
molecular characterization of gastric adenocarcinoma.
Nature 2014;513:202–209.
4. Correa P. Human gastric carcinogenesis: a multistep and
multifactorial process—first American Cancer Society
Award Lecture on cancer epidemiology and prevention.
Cancer Res 1992;52:6735–6740.
Pathogenesis of Gastric Adenocarcinoma 1161
5. Almeida R, Silva E, Santos-Silva F, et al. Expression of
intestine-specific transcription factors, CDX1 and CDX2,
in intestinal metaplasia and gastric carcinomas. J Pathol
2003;199:36–40.
6. Goldenring JR, Nomura S. Differentiation of the gastric
mucosa III. Animal models of oxyntic atrophy and
metaplasia. Am J Physiol Gastrointest Liver Physiol
GENOMICS
2006;291:G999–1004.
7. Goldenring JR, Nam KT. Oxyntic atrophy, metaplasia,
and gastric cancer. Dev Diff Dis 2010;96:117–131.
8. Karin M. Inflammation and cancer: the long reach of Ras.
Nat Med 2005;11:20–21.
9. Eaton KA, Logan SM, Baker PE, et al. Helicobacter pylori
with a truncated lipopolysaccharide O chain fails to
induce gastritis in SCID mice injected with splenocytes
from wild-type C57BL/6J mice. Infect Immun 2004;
72:3925–3931.
10. Lochhead P, El-Omar EM. Gastric cancer. Br Med Bull
2008;85:87–100.
11. Tsugane S, Sasazuki S. Diet and the risk of gastric
cancer: review of epidemiological evidence. Gastric
Cancer 2007;10:75–83.
12. Noto JM, Gaddy JA, Lee JY, et al. Iron deficiency ac-
celerates Helicobacter pylori-induced carcinogenesis in
rodents and humans. J Clin Invest 2013;123:479–492.
13. Iwakiri D TK. Epstein-Barr virus and gastric cancers. In:
ES R, ed. Epstein-Barr virus. Norfolk, VA: Caister Aca-
demic Press, 2005:157–169.
14. Murphy G, Pfeiffer R, Camargo MC, et al. Meta-analysis
shows that prevalence of Epstein-Barr virus-positive
gastric cancer differs based on sex and anatomic loca-
tion. Gastroenterology 2009;137:824–833.
15. Peleteiro B, Bastos A, Ferro A, et al. Prevalence of Hel-
icobacter pylori infection worldwide: a systematic review
of studies with national coverage. Dig Dis Sci 2014;
59:1698–1709.
16. Odenbreit S, Puls J, Sedlmaier B, et al. Translocation of
Helicobacter pylori CagA into gastric epithelial cells by
type IV secretion. Science 2000;287:1497–1500.
17. Ohnishi N, Yuasa H, Tanaka S, et al. Transgenic
expression of Helicobacter pylori CagA induces
gastrointestinal and hematopoietic neoplasms in
mouse. Proc Natl Acad Sci U S A 2008;105:
1003–1008.
18. Higashi H, Tsutsumi R, Fujita A, et al. Biological activity
of the Helicobacter pylori virulence factor CagA is
determined by variation in the tyrosine phosphorylation
sites. Proc Natl Acad Sci U S A 2002;99:14428–14433.
19. Higashi H, Tsutsumi R, Muto S, et al. SHP-2 tyrosine
phosphatase as an intracellular target of Helicobacter
pylori CagA protein. Science 2002;295:683–686.
20. Amieva MR, Vogelmann R, Covacci A, et al. Disruption of
the epithelial apical-junctional complex by Helicobacter
pylori CagA. Science 2003;300:1430–1434.
21. Saadat I, Higashi H, Obuse C, et al. Helicobacter pylori
CagA targets PAR1/MARK kinase to disrupt epithelial
cell polarity. Nature 2007;447:330.
22. Murata-Kamiya N, Kurashima Y, Teishikata Y, et al.
Helicobacter pylori CagA interacts with E-cadherin and
deregulates the beta-catenin signal that promotes in-
 1162 Tan and Yeoh
testinal transdifferentiation in gastric epithelial cells.
