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Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy.

Strong MJ, Xu G, Coco J, Baribault C, Vinay DS, Lacey MR, Strong AL, Lehman TA, Seddon MB, Lin Z, Concha M, Baddoo M, Ferris M, Swan KF, Sullivan DE, Burow ME, Taylor CM, Flemington EK - PLoS Pathog. (2013)

Bottom Line: Epstein-Barr virus (EBV) is associated with roughly 10% of gastric carcinomas worldwide (EBVaGC).In four samples with the highest EBV coverage (hiEBVaGC - high EBV associated gastric carcinoma), transcripts from the BamHI A region comprised the majority of EBV reads.These results were confirmed in a separate cohort of 21 Vietnamese gastric carcinoma samples using qRT-PCR and on tissue samples using in situ hybridization and immunohistochemistry.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America.

ABSTRACT
Epstein-Barr virus (EBV) is associated with roughly 10% of gastric carcinomas worldwide (EBVaGC). Although previous investigations provide a strong link between EBV and gastric carcinomas, these studies were performed using selected EBV gene probes. Using a cohort of gastric carcinoma RNA-seq data sets from The Cancer Genome Atlas (TCGA), we performed a quantitative and global assessment of EBV gene expression in gastric carcinomas and assessed EBV associated cellular pathway alterations. EBV transcripts were detected in 17% of samples but these samples varied significantly in EBV coverage depth. In four samples with the highest EBV coverage (hiEBVaGC - high EBV associated gastric carcinoma), transcripts from the BamHI A region comprised the majority of EBV reads. Expression of LMP2, and to a lesser extent, LMP1 were also observed as was evidence of abortive lytic replication. Analysis of cellular gene expression indicated significant immune cell infiltration and a predominant IFNG response in samples expressing high levels of EBV transcripts relative to samples expressing low or no EBV transcripts. Despite the apparent immune cell infiltration, high levels of the cytotoxic T-cell (CTL) and natural killer (NK) cell inhibitor, IDO1, was observed in the hiEBVaGCs samples suggesting an active tolerance inducing pathway in this subgroup. These results were confirmed in a separate cohort of 21 Vietnamese gastric carcinoma samples using qRT-PCR and on tissue samples using in situ hybridization and immunohistochemistry. Lastly, a panel of tumor suppressors and candidate oncogenes were expressed at lower levels in hiEBVaGC versus EBV-low and EBV-negative gastric cancers suggesting the direct regulation of tumor pathways by EBV.

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Cluster analysis of EBV-associated gastric carcinoma samples.(A) A representative cohort of 32 gastric carcinoma samples (12 EBV-positive and 20 EBV-negative) were grouped using hierarchical clustering and are displayed with an expression heat map of the 490 genes that were found to be significantly differentially expressed in high EBV. (B) The cohort of 32 gastric carcinoma samples was divided into three categories (high EBV, low EBV, and negative). These categories were subjected to differential gene expression analysis using edgeR. The Venn diagram displays the numbers of all statistically significant differentially expressed genes. Statistical significance was determined by an adjusted P value<0.05.
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ppat-1003341-g007: Cluster analysis of EBV-associated gastric carcinoma samples.(A) A representative cohort of 32 gastric carcinoma samples (12 EBV-positive and 20 EBV-negative) were grouped using hierarchical clustering and are displayed with an expression heat map of the 490 genes that were found to be significantly differentially expressed in high EBV. (B) The cohort of 32 gastric carcinoma samples was divided into three categories (high EBV, low EBV, and negative). These categories were subjected to differential gene expression analysis using edgeR. The Venn diagram displays the numbers of all statistically significant differentially expressed genes. Statistical significance was determined by an adjusted P value<0.05.

Mentions: To investigate influences of EBV dependent alterations in tumor signaling pathways, we analyzed global cellular gene expression in all 12 EBV positive specimens plus an additional 20 randomly selected EBV negative samples. EBV gene expression data was not included in this analysis to ensure that clustering occurred based only on differences in cellular gene expression (i.e. that it occurred independently of biases incurred by the presence of EBV gene expression signatures). Strikingly, when the set of samples were analyzed using hierarchical clustering, the four gastric carcinoma samples with higher numbers of EBV reads (BR-4253, BR-4271, BR-4376, and BR-4298) formed its own well-separated group (Figure 7A). One of the EBV negative samples, BR-4294, clustered independently of the others and subsequent analysis revealed that this sample was likely an outlier (Figure S5). Nevertheless, this sample was retained in the subsequent differential expression analysis as a conservative measure.


Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy.

