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In silico analysis of stomach lineage specific gene set expression pattern in gastric cancer. Biochem Biophys Res Commun 2013; 439:539-46. [DOI: 10.1016/j.bbrc.2013.09.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 09/02/2013] [Indexed: 01/28/2023]
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Tan IB, Ng I, Tai WM, Tan P. Understanding the genetic basis of gastric cancer: recent advances. Expert Rev Gastroenterol Hepatol 2012; 6:335-41. [PMID: 22646255 DOI: 10.1586/egh.12.7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Two major gastric cancer histological subtypes are recognized with distinct morphology, epidemiology, pathogenesis and clinical behavior. Genetically, the intestinal and diffuse subtypes are also characterized by distinct germline susceptibility patterns and somatic aberrations. Helicobacter pylori is strongly associated with both Lauren's subtypes, although the underlying carcinogenic mechanisms are unique. Risk is modulated by strain-specific virulence factors, host responses and specific host-microbe interactions. Somatic aberrations in gastric cancer are driven by three major mechanisms, namely chromosomal instability, microsatellite instability and epigenetic alterations. These processes drive carcinogenesis in both Lauren's subtypes; however, the relative contribution of these processes and the specific genes aberrated differ. Moving beyond Lauren's subtypes, next-generation techniques have identified major genomic subtypes that have prognostic impact and exhibit distinct response patterns to standard cytotoxics.
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Affiliation(s)
- Iain Beehuat Tan
- Department of Medical Oncology, National Cancer Centre Singapore, Singapore.
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THBS4, a novel stromal molecule of diffuse-type gastric adenocarcinomas, identified by transcriptome-wide expression profiling. Mod Pathol 2011; 24:1390-403. [PMID: 21701537 DOI: 10.1038/modpathol.2011.99] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastric adenocarcinomas can be divided into two major histological types, the diffuse and intestinal type (Laurén classification). Since they diverge in many clinical and molecular characteristics, it is widely accepted that they represent distinct disease entities that may benefit from different therapeutic approaches. Gene expression profiling studies have identified numerous genes that are differentially expressed between them. However, none of these studies covered the whole transcriptome and the published gene lists reveal little overlap, raising the need for further, more comprehensive analyses. Here, we present the first transcriptome-wide expression profiling study comparing the two types (diffuse n=19, intestinal n=24), which identified >1000 genes that are differentially expressed. Among them, thrombospondin 4 (THBS4) showed the strongest correlation to histological type, with vast overexpression in the diffuse type. Quantitative real-time PCR validated this strong overexpression and revealed that intestinal tumors generally lack THBS4 expression. Immunohistochemistry demonstrated THBS4 overexpression on the protein level (n=10) and localized THBS4 to the stromal aspect. Its expression was primarily observed within the extracellular matrix surrounding the tumor cells, with the highest intensities found in regions of high tumor cell density and invasion. Intestinal tumors and matched non-neoplastic gastric epithelium and stroma did not feature any relevant THBS4 expression in a preliminary selection of analyzed cases (n=5). Immunohistochemical colocalization and in vitro studies revealed that THBS4 is expressed and secreted by cancer-associated fibroblasts. Furthermore, we show that THBS4 transcription in fibroblasts is stimulated by tumor cells. This study is the first to identify THBS4 as a powerful marker for diffuse-type gastric adenocarcinomas and to provide an initial characterization of its expression in the course of this disease.
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Marimuthu A, Jacob HK, Jakharia A, Subbannayya Y, Keerthikumar S, Kashyap MK, Goel R, Balakrishnan L, Dwivedi S, Pathare S, Dikshit JB, Maharudraiah J, Singh S, Sameer Kumar GS, Vijayakumar M, Veerendra Kumar KV, Premalatha CS, Tata P, Hariharan R, Roa JC, Prasad T, Chaerkady R, Kumar RV, Pandey A. Gene Expression Profiling of Gastric Cancer. JOURNAL OF PROTEOMICS & BIOINFORMATICS 2011; 4:74-82. [PMID: 27030788 PMCID: PMC4809432 DOI: pmid/27030788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Gastric cancer is the second leading cause of cancer death worldwide, both in men and women. A genomewide gene expression analysis was carried out to identify differentially expressed genes in gastric adenocarcinoma tissues as compared to adjacent normal tissues. We used Agilent's whole human genome oligonucleotide microarray platform representing ~41,000 genes to carry out gene expression analysis. Two-color microarray analysis was employed to directly compare the expression of genes between tumor and normal tissues. Through this approach, we identified several previously known candidate genes along with a number of novel candidate genes in gastric cancer. Testican-1 (SPOCK1) was one of the novel molecules that was 10-fold upregulated in tumors. Using tissue microarrays, we validated the expression of testican-1 by immunohistochemical staining. It was overexpressed in 56% (160/282) of the cases tested. Pathway analysis led to the identification of several networks in which SPOCK1 was among the topmost networks of interacting genes. By gene enrichment analysis, we identified several genes involved in cell adhesion and cell proliferation to be significantly upregulated while those corresponding to metabolic pathways were significantly downregulated. The differentially expressed genes identified in this study are candidate biomarkers for gastric adenoacarcinoma.
