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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

Gene Expression Alterations in Biliary Tract Cancers. Heat maps showing the top 40 overexpressed (red) and top 40 underexpressed (green) genes for (a) EHC, (b) IHC, and (c) GBC. (d) All malignant subtypes were also combined for analysis and compared in terms of gene expression with benign bile duct and gallbladder controls. Genes were ranked based on FDR values. (e) A Venn diagram is used to depict the relationship of transcriptional changes among biliary cancer subtypes. There were 165 common genes with significantly altered expression in all three biliary tract cancer subtypes.
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Figure 1: Gene Expression Alterations in Biliary Tract Cancers. Heat maps showing the top 40 overexpressed (red) and top 40 underexpressed (green) genes for (a) EHC, (b) IHC, and (c) GBC. (d) All malignant subtypes were also combined for analysis and compared in terms of gene expression with benign bile duct and gallbladder controls. Genes were ranked based on FDR values. (e) A Venn diagram is used to depict the relationship of transcriptional changes among biliary cancer subtypes. There were 165 common genes with significantly altered expression in all three biliary tract cancer subtypes.

Mentions: We analyzed alterations in gene expression in EHC, IHC, and GBC compared with non-cancerous bile duct or gallbladder controls using the Human Genome U133A GeneChip. Figure 1 depicts the 40 top ranking overexpressed and underexpressed genes for (a) extrahepatic cholangiocarcinoma, (b) IHC, and (c) GBC. Ranking was based on FDR values. Table 2 summarizes the extent of gene expression alterations for each type of biliary tract cancer. In the EHC specimens, differential expression was noted in 545 genes compared with 2,354 in IHC and 1,281 in GBC (See additional files 1, additional file 2, and additional file 3). There was a near equal distribution of overexpressed and underexpressed genes for each tumor type. However, higher fold changes in expression levels were seen more commonly with underexpressed genes. In particular, depending on cancer subtype, 16–22% of genes with decreased expression had greater than 10-fold changes expression levels compared with controls. Conversely, only 2–12% of genes with increased expression had alterations of 10-fold or greater (Table 2).


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)

Gene Expression Alterations in Biliary Tract Cancers. Heat maps showing the top 40 overexpressed (red) and top 40 underexpressed (green) genes for (a) EHC, (b) IHC, and (c) GBC. (d) All malignant subtypes were also combined for analysis and compared in terms of gene expression with benign bile duct and gallbladder controls. Genes were ranked based on FDR values. (e) A Venn diagram is used to depict the relationship of transcriptional changes among biliary cancer subtypes. There were 165 common genes with significantly altered expression in all three biliary tract cancer subtypes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Gene Expression Alterations in Biliary Tract Cancers. Heat maps showing the top 40 overexpressed (red) and top 40 underexpressed (green) genes for (a) EHC, (b) IHC, and (c) GBC. (d) All malignant subtypes were also combined for analysis and compared in terms of gene expression with benign bile duct and gallbladder controls. Genes were ranked based on FDR values. (e) A Venn diagram is used to depict the relationship of transcriptional changes among biliary cancer subtypes. There were 165 common genes with significantly altered expression in all three biliary tract cancer subtypes.
Mentions: We analyzed alterations in gene expression in EHC, IHC, and GBC compared with non-cancerous bile duct or gallbladder controls using the Human Genome U133A GeneChip. Figure 1 depicts the 40 top ranking overexpressed and underexpressed genes for (a) extrahepatic cholangiocarcinoma, (b) IHC, and (c) GBC. Ranking was based on FDR values. Table 2 summarizes the extent of gene expression alterations for each type of biliary tract cancer. In the EHC specimens, differential expression was noted in 545 genes compared with 2,354 in IHC and 1,281 in GBC (See additional files 1, additional file 2, and additional file 3). There was a near equal distribution of overexpressed and underexpressed genes for each tumor type. However, higher fold changes in expression levels were seen more commonly with underexpressed genes. In particular, depending on cancer subtype, 16–22% of genes with decreased expression had greater than 10-fold changes expression levels compared with controls. Conversely, only 2–12% of genes with increased expression had alterations of 10-fold or greater (Table 2).

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