Oncogene 2007;26:4617–4626.
23. Wong BC, Lam SK, Wong WM, et al. Helicobacter pylori
eradication to prevent gastric cancer in a high-risk region
of China: a randomized controlled trial. JAMA 2004;
291:187–194.
24. Lee YC, Chen TH, Chiu HM, et al. The benefit of mass
GENOMICS
eradication of Helicobacter pylori infection: a
community-based study of gastric cancer prevention.
Gut 2013;62:676–682.
25. Fuccio L, Zagari RM, Eusebi LH, et al. Meta-analysis: can
Helicobacter pylori eradication treatment reduce the risk
for gastric cancer? Ann Intern Med 2009;151:121–128.
26. Shiota S, Yamaoka Y. Strategy for the treatment of
Helicobacter pylori infection. Curr Pharm Des 2014;
20:4489–4500.
27. Nomura AM, Wilkens LR, Henderson BE, et al. The associ-
ation of cigarette smoking with gastric cancer: the multi-
ethnic cohort study. Cancer Causes Control 2012;23:51–58.
28. Dyke GW, Craven JL, Hall R, et al. Smoking-related DNA
adducts in human gastric cancers. Int J Cancer 1992;
52:847–850.
29. Kneller RW, You WC, Chang YS, et al. Cigarette smoking
and other risk factors for progression of precancerous
stomach lesions. J Natl Cancer Inst 1992;84:1261–1266.
30. Kaneda A, Matsusaka K, Aburatani H, et al. Epstein-Barr
virus infection as an epigenetic driver of tumorigenesis.
Cancer Res 2012;72:3445–3450.
31. Pfeffer S, Zavolan M, Grasser FA, et al. Identification of
virus-encoded microRNAs. Science 2004;304:734–736.
32. Marquitz AR, Mathur A, Nam CS, et al. The Epstein-Barr
Virus BART microRNAs target the pro-apoptotic protein
Bim. Virology 2011;412:392–400.
33. Shinozaki-Ushiku A, Kunita A, Isogai M, et al. Profiling of
virus-encoded microRNAs in Epstein-Barr virus-associ-
ated gastric carcinoma and their roles in gastric carci-
nogenesis. J Virol 2015;89:5581–5591.
34. El-Omar EM, Carrington M, Chow WH, et al. Interleukin-1
polymorphisms associated with increased risk of gastric
cancer. Nature 2000;404:398–402.
35. El-Omar EM, Rabkin CS, Gammon MD, et al. Increased
risk of noncardia gastric cancer associated with proin-
flammatory cytokine gene polymorphisms. Gastroenter-
ology 2003;124:1193–1201.
36. Figueiredo C, Machado JC, Pharoah P, et al. Heli-
cobacter pylori and interleukin 1 genotyping: an oppor-
tunity to identify high-risk individuals for gastric
carcinoma. J Natl Cancer Inst 2002;94:1680–1687.
37. Persson C, Canedo P, Machado JC, et al. Polymorphisms
in inflammatory response genes and their association with
gastric cancer: A HuGE systematic review and meta-an-
alyses. Am J Epidemiol 2011;173:259–270.
38. Study Group of Millennium Genome Project for C,
Sakamoto H, Yoshimura K, et al. Genetic variation in
PSCA is associated with susceptibility to diffuse-type
gastric cancer. Nat Genet 2008;40:730–740.
39. Lochhead P, Frank B, Hold GL, et al. Genetic variation in
the prostate stem cell antigen gene and upper
Gastroenterology Vol. 149, No. 5
gastrointestinal cancer in white individuals. Gastroen-
terology 2011;140:435–441.
40. Oliveira C, Pinheiro H, Figueiredo J, et al. Familial
gastric cancer: genetic susceptibility, pathology, and
implications for management. Lancet Oncol 2015;16:
e60–e70.