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Affiliation(s)
- Arivusudar Marimuthu
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
| | - Harrys K.C. Jacob
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
| | - Aniruddha Jakharia
- Department of Zoology, Gauhati University, Guwahati 781014, Assam, India
- Imgenex India, Bhubaneswar 751024, Orissa, India
| | - Yashwanth Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Rajiv Gandhi University of Health Sciences, Bangalore, 560041, Karnataka, India
| | | | - Manoj Kumar Kashyap
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Renu Goel
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Lavanya Balakrishnan
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - Sutopa Dwivedi
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- School of Biotechnology, Amrita Vishwa Vidyapeetham University, Kollam 690525, Kerala, India
| | | | | | - Jagadeesha Maharudraiah
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- RajaRajeswari Medical college, Bangalore, 560074, India
| | - Sujay Singh
- Imgenex India, Bhubaneswar 751024, Orissa, India
- Imgenex Corporation, San Diego 92121, California, USA
| | - Ghantasala S Sameer Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Department of Biotechnology, Kuvempu University, Shimoga 577451, Karnataka, India
| | - M. Vijayakumar
- Departments of Surgical Oncology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India
| | | | | | - Pramila Tata
- Strand Life Sciences, Bangalore 560024, Karnataka, India
| | | | - Juan Carlos Roa
- Department of Pathology, Universidad de La Frontera, Temuco, Chile
| | - T.S.K Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
| | - Raghothama Chaerkady
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India
- Manipal University, Madhav Nagar, Manipal, Karnataka 576104; India
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
| | - Rekha Vijay Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore 560029, Karnataka; India
- Corresponding authors: Akhilesh Pandey MD, PhD, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, Tel: 410-502-6662; Fax: 410-502-7544; , Rekha V. Kumar, MD, Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029; India. Tel: 091-080-6560708; Fax: 091-080-6560723;
| | - Akhilesh Pandey
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205, Maryland, USA
- Corresponding authors: Akhilesh Pandey MD, PhD, McKusick-Nathans Institute of Genetic Medicine, 733 N. Broadway, BRB 527, Johns Hopkins University, Baltimore, MD 21205, Tel: 410-502-6662; Fax: 410-502-7544; , Rekha V. Kumar, MD, Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, Karnataka 560029; India. Tel: 091-080-6560708; Fax: 091-080-6560723;
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Mukherjee K, Peng D, Brifkani Z, Belkhiri A, Pera M, Koyama T, Koehler EAS, Revetta FL, Washington MK, El-Rifai W. Dopamine and cAMP regulated phosphoprotein MW 32 kDa is overexpressed in early stages of gastric tumorigenesis. Surgery 2010; 148:354-63. [PMID: 20580047 PMCID: PMC2919779 DOI: 10.1016/j.surg.2010.05.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 05/14/2010] [Indexed: 12/17/2022]
Abstract
BACKGROUND Gastric adenocarcinoma is a leading cause of cancer mortality. The role of dopamine and cAMP regulated phosphoprotein MW 32 kDa (DARPP-32) overexpression in the gastric tumorigenesis cascade remains unclear. METHODS The expression of DARPP-32 in the multistep carcinogenesis cascade was examined using immunohistochemistry analysis on 533 samples. The contribution of DARPP-32 in cellular transformation and molecular signaling was investigated using NIH3T3, AGS, and SNU16 cells. RESULTS The composite expression score (CES), calculated from immunostaining patterns, increased significantly from normal or gastritis to metaplasia, dysplasia, and adenocarcinoma (P < .001). In patients with normal stomach or gastritis and tumor samples, a 76% and 77% chance, respectively, was found (P < .001) that CES was higher in the tumor. High median CES correlated with well- or moderately differentiated (P = .03) gastric adenocarcinomas. NIH3T3 cells transfected with DARPP-32 demonstrated increased levels of phospho-AKT and a 5-fold increase in the number of foci as compared with the control (P = .02). DARPP-32 expression in AGS cells led to increased protein levels of phospho-AKT and BCL-2. For validation, the knockdown of endogenous DARPP-32 expression in SNU16 cells using shRNA resulted in decreased levels of phospho-AKT phosphorylation and BCL-2. CONCLUSION Our results suggest that DARPP-32 overexpression may participate in the transition to intestinal metaplasia and in the progression to neoplasia. The ability of DARPP-32 to transform NIH3T3 cells and to regulate AKT and BCL-2 underscores its possible oncogenic potential.
