Inferred inactivation of the Cftr gene in the duodena of mice exposed to hexavalent chromium (Cr(VI)) in drinking water supports its tumor-suppressor status and implies its potential role in Cr(VI)-induced carcinogenesis of the small intestines

Abstract

Carcinogenicity of hexavalent chromium [Cr (VI)] has been supported by a number of epidemiological and animal studies; however, its carcinogenic mode of action is still incompletely understood. To identify mechanisms involved in cancer development, we analyzed gene expression data from duodena of mice exposed to Cr(VI) in drinking water. This analysis included (i) identification of upstream regulatory molecules that are likely responsible for the observed gene expression changes, (ii) identification of annotated gene expression data from public repositories that correlate with gene expression changes in duodena of Cr(VI)-exposed mice, and (iii) identification of hallmark and oncogenic signature gene sets relevant to these data. We identified the inactivated CFTR gene among the top scoring upstream regulators, and found positive correlations between the expression data from duodena of Cr(VI)-exposed mice and other datasets in public repositories associated with the inactivation of the CFTR gene. In addition, we found enrichment of signatures for oncogenic signaling, sustained cell proliferation, impaired apoptosis and tissue remodeling. Results of our computational study support the tumor-suppressor role of the CFTR gene. Furthermore, our results support human relevance of the Cr(VI)-mediated carcinogenesis observed in the small intestines of exposed mice and suggest possible groups that may be more vulnerable to the adverse outcomes associated with the inactivation of CFTR by hexavalent chromium or other agents. Lastly, our findings predict, for the first time, the role of CFTR inactivation in chemical carcinogenesis and expand the range of plausible mechanisms that may be operative in Cr(VI)-mediated carcinogenesis of intestinal and possibly other tissues.

Keywords: CFTR; Carcinogenesis; Chromium; Duodenal cancer; Toxicogenomics.

Figure 1. Upstream regulators inferred from differentially expressed genes in the duodena of mice exposed to hexavalent chromium in drinking water for 8 days.

Upstream regulators are ordered based on absolute values of Z-scores (A) and p-values (B). CFTR ranks 3^rd (A) and 11^th (B) among the inferred upstream regulators. A – color coding indicates Z scores; B- color coding indicates enrichment p-values. Dots: (A) |Z|<2; (B): p>0.05

Figure 2. Upstream regulators inferred from differentially expressed genes in the duodena of mice exposed to hexavalent chromium in drinking water for 91 days.

Upstream regulators are ordered based on absolute values of Z-scores (A) and p-values (B).CFTR ranks 15^th (A) and 12^th (B) among the inferred upstream regulators. A – color coding indicates Z scores; B- color coding indicates enrichment p-values. Dots: (A) |Z|<2; (B): p>0.05

Figure 3

Heatmap depicting differentially expressed genes that support inactivated status of Cftr in the duodena of mice exposed to hexavalent chromium for 8 days (A) and 91 days (B). Color coding indicates log expression values (green-red) and CFTR upstream activator z-score (blue-white-red).

Figure 4. Differentially expressed genes supporting inactivated status of Cftr in the duodena of mice exposed to hexavalent chromium for: (A) 8 days at 60 ppm; (B) 91 days 170 ppm.

Color coding: Green shapes- down-regulated; red shapes- up-regulated; blue shape- inferred inactivated; blue edges- activating relationship consistent with prediction; brown edges- inactivating relationship consistent with prediction; yellow edge- relationship inconsistent with prediction. More details on figure legend are available at: https://qiagen.secure.force.com/KnowledgeBase/KnowledgeIPAPage?id=kA41i000000L5rTCAS

Figure 5. Correlation of biosets for the duodena of mice exposed to Cr(VI) and the ilea of mice with Cftr-knockout.

Exposure: 60 mg/L SDD for 8 days. Depicted are numbers of unique and overlapping genes between the two datasets and statistical significance of their overlaps. P-values are determined using the running Fischer test that is implement in BSCE.

Figure 6. Hallmark Gene Sets (H) enriched in the duodena of mice exposed to SDD for 8 days at 0.3–520 mg/L.

(p-value<0.01 and FDR q-value<0.1. Color coding: concentration of SDD. Description of gene sets is available at: http://www.gsea-msigdb.org/gsea/msigdb/index.jsp

Figure 7. Hallmark Gene Sets (H) enriched in the duodena of mice exposed to SDD for 91 days at 0.3–520 mg/L.

(p-value<0.01 and FDR q-value<0.1. Color coding: concentration of SDD. Description of gene sets is available at: http://www.gsea-msigdb.org/gsea/msigdb/index.jsp