41. Huntsman DG, Carneiro F, Lewis FR, et al. Early gastric
cancer in young, asymptomatic carriers of germ-line E-
cadherin mutations. N Engl J Med 2001;344:1904–1909.
42. Hansford S, Kaurah P, Li-Chang H, et al. Hereditary
Diffuse Gastric Cancer Syndrome: CDH1 Mutations and
Beyond. JAMA Oncol 2015;1:23–32.
43. Worthley DL, Phillips KD, Wayte N, et al. Gastric
adenocarcinoma and proximal polyposis of the stomach
(GAPPS): a new autosomal dominant syndrome. Gut
2012;61:774–779.
44. Lauren P. The two histological main types of gastric
carcinoma: diffuse and so-called intestinal-type carci-
noma. An attempt at a histo-clinical classification. Acta
Pathol Microbiol Scand 1965;64:31–49.
45. Kaneko S, Yoshimura T. Time trend analysis of gastric
cancer incidence in Japan by histological types, 1975-
1989. Br J Cancer 2001;84:400–405.
46. Adachi Y, Yasuda K, Inomata M, et al. Pathology and
prognosis of gastric carcinoma: well versus poorly
differentiated type. Cancer 2000;89:1418–1424.
47. Bosman FT. WHO classification of tumours of the
digestive system. Lyon, Paris: IARC Press, 2010.
48. Lawrence MS, Stojanov P, Polak P, et al. Mutational
heterogeneity in cancer and the search for new cancer-
associated genes. Nature 2013;499:214–218.
49. Gonzalgo ML, Jones PA. Mutagenic and epigenetic ef-
fects of DNA methylation. Mutat Res 1997;386:107–118.
50. Hanazono K, Natsugoe S, Stein HJ, et al. Distribution of
p53 mutations in esophageal and gastric carcinomas and
the relationship with p53 expression. Oncol Rep 2006;
15:821–824.
Received March 25, 2015. Accepted May 20, 2015.
Reprint requests
Address requests for reprints to: Patrick Tan, Cancer and Stem Cell Biology
Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore
169857. e-mail: gmstanp@duke-nus.edu.sg; fax: (þ65) 6226 5294; or Khay
Guan Yeoh, Department of Medicine, Yong Loo Lin School of Medicine, 1E
Kent Ridge Road, NUHS Tower Block, Level 11, Singapore 119228. e-mail:
khay_guan_yeoh@nuhs.edu.sg; fax: (þ65) 6778 5743.
Acknowledgements
We thank Beatrice Tan, Jennie Wong, Tze Wei Chua, and Feng Zhu for
assistance with manuscript preparation and Wei Peng Yong and Matthew Ng
for valuable feedback. We thank Prof Teh Ming and Dr Supriya Srivastava,
Dept of Pathology, National University of Singapore for supplying the
histopathology images for Figure 1. Due to length restrictions, we apologize
to those clinicians and scientists in the GC community whose work we may
have inadvertently missed.
Conflicts of interest
The authors disclose no conflicts.
Funding
This work was supported by the Singapore Gastric Cancer Consortium, funded
through the National Medical Research Council/National Research Foundation
Translational and Clinical Research Flagship Program (NMRC/TCR/009-NUHS/
2013).
October 2015
Supplementary References
51. Lei Z, Tan IB, Das K, et al. Identification of molecular
subtypes of gastric cancer with different responses to
PI3-kinase inhibitors and 5-fluorouracil. Gastroenter-
ology 2013;145:554–565.
52. Grabsch HI, Tan P. Gastric cancer pathology and un-
derlying molecular mechanisms. Dig Surg 2013;
30:150–158.
53. Jaiswal BS, Kljavin NM, Stawiski EW, et al. Oncogenic
ERBB3 mutations in human cancers. Cancer Cell 2013;
23:603–617.
54. Chen K, Yang D, Li X, et al. Mutational landscape of
gastric adenocarcinoma in Chinese: implications for
prognosis and therapy. Proc Natl Acad Sci U S A 2015;
112:1107–1112.