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Affiliation(s)
- Kaushik Mukherjee
- Department of Surgery, Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Dunfa Peng
- Department of Surgery, Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Zaid Brifkani
- Department of Medicine, Meharry Medical College, Nashville TN
| | - Abbes Belkhiri
- Department of Surgery, Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, TN
| | - Manuel Pera
- Section of Gastrointestinal Surgery, Hospital Clinic, CIBERehd, University of Barcelona (IDIBAPS), Barcelona, Spain
| | - Tatsuki Koyama
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN
| | | | - Frank L. Revetta
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN
| | - Mary K. Washington
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN
| | - Wael El-Rifai
- Department of Surgery, Section of Surgical Sciences, Vanderbilt University Medical Center, Nashville, TN
- Department of Cancer Biology and, Vanderbilt University Medical Center, Nashville, TN
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Tomioka N, Morita K, Kobayashi N, Tada M, Itoh T, Saitoh S, Kondo M, Takahashi N, Kataoka A, Nakanishi K, Takahashi M, Kamiyama T, Ozaki M, Hirano T, Todo S. Array comparative genomic hybridization analysis revealed four genomic prognostic biomarkers for primary gastric cancers. ACTA ACUST UNITED AC 2010; 201:6-14. [PMID: 20633762 DOI: 10.1016/j.cancergencyto.2010.04.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Revised: 03/29/2010] [Accepted: 04/21/2010] [Indexed: 12/14/2022]
Abstract
Unlike the case with some other solid tumors, whole genome array screening has not revealed prognostic genetic aberrations in primary gastric cancer. Comparative genomic hybridization (CGH) using bacterial artificial chromosome (BAC) arrays for 56 primary gastric cancers resulted in identification of four prognostic loci in this study: 6q21 (harboring FOXO3A; previously FKHRL1), 9q32 (UGCG), 17q21.1 approximately q21.2 (CASC3), and 17q21.32 (HOXB3 through HOXB9). If any one of these four loci was deleted, the prognosis of the patient was significantly worse (P = 0.0019). This was true even for advanced tumors (stage IIIA, IIB, or IV, n = 39) (P = 0.0113), whereas only 1 of the 17 patients with less advanced tumors (stage IA, IB, or II; n = 17) died of disease after surgery. Multivariate analysis according to the status of four BACs or pathological stage based on the Japanese Classification of Gastric Carcinoma (stages IA, IB, and II vs. stages IIIA, IIIB, and IV) demonstrated that the BAC clone status was also an independent prognostic factor (P = 0.006). These findings may help predict which patients with malignant potential need more intensive therapy, or may point to new therapeutic approaches especially for advanced tumors. The parameter here termed the integrated genomic prognostic biomarker may therefore be of clinical utility as a prognostic biomarker.
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Affiliation(s)
- Nobumoto Tomioka
- Department of General Surgery, Hokkaido University Graduate School of Medicine, N-15 W-7 Kita-ku, Sapporo, Japan.
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Perineural invasion after preoperative chemotherapy predicts poor survival in patients with locally advanced gastric cancer: gene expression analysis with pathologic validation. Am J Clin Oncol 2009; 32:356-62. [PMID: 19381079 DOI: 10.1097/coc.0b013e31818c08e8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND We examined gene expression profiles and clinicopathologic features (tumor location, stage, graded pathologic response, perineural invasion (PNI), Lauren's classification, and survival) of patients with gastric cancer who received preoperative chemotherapy to identify prognostic markers. METHODS Thirty-eight patients with locally advanced gastric cancer received preoperative chemotherapy on a phase II trial. Twelve fresh-frozen tumor samples were available for RNA expression analysis. Differential gene expression between tumors with and without PNI was identified and correlated with clinicopathologic features. RESULTS Preliminary hierarchical clustering suggested a separation between long- and short-term survivors. The close association between PNI and overall survival was identified and validated immunohistochemically in 31 completely resected gastric tumors. Five-year survival for patients with PNI and without PNI was 5% and 65%, respectively (P < 0.01). PNI added significant prognostic value to posttreatment pathologic stage, (P < 0.01). Differential gene expression profile for PNI and non-PNI tumors identified 111 potentially relevant genes. CONCLUSIONS Our results demonstrate that the presence of PNI after preoperative chemotherapy is associated with poor survival. These results need to be validated in prospective studies, to help establish whether patients with evidence of PNI would be candidates for more aggressive therapy or enrollment into clinical trials. The presence of PNI provides additional prognostic importance to posttreatment pathologic stage and may indicate treatment resistance. Understanding the molecular events associated with PNI, may provide insight into new therapeutic agents for this subset of patients with resistant tumors.