Strong MJ, Xu G, Coco J, Baribault C, Vinay DS, Lacey MR, Strong AL, Lehman TA, Seddon MB, Lin Z, Concha M, Baddoo M, Ferris M, Swan KF, Sullivan DE, Burow ME, Taylor CM, Flemington EK - PLoS Pathog. (2013)

Cluster analysis of EBV-associated gastric carcinoma samples.(A) A representative cohort of 32 gastric carcinoma samples (12 EBV-positive and 20 EBV-negative) were grouped using hierarchical clustering and are displayed with an expression heat map of the 490 genes that were found to be significantly differentially expressed in high EBV. (B) The cohort of 32 gastric carcinoma samples was divided into three categories (high EBV, low EBV, and negative). These categories were subjected to differential gene expression analysis using edgeR. The Venn diagram displays the numbers of all statistically significant differentially expressed genes. Statistical significance was determined by an adjusted P value<0.05.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3649992&req=5

ppat-1003341-g007: Cluster analysis of EBV-associated gastric carcinoma samples.(A) A representative cohort of 32 gastric carcinoma samples (12 EBV-positive and 20 EBV-negative) were grouped using hierarchical clustering and are displayed with an expression heat map of the 490 genes that were found to be significantly differentially expressed in high EBV. (B) The cohort of 32 gastric carcinoma samples was divided into three categories (high EBV, low EBV, and negative). These categories were subjected to differential gene expression analysis using edgeR. The Venn diagram displays the numbers of all statistically significant differentially expressed genes. Statistical significance was determined by an adjusted P value<0.05.
Mentions: To investigate influences of EBV dependent alterations in tumor signaling pathways, we analyzed global cellular gene expression in all 12 EBV positive specimens plus an additional 20 randomly selected EBV negative samples. EBV gene expression data was not included in this analysis to ensure that clustering occurred based only on differences in cellular gene expression (i.e. that it occurred independently of biases incurred by the presence of EBV gene expression signatures). Strikingly, when the set of samples were analyzed using hierarchical clustering, the four gastric carcinoma samples with higher numbers of EBV reads (BR-4253, BR-4271, BR-4376, and BR-4298) formed its own well-separated group (Figure 7A). One of the EBV negative samples, BR-4294, clustered independently of the others and subsequent analysis revealed that this sample was likely an outlier (Figure S5). Nevertheless, this sample was retained in the subsequent differential expression analysis as a conservative measure.

Bottom Line: Epstein-Barr virus (EBV) is associated with roughly 10% of gastric carcinomas worldwide (EBVaGC).In four samples with the highest EBV coverage (hiEBVaGC - high EBV associated gastric carcinoma), transcripts from the BamHI A region comprised the majority of EBV reads.These results were confirmed in a separate cohort of 21 Vietnamese gastric carcinoma samples using qRT-PCR and on tissue samples using in situ hybridization and immunohistochemistry.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology, Tulane University, New Orleans, Louisiana, United States of America.

ABSTRACT
Epstein-Barr virus (EBV) is associated with roughly 10% of gastric carcinomas worldwide (EBVaGC). Although previous investigations provide a strong link between EBV and gastric carcinomas, these studies were performed using selected EBV gene probes. Using a cohort of gastric carcinoma RNA-seq data sets from The Cancer Genome Atlas (TCGA), we performed a quantitative and global assessment of EBV gene expression in gastric carcinomas and assessed EBV associated cellular pathway alterations. EBV transcripts were detected in 17% of samples but these samples varied significantly in EBV coverage depth. In four samples with the highest EBV coverage (hiEBVaGC - high EBV associated gastric carcinoma), transcripts from the BamHI A region comprised the majority of EBV reads. Expression of LMP2, and to a lesser extent, LMP1 were also observed as was evidence of abortive lytic replication. Analysis of cellular gene expression indicated significant immune cell infiltration and a predominant IFNG response in samples expressing high levels of EBV transcripts relative to samples expressing low or no EBV transcripts. Despite the apparent immune cell infiltration, high levels of the cytotoxic T-cell (CTL) and natural killer (NK) cell inhibitor, IDO1, was observed in the hiEBVaGCs samples suggesting an active tolerance inducing pathway in this subgroup. These results were confirmed in a separate cohort of 21 Vietnamese gastric carcinoma samples using qRT-PCR and on tissue samples using in situ hybridization and immunohistochemistry. Lastly, a panel of tumor suppressors and candidate oncogenes were expressed at lower levels in hiEBVaGC versus EBV-low and EBV-negative gastric cancers suggesting the direct regulation of tumor pathways by EBV.

Show MeSH
Related in: MedlinePlus