55. Wang K, Yuen ST, Xu J, et al. Whole-genome
sequencing and comprehensive molecular profiling
identify new driver mutations in gastric cancer. Nat
Genet 2014;46:573–582.
56. Wang K, Kan J, Yuen ST, et al. Exome sequencing
identifies frequent mutation of ARID1A in molecular
subtypes of gastric cancer. Nat Genet 2011;
43:1219–1223.
57. Zang ZJ, Cutcutache I, Poon SL, et al. Exome
sequencing of gastric adenocarcinoma identifies recur-
rent somatic mutations in cell adhesion and chromatin
remodeling genes. Nat Genet 2012;44:570–574.
58. Kakiuchi M, Nishizawa T, Ueda H, et al. Recurrent gain-
of-function mutations of RHOA in diffuse-type gastric
carcinoma. Nat Genet 2014;46:583–587.
59. Nagarajan N, Bertrand D, Hillmer AM, et al. Whole-
genome reconstruction and mutational signatures in
gastric cancer. Genome Biol 2012;13:R115.
60. Wong SS, Kim KM, Ting JC, et al. Genomic landscape
and genetic heterogeneity in gastric adenocarcinoma
revealed by whole-genome sequencing. Nat Commun
2014;5:5477.
61. Takeshima H, Niwa T, Takahashi T, et al. Frequent
involvement of chromatin remodeler alterations in gastric
field cancerization. Cancer Lett 2015;357:328–338.
62. Kim TM, Jung SH, Kim MS, et al. The mutational burdens
and evolutionary ages of early gastric cancers are
comparable to those of advanced gastric cancers.
J Pathol 2014;234:365–374.
63. Yoon K, Lee S, Han TS, et al. Comprehensive genome-
and transcriptome-wide analyses of mutations associ-
ated with microsatellite instability in Korean gastric
cancers. Genome Res 2013;23:1109–1117.
64. Alexandrov LB, Nik-Zainal S, Wedge DC, et al. Signa-
tures of mutational processes in human cancer. Nature
2013;500:415–421.
65. Matsumoto Y, Marusawa H, Kinoshita K, et al. Heli-
cobacter pylori infection triggers aberrant expression of
activation-induced cytidine deaminase in gastric
epithelium. Nat Med 2007;13:470–476.
66. Nadauld LD, Garcia S, Natsoulis G, et al. Metastatic tu-
mor evolution and organoid modeling implicate TGFBR2
as a cancer driver in diffuse gastric cancer. Genome Biol
2014;15:428.
Pathogenesis of Gastric Adenocarcinoma 1162.e1
67. Deng N, Goh LK, Wang H, et al. A comprehensive survey
of genomic alterations in gastric cancer reveals sys-
tematic patterns of molecular exclusivity and co-
occurrence among distinct therapeutic targets. Gut
2012;61:673–684.
68. Dulak AM, Schumacher SE, van Lieshout J, et al.
Gastrointestinal adenocarcinomas of the esophagus,
stomach, and colon exhibit distinct patterns of genome
instability and oncogenesis. Cancer Res 2012;
72:4383–4393.
69. Ohtsu A, Shah MA, Van Cutsem E, et al. Bevacizumab in
combination with chemotherapy as first-line therapy in
advanced gastric cancer: a randomized, double-blind,
placebo-controlled phase III study. J Clin Oncol 2011;
29:3968–3976.
70. Kim J, Fox C, Peng S, et al. Preexisting oncogenic
events impact trastuzumab sensitivity in ERBB2-
amplified gastroesophageal adenocarcinoma. J Clin
Invest 2014;124:5145–5158.
71. Scaltriti M, Eichhorn PJ, Cortes J, et al. Cyclin E ampli-
fication/overexpression is a mechanism of trastuzumab
resistance in HER2þ breast cancer patients. Proc Natl
Acad Sci U S A 2011;108:3761–3766.
72. Sulahian R, Casey F, Shen J, et al. An integrative analysis
reveals functional targets of GATA6 transcriptional regu-
lation in gastric cancer. Oncogene 2014;33:5637–5648.
