Pan-cancer chromatin analysis of the human vtRNA genes uncovers their association with cancer biology

Abstract

Background: The vault RNAs (vtRNAs) are a class of 84-141-nt eukaryotic non-coding RNAs transcribed by RNA polymerase III, associated to the ribonucleoprotein complex known as vault particle. Of the four human vtRNA genes, vtRNA1-1, vtRNA1-2 and vtRNA1-3, clustered at locus 1, are integral components of the vault particle, while vtRNA2-1 is a more divergent homologue located in a second locus. Gene expression studies of vtRNAs in large cohorts have been hindered by their unsuccessful sequencing using conventional transcriptomic approaches. Methods: VtRNA expression in The Cancer Genome Atlas (TCGA) Pan-Cancer cohort was estimated using the genome-wide DNA methylation and chromatin accessibility data (ATAC-seq) of their genes as surrogate variables. The association between vtRNA expression and patient clinical outcome, immune subtypes and transcriptionally co-regulated gene programs was analyzed in the dataset. Results: VtRNAs promoters are enriched in transcription factors related to viral infection. VtRNA2-1 is likely the most independently regulated homologue. VtRNA1-1 has the most accessible chromatin, followed by vtRNA1-2, vtRNA2-1 and vtRNA1-3. VtRNA1-1 and vtRNA1-3 chromatin status does not significantly change in cancer tissues. Meanwhile, vtRNA2-1 and vtRNA1-2 expression is widely deregulated in neoplastic tissues and its alteration is compatible with a broad oncogenic role for vtRNA1-2, and both tumor suppressor and oncogenic functions for vtRNA2-1. Yet, vtRNA1-1, vtRNA1-2 and vtRNA2-1 promoter DNA methylation predicts a shorter patient overall survival cancer-wide. In addition, gene ontology analyses of vtRNAs co-regulated genes identify a chromosome regulatory domain, epithelial differentiation, immune and thyroid cancer gene sets for specific vtRNAs. Furthermore, vtRNA expression patterns are associated with cancer immune subtypes and vtRNA1-2 expression is positively associated with cell proliferation and wound healing. Conclusions: Our study presents the landscape of vtRNA chromatin status cancer-wide, identifying co-regulated gene networks and ontological pathways associated with the different vtRNA genes that may account for their diverse roles in cancer.

Small but Powerful: The Human Vault RNAs as Multifaceted Modulators of Pro-Survival Characteristics and Tumorigenesis

“…In tumors, the vtRNA1-1 paralogue usually has the lowest levels of promoter methylation and the highest chromatin accessibility [ 68 ]. Indeed, in cancer cell lines, vtRNA1-1 is commonly the most strongly expressed among the four vault RNAs [ 47 ].…”

“…On the contrary, its function is probably so crucial that it has been impossible so far to KO vtRNA1-2 to perform single-gene deletion analysis in human cell lines (our unpublished data). The most relevant information regarding vtRNA1-2 comes from The Cancer Genome Atlas data analysis, specifically the methylation state of its promoter [ 68 , 72 , 73 ]. The expression of vault RNA1-2 on average is suppressed in tumors compared to normal tissues according to the elevated level of promoter methylation [ 68 , 74 , 75 ].…”

“…The most relevant information regarding vtRNA1-2 comes from The Cancer Genome Atlas data analysis, specifically the methylation state of its promoter [ 68 , 72 , 73 ]. The expression of vault RNA1-2 on average is suppressed in tumors compared to normal tissues according to the elevated level of promoter methylation [ 68 , 74 , 75 ]. This trend of gene silencing in neoplastic tissue is characteristic of tumor suppressor genes, and based on these data, it is reasonable to speculate about vtRNA1-2 being an anti-oncogene [ 68 ].…”

“…The expression of vault RNA1-2 on average is suppressed in tumors compared to normal tissues according to the elevated level of promoter methylation [ 68 , 74 , 75 ]. This trend of gene silencing in neoplastic tissue is characteristic of tumor suppressor genes, and based on these data, it is reasonable to speculate about vtRNA1-2 being an anti-oncogene [ 68 ]. Nevertheless, in liver-derived metastasis, vtRNA1-2 levels are as high as the pro-proliferative vtRNA1-1 and, thus, significantly upregulated compared to the surrounding healthy liver tissue ( Figure 2 ).…”

“…However, this conflicting role of vtRNA2-1-derived fragments was not unanticipated since the vtRNA2-1 expression is inconsistent and regulated in a cancer type-specific manner. More precisely, it is upregulated or unaffected in the cancer of all tissues, except for kidney tumors [ 68 ]. Nevertheless, excluding renal cancer, overall miR886-3p, similarly to its precursor vtRNA2-1, suggests a tumor suppressor role.…”