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miRNA next generation sequencing

Qiyu Lu, Yi Sun, Yuyin Duan, Bin Li, Jianming Xia, Songhua Yu, Guimin Zhang
BACKGROUND: Valvular heart disease is a leading cause of cardiovascular mortality, especially in China. More than a half of valvular heart diseases are caused by acute rheumatic fever. microRNA is involved in many physiological and pathological processes. However, the miRNA profile of the rheumatic valvular heart disease is unknown. This research is to discuss microRNAs and their target gene pathways involved in rheumatic heart valve disease. METHODS: Serum miRNA from one healthy individual and four rheumatic heart disease patients were sequenced...
March 16, 2018: BMC Cardiovascular Disorders
Cristian De Gregorio, Paula Díaz, Rodrigo López-Leal, Patricio Manque, Felipe A Court
Exosomes are small (30-150 nm) vesicles of endosomal origin secreted by most cell types. Exosomes contain proteins, lipids, and RNA species including microRNA, mRNA, rRNA, and long noncoding RNAs. The mechanisms associated with exosome synthesis and cargo loading are still poorly understood. A role for exosomes in intercellular communication has been reported in physiological and pathological conditions both in vitro and in vivo. Previous studies have suggested that Schwann cell-derived exosomes regulate neuronal functions, but the mechanisms are still unclear...
2018: Methods in Molecular Biology
Akira Inoue, Tsunekazu Mizushima, Xin Wu, Daisuke Okuzaki, Nanami Kambara, Sho Ishikawa, Jiaqi Wang, Yamin Qian, Haruka Hirose, Yuhki Yokoyama, Ryo Ikeshima, Masayuki Hiraki, Norikatsu Miyoshi, Hidekazu Takahashi, Naotsugu Haraguchi, Taishi Hata, Chu Matsuda, Yuichiro Doki, Masaki Mori, Hirofumi Yamamoto
We previously demonstrated that miR-29b-3p is a hopeful microRNA (miRNA)-based therapies against colorectal cancer (CRC). In this study, we aimed to clarify a value of miR-29b-1-5p as a next generation treatment, especially for KRAS mutant CRC. RT-PCR assay showed that expression of miR-29b-3p was high and its partner strand, miR-29b-1-5p level was only negligible in clinical CRC samples. Mimic-miR-29b-1-5p significantly inhibited proliferation of KRAS mutant CRC cell lines DLD1 and SW480 and KRAS wild type HT29 cells...
March 15, 2018: Molecular Cancer Therapeutics
Hong Shen, Shuyang Lu, Lili Dong, Yuan Xue, Chenling Yao, Chaoyang Tong, Chunsheng Wang, Xianhong Shu
Abnormal expression of microRNAs (miRNAs) has been associated with aortic dissection (AD). Next generation sequencing was performed to identify the differentially expressed miRNAs in aortic tissue samples between AD and non-diseased individuals. Selected miRNAs which showed significant variation between the two groups, were then transfected into human aortic vascular smooth muscle cells (HA-VSMC), and assessed for effects on cell migration and induced apoptosis. The changes in gene expression pattern in HA-VSMC cells transfected with the miRNAs were also investigated...
March 9, 2018: Journal of Cardiovascular Pharmacology
Tadashige Nozaki, Yuka Sasaki, Itsuko Fukuda, Mayu Isumi, Keitaro Nakamoto, Takae Onodera, Mitsuko Masutani
Poly (ADP-ribose) polymerase family, member 1 (Parp1) has pleiotropic and disparate functions in multiple cellular signaling pathways through post-translational protein modification. It contributes to the regulation of various cellular processes, including DNA damage repair, cell death, and cell differentiation, genetically or epigenetically. Meanwhile, the functions of Parp1 in intercellular signaling remain to be established. To examine the functions of Parp1 in intercellular signaling, we examined microRNA (miRNA) regulation in exosomes derived from Parp1-deficient (Parp1-/- ) embryonic stem (ES) cells...
March 10, 2018: Biochemical and Biophysical Research Communications
Xinyu Feng, Xiaojian Zhou, Shuisen Zhou, Jingwen Wang, Wei Hu
BACKGROUND: microRNAs (miRNAs) are small non-coding RNAs widely identified in many mosquitoes. They are reported to play important roles in development, differentiation and innate immunity. However, miRNAs in Anopheles sinensis, one of the Chinese malaria mosquitoes, remain largely unknown. METHODS: We investigated the global miRNA expression profile of An. sinensis using Illumina Hiseq 2000 sequencing. Meanwhile, we applied a bioinformatic approach to identify potential miRNAs in An...
March 12, 2018: Parasites & Vectors
Linping Yan, Jie Feng, Feng Cheng, Xianwei Cui, Lingjuan Gao, Yajun Chen, Fei Wang, Tianying Zhong, Yun Li, Lan Liu
Circular RNAs (circRNAs) have recently been shown to exert their effects on multiple pathological processes by acting as microRNA (miRNA) sponges. However, the roles of circRNAs in gestational diabetes mellitus (GDM) are largely unknown. This study aimed to identify the circRNAs involved in GDM and predict their potential biological functions. We first performed next-generation sequencing (NGS) to generate unbiased placental villi circRNA expression profiles of GDM and normal controls. In total, 48,270 circRNAs from the placental villi of the two groups were sequenced...
