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Molecular classification and prediction in gastric cancer.

Lin X, Zhao Y, Song WM, Zhang B - Comput Struct Biotechnol J (2015)

Bottom Line: Unprecedented whole-genome-scale data have been catalyzing and advancing the molecular subtyping approach.We identified the consensus patterns across these signatures and identified the underlying molecular pathways and biological functions.The identification of molecular subtyping of gastric adenocarcinoma and the development of integrated genomics approaches for clinical applications such as prediction of clinical intervening emerge as an essential phase toward personalized medicine in treating gastric cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, NY 10029, USA ; Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fujian Provincial Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, Fujian 350014, PR China.

ABSTRACT
Gastric cancer, a highly heterogeneous disease, is the second leading cause of cancer death and the fourth most common cancer globally, with East Asia accounting for more than half of cases annually. Alongside TNM staging, gastric cancer clinic has two well-recognized classification systems, the Lauren classification that subdivides gastric adenocarcinoma into intestinal and diffuse types and the alternative World Health Organization system that divides gastric cancer into papillary, tubular, mucinous (colloid), and poorly cohesive carcinomas. Both classification systems enable a better understanding of the histogenesis and the biology of gastric cancer yet have a limited clinical utility in guiding patient therapy due to the molecular heterogeneity of gastric cancer. Unprecedented whole-genome-scale data have been catalyzing and advancing the molecular subtyping approach. Here we cataloged and compared those published gene expression profiling signatures in gastric cancer. We summarized recent integrated genomic characterization of gastric cancer based on additional data of somatic mutation, chromosomal instability, EBV virus infection, and DNA methylation. We identified the consensus patterns across these signatures and identified the underlying molecular pathways and biological functions. The identification of molecular subtyping of gastric adenocarcinoma and the development of integrated genomics approaches for clinical applications such as prediction of clinical intervening emerge as an essential phase toward personalized medicine in treating gastric cancer.

No MeSH data available.


Related in: MedlinePlus

Enrichment of MSigDB and gastric specific gene sets in the GC gene signatures. The c2 and c5 sets include biological processes and KEGG from MSigDB version 5.0 were employed for enrichment of the analysis of gene sets listed in Table 3.
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f0015: Enrichment of MSigDB and gastric specific gene sets in the GC gene signatures. The c2 and c5 sets include biological processes and KEGG from MSigDB version 5.0 were employed for enrichment of the analysis of gene sets listed in Table 3.

Mentions: The c2 and c5 sets in MSigDB version 5.0, including biological processes and KEGG pathways, respectively, were tested for enrichment in the gene signatures listed in Table 3. The result was represented by the heat map in Fig. 3. Many cancer-associated molecular pathways have been captured in terms of highly overlapped with GC gene signatures. Notably, the digestion and pyrimidine signaling pathways highly enriched in many signatures, indicating they are GC specific and related to inflammation.


Molecular classification and prediction in gastric cancer.

Lin X, Zhao Y, Song WM, Zhang B - Comput Struct Biotechnol J (2015)

Enrichment of MSigDB and gastric specific gene sets in the GC gene signatures. The c2 and c5 sets include biological processes and KEGG from MSigDB version 5.0 were employed for enrichment of the analysis of gene sets listed in Table 3.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4556804&req=5

f0015: Enrichment of MSigDB and gastric specific gene sets in the GC gene signatures. The c2 and c5 sets include biological processes and KEGG from MSigDB version 5.0 were employed for enrichment of the analysis of gene sets listed in Table 3.
Mentions: The c2 and c5 sets in MSigDB version 5.0, including biological processes and KEGG pathways, respectively, were tested for enrichment in the gene signatures listed in Table 3. The result was represented by the heat map in Fig. 3. Many cancer-associated molecular pathways have been captured in terms of highly overlapped with GC gene signatures. Notably, the digestion and pyrimidine signaling pathways highly enriched in many signatures, indicating they are GC specific and related to inflammation.

Bottom Line: Unprecedented whole-genome-scale data have been catalyzing and advancing the molecular subtyping approach.We identified the consensus patterns across these signatures and identified the underlying molecular pathways and biological functions.The identification of molecular subtyping of gastric adenocarcinoma and the development of integrated genomics approaches for clinical applications such as prediction of clinical intervening emerge as an essential phase toward personalized medicine in treating gastric cancer.

View Article: PubMed Central - PubMed

Affiliation: Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, NY 10029, USA ; Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fujian Provincial Cancer Hospital, No. 420 Fuma Road, Jinan District, Fuzhou, Fujian 350014, PR China.

ABSTRACT
Gastric cancer, a highly heterogeneous disease, is the second leading cause of cancer death and the fourth most common cancer globally, with East Asia accounting for more than half of cases annually. Alongside TNM staging, gastric cancer clinic has two well-recognized classification systems, the Lauren classification that subdivides gastric adenocarcinoma into intestinal and diffuse types and the alternative World Health Organization system that divides gastric cancer into papillary, tubular, mucinous (colloid), and poorly cohesive carcinomas. Both classification systems enable a better understanding of the histogenesis and the biology of gastric cancer yet have a limited clinical utility in guiding patient therapy due to the molecular heterogeneity of gastric cancer. Unprecedented whole-genome-scale data have been catalyzing and advancing the molecular subtyping approach. Here we cataloged and compared those published gene expression profiling signatures in gastric cancer. We summarized recent integrated genomic characterization of gastric cancer based on additional data of somatic mutation, chromosomal instability, EBV virus infection, and DNA methylation. We identified the consensus patterns across these signatures and identified the underlying molecular pathways and biological functions. The identification of molecular subtyping of gastric adenocarcinoma and the development of integrated genomics approaches for clinical applications such as prediction of clinical intervening emerge as an essential phase toward personalized medicine in treating gastric cancer.

No MeSH data available.


Related in: MedlinePlus