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Abstract
Neuroendocrine tumours (NETs) comprise a heterogenous group of malignancies with an often unpredictable course, and with limited treatment options. Thus, new diagnostic, prognostic, and therapeutic markers are needed. To shed new lights into the biology of NETs, we have by cDNA transcript profiling, sought to identify genes that are either up- or downregulated in NE as compared with non-NE tumour cells. A panel of six NET and four non-NET cell lines were examined, and out of 12 743 genes examined, we studied in detail the 200 most significantly differentially expressed genes in the comparison. In addition to potential new diagnostic markers (NEFM, CLDN4, PEROX2), the results point to genes that may be involved in the tumorigenesis (BEX1, TMEPAI, FOSL1, RAB32), and in the processes of invasion, progression and metastasis (MME, STAT3, DCBLD2) of NETs. Verification by real time qRT–PCR showed a high degree of consistency to the microarray results. Furthermore, the protein expression of some of the genes were examined. The results of our study has opened a window to new areas of research, by uncovering new candidate genes and proteins to be further investigated in the search for new prognostic, predictive, and therapeutic markers in NETs.
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Myllykangas S, Junnila S, Kokkola A, Autio R, Scheinin I, Kiviluoto T, Karjalainen-Lindsberg ML, Hollmén J, Knuutila S, Puolakkainen P, Monni O. Integrated gene copy number and expression microarray analysis of gastric cancer highlights potential target genes. Int J Cancer 2008; 123:817-25. [PMID: 18506690 DOI: 10.1002/ijc.23574] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We performed an integrated array comparative genomic hybridization (aCGH) and expression microarray analysis of 8 normal gastric tissues and 38 primary tumors, including 25 intestinal and 13 diffuse gastric adenocarcinomas to identify genes whose expression is deregulated in association with copy number alteration. Our aim was also to identify molecular genetic alterations that are specific to particular clinicopathological characteristics of gastric cancer. Distinct molecular genetic profiles were identified for intestinal and diffuse gastric cancers and for tumors obtained from 2 different locations of the stomach. Interestingly, the ERBB2 amplification and gains at 20q13.12-q13.33 almost exclusively discriminated intestinal cancers from the diffuse type. In addition, the 17q12-q25 gain was characteristic to cancers located in corpus and the 20q13.12-q13.13 gain was more common in the antrum. Statistical analysis was performed using integrated copy number and expression data to identify genes showing differential expression associated with a copy number alteration. Genes with the highest statistical significance included ERBB2, MUC1, GRB7, PPP1R1B and PPARBP with concomitant changes in copy number and expression. Immunohistochemical analysis of ERBB2 and MUC1 on a tissue microarray containing 78 independent gastric tissues showed statistically significant differences (p < 0.05 and <0.001) in immunopositivity in the intestinal (31 and 70%) and diffuse subtypes (14 and 41%), respectively. In conclusion, our results demonstrate that intestinal and diffuse type gastric cancers as well as cancers located in different sites of the stomach have distinct molecular profiles which may have clinical value.
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Affiliation(s)
- Samuel Myllykangas
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
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Galamb O, Sipos F, Molnar B, Szoke D, Spisak S, Tulassay Z. Evaluation of malignant and benign gastric biopsy specimens by mRNA expression profile and multivariate statistical methods. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2007; 72:299-309. [PMID: 17366642 DOI: 10.1002/cyto.b.20189] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND mRNA expression array and multivariate statistical analysis of gastric biopsies can yield insight into the molecular biology basis of local alterations, supporting expression-based identification of morphological alterations. METHODS From 11 patients with erosive gastritis(EG), 5 with adenocarcinoma (GC), 11 with atrophic gastritis (AG) gastric biopsies were collected, total RNA isolated, T7 amplification and expression analysis of 1047 mRNAs was performed using commercial glass arrays (Clontech, USA). After microarray quality control, applicable data were available from 7 EG, 4 GC, and 5 AG. Multivariate statistical and cell functional analysis were performed. Real-time RT-PCR and immunohistochemistry were used for validation. RESULTS GC was characterized by overregulated v-raf, v-erb-a, BCL2-associated- athanogene, immediate-early-response-3, Polo-like kinase, CDK-2, cyclin-C, Pin1 genes, and downregulated ADP-ribosyltransferase, sialophorin and DCC. AG cases had increased PDGF-receptor, TGF-beta-receptor-3, and decreased death-associated-protein-3, beta-1-catenin, topoisomerase-1 levels. In EG upregulation of IGF-receptor-1, CD9, transferrin receptor, integrins, and underexpression of keratin-5, caspase-4 was found. Discriminant analysis could reclassify all samples correctly using four parameters. CONCLUSIONS mRNA expression array analysis of gastric biopsies yields previously known and new data in the evaluation of local gastric alterations.