March 8, 2018: Biochemical and Biophysical Research Communications
Jyoti Roy, Bibekanand Mallick
Remarkable attempts have been exercised in recent years using high-throughput technologies to identify and decipher the functions of piRNAs in various abnormalities like cancer. However, piRNAs in the oncogenesis of neuroblastoma (NB) has not been reported yet even after their illustrated roles in neurological processes. Therefore, we investigated the piRNA transcriptome in IMR-32 and SH-SY-5Y NB cell lines by employing high-throughput next-generation sequencing after confirming the expression of three associated PIWILs both at mRNAs and protein level by qRT-PCR and immunofluroscence respectively...
March 8, 2018: Genes, Chromosomes & Cancer
Leilei Liang, Jingchao Xu, Meng Wang, Gaoran Xu, Ning Zhang, Guangzhi Wang, Yongfu Zhao
Long non-coding RNAs (lncRNAs), which are important functional regulators in cancer, have received increased attention in recent years. In this study, next-generation sequencing technology was used to identify aberrantly expressed lncRNAs in follicular thyroid carcinoma (FTC). The long non-coding RNA-HLA complex P5 (HCP5) was found to be overexpressed in FTC. The results of the qPCR analysis were consistent with the sequencing results. In addition, functional experiments showed that overexpression of HCP5 can promote the proliferation, migration, invasiveness and angiogenic ability of FTC cells...
March 7, 2018: Cell Death & Disease
P Scott Pine, Steven P Lund, Jerod R Parsons, Lindsay K Vang, Ashish A Mahabal, Luca Cinquini, Sean C Kelly, Heather Kincaid, Daniel J Crichton, Avrum Spira, Gang Liu, Adam C Gower, Harvey I Pass, Chandra Goparaju, Steven M Dubinett, Kostyantyn Krysan, Sanford A Stass, Debra Kukuruga, Kendall Van Keuren-Jensen, Amanda Courtright-Lim, Karol L Thompson, Barry A Rosenzweig, Lynn Sorbara, Sudhir Srivastava, Marc L Salit
BACKGROUND: The potential utility of microRNA as biomarkers for early detection of cancer and other diseases is being investigated with genome-scale profiling of differentially expressed microRNA. Processes for measurement assurance are critical components of genome-scale measurements. Here, we evaluated the utility of a set of total RNA samples, designed with between-sample differences in the relative abundance of miRNAs, as process controls. RESULTS: Three pure total human RNA samples (brain, liver, and placenta) and two different mixtures of these components were evaluated as measurement assurance control samples on multiple measurement systems at multiple sites and over multiple rounds...
March 6, 2018: BMC Genomics
Xiaonan Fu, Daoyuan Dong
The vital role of microRNAs (miRNAs) involved in gene expression regulation has been confirmed in many biological processes. With the growing power and reducing cost of next-generation sequencing, more and more researchers turn to apply this high-throughput method to solve their biological problems. For miRNAs with known sequences, their expression profiles can be generated from the sequencing data. It also allows us to identify some novel miRNAs and explore the sequence variations under different conditions...
2018: Methods in Molecular Biology
Jiyoun Yeo, Diego A Morales, Tian Chen, Erin L Crawford, Xiaolu Zhang, Thomas M Blomquist, Albert M Levin, Pierre P Massion, Douglas A Arenberg, David E Midthun, Peter J Mazzone, Steven D Nathan, Ronald J Wainz, Patrick Nana-Sinkam, Paige F S Willey, Taylor J Arend, Karanbir Padda, Shuhao Qiu, Alexei Federov, Dawn-Alita R Hernandez, Jeffrey R Hammersley, Youngsook Yoon, Fadi Safi, Sadik A Khuder, James C Willey
BACKGROUND: There is a need for more powerful methods to identify low-effect SNPs that contribute to hereditary COPD pathogenesis. We hypothesized that SNPs contributing to COPD risk through cis-regulatory effects are enriched in genes comprised by bronchial epithelial cell (BEC) expression patterns associated with COPD. METHODS: To test this hypothesis, normal BEC specimens were obtained by bronchoscopy from 60 subjects: 30 subjects with COPD defined by spirometry (FEV1/FVC < 0...
March 5, 2018: BMC Pulmonary Medicine
Sergei A Korneev, Dimitris V Vavoulis, Souvik Naskar, Varvara E Dyakonova, Ildikó Kemenes, György Kemenes
Although single-trial induced long-term memories (LTM) have been of major interest in neuroscience, how LTM can form after a single episode of learning remains largely unknown. We hypothesized that the removal of molecular inhibitory constraints by microRNAs (miRNAs) plays an important role in this process. To test this hypothesis, first we constructed small non-coding RNA (sncRNA) cDNA libraries from the CNS of Lymnaea stagnalis subjected to a single conditioning trial. Then, by next generation sequencing of these libraries, we identified a specific pool of miRNAs regulated by training...
