1
|
Lin X, Zhao Y, Song WM, Zhang B. Molecular classification and prediction in gastric cancer. Comput Struct Biotechnol J 2015; 13:448-58. [PMID: 26380657 PMCID: PMC4556804 DOI: 10.1016/j.csbj.2015.08.001] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 07/23/2015] [Accepted: 08/01/2015] [Indexed: 12/19/2022] Open
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.
Collapse
Affiliation(s)
- Xiandong Lin
- 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
| | - Yongzhong Zhao
- 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
| | - Won-min Song
- 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
| | - Bin Zhang
- 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
| |
Collapse
|
2
|
Zang S, Guo R, Xing R, Zhang L, Li W, Zhao M, Fang J, Hu F, Kang B, Ren Y, Zhuang Y, Liu S, Wang R, Li X, Yu Y, Cheng J, Lu Y. Identification of differentially-expressed genes in intestinal gastric cancer by microarray analysis. GENOMICS PROTEOMICS & BIOINFORMATICS 2014; 12:276-83. [PMID: 25500430 PMCID: PMC4411479 DOI: 10.1016/j.gpb.2014.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 09/18/2014] [Accepted: 09/30/2014] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is one of the most frequent malignant tumors. In order to systematically characterize the cellular and molecular mechanisms of intestinal GC development, in this study, we used 22K oligonucleotide microarrays and bioinformatics analysis to evaluate the gene expression profiles of GC in 45 tissue samples, including 20 intestinal GC tissue samples, 20 normal appearing tissues (NATs) adjacent to tumors and 5 noncancerous gastric mucosa tissue samples. These profiles allowed us to explore the transcriptional characteristics of GC and determine the change patterns in gene expression that may be of clinical significance. 1519 and 1255 differentially-expressed genes (DEGs) were identified in intestinal GC tissues and NATs, respectively, as determined by Bayesian analysis (P<0.001). These genes were associated with diverse functions such as mucosa secretion, metabolism, proliferation, signaling and development, which occur at different stages of GC development.
Collapse
Affiliation(s)
- Shizhu Zang
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Ruifang Guo
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Rui Xing
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Liang Zhang
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Wenmei Li
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Min Zhao
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jingyuan Fang
- Department of Gastroenterology, Renji Hospital of Shanghai Second Medical University, Shanghai 200001, China
| | - Fulian Hu
- Department of Gastroenterology, Peking University First Hospital, Beijing 100034, China
| | - Bin Kang
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yonghong Ren
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Yonglong Zhuang
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Siqi Liu
- Beijing Institutes of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rong Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Xianghong Li
- Department of Pathology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Yingyan Yu
- Shanghai Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai 200025, China
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology and Tsinghua University School of Medicine, Beijing 102206, China
| | - Youyong Lu
- Laboratory of Molecular Oncology, MOE Key Laboratory of Carcinogenesis and Translational Research, Peking University Cancer Hospital & Institute, Beijing 100142, China.
| |
Collapse
|
3
|
Laurindo FRM, Pescatore LA, Fernandes DDC. Protein disulfide isomerase in redox cell signaling and homeostasis. Free Radic Biol Med 2012; 52:1954-69. [PMID: 22401853 DOI: 10.1016/j.freeradbiomed.2012.02.037] [Citation(s) in RCA: 174] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2011] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 12/16/2022]
Abstract
Thiol proteins may potentially act as redox signaling adaptor proteins, adjusting reactive oxygen species intermediates to specific signals and redox signals to cell homeostasis. In this review, we discuss redox effects of protein disulfide isomerase (PDI), a thioredoxin superfamily oxidoreductase from the endoplasmic reticulum (ER). Abundantly expressed PDI displays ubiquity, interactions with redox and nonredox proteins, versatile effects, and several posttranslational modifications. The PDI family contains >20 members with at least some apparent complementary actions. PDI has oxidoreductase, isomerase, and chaperone effects, the last not directly dependent on its thiols. PDI is a converging hub for pathways of disulfide bond introduction into ER-processed proteins, via hydrogen peroxide-generating mechanisms involving the oxidase Ero1α, as well as hydrogen peroxide-consuming reactions involving peroxiredoxin IV and the novel peroxidases Gpx7/8. PDI is a candidate pathway for coupling ER stress to oxidant generation. Emerging information suggests a convergence between PDI and Nox family NADPH oxidases. PDI silencing prevents Nox responses to angiotensin II and inhibits Akt phosphorylation in vascular cells and parasite phagocytosis in macrophages. PDI overexpression spontaneously enhances Nox activation and expression. In neutrophils, PDI redox-dependently associates with p47phox and supports the respiratory burst. At the cell surface, PDI exerts transnitrosation, thiol reductase, and apparent isomerase activities toward targets including adhesion and matrix proteins and proteases. Such effects mediate redox-dependent adhesion, coagulation/thrombosis, immune functions, and virus internalization. The route of PDI externalization remains elusive. Such multiple redox effects of PDI may contribute to its conspicuous expression and functional role in disease, rendering PDI family members putative redox cell signaling adaptors.
Collapse
Affiliation(s)
- Francisco R M Laurindo
- Vascular Biology Laboratory, Heart Institute (InCor), University of São Paulo School of Medicine, 05403-000 São Paulo, Brazil.
| | | | | |
Collapse
|