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Affiliation(s)
- Orsolya Galamb
- 2nd Department of Internal Medicine, University Semmelweis, Faculty of Medicine, Budapest, Hungary.
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Vecchi M, Nuciforo P, Romagnoli S, Confalonieri S, Pellegrini C, Serio G, Quarto M, Capra M, Roviaro GC, Contessini Avesani E, Corsi C, Coggi G, Di Fiore PP, Bosari S. Gene expression analysis of early and advanced gastric cancers. Oncogene 2007; 26:4284-94. [PMID: 17297478 DOI: 10.1038/sj.onc.1210208] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Gastric carcinoma is one of the major causes of cancer mortality worldwide. Early detection results in excellent prognosis for patients with early cancer (EGC), whereas the prognosis of advanced cancer (AGC) patients remains poor. It is not clear whether EGC and AGC are molecularly distinct, and whether they represent progressive stages of the same tumor or different entities ab initio. Gene expression profiles of EGC and AGC were determined by Affymetrix technology and quantitative polymerase chain reaction. Representative regulated genes were further analysed by in situ hybridization (ISH) on tissue microarrays. Expression analysis allowed the identification of a signature that differentiates AGC from EGC. In addition, comparison with normal gastric mucosa indicated that the majority of alterations associated with EGC are retained in AGC, and that further expression changes mark the transition from EGC to AGC. Finally, ISH analysis showed that representative genes, differentially expressed in the invasive areas of EGC and AGC, are not differentially expressed in the non-invasive areas of the same tumors. Our data are more directly compatible with a progression model of gastric carcinogenesis, whereby EGC and AGC may represent different molecular stages of the same tumor. Finally, the identification of an AGC-specific signature might help devising novel therapeutic strategies for advanced gastric cancer.
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Affiliation(s)
- M Vecchi
- IFOM Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
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Wang D, Lv Y, Guo Z, Li X, Li Y, Zhu J, Yang D, Xu J, Wang C, Rao S, Yang B. Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules. Bioinformatics 2006; 22:2883-9. [PMID: 16809389 DOI: 10.1093/bioinformatics/btl339] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
MOTIVATION Microarrays datasets frequently contain a large number of missing values (MVs), which need to be estimated and replaced for subsequent data mining. The focus of the paper is to study the effects of different MV treatments for cDNA microarray data on disease classification analysis. RESULTS By analyzing five datasets, we demonstrate that among three kinds of classifiers evaluated in this study, support vector machine (SVM) classifiers are robust to varied MV imputation methods [e.g. replacing MVs by zero, K nearest-neighbor (KNN) imputation algorithm, local least square imputation and Bayesian principal component analysis], while the classification and regression tree classifiers are sensitive in terms of classification accuracy. The KNNclassifiers built on differentially expressed genes (DEGs) are robust to the varied MV treatments, but the performances of the KNN classifiers based on all measured genes can be significantly deteriorated when imputing MVs for genes with larger missing rate (MR) (e.g. MR > 5%). Generally, while replacing MVs by zero performs relatively poor, the other imputation algorithms have little difference in affecting classification performances of the SVM or KNN classifiers. We further demonstrate the power and feasibility of our recently proposed functional expression profile (FEP) approach as means to handle microarray data with MVs. The FEPs, which are derived from the functional modules that are enriched with sets of DEGs and thus can be consistently identified under varied MV treatments, achieve precise disease classification with better biological interpretation. We conclude that the choice of MV treatments should be determined in context of the later approaches used for disease classification. The suggested exclusion criterion of ignoring the genes with larger MR (e.g. >5%), while justifiable for some classifiers such as KNN classifiers, might not be considered as a general rule for all classifiers.
