Comprehensive Analysis Of miRNA Profiles Research Articles

Comprehensive analysis of miRNA profiles reveals the role of Schistosoma japonicum miRNAs at different developmental stages

Schistosomiasis is an important zoonotic disease affecting up to 40 kinds of animals and 250 million people. It has been reported that the miRNAs play a role in the metabolism, differentiation, development and reproduction in many organisms. However, the roles of miRNAs regulating the development, maturation and production in schistosome in both females and males remains unclear. Here we present the dynamic transcriptome analysis of all 79 known Schistosoma japonicum miRNAs from pairing to production, including 14 days post-infection (dpi), 16, 18, 20, 22, 24, 26, 28 dpi female and male, by small RNA sequencing. The miRNA expression profiles showed time-related characteristics in male and female from paring to production, which could be clustered into three patterns, characterized by pairing stage highly expressed (cluster 1), maturating stage highly expressed (cluster 2), and egg producing stage highly expressed (cluster 3). The enrichment of miRNA cluster targeted genes in female and male were distinctly different. Network analysis of miRNAs and their target regulation showed that cluster 1 had 15 miRNAs involved in the regulation of interaction, communication, immune response in female–male and parasite–host. The other 11 miRNAs were involved in gender differentiation and the meiotic cell cycle process. In cluster 2, 11 miRNAs were involved in development and sexual maturation. In cluster 3, 45 miRNAs possibly regulate metabolism and synthesis of the substance for egg production. Analysis of the miRNA regulation network would contribute to understanding the molecular mechanism in S. japonicum development and egg production.

Abstract 3075: Analysis of microRNA profiles involved in the resistance to trifluridine

Abstract Background: Trifluridine (FTD) is a key component of the novel oral antitumor drug trifluridine/tipiracil, which was approved for the treatment of patients with metastatic colorectal cancer refractory to standard chemotherapies. A comprehensive analysis of miRNA profiles was performed in cell lines resistant to FTD established by ourselves, in order to explore the underlying mechanisms of resistance to the drug. Method: We established subline resistance to FTD through continuous administration and increasing dose of the drug for 5 months using the colorectal cancer cell line DLD-1. Total RNA was extracted at intervals whilst establishing FTD resistant sublines, and miRNA expression was analyzed by microarray. The expression of miRNA that was significantly downregulated in the FTD resistant subline was knocked down to test its involvement in resistance to FTD. Cell viability was evaluated by crystal violet cytotoxicity test. Results: The established FTD-resistant sublines showed more than 22-fold higher resistance to FTD and no cross-resistance to 5-FU. miRNA and mRNA clustered in the genome locus located in chromosome 9, 9p22.32 were downregulated in the FTD-resistant cell line, one of which was the miRNA let-7d-5p, which is one of the let-7 family and is known to target oncogenes and several key components of the cell cycle and cell proliferation. Anti-let-7d-5p treated DLD-1 was less sensitive to FTD than compared to control. The IC50 values of FTD were 16.8 µM and 7.6 µM for the anti-let-7d-5p treated cells and control respectively. On the other hand, overexpression of let-7d-5p in DLD-1 using let-7d-5p mimic increased the sensitivity to FTD compared to control. The IC50 values of FTD were 3.7 µM and 13.9 µM in the let-7d-5p overexpression cells and control respectively. 5FU sensitivity was only altered slightly in anti- let-7d-5p treated or let-7d-5p mimic treated cells. These data suggest that let-7d-5p is more relevant to sensitivity for FTD than that of 5FU. Conclusion: Let-7d-5p expression level influenced FTD sensitivity more effectively than 5FU. It suggests that the let-7d-5p is a potential predictive marker for trifluridine/tipiracil treatment in the clinical setting. Citation Format: Kenta Tsunekuni, Jun Koseki, Masamitsu Konno, Ayumu Asai, Norihiro Nishida, Hugh Colvin, Koichi Kawamoto, Yuichiro Doki, Masaki Mori, Hideshi Ishii. Analysis of microRNA profiles involved in the resistance to trifluridine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3075. doi:10.1158/1538-7445.AM2017-3075

Identification and Analysis of the Porcine MicroRNA in Porcine Cytomegalovirus-Infected Macrophages Using Deep Sequencing.

Porcine cytomegalovirus (PCMV; genus Cytomegalovirus, subfamily Betaherpesvirinae, family Herpesviridae) is an immunosuppressive virus that mainly inhibits the immune function of T lymphocytes and macrophages, which has caused substantial damage in the farming industry. In this study, we obtained the miRNA expression profiles of PCMV-infected porcine macrophages via high-throughput sequencing. The comprehensive analysis of miRNA profiles showed that 239 miRNA database-annotated and 355 novel pig-encoded miRNAs were detected. Of these, 130 miRNAs showed significant differential expression between the PCMV-infected and uninfected porcine macrophages. The 10 differentially expressed pig-encoded miRNAs were further determined by stem-loop reverse-transcription polymerase chain reaction, and the results were consistent with the high-throughput sequencing. Gene Ontology analysis of the target genes of miRNAs in PCMV-infected porcine macrophages showed that the differentially expressed miRNAs are mainly involved in immune and metabolic processes. This is the first report of the miRNA transcriptome in porcine macrophages and an analysis of the miRNA regulatory mechanisms during PCMV infection. Further research into the regulatory mechanisms of miRNAs during immunosuppressive viral infections should contribute to the treatment and prevention of immunosuppressive viruses.