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Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE40967 | GEO | 2013/05/22

SECONDARY ACCESSION(S): PRJNA175448

REPOSITORIES: GEO

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Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-05-22 | E-GEOD-40967 | biostudies-arrayexpress

Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]

Project description:From a clinical and molecular perspective, colon cancer (CC) is a heterogeneous disease but to date no classification based on high-density transcriptome data has been established. The aim of this study was to build up a robust molecular classification ofÂ mRNA expression profiles (Affymetrix U133Plus2) ofÂ a large series of 443 CC and to validate it on an independent serie of 123 CC and 906 public dataset.Â We identified and validated six molecular subtypes in this large cohort as a combination of multiple molecular processes that complement current disease stratification based on clinicopathological variables and molecular markers. The biological relevance of these subtypes was consolidated by significant differences in survival. These insights open new perspectives for improving prognostic models and targeted therapies. Among a large series of colon cancers collected for the Cartes d'IdentitÃ© des Tumeurs (CIT) program from the French Ligue Nationale Contre le Cancer (http://cit.ligue-cancer.net), 566 were analyzed for mRNA expression profiles using Affymetrix U133plus2 chip and, among theses, 463 could also be analyzed for DNA alteration profiles using the CGH Array (Â CIT-CGHarray V6). The 566 tumors was divided into a discovery dataset of 443 CC and a validation dataset of 123 CC.

2013-05-22 | E-GEOD-39582 | biostudies-arrayexpress

Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [CGH]

2013-05-22 | E-GEOD-40966 | biostudies-arrayexpress

Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [CGH]

2013-05-22 | GSE40966 | GEO

Gene expression Classification of Colon Cancer defines six molecular subtypes with distinct clinical, molecular and survival characteristics [Expression]

2013-05-22 | GSE39582 | GEO

Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-04-17 | E-GEOD-66229 | biostudies-arrayexpress

Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-04-17 | GSE66229 | GEO

Calcium intake and colon cancer risk subtypes by tumor molecular characteristics.

Project description:BackgroundA preventive potential of high calcium intake against colorectal cancer has been indicated for distal colon cancer, which is inversely associated with high-level CpG island methylator phenotype (CIMP), high-level microsatellite instability (MSI), and BRAF and PIK3CA mutations. In addition, BRAF mutation is strongly inversely correlated with KRAS mutation. We hypothesized that the association between calcium intake and colon cancer risk might vary by these molecular features.MethodsWe prospectively followed 88,506 women from the Nurses' Health Study and 47,733 men from the Health Professionals Follow-up Study for up to 30 years. Duplication-method Cox proportional cause-specific hazards regression was used to estimate multivariable hazard ratios (HRs), and 95% confidence intervals (95% CIs) for the associations between calcium intake and the risk of colon cancer subtypes. By Bonferroni correction, the α-level was adjusted to 0.01.ResultsBased on 853 colon cancer cases, the inverse association between dietary calcium intake and colon cancer risk differed by CIMP status (pheterogeneity = 0.01). Per each 300 mg/day increase in intake, multivariable HRs were 0.84 (95% CI 0.76-0.94) for CIMP-negative/low and 1.12 (95% CI 0.93-1.34) for CIMP-high. Similar differential associations were suggested for MSI subtypes (pheterogeneity = 0.02), with the corresponding HR being 0.86 (95% CI 0.77-0.95) for non-MSI-high and 1.10 (95% CI 0.92-1.32) for MSI-high. No differential associations were observed by BRAF, KRAS, or PIK3CA mutations.ConclusionThe inverse association between dietary calcium intake and colon cancer risk may be specific to CIMP-negative/low and possibly non-MSI-high subtypes.

| S-EPMC6546870 | biostudies-literature

Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study [gastric tumors]

Project description:Gastric cancer, a leading cause of cancer related deaths, is a heterogeneous disease, with little consensus on molecular subclasses and their clinical relevance. We describe four molecular subtypes linked with distinct patterns of molecular alterations, disease progression and prognosis viz. a) Microsatellite Instable: hypermutated intestinal subtype tumors occurring in antrum, best overall prognosis, lower frequency of recurrence (22%), with liver metastasis in 23% of recurred cases b) Mesenchymal-like: diffuse tumors with worst prognosis, a tendency to occur at an earlier age and highest recurrence (63%) with peritoneal seeding in 64% of recurred cases, low frequency of molecular alterations c) TP53-inactive with TP53 loss, presence of focal amplifications and chromosomal instability d) TP53-active marked by EBV infection and PIK3CA mutations. The key molecular mechanisms and associated survival patterns are validated in multiple independent cohorts, to provide a consistent and unified framework for further preclinical and clinical research. ACRG Gastric cohort: microarray profiles from 300 gastric tumors from gastric cancer patients.

2015-04-17 | E-GEOD-62254 | biostudies-arrayexpress

A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues

Project description:This work presents a novel Consensus Molecular Subtypes (CMS) classifier for colorectal cancer (CRC), optimized for degraded RNA stemming from clinical formalin-fixed paraffin-embedded tissue samples.

2024-05-22 | GSE267010 | GEO

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