The functionally relevant role of sdRNA-19b and sdRNA-24 in prostate cancer

In recent studies small nucleolar RNAs (snoRNA) have been shown to be processed into smaller microRNA-like fragments known as sno-derived RNA (sdRNA). We recently identified 9 snoRNAs that contribute to prostate malignancy using The Cancer Genome Atlas (TCGA) patient prostate tumor next-generation sequencing datasets. These snoRNA were found to be processed into sdRNAs, heavily misexpressed in prostate cancer cell types 8140 and 8550, and shown to function by binding Ago proteins in order to impact mRNA translation. SdRNA-19b and sdRNA-24 in particular stood out as having significant differential expression in prostate cancer vs. control tissue. Interestingly, the targets for sdRNA-19b and sdRNA-24 were then predicted to be well known tumor suppressors and oncogenes. SdRNA-19b aligned with STAT5b, CDK6 and CD44 while sdRNA-24 aligned with were predicted to be RHOH, Timp3 and AR, all of which were confirmed through the use of luciferase assays. Additionally, our phenotypic assays show that over-expressions of sdRNA-19b and sdRNA-24 lead to increased cell proliferation and over expressions of sdRNA-19b lead to increased cell migration rates, indicating a direct impact on sdRNA levels to the proliferative and migratory ability of prostate cancer cells. Current results also strongly indicate that when sdRNA-19b and sdRNA-24 are inhibited they are significantly less likely to survive the presence of chemotherapeutic agents, providing a new potential target for effective chemotherapy treatment. In summary, our results indicate that sdRNA-19b and sdRNA-24 actively contribute to the malignant phenotype of prostate cancer through miRNA-like regulation

Characterization of novel small RNAs (sRNAs) contributing to the desiccation response of Salmonella enterica serovar Typhimurium

Noncoding RNA (ncRNA) modulation of gene expression has now been ubiquitously observed across all domains of life. An increasingly apparent role of ncRNAs is to coordinate changes in gene expressions in response to environmental stress. Salmonella enterica, a common food-born pathogen, is known for its striking ability to survive, adapt, and thrive in various unfavourable environments which makes it a particularly difficult pathogen to eliminate as well as an interesting model in which to study ncRNA contributions to cellular stress response. Mounting evidence now suggests that small RNAs (sRNAs) represent key regulators of Salmonella stress adaptation. Approximately 50-500 nucleotides in length, sRNAs regulate gene expression through complementary base pairing with molecular targets and have recently been suggested to outnumber protein-coding genes in bacteria. In this work, we employ small RNA transcriptome sequencing to characterize changes in the sRNA profiles of Salmonella in response to desiccation. In all, we identify 102 previously annotated sRNAs significantly differentially expressed during desiccation; and excitingly, 71 novel sRNAs likewise differentially expressed. Small transcript northern blotting and qRT-PCRs confirm the identities and expressions of several of our novel sRNAs, and computational analyses indicate the majority are highly conserved and structurally related to characterized sRNAs. Predicted sRNA targets include several proteins necessary for desiccation survival and this, in part, suggests a role for desiccation-regulated sRNAs in this stress response. Furthermore, we find individual knock-outs of two of the novel sRNAs identified herein, either sRNA1320429 or sRNA3981754, significantly impairs the ability of Salmonella to survive desiccation, confirming their involvements (and suggesting the potential involvements of other sRNAs we identify in this work) in the Salmonella response to desiccation161116431657CONSELHO NACIONAL DE DESENVOLVIMENTO CIENTÍFICO E TECNOLÓGICO - CNPQFUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULO - FAPESP302763/2014-7; 305804/2017-02014/17387-8; 2015/19400-4Funding was provided in part by NSF CAREER grant 1350064 (GMB) awarded by Division of Molecular and Cellular Biosciences (with cofunding provided by the NSF EPSCoR program). Graduate funding was also provided in part by Alabama Commission on Higher Education ALEPSCoR grants 150380 (JTR),160330 (VMK), and 180435 (DH). Postdoctoral funding was provided by São Paulo Research Foundation (FAPESP) Grants # 2014/17387-8 and # 2015/19400-4 (AC). A.S. Sant’Ana acknowledges the support of ‘Conselho Nacional de Desenvolvimento Cientifico e Tecnológico’ (CNPq) (Grants #302763/2014-7; #305804/2017-0); Alabama Commission on Higher Education [180435]; Alabama Commission on Higher Education [160330]; Alabama Commission on Higher Education [150380]; Conselho Nacional de Desenvolvimento Científico e Tecnológico [305804/2017-0]; Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas [2015/19400-4]; Fundo de Apoio ao Ensino, à Pesquisa e Extensão, Universidade Estadual de Campinas (BR) [2014/17387-8]; Conselho Nacional de Desenvolvimento Científico e Tecnológico (BR) [302763/2014-7

MicroRNA-like snoRNA-Derived RNAs (sdRNAs) Promote Castration-Resistant Prostate Cancer

We have identified 38 specifically excised, differentially expressed snoRNA fragments (sdRNAs) in TCGA prostate cancer (PCa) patient samples as compared to normal prostate controls. SnoRNA-derived fragments sdRNA-D19b and -A24 emerged among the most differentially expressed and were selected for further experimentation. We found that the overexpression of either sdRNA significantly increased PC3 (a well-established model of castration-resistant prostate cancer (CRPC)) cell proliferation, and that sdRNA-D19b overexpression also markedly increased the rate of PC3 cell migration. In addition, both sdRNAs provided drug-specific resistances with sdRNA-D19b levels correlating with paclitaxel resistance and sdRNA-24A conferring dasatinib resistance. In silico and in vitro analyses revealed that two established PCa tumor suppressor genes, CD44 and CDK12, represent targets for sdRNA-D19b and sdRNA-A24, respectively. This outlines a biologically coherent mechanism by which sdRNAs downregulate tumor suppressors in AR-PCa to enhance proliferative and metastatic capabilities and to encourage chemotherapeutic resistance. Aggressive proliferation, rampant metastasis, and recalcitrance to chemotherapy are core characteristics of CRPC that synergize to produce a pathology that ranks second in cancer-related deaths for men. This study defines sdRNA-D19b and -A24 as contributors to AR-PCa, potentially providing novel biomarkers and therapeutic targets of use in PCa clinical intervention