73. Chia NY, Deng N, Das K, et al. Regulatory crosstalk
between lineage-survival oncogenes KLF5, GATA4 and
GATA6 cooperatively promotes gastric cancer develop-
ment. Gut 2015;64:707–719.
74. Haveri H, Westerholm-Ormio M, Lindfors K, et al. Tran-
scription factors GATA-4 and GATA-6 in normal and
neoplastic human gastrointestinal mucosa. BMC Gas-
troenterol 2008;8:9.
75. Qian J, Kong X, Deng N, et al. OCT1 is a determinant of
synbindin-related ERK signalling with independent
prognostic significance in gastric cancer. Gut 2015;
64:37–48.
76. Yan C, Higgins PJ. Drugging the undruggable: tran-
scription therapy for cancer. Biochim Biophys Acta 2013;
1835:76–85.
77. Corso G, Carvalho J, Marrelli D, et al. Somatic mutations
and deletions of the E-cadherin gene predict poor sur-
vival of patients with gastric cancer. J Clin Oncol 2013;
31:868–875.
78. Carvalho J, van Grieken NC, Pereira PM, et al. Lack of
microRNA-101 causes E-cadherin functional deregula-
tion through EZH2 up-regulation in intestinal gastric
cancer. J Pathol 2012;228:31–44.
79. Lin DC, Xu L, Ding LW, et al. Genomic and functional
characterizations of phosphodiesterase subtype 4D in
human cancers. Proc Natl Acad Sci U S A 2013;
110:6109–6114.
80. Palanisamy N, Ateeq B, Kalyana-Sundaram S, et al.
Rearrangements of the RAF kinase pathway in prostate
cancer, gastric cancer and melanoma. Nat Med 2010;
16:793–798.
81. Tao J, Deng NT, Ramnarayanan K, et al. CD44-SLC1A2
gene fusions in gastric cancer. Sci Transl Med 2011;
3:77ra30.
1162.e2 Tan and Yeoh
82. Giacomini CP, Sun S, Varma S, et al. Breakpoint analysis
of transcriptional and genomic profiles uncovers novel
gene fusions spanning multiple human cancer types.
PLoS Genet 2013;9:e1003464.
83. Shinmura K, Kato H, Igarashi H, et al. CD44–SLC1A2
Fusion Transcripts in Primary Colorectal Cancer. Pathol
Oncol Res 2015;21:759–764.
84. Lee J, Lee SE, Kang SY, et al. Identification of ROS1
rearrangement in gastric adenocarcinoma. Cancer 2013;
119:1627–1635.
85. Yao F, Kausalya JP, Sia YY, et al. Recurrent fusion genes
in gastric cancer: CLDN18-ARHGAP26 induces loss of
epithelial integrity. Cell Rep 2015;12:272–285.
86. Niwa T, Tsukamoto T, Toyoda T, et al. Inflammatory
processes triggered by Helicobacter pylori infection
cause aberrant DNA methylation in gastric epithelial
cells. Cancer Res 2010;70:1430–1440.
87. Asada K, Nakajima T, Shimazu T, et al. Demonstration of
the usefulness of epigenetic cancer risk prediction by a
multicentre prospective cohort study. Gut 2015;
64:388–396.
88. Nakamura J, Tanaka T, Kitajima Y, et al. Methylation-
mediated gene silencing as biomarkers of gastric cancer:
a review. World J Gastroenterol 2014;20:11991–12006.
89. Ganesan K, Ivanova T, Wu Y, et al. Inhibition of gastric
cancer invasion and metastasis by PLA2G2A, a novel
beta-catenin/TCF target gene. Cancer Res 2008;
68:4277–4286.
90. Wang L, Xie L, Wang J, et al. Correlation between the
methylation of SULF2 and WRN promoter and the iri-
notecan chemosensitivity in gastric cancer. BMC Gas-
troenterol 2013;13:173.
91. Ivanova T, Zouridis H, Wu Y, et al. Integrated epi-
genomics identifies BMP4 as a modulator of cisplatin
sensitivity in gastric cancer. Gut 2013;62:22–33.