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Affiliation(s)
- Dong Wang
- Department of Bioinformatics and Bio-pharmaceutical Key Laboratory of Heilongjiang Province and State, Harbin Medical University Harbin 150086, China
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Beisvag V, Lehre PK, Midelfart H, Aass H, Geiran O, Sandvik AK, Laegreid A, Komorowski J, Ellingsen O. Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data. Eur J Heart Fail 2006; 8:381-9. [PMID: 16753336 DOI: 10.1016/j.ejheart.2006.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Revised: 03/07/2006] [Accepted: 05/09/2006] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The objective of the present study was to use gene expression profiling, functional annotations and classification to identify aetiology-specific biological processes and potential molecular markers for different aetiologies of end-stage heart failure. METHODS AND RESULTS Individual left ventricular myocardial samples from eleven coronary artery disease and nine dilated cardiomyopathy transplant patients were co-hybridized with pooled RNA from four non-failing hearts on custom-made arrays of 7000 human genes. Significance analysis identified differential expression of 153 and 147 genes, respectively, in coronary artery disease or dilated cardiomyopathy versus non-failing hearts. Analysis of Gene Ontology biological process annotations indicated aetiology-specific patterns, primarily related to genes involved in catabolism and in regulation of protein kinase activity. Gene expression classifiers were obtained and used for class prediction of random samples of coronary artery diseased and dilated cardiomyopathic hearts. Best classifiers frequently included matrix metalloproteinase 3, fibulin 1, ATP-binding cassette, sub-family B member 1 and iroquois homeobox protein 5. CONCLUSION Combining functional annotation from microarray data and classification analysis constitutes a potent strategy to identify disease-specific biological processes and gene expression markers in e.g. end-stage coronary artery disease and dilated cardiomyopathy.
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Affiliation(s)
- Vidar Beisvag
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.
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Shi SL, Wang YY, Liang Y, Li QF. Effects of tachyplesin and n-sodium butyrate on proliferation and gene expression of human gastric adenocarcinoma cell line BGC-823. World J Gastroenterol 2006; 12:1694-8. [PMID: 16586536 PMCID: PMC4124342 DOI: 10.3748/wjg.v12.i11.1694] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the effects of tachyplesin and n-sodium butyrate on proliferation and gene expression of human gastric adenocarcinoma cell line BGC-823.
METHODS: Effects of tachyplesin and n-sodium
butyrate on proliferation of BGC-823 cells were determined with trypan blue dye exclusion test and HE staining. Effects of tachyplesin and n-sodium butyrate on cell cycle were detected by flow cytometry. Protein levels of c-erbB-2, c-myc, p53 and p16 were examined by immunocytochemistry.
RESULTS: The inhibiting effects were similar after 2.0 mg/L tachyplesin and 2.0 mmol/L n-sodium butyrate treatment, the inhibitory rate of cellular growth was 62.66% and 60.19% respectively, and the respective maximum mitotic index was decreased by 49.35% and 51.69% respectively. Tachyplesin and n-sodium butyrate treatment could markedly increase the proportion of cells at G0/G1 phase and decrease the proportion at S phase. The expression levels of oncogene c-erbB-2, c-myc, and mtp53 proteins were down-regulated while the expression level of tumor suppressor gene p16 protein was up-regulated after the treatment with tachyplesin or n-sodium butyrate. The effects of 1.0 mg/L tachyplesin in combination with 1.0 mmol/L n-sodium butyrate were obviously superior to their individual treatment in changing cell cycle distribution and expression of c-erbB-2, c-myc, mtp53 and p16 protein. The inhibitory rate of cellular growth of BGC-823 cells after combination treatment was 62.29% and the maximum mitotic index was decreased by 51.95%.
CONCLUSION: Tachyplesin as a differentiation inducer of tumor cells has similar effects as n-sodium butyrate on proliferation of tumor cells, expression of correlative oncogene and tumor suppressor gene. It also has a synergistic effect on differentiation of tumor cells.
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Affiliation(s)
- Song-Lin Shi
- The Key Laboratory of Chinese Ministry of Education for Cell Biology & Tumor Cell Engineering, School of Life Science, Xiamen University, Xiamen 361005, Fujian Province, China
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Wu MS, Lin YS, Chang YT, Shun CT, Lin MT, Lin JT. Gene expression profiling of gastric cancer by microarray combined with laser capture microdissection. World J Gastroenterol 2006; 11:7405-12. [PMID: 16437709 PMCID: PMC4725172 DOI: 10.3748/wjg.v11.i47.7405] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To examine the gene expression profile of gastric cancer (GC) by combination of laser capture microdissection (LCM) and microarray and to correlate the profiling with histological subtypes. METHODS Using LCM, pure cancer cells were procured from 45 cancerous tissues. After procurement of about 5000 cells, total RNA was extracted and the quality of RNA was determined before further amplification and hybridization. One microgram of amplified RNA was converted to cDNA and hybridized to cDNA microarray. RESULTS Among 45 cases, only 21 were qualified for their RNAs. A total of 62 arrays were performed. These included 42 arrays for cancer (21 cases with dye-swab duplication) and 20 arrays for non-tumorous cells (10 cases with dye-swab duplication) with universal reference. Analyzed data showed 504 genes were differentially expressed and could distinguish cancerous and non-cancerous groups with more than 99% accuracy. Of the 504 genes, trefoil factors 1, 2, and 3 were in the list and their expression patterns were consistent with previous reports. Immunohistochemical staining of trefoil factor 1 was also consistent with the array data. Analyses of the tumor group with these 504 genes showed that there were 3 subgroups of GC that did not correspond to any current classification system, including Lauren's classification. CONCLUSION By using LCM, linear amplification of RNA, and cDNA microarray, we have identified a panel of genes that have the power to discriminate between GC and non-cancer groups. The new molecular classification and the identified novel genes in gastric carcinogenesis deserve further investigations to elucidate their clinicopathological significance.