March 2, 2018: Scientific Reports
Cindy M Yamamoto, Melanie L Oakes, Taku Murakami, Michael G Muto, Ross S Berkowitz, Shu-Wing Ng
BACKGROUND: Extracellular vesicles (EVs) are considered as a new class of resources for potential biomarkers. We analyzed expression of specific mRNA and miRNA in EVs derived from ovarian cancer ascites and the ideal controls, peritoneal fluids from benign patients for potential early detection and prognostic biomarkers. METHODS: Fluids were collected from subjects with benign cysts or endometrioma (n = 10), or low/high grade serous ovarian carcinoma (n = 8)...
March 2, 2018: Journal of Ovarian Research
Anita Tripathi, Osmani Chacon, Sneh Lata Singla-Pareek, Sudhir K Sopory, Neeti Sanan-Mishra
In the recent years, glyoxalase pathway has been an active area of research in both human and plants. This pathway is reported to confer stress tolerance in plants, by modulating the glutathione homeostasis to achieve detoxification of a potent cytotoxic and mutagenic compound, methylglyoxal. The microRNAs (miRNAs) are also reported to play significant role in stress tolerance for plants. However, the cross-talk of miRNAs with the metabolism regulated by glyoxalase in the salinity-tolerance is unexplored. We therefore investigated whether expression profiles of miRNAs are altered in response to glyoxalase overexpression, and if any of these are also responsible for modulating the stress responses of plants...
January 2018: Current Genomics
Ying Si, Xianqin Cui, David K Crossman, Jiaying Hao, Mohamed Kazamel, Yuri Kwon, Peter H King
ALS is a fatal neurodegenerative disorder of motor neurons leading to progressive atrophy and weakness of muscles. Some of the earliest pathophysiological changes occur at the level of skeletal muscle and the neuromuscular junction. We previously identified distinct mRNA patterns, including members of the Smad and TGF-β family, that emerge in muscle tissue at the earliest (pre-clinical) stages. These patterns track disease progression in the mutant SOD1 mouse and are present in human ALS muscle. Because miRNAs play a direct regulatory role in mRNA expression, we hypothesized in this study that there would be distinct miRNA patterns in ALS muscle appearing in early stages that could track disease progression...
February 24, 2018: Neurobiology of Disease
Takuma Iguchi, Ken Sakurai, Satoshi Tamai, Kazuhiko Mori
Circulating microRNAs (miRNAs) can potentially be used as sensitive and specific biomarkers for tissue injury. However, the usefulness of circulating miRNAs as safety biomarkers in nonclinical toxicological studies using nonhuman primates is debatable owing to the limited information on organ-specific miRNAs. Therefore, a systematic investigation was performed to address this point. We identified organ-specific miRNAs from cynomolgus monkeys by next-generation sequencing analysis, which revealed that miR-122 was only abundant in the liver, whereas miR-192 was abundant in the liver, stomach, intestines, and kidney...
January 2018: Journal of Toxicologic Pathology
Halil Bisgin, Binsheng Gong, Yuping Wang, Weida Tong
MicroRNAs (miRNAs) are key post-transcriptional regulators that affect protein translation by targeting mRNAs. Their role in disease etiology and toxicity are well recognized. Given the rapid advancement of next-generation sequencing techniques, miRNA profiling has been increasingly conducted with RNA-seq, namely miRNA-seq. Analysis of miRNA-seq data requires several steps: (1) mapping the reads to miRBase, (2) considering mismatches during the hairpin alignment (windowing), and (3) counting the reads (quantification)...
2018: Frontiers in Genetics
Veena B Nair, V G Manasa, M S Sinto, K Jayasree, Francis V James, S Kannan
OBJECTIVES: Cervical cancer is the second most common cancer in women in developing countries, including India. Recently, microRNAs (miRNAs) are gaining importance in cancer biology because of their involvement in various cellular processes. The present study aimed to profile miRNA expression pattern in cervical cancer, identify their target genes, and understand their role in carcinogenesis. METHODS: Human papillomavirus (HPV) infection statuses in samples were assessed by heminested polymerase chain reaction followed by direct DNA sequencing...
March 2018: International Journal of Gynecological Cancer
Maria Vila-Casadesús, Elena Vila-Navarro, Giulia Raimondi, Cristina Fillat, Antoni Castells, Juan José Lozano, Meritxell Gironella
MiRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression. They play important roles in cancer but little is known about the specific functions that each miRNA exerts in each type of cancer. More knowledge about their specific targets is needed to better understand the complexity of molecular networks taking part in cancer. In this study we report the miRNA-mRNA interactome occurring in pancreatic cancer by using a bioinformatic approach called miRComb, which combines tissue expression data with miRNA-target prediction databases (TargetScan, miRSVR and miRDB)...
January 19, 2018: Oncotarget
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