92. Toyota M, Ahuja N, Suzuki H, et al. Aberrant methylation
in gastric cancer associated with the CpG island meth-
ylator phenotype. Cancer Res 1999;59:5438–5442.
93. Zouridis H, Deng N, Ivanova T, et al. Methylation sub-
types and large-scale epigenetic alterations in gastric
cancer. Sci Transl Med 2012;4:156ra140.
94. Matsusaka K, Kaneda A, Nagae G, et al. Classification of
Epstein-Barr virus-positive gastric cancers by definition
of DNA methylation epigenotypes. Cancer Res 2011;
71:7187–7197.
95. Grogg KL, Lohse CM, Pankratz VS, et al. Lymphocyte-
rich gastric cancer: associations with Epstein-Barr virus,
microsatellite instability, histology, and survival. Mod
Pathol 2003;16:641–651.
96. Liang Q, Yao X, Tang S, et al. Integrative identification of
Epstein-Barr virus-associated mutations and epigenetic
alterations in gastric cancer. Gastroenterology 2014;
147:1350–1362.
97. Zhang L, Zhong K, Dai Y, et al. Genome-wide analysis of
histone H3 lysine 27 trimethylation by ChIP-chip in
gastric cancer patients. J Gastroenterol 2009;
44:305–312.
98. Muratani M, Deng N, Ooi WF, et al. Nanoscale chromatin
profiling of gastric adenocarcinoma reveals cancer-
Gastroenterology Vol. 149, No. 5
associated cryptic promoters and somatically acquired
regulatory elements. Nat Commun 2014;5:4361.
99. Tay ST, Leong SH, Yu K, et al. A combined comparative
genomic hybridization and expression microarray anal-
ysis of gastric cancer reveals novel molecular subtypes.
Cancer Res 2003;63:3309–3316.
100.Boussioutas A, Li H, Liu J, et al. Distinctive patterns of
gene expression in premalignant gastric mucosa and
gastric cancer. Cancer Res 2003;63:2569–2577.
101.Chen X, Leung SY, Yuen ST, et al. Variation in gene
expression patterns in human gastric cancers. Mol Biol
Cell 2003;14:3208–3215.
102.Tan IB, Ivanova T, Lim KH, et al. Intrinsic subtypes of
gastric cancer, based on gene expression pattern, pre-
dict survival and respond differently to chemotherapy.
Gastroenterology 2011;141:476–485.
103.Cristescu R, Lee J, Nebozhyn M, et al. Molecular anal-
ysis of gastric cancer identifies discrete subtypes asso-
ciated with distinct clinical characteristics and survival
outcomes: the ACRG (Asian Cancer Research Group)
study. Nature Medicine 2015;21:449–456.
104.Cho JY, Lim JY, Cheong JH, et al. Gene expression
signature-based prognostic risk score in gastric cancer.
Clin Cancer Res 2011;17:1850–1857.
105.Lee J, Sohn I, Do IG, et al. Nanostring-based multigene
assay to predict recurrence for gastric cancer patients
after surgery. PLoS One 2014;9:e90133.
106.Ooi CH, Ivanova T, Wu J, et al. Oncogenic pathway
combinations predict clinical prognosis in gastric cancer.
PLoS Genet 2009;5:e1000676.
107.Chang HR, Nam S, Kook MC, et al. HNF4alpha is a
therapeutic target that links AMPK to WNT signalling in
early-stage gastric cancer. Gut 2014 [Epub ahead of
print]; pii: gutjnl-2014-307918.
108.Kim YH, Liang H, Liu X, et al. AMPKalpha modulation in
cancer progression: multilayer integrative analysis of the
whole transcriptome in Asian gastric cancer. Cancer Res
2012;72:2512–2521.
109.Kim HK, Choi IJ, Kim CG, et al. A gene expression
signature of acquired chemoresistance to cisplatin and
fluorouracil combination chemotherapy in gastric cancer
patients. PLoS One 2011;6:e16694.