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Affiliation(s)
- Ming-Shiang Wu
- Department of Internal Medicine and Primary Care Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan, China
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17
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Tsai CJ, Herrera-Goepfert R, Tibshirani RJ, Yang S, Mohar A, Guarner J, Parsonnet J. Changes of Gene Expression in Gastric Preneoplasia following Helicobacter pylori Eradication Therapy. Cancer Epidemiol Biomarkers Prev 2006; 15:272-80. [PMID: 16492915 DOI: 10.1158/1055-9965.epi-05-0632] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Helicobacter pylori causes gastric preneoplasia and neoplasia. Eradicating H. pylori can result in partial regression of preneoplastic lesions; however, the molecular underpinning of this change is unknown. To identify molecular changes in the gastric mucosa following H. pylori eradication, we used cDNA microarrays (with each array containing approximately 30,300 genes) to analyze 54 gastric biopsies from a randomized, placebo-controlled trial of H. pylori therapy. The 54 biopsies were obtained from 27 subjects (13 from the treatment and 14 from the placebo group) with chronic gastritis, atrophy, and/or intestinal metaplasia. Each subject contributed one biopsy before and another biopsy 1 year after the intervention. Significant analysis of microarrays (SAM) was used to compare the gene expression profiles of pre-intervention and post-intervention biopsies. In the treatment group, SAM identified 30 genes whose expression changed significantly from baseline to 1 year after treatment (0 up-regulated and 30 down-regulated). In the placebo group, the expression of 55 genes differed significantly over the 1-year period (32 up-regulated and 23 down-regulated). Five genes involved in cell-cell adhesion and lining (TACSTD1 and MUC13), cell cycle differentiation (S100A10), and lipid metabolism and transport (FABP1 and MTP) were down-regulated over time in the treatment group but up-regulated in the placebo group. Immunohistochemistry for one of these differentially expressed genes (FABP1) confirmed the changes in gene expression observed by microarray. In conclusion, H. pylori eradication may stop or reverse ongoing molecular processes in the stomach. Further studies are needed to evaluate the use of these genes as markers for gastric cancer risk.
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Affiliation(s)
- Chiaojung Jillian Tsai
- Department of Health Research and Policy, Stanford University School, California 94305-5107, USA
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18
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Sandvik AK, Alsberg BK, Nørsett KG, Yadetie F, Waldum HL, Laegreid A. Gene expression analysis and clinical diagnosis. Clin Chim Acta 2006; 363:157-64. [PMID: 16168978 DOI: 10.1016/j.cccn.2005.05.046] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2005] [Revised: 04/28/2005] [Accepted: 05/16/2005] [Indexed: 01/23/2023]
Abstract
BACKGROUND A new basis for diagnostic tests is being provided by the vast amount of data on gene expression that are now becoming available through large-scale measurement of mRNA abundance. The insights gained from these resources are most likely going to provide both a better basic understanding of disease mechanisms, and to identify molecular markers for more precise diagnoses and for prediction of prognosis and treatment response. METHODS Some quantitative RT-PCR assays are utilized today for diagnosis of both malignant and non-malignant disease, but the use of gene expression measurements in clinical medicine can be expected to increase dramatically. CONCLUSIONS There are important technical issues that must be adequately solved in order to obtain robust assays, such as standardized protocols with appropriate quality controls that ensure reliable data for the specific samples being analysed and good inter-laboratory reproducibility.
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Affiliation(s)
- A K Sandvik
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim.
