Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders

Abstract

the mechanistic relevance of intergenic disease-associated genetic loci (IDAGL) containing highly statistically significant disease-linked SNPs remains unknown. Here, we present experimental and clinical evidence supporting the importantance of the role of IDAGL in human diseases. A targeted rt-PCr screen coupled with sequencing of purified PCr products detects widespread transcription at multiple IDAGL and identifies 96 small noncoding trans-regulatory rNAs of ~100-300 nt in length containing SNPs (snprNAs) associated with 21 common disorders. Multiple independent lines of experimental evidence support functionality of snprNAs by documenting their cell type-specific expression and evolutionary conservation of sequences, genomic coordinates and biological effects. Chromatin state signatures, expression profiling experiments and luciferase reporter assays demonstrate that many IDAGL are Polycomb-regulated long-range enhancers. expression of snprNAs in human and mouse cells markedly affects cellular behavior and induces allele-specific clinically relevant phenotypic changes: NLRP1-locus snprNAs rs2670660 exert regulatory effects on monocyte/macrophage transdifferentiation, induce prostate cancer (PC) susceptibility snprNAs and transform lowmalignancy hormone-dependent human PC cells into highly malignant androgen-independent PC. Q-PCr analysis and luciferase reporter assays demonstrate that snprNA sequences represent allele-specific "decoy" targets of microrNAs that function as SNP allele-specific modifiers of microrNA expression and activity. We demonstrate that trans-acting rNA molecules facilitating resistance to androgen depletion (rAD) in vitro and castration-resistant phenotype (CrP) in vivo of PC contain intergenic 8q24-locus SNP variants (rs1447295; rs16901979; rs6983267) that were recently linked with increased risk of PC. Q-PCr analysis of clinical samples reveals markedly increased and highly concordant (r = 0.896; p < 0.0001) snprNA expression levels in tumor tissues compared with the adjacent normal prostate [122-fold and 45-fold in Gleason 7 tumors (p = 0.03); 370-fold and 127-fold in Gleason 8 tumors (p = 0.0001) for NLRP1-locus and 8q24-locus snprNAs, respectively]. Our experiments indicate that rAD and Cr phenotype of human PC cells can be triggered by ncrNA molecules transcribed from the NLRP1-locus intergenic enhancer at 17p13 and by downstream activation of the 8q24-locus snprNAs. Our results define the IDAGL at 17p13 and 8q24 as candidate regulatory loci of rAD and Cr phenotypes of PC, reveal previously unknown molecular links between the innate immunity/inflammasome system and development of hormone-independent PC and identify novel molecular and genetic targets with diagnostic and therapeutic potentials, exploration of which should be highly beneficial for personalized clinical management of PC. Networks of intergenic long-range enhancers

Association of 8 Loci on Chromosome 8q24 with Prostate Carcinoma Risk in Northern Chinese Men

“…The alleles of rs6983267 are known to differentially bind transcription regulating elements such as TCF7L2/TCF4 (Ahmadiyeh et al, 2010;Wright et al, 2010). The downstream activation of corresponding snpRNAs have also been involved in the phenotypic orientation of prostate cancer (Glinskii et al, 2011). An in vivo functional study demonstrated that the cancer associated variant rs6983267 lies in a prostate enhancer sequence, of which expression mimics that of a nearby proto-oncogene Myc (Wasserman et al, 2010).…”

RNA-guided diagnostics and therapeutics for next-generation individualized nanomedicine

“…Transcriptional outputs from genomic regions around the 22,000 protein-coding genes in the human genome generate an average of 10 transcripts each, including transcripts from sense, antisense, intronic, intergenic, pseudogenes, retrotransposons, and repetitive elements sequences. Emerging experimental and clinical evidence is mechanistically linking novel classes of sncRNAs and lncRNAs to a broad spectrum of common, polygenic human disorders (11)(12)(13). However, the lack of reliable quantitative labora tory tests for measurements of lncRNAs and sncRNAs in archived, formalin-fixed paraffin-embedded (FFPE) human samples with sufficient specificity and sensitivity has significantly limited the development of clinically relevant noncoding RNA-based translational applications.…”

Malignant field expression signatures in biopsy samples at diagnosis predict the likelihood of lethal disease in patients with localized prostate cancer

“…[17][18][19][20] GES were built based on selection of co-regulated transcripts in various experimental conditions and clinically-relevant models, including prostate cancer predisposition and longevity models. [16][17][18][19][20] Underlying concept at this stage of the analysis was to identify GES with concordant expression profiles across multiple data sets. [17][18][19][20] Cox regression analysis was carried out to identify statistically significant candidate GES associated with patients' survival status.…”

“…All 6,144 genes were evaluated for association with clinical and pathological variables (except survival status) using correlation analysis. Different thresholds on the P-values (0.05; 0.01; 0.001) were used for selection of gene sets with common patterns of association and concordance analysis was performed using expression profiling data of snpRNA-driven cell line-based models of prostate cancer predisposition [15,16] to identify concordant and discordant GES in cell lines and clinical samples. [17][18][19][20] GES were built based on selection of co-regulated transcripts in various experimental conditions and clinically-relevant models, including prostate cancer predisposition and longevity models.…”