110.Lau WM, Teng E, Chong HS, et al. CD44v8-10 is a
cancer-specific marker for gastric cancer stem cells.
Cancer Res 2014;74:2630–2641.
111.Ishimoto T, Nagano O, Yae T, et al. CD44 variant regu-
lates redox status in cancer cells by stabilizing the xCT
subunit of system xc(-) and thereby promotes tumor
growth. Cancer Cell 2011;19:387–400.
112.Liu J, McCleland M, Stawiski EW, et al. Integrated exome
and transcriptome sequencing reveals ZAK isoform us-
age in gastric cancer. Nat Commun 2014;5:3830.
113.Yun SM, Yoon K, Lee S, et al. PPP1R1B-STARD3
chimeric fusion transcript in human gastric cancer pro-
motes tumorigenesis through activation of PI3K/AKT
signaling. Oncogene 2014;33:5341–5347.
114.Song JH, Meltzer SJ. MicroRNAs in pathogenesis,
diagnosis, and treatment of gastroesophageal cancers.
Gastroenterology 2012;143:35–47.
October 2015
115.Song S, Ajani JA. The role of microRNAs in cancers of
the upper gastrointestinal tract. Nat Rev Gastroenterol
Hepatol 2013;10:109–118.
116.Lu Z, Liu M, Stribinskis V, et al. MicroRNA-21 promotes
cell transformation by targeting the programmed cell
death 4 gene. Oncogene 2008;27:4373–4379.
117.Lai KW, Koh KX, Loh M, et al. MicroRNA-130b regulates
the tumour suppressor RUNX3 in gastric cancer. Eur J
Cancer 2010;46:1456–1463.
118.Zhang BG, Li JF, Yu BQ, et al. microRNA-21 promotes
tumor proliferation and invasion in gastric cancer by
targeting PTEN. Oncol Rep 2012;27:1019–1026.
119.Tsukamoto Y, Nakada C, Noguchi T, et al. MicroRNA-
375 is downregulated in gastric carcinomas and regu-
lates cell survival by targeting PDK1 and 14-3-3zeta.
Cancer Res 2010;70:2339–2349.
120.Oh HK, Tan AL, Das K, et al. Genomic loss of miR-486
regulates tumor progression and the OLFM4 anti-
apoptotic factor in gastric cancer. Clin Cancer Res 2011;
17:2657–2667.
121.Han TS, Hur K, Xu G, et al. MicroRNA-29c mediates
initiation of gastric carcinogenesis by directly targeting
ITGB1. Gut 2015;64:203–214.
122.Guo SL, Ye H, Teng Y, et al. Akt-p53-miR-365-cyclin D1/
cdc25A axis contributes to gastric tumorigenesis
induced by PTEN deficiency. Nat Commun 2013;4:2544.
123.Kiga K, Mimuro H, Suzuki M, et al. Epigenetic silencing
of miR-210 increases the proliferation of gastric epithe-
lium during chronic Helicobacter pylori infection. Nat
Commun 2014;5:4497.
124.Li X, Zhang Y, Zhang Y, et al. Survival prediction of
gastric cancer by a seven–microRNA signature. Gut
2010;59:579–585.
125.Ueda T, Volinia S, Okumura H, et al. Relation between
microRNA expression and progression and prognosis of
gastric cancer: a microRNA expression analysis. Lancet
Oncol 2010;11:136–146.
126.Song F, Yang D, Liu B, et al. Integrated microRNA
network analyses identify a poor-prognosis subtype of
gastric cancer characterized by the miR-200 family. Clin
Cancer Res 2014;20:878–889.
127.Okugawa Y, Toiyama Y, Hur K, et al. Metastasis-asso-
ciated long non-coding RNA drives gastric cancer
development and promotes peritoneal metastasis.
Carcinogenesis 2014;35:2731–2739.
128.Hu Y, Wang J, Qian J, et al. Long noncoding RNA
GAPLINC regulates CD44-dependent cell invasiveness
and associates with poor prognosis of gastric cancer.
Cancer Res 2014;74:6890–6902.
