We use cookies to understand how you use our site and to improve your experience. This includes personalizing content and advertising. To learn more, click here. By continuing to use our site, you accept our use of cookies. Cookie Policy.

Features Partner Sites Information LinkXpress hp
Sign In
Advertise with Us
LGC Clinical Diagnostics

Download Mobile App




Gastric Cancer Analysis Identifies Four Subtypes

By LabMedica International staff writers
Posted on 28 Feb 2019
Print article
Image: A histopathology of gastric adenocarcinoma representing a signet ring cell variant identified in an endoscopic biopsy specimen (Photo courtesy of KGH).
Image: A histopathology of gastric adenocarcinoma representing a signet ring cell variant identified in an endoscopic biopsy specimen (Photo courtesy of KGH).
In previous studies of gastric cancers (GCs), genomic and transcriptomic analyses have identified molecular signatures associated with phenotypes of the disease, such as patient subtypes and survival. New proteogenomic analysis of diffuse gastric cancers (GCs) in young populations identified four subtypes of the disease.

The Cancer Genome Atlas (TCGA) identified four GC subtypes and associated molecular signatures: Epstein-Barr virus (EBV)-positive tumors with recurrent PIK3CA mutations, DNA hypermethylation, and amplification of JAK2, CD274, and PDCD1LG2; tumors with microsatellite instability with high mutation rates; genomically stable tumors enriched for diffuse histological variants and mutations in RHOA; and tumors with chromosomal instability showing aneuploidy and amplifications of genes encoding receptor tyrosine kinases.

A large team of scientists collaborating with the Korea University, Seoul, Republic of Korea) collected paired tumor and adjacent normal tissues, as well as blood samples, from 80 patients with early-onset GCs (EOGCs) under 45 years of age. These 80 tumors included 74 diffuse, three intestinal, two mixed types, and one inflammatory myoblastic tumor. For each patient, the team performed exome sequencing of the tumors and peripheral blood mononuclear cells, as well as mRNA sequencing of the paired tumor and adjacent normal tissues.

The team used exome sequencing data, and identified 56,502 non-synonymous single-nucleotide variants and 3,598 frameshift indels. Further, they found 11,938 genes were expressed in the tumor and adjacent normal samples, on average, in the mRNA data. They then used these variants and expressed transcripts from each patient to build a sample-specific database and identified 156,135 peptides, 28,944 phosphopeptides, and 4,376 N-glycopeptides from the global proteomes, phosphoproteomes, and N-glycoproteomes, respectively. These peptides were mapped to 10,295 protein-coding genes, on average.

The scientists compared their own GC subtypes to GC subgroups in TCGA data, and found that subtype 2- and 4-like TCGA subgroups showed the best and worst survivals, respectively. MSI- and EBV-positive GCs were significantly enriched in the subtype 2-like subgroup, while genomically stable GCs were enriched in the subtype 4-like subgroup. They defined subtype 2 as representing immune response-related processes (antigen presentation, BCR/TNF/Toll-like receptor signaling, TCR signaling, and phagosome). Subtype 3 uniquely represented metabolism-related processes (oxidative phosphorylation, fatty acid b-oxidation, and citrate cycle). Subtype 4 mainly represented invasion-related processes (actin cytoskeleton and MAPK, PI3K-AKT, WNT, RHOA, and cadherin signaling).

The authors concluded that based on their data, subtypes 2 and 4 can be characterized as immunogenic and invasive tumors with possibly good and poor survival rates, respectively, similar to subtypes 2- and 4-like subgroups in TCGA cohort. They noted that the tumors in subtype 2 show strong immune activity that may contribute to a good prognosis and that the tumors in subtype 4 show strong invasion potential that may contribute to a poor prognosis. The study was published on January 14, 2019, on the journal Cancer Cell.

Related Links:
Korea University

Gold Member
Flocked Fiber Swabs
Puritan® Patented HydraFlock®
Verification Panels for Assay Development & QC
Seroconversion Panels
New
Coagulation Analyzer
CS-2400
New
cTnI/CK-MB/Myo Test
Finecare cTnI/CK-MB/Myo Rapid Quantitative Test

Print article

Channels

Clinical Chemistry

view channel
Image: The tiny clay-based materials can be customized for a range of medical applications (Photo courtesy of Angira Roy and Sam O’Keefe)

‘Brilliantly Luminous’ Nanoscale Chemical Tool to Improve Disease Detection

Thousands of commercially available glowing molecules known as fluorophores are commonly used in medical imaging, disease detection, biomarker tagging, and chemical analysis. They are also integral in... Read more

Immunology

view channel
Image: The cancer stem cell test can accurately choose more effective treatments (Photo courtesy of University of Cincinnati)

Stem Cell Test Predicts Treatment Outcome for Patients with Platinum-Resistant Ovarian Cancer

Epithelial ovarian cancer frequently responds to chemotherapy initially, but eventually, the tumor develops resistance to the therapy, leading to regrowth. This resistance is partially due to the activation... Read more

Microbiology

view channel
Image: The lab-in-tube assay could improve TB diagnoses in rural or resource-limited areas (Photo courtesy of Kenny Lass/Tulane University)

Handheld Device Delivers Low-Cost TB Results in Less Than One Hour

Tuberculosis (TB) remains the deadliest infectious disease globally, affecting an estimated 10 million people annually. In 2021, about 4.2 million TB cases went undiagnosed or unreported, mainly due to... Read more

Pathology

view channel
Image: The ready-to-use DUB enzyme assay kits accelerate routine DUB activity assays without compromising data quality (Photo courtesy of Adobe Stock)

Sensitive and Specific DUB Enzyme Assay Kits Require Minimal Setup Without Substrate Preparation

Ubiquitination and deubiquitination are two important physiological processes in the ubiquitin-proteasome system, responsible for protein degradation in cells. Deubiquitinating (DUB) enzymes contain around... Read more

Technology

view channel
Image: The HIV-1 self-testing chip will be capable of selectively detecting HIV in whole blood samples (Photo courtesy of Shutterstock)

Disposable Microchip Technology Could Selectively Detect HIV in Whole Blood Samples

As of the end of 2023, approximately 40 million people globally were living with HIV, and around 630,000 individuals died from AIDS-related illnesses that same year. Despite a substantial decline in deaths... Read more

Industry

view channel
Image: The collaboration aims to leverage Oxford Nanopore\'s sequencing platform and Cepheid\'s GeneXpert system to advance the field of sequencing for infectious diseases (Photo courtesy of Cepheid)

Cepheid and Oxford Nanopore Technologies Partner on Advancing Automated Sequencing-Based Solutions

Cepheid (Sunnyvale, CA, USA), a leading molecular diagnostics company, and Oxford Nanopore Technologies (Oxford, UK), the company behind a new generation of sequencing-based molecular analysis technologies,... Read more
Copyright © 2000-2025 Globetech Media. All rights reserved.