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Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract.

Miller G, Socci ND, Dhall D, D'Angelica M, DeMatteo RP, Allen PJ, Singh B, Fong Y, Blumgart LH, Klimstra DS, Jarnagin WR - J. Exp. Clin. Cancer Res. (2009)

Bottom Line: Results were confirmed by RT-PCR.Clinical-pathologic correlation was made using functional over-representation analysis of the top 100 mutations associated with each variable.The findings have implications for identification of therapeutic targets, screening, and prognostication.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. george.miller@med.nyu.edu

ABSTRACT

Background: The pathogenesis of biliary cancers is ill-defined. This study investigates changes in gene expression and copy number in biliary cancers and correlates these changes with anatomical site of origin, histopathology and outcome.

Methods: We performed gene expression and CGH analysis on 34 biliary tract cancer specimens. Results were confirmed by RT-PCR. Clinical-pathologic correlation was made using functional over-representation analysis of the top 100 mutations associated with each variable.

Results: There were 545 genes with altered expression in extrahepatic cholangiocarcinoma, 2,354 in intrahepatic cholangiocarcinoma, and 1,281 in gallbladder cancer. Unsupervised hierarchical clustering analysis indicated there was no difference in the global gene expression patterns between each biliary cancer subgroup. CGH analysis revealed that short segments of chromosomes 1p, 3p, 6q, 8p, 9p, and 14q were commonly deleted across all cancer subtypes. Commonly amplified regions included segments of 1q, 3q, 5p, 7p, 7q, 8q, and 20q. Over-representation analysis revealed an association between altered expression of functional gene groupings and pathologic features.

Conclusion: This study defined regions of the genome associated with changes in DNA copy number and gene expression in specific subtypes of biliary cancers. The findings have implications for identification of therapeutic targets, screening, and prognostication.

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Related in: MedlinePlus

Real-Time PCR Based Validation of Gene Expression Findings. To confirm the gene expression changes in biliary tract cancers identified on microarray analysis, selected genes were tested in tumor and control specimens by RT PCR and normalized to HRPT which is similarly expressed in tumors and normal biliary epithelia. Results are shown for (g) IL6, (h) FOSB, (i) CDKN1C, (j) NR4A2, and (k) DLC.
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Figure 4: Real-Time PCR Based Validation of Gene Expression Findings. To confirm the gene expression changes in biliary tract cancers identified on microarray analysis, selected genes were tested in tumor and control specimens by RT PCR and normalized to HRPT which is similarly expressed in tumors and normal biliary epithelia. Results are shown for (g) IL6, (h) FOSB, (i) CDKN1C, (j) NR4A2, and (k) DLC.

Mentions: In addition, to externally validate our data, selected differentially expressed genes were measured for transcript levels in biliary carcinoma specimens and in normal biliary epithelial controls using quantitative reverse transcriptase PCR. We assayed 11 genes with differing biologic functions and involvement in diverse molecular pathways but with known importance in carcinogenesis. These included genes which were overexpressed in EHC (SRDA21, STAT1, UBD, TYMS), underexpressed in EHC (FOSB, CDKN1C, IL6), overexpressed in IHC (SRDA21, STAT1, UBD, TYMS), underexpressed in IHC (DLC1, NR4A2, IL6), and overexpressed in GBC (UBD, TYMS, CDC2, CCNB2). PCR data was normalized to HPRT which was expressed at similar levels in both the cancerous and the control biliary epithelium (not shown). Results are shown in Figures (3a–f, 4g–k) and, for each gene tested, confirm the Affymetrix U133A gene expression array data. The array-based CGH results were internally validated by correlation of the X chromosome copy number with patient gender.


Genome wide analysis and clinical correlation of chromosomal and transcriptional mutations in cancers of the biliary tract.

Miller G, Socci ND, Dhall D, D'Angelica M, DeMatteo RP, Allen PJ, Singh B, Fong Y, Blumgart LH, Klimstra DS, Jarnagin WR - J. Exp. Clin. Cancer Res. (2009)

Real-Time PCR Based Validation of Gene Expression Findings. To confirm the gene expression changes in biliary tract cancers identified on microarray analysis, selected genes were tested in tumor and control specimens by RT PCR and normalized to HRPT which is similarly expressed in tumors and normal biliary epithelia. Results are shown for (g) IL6, (h) FOSB, (i) CDKN1C, (j) NR4A2, and (k) DLC.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2698861&req=5

Figure 4: Real-Time PCR Based Validation of Gene Expression Findings. To confirm the gene expression changes in biliary tract cancers identified on microarray analysis, selected genes were tested in tumor and control specimens by RT PCR and normalized to HRPT which is similarly expressed in tumors and normal biliary epithelia. Results are shown for (g) IL6, (h) FOSB, (i) CDKN1C, (j) NR4A2, and (k) DLC.
Mentions: In addition, to externally validate our data, selected differentially expressed genes were measured for transcript levels in biliary carcinoma specimens and in normal biliary epithelial controls using quantitative reverse transcriptase PCR. We assayed 11 genes with differing biologic functions and involvement in diverse molecular pathways but with known importance in carcinogenesis. These included genes which were overexpressed in EHC (SRDA21, STAT1, UBD, TYMS), underexpressed in EHC (FOSB, CDKN1C, IL6), overexpressed in IHC (SRDA21, STAT1, UBD, TYMS), underexpressed in IHC (DLC1, NR4A2, IL6), and overexpressed in GBC (UBD, TYMS, CDC2, CCNB2). PCR data was normalized to HPRT which was expressed at similar levels in both the cancerous and the control biliary epithelium (not shown). Results are shown in Figures (3a–f, 4g–k) and, for each gene tested, confirm the Affymetrix U133A gene expression array data. The array-based CGH results were internally validated by correlation of the X chromosome copy number with patient gender.

Bottom Line: Results were confirmed by RT-PCR.Clinical-pathologic correlation was made using functional over-representation analysis of the top 100 mutations associated with each variable.The findings have implications for identification of therapeutic targets, screening, and prognostication.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA. george.miller@med.nyu.edu

ABSTRACT

Background: The pathogenesis of biliary cancers is ill-defined. This study investigates changes in gene expression and copy number in biliary cancers and correlates these changes with anatomical site of origin, histopathology and outcome.

Methods: We performed gene expression and CGH analysis on 34 biliary tract cancer specimens. Results were confirmed by RT-PCR. Clinical-pathologic correlation was made using functional over-representation analysis of the top 100 mutations associated with each variable.

Results: There were 545 genes with altered expression in extrahepatic cholangiocarcinoma, 2,354 in intrahepatic cholangiocarcinoma, and 1,281 in gallbladder cancer. Unsupervised hierarchical clustering analysis indicated there was no difference in the global gene expression patterns between each biliary cancer subgroup. CGH analysis revealed that short segments of chromosomes 1p, 3p, 6q, 8p, 9p, and 14q were commonly deleted across all cancer subtypes. Commonly amplified regions included segments of 1q, 3q, 5p, 7p, 7q, 8q, and 20q. Over-representation analysis revealed an association between altered expression of functional gene groupings and pathologic features.

Conclusion: This study defined regions of the genome associated with changes in DNA copy number and gene expression in specific subtypes of biliary cancers. The findings have implications for identification of therapeutic targets, screening, and prognostication.

Show MeSH
Related in: MedlinePlus