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Galamb O, Sipos F, Fischer K, Tulassay Z, Molnar B. The results of the expression array studies correlate and enhance the known genetic basis of gastric and colorectal cancer. CYTOMETRY. PART B, CLINICAL CYTOMETRY 2005; 68:1-17. [PMID: 16208682 DOI: 10.1002/cyto.b.20069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Gastric and colorectal cancers belong to the most frequent cancer types in the world today. This fact emphasizes the importance of identification of useful diagnostic and prognostic markers, in the earliest stage of the disease. The examination of gene expression profile in gastric and colorectal cancer may develop the bases of early diagnosis and of individual therapeutic strategies. In the microarray examinations done so far for these types of cancers, the expression of hundreds and thousands of genes were studied, however, both the sample collection and the results showed wide variations. The diversity of expression array methods and data analysis makes the comparison of microarray results difficult. Beside the exposition of the practical aspects of the chip technology, our aims are the systematization of data that are currently available in the international scientific literature and the description of the results in a comprehensive way. Microarray results show that the gene expression pattern, detected in gastric and colon cancers, highly depends on the histological type and heterogeneity of the sample, array type, and softwares, used for data analysis. Recent experiments point out not just the changes of the alterations of tumor suppression, apoptosis, cell-cycle regulation, and signal transduction, but tumor cell metabolism and cell-microenvironment interactions also. Results show connection to and make more complete the already known molecular background of gastric and colorectal cancers. Based on the accumulation of recent and further data, such kind of multifunctional diagnostic microarrays that can be suited for completing the conventional histological diagnostics and subtypization will certainly become available in the near future.
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Affiliation(s)
- Orsolya Galamb
- II Department of Medicine, Semmelweis University, Faculty of Medicine Budapest, Hungary.
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Velmurugan B, Mani A, Nagini S. Combination of S-allylcysteine and lycopene induces apoptosis by modulating Bcl-2, Bax, Bim and caspases during experimental gastric carcinogenesis. Eur J Cancer Prev 2005; 14:387-93. [PMID: 16030430 DOI: 10.1097/00008469-200508000-00012] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Combination chemoprevention by diet-derived agents that induce apoptosis is a promising strategy to control gastric cancer, the second most common malignancy worldwide. The present study was undertaken to investigate the apoptosis-inducing potential of a combination of S-allylcysteine (SAC), an organosulphur constituent of garlic and lycopene, a tomato carotenoid during N-methyl-N'-nitro-N-nitroso-guanidine (MNNG) and saturated sodium chloride (S-NaCl)-induced gastric carcinogenesis in Wistar rats using the apoptosis-associated proteins Bcl-2, Bax, Bim, caspase 8 and caspase 3 as markers. Animals administered MNNG followed by S-NaCl developed squamous cell carcinomas of the stomach associated with increased Bcl-2 expression and decreased expression of Bax, Bim, caspase 8 and caspase 3. Although SAC and lycopene alone significantly suppressed the development of gastric cancer, administration of SAC and lycopene in combination was more effective in inhibiting MNNG-induced stomach tumours and modulating the expression of apoptosis-associated proteins. Our results suggest that induction of apoptosis by SAC and lycopene combination represents one of the possible mechanisms that could account for their synergistic chemopreventive activity against gastric cancer.
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Affiliation(s)
- B Velmurugan
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar-608 002, Tamil Nadu, India
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Hofsli E, Thommesen L, Yadetie F, Langaas M, Kusnierczyk W, Falkmer U, Sandvik AK, Laegreid A. Identification of novel growth factor-responsive genes in neuroendocrine gastrointestinal tumour cells. Br J Cancer 2005; 92:1506-16. [PMID: 15846300 PMCID: PMC2361991 DOI: 10.1038/sj.bjc.6602535] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Targeting growth-regulatory pathways is a promising approach in cancer treatment. A prerequisite to the development of such therapies is characterisation of tumour growth regulation in the particular tumour cell type of interest. In order to gain insight into molecular mechanisms underlying proliferative responses in neuroendocrine (NE) gastrointestinal (GI) tumours, we investigated gene expression in human carcinoid BON cells after exposure to gastrin, hepatocyte growth factor (HGF), pituitary adenylate cyclase-activating polypeptide or epidermal growth factor. We particularly focused on gastrin- and HGF-induced gene expression, and identified 95 gastrin- and 101 HGF-responsive genes. The majority of these genes are known mediators of processes central in tumour biology, and a number of them have been associated with poor prognosis and metastasis in cancer patients. Furthermore, we identified 12 genes that were regulated by all four factors, indicating that they may be universally regulated during NE GI tumour cell proliferation. Our findings provide useful hypotheses for further studies aimed to search for new therapeutic targets as well as tumour markers in NE GI tumours.
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Affiliation(s)
- E Hofsli
- Department of Cancer Research and Molecular Medicine, Faculty of Medicine, Norwegian University of Science and Technology, Medisinsk Teknisk Forskningssenter, Trondheim N-7489, Norway.
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