Integrative genomic approaches to dissect clinically-significant relationships between the VDR cistrome and gene expression in primary colon cancer

- VDR is commonly and uniquely down-regulated in the colon cancer TCGA cohort therefore supporting VDR binding-gene expression (cistrome-transcriptome) relationships.
- Re-analyses of VDR ChIP-Seq in LS180 colon cancer cells revealed 1809 significant 1,25(OH)2D3 induced VDR binding peaks that mapped to 672 unique genes including DOCK1, LGALS4 and CA9.
- Examination of these 672 genes in the TCGA colon cancer cohort of 286 tumors a significant correlation with VDR and revealed 27 commonly and significantly genes that associated with worse tumor grade.
- Kaplan-Meier analyses identified significant relationships with disease free survival for example with LGALS4 expression and male patients.
- These findings support both positive and negative cistrome-transcriptome relationships between VDR and target genes that are clinically significant and suggest that in the clinical setting that, in the presence of physiological levels of the ligand, that the level of VDR is a stronger determinant of tumor outcome.

Recently, we undertook a pan-cancer analyses of the nuclear hormone receptor (NR) superfamily in The Cancer Genome Atlas (TCGA), and revealed that the vitamin D receptor (NR1I1/VDR) was commonly and significantly down-regulated specifically in colon adenocarcinoma cohort (COAD). To examine the consequence of down-regulated VDR expression we re-analyzed VDR chromatin immunoprecipitation sequencing (ChIP-Seq) data from LS180 colon cancer cells (GSE31939). This analysis identified 1809 loci that displayed significant (p.adj < 0.01) differential binding of the VDR in response 1,25(OH)2D3 treatment; 947 peaks annotated to 672 genes. We examined expression patterns in the COAD cohort of 286 tumors compared to 41 normal samples and revealed that VDR bound genes were significantly positively correlated to VDR expression compared to the background transcriptome, suggesting direct regulation by VDR. Gene set enrichment analyses revealed significant enrichment for genes known to be regulated by a number of other transcription factors including SMADs and JUN. Filtering VDR associated genes for those that were commonly and significantly altered in COAD revealed a cohort of 27 differentially expressed genes. The expression patterns of these genes clustered tumors and significantly associated with disease free survival. For instance, males with low expression of Lectin, Galactoside Binding Soluble 4 (LGALS4, encodes the colon tumor suppressor, Galactin 4) had significantly shorted disease free survival. These analyses suggest that reduced expression of VDR in colon cancer (but neither loss nor mutation) changes the actions of the VDR by both dampening the expression of tumor suppressors (e.g. LGALS4) whilst either stabilizing or not down-regulating expression of oncogenes (e.g. Carbonic Anhydrase 9 (CA9)). These integrative genomic approaches are relatively generic and applicable to the study of any transcription factor.