Comparative microRNA Profiling of Prostate Carcinomas with Increasing Tumor Stage by Deep Sequencing

Abstract

MicroRNAs (miRNA) posttranscriptionally regulate gene expression and are important in tumorigenesis. Previous deep sequencing identified the miRNA profile of prostate carcinoma versus nonmalignant prostate tissue. Here, we generated miRNA expression profiles of prostate carcinoma by deep sequencing, with increasing tumor stage relative to corresponding nonmalignant and healthy prostate tissue, and detected clearly changed miRNA expression patterns. The miRNA profiles of the healthy and nonmalignant tissues were consistent with our previous findings, indicating a high fidelity of the method employed. In the tumors, quantitative real-time PCR (qRT-PCR) analysis of 40 paired samples of prostate carcinoma versus normal tissue revealed significant upregulation of miR-20a, miR-148a, miR-200b, and miR-375 and downregulation of miR-143 and miR-145. Hereby, miR-375 increased from normal to organ-confined tumors (pT2 pN0), slightly decreased in tumors with extracapsular growth (pT3 pN0), but was then expressed again at higher levels in lymph node metastasizing (pN1) tumors. The sequencing data for miR-375 were confirmed by Northern blotting and qRT-PCR. The regulation for other selected miRNAs could, however, not be confirmed by qRT-PCR in individual tumor stages. MiR-200b, in addition to miR-200c and miR-375 reduced the expression of SEC23A. Interestingly, miR-375, found by sequencing in pT2 upregulated by us and others in tumor versus normal tissue, and miR-15a, found by sequencing in pT2 and pT3 and in the metastasizing tumors, target the phosphatases PHLPP1 and PHLPP2, respectively. PHLPP1 and PHLPP2 dephosphorylate members of the AKT family of signal transducers, thereby inhibiting cell growth. Coexpression of miR-15a and miR-375 resulted in downregulation of PHLPP1/2 and strongly increased prostate carcinoma cell growth.Implications: These genomic data reveal relevant miRNAs in prostate cancer that may have biomarker and therapeutic potential. Mol Cancer Res; 12(2); 250-63. Ó2013 AACR. IntroductionProstate carcinoma is the second most frequently diagnosed malignancy and a leading cause of cancer-related death in men worldwide (1). The underlying mechanisms resulting in invasive growth after dissemination of the primary tumor from the initial site in the prostate are not completely understood. MicroRNAs (miRNAs) are now recognized as contributing factors to the induction, growth, and metastasis

Roles of the canonical myomiRs miR-1, -133 and -206 in cell development and disease

“…Importantly, such deep sequencing analyses also question the canonical view that miR133b is not expressed in cardiac tissue, reinforcing the need to employ sensitive and accurate analysis to extend our understanding of miR involvement in biological processes. Discrepancies in miR profiles detected between deep sequencing analysis of liver cancer [344] and microarray/Taqman expression profiling [95] , and in comparison of level 3 expression data from the Cancer Genome Atlas (TCGA) with deep sequence data from ovarian cancer patients [119] prostate tumors from individual patients by deep sequencing revealed that the expression of numerous miRs changed according to tumor stage [125] ; however qRTPCR of individual miRs at each tumor stage could not consistently confirm these alterations. A detailed survey of miRs using qRTPCR accompanied by in situ hybridization to confirm the identity of the changed miR expression in matched prostate tumor tissue found less than 50% identity between major altered species when compared with deep sequencing analysis of pooled tumors by the same authors [126] .…”

“…Several large cohort studies have examined the changes in expressed miR networks in a variety of cancers. Navon et al [95] , Hart et al [125] , Han et al [127] , Itesako et al [128] and Volinia et al [145] noted that the downregulated expression of the miR-133/-1/-206 genes is associated with a variety of solid tissue cancers, with numerous other miRs also having highly significant oncogenic roles in particular cancer types. In sum, the downregulation of the various myomiRs contributes significantly to the upregulation of oncogenic proteins linked to regulation of cell cycle progression in solid tumors, sarcomas and carcinomas.…”

Prostasomes as a source of diagnostic biomarkers for prostate cancer

“…Prostasome-associated miRNA PCa markers miRNAs regulate the expression of protein-coding genes at the translational level (38,94), and miRNA expression is altered by epigenetic repression, genomic deletion, amplification, or mutation in many types of cancer, including PCa (95,96). The ability of some miRNAs to inhibit translation of oncogenes and tumor suppressors may explain their involvement in carcinogenesis.…”

Novel RNA Markers in Prostate Cancer: Functional Considerations and Clinical Translation

“…Other analyses revealed the association of miRNA expression with distinct PCa: for instance, miR-375 expression was reported to be dependent on pT and pN status (TNM staging system) of PCa patients, with the highest enrichment in pN1 tumors [16]. Moreover, ten miRNAs (including miR-145 , miR-221 , and miR-222 ) were downregulated and five (including miR-375 and miR-96 ) upregulated in advanced PCa, whereas miR-96 was associated with tumor recurrence after radical prostatectomy [17].…”

“…The authors suggested that miR-375 -mediated SEC23A downregulation impairs cellular immunogenicity of PCa by reducing HLA class I cell surface receptors [19]. MiR-375 was also shown to downregulate the phosphatase PHLPP2 and to strongly increase prostate carcinoma cell growth [16]. MiR-141 , which is upregulated in PCa tissue, was found to downregulate the gene coding for the nuclear receptor subfamily 0, group B, member 2 ( NR0B2 ) in prostate epithelial cells.…”