129.Busuttil RA, George J, Tothill RW, et al. A signature
predicting poor prognosis in gastric and ovarian cancer
represents a coordinated macrophage and stromal
response. Clin Cancer Res 2014;20:2761–2772.
130.Wu Y, Grabsch H, Ivanova T, et al. Comprehensive
genomic meta-analysis identifies intra-tumoural stroma
as a predictor of survival in patients with gastric cancer.
Gut 2013;62:1100–1111.
131.Saadi A, Shannon NB, Lao-Sirieix P, et al. Stromal genes
discriminate preinvasive from invasive disease, predict
Pathogenesis of Gastric Adenocarcinoma 1162.e3
outcome, and highlight inflammatory pathways in
digestive cancers. Proc Natl Acad Sci U S A 2010;
107:2177–2182.
132.Rajski M, Zanetti-Dallenbach R, Vogel B, et al. IGF-I
induced genes in stromal fibroblasts predict the clinical
outcome of breast and lung cancer patients. BMC Med
2010;8:1.
133.Quail DF, Joyce JA. Microenvironmental regulation of
tumor progression and metastasis. Nat Med 2013;
19:1423–1437.
134.Merchant JL, Saqui-Salces M. Inhibition of Hedgehog
signaling in the gastrointestinal tract: targeting the can-
cer microenvironment. Cancer Treat Rev 2014;40:12–21.
135.Wilke H, Muro K, Van Cutsem E, et al. Ramucirumab plus
paclitaxel versus placebo plus paclitaxel in patients with
previously treated advanced gastric or gastro-
oesophageal junction adenocarcinoma (RAINBOW): a
double-blind, randomised phase 3 trial. Lancet Oncol
2014;15:1224–1235.
136.Fuchs CS, Tomasek J, Yong CJ, et al. Ramucirumab
monotherapy for previously treated advanced gastric or
gastro-oesophageal junction adenocarcinoma (RE-
GARD): an international, randomised, multicentre,
placebo-controlled, phase 3 trial. Lancet 2014;383:31–39.
137.Haas M, Dimmler A, Hohenberger W, et al. Stromal
regulatory T-cells are associated with a favourable
prognosis in gastric cancer of the cardia. BMC Gastro-
enterol 2009;9:65.
138.Zhuang Y, Peng LS, Zhao YL, et al. CD8(þ) T cells that
produce interleukin-17 regulate myeloid-derived sup-
pressor cells and are associated with survival time of
patients with gastric cancer. Gastroenterology 2012;
143:951–962.
139.Fridman WH, Pages F, Sautes-Fridman C, et al. The
immune contexture in human tumours: impact on clinical
outcome. Nat Rev Cancer 2012;12:298–306.
140.Lin SJ, Gagnon-Bartsch JA, Tan IB, et al. Signatures of
tumour immunity distinguish Asian and non-Asian
gastric adenocarcinomas. Gut 2014 [Epub ahead of
print]; pii: gutjnl-2014-308252.
141.Sunakawa Y, Stremitzer S, Cao S, et al. Association of
variants in genes encoding for macrophage-related
functions with clinical outcome in patients with
locoregional gastric cancer. Ann Oncol 2015;
26:332–339.
142.Abreu MT, Peek RM Jr. Gastrointestinal malignancy and
the microbiome. Gastroenterology 2014;146:1534–1546.
143.Yasui W, Oue N, Aung PP, et al. Molecular-pathological
prognostic factors of gastric cancer: a review. Gastric
Cancer 2005;8:86–94.
144.Wroblewski LE, Peek RM Jr, Wilson KT. Helicobacter
pylori and gastric cancer: factors that modulate disease
risk. Clin Microbiol Rev 2010;23:713–739.
145.Loh M, Koh KX, Yeo BH, et al. Meta-analysis of genetic
polymorphisms and gastric cancer risk: variability in
associations according to race. Eur J Cancer 2009;
45:2562–2568.
146.Hanahan D, Weinberg RA. The hallmarks of cancer. Cell
2000;100:57–70.