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miRNA next generation sequencing

Poching Liu
MicroRNAs are a class of small noncoding RNAs that function as regulators involving in many biological processes. The evaluation of miRNAs and their targets has been aided by miRNA expression profiling studies including multiplex PCR, microarrays, and recent next-generation sequencing tools. Next-generation sequencing has enabled us to profile thousands of genes in a single experiment and overcome the background signal and cross-hybridization issues of microarrays. Next-generation sequencing also allows for the simultaneous confirmation of known miRNAs and discovery of new miRNAs, and significantly reduces costs while providing billions of nucleotide information within a single experiment...
2018: Methods in Molecular Biology
Barbara Pardini, Francesca Cordero, Alessio Naccarati, Clara Viberti, Giovanni Birolo, Marco Oderda, Cornelia Di Gaetano, Maddalena Arigoni, Federica Martina, Raffaele A Calogero, Carlotta Sacerdote, Paolo Gontero, Paolo Vineis, Giuseppe Matullo
Bladder cancer (BC) is the most frequent malignancy of the urinary tract with a high incidence in men and smokers. Currently, there are no non-invasive markers useful for BC diagnosis and subtypes classification that could overcome invasive procedures such as cystoscopy. Dysregulated miRNA profiles have been associated with numerous cancers, including BC. Cell-free miRNAs are abundantly present in a variety of biofluids including urine and make them promising candidates in cancer biomarker discovery. In the present study, the identification of miRNA fingerprints associated with different BC status was performed by next-generation sequencing on urine samples from 66 BC and 48 controls...
April 17, 2018: Oncotarget
H Wang, J Zhong, Z Chai, J Zhu, J Xin
microRNA (miRNA) and piwi-interacting RNA (piRNA) are two classes small non-coding regulatory RNAs that play crucial roles in multiple biological processes such as spermatogenesis. However, there are no published studies on conjoint analysis of miRNA and piRNA profiles among cattle, yak and their interspecies (the dzo) using sequencing technology. Next-generation sequencing technology was used to profile miRNAs and piRNAs among those three ruminants to elucidate their functions. A total of 119, 14 and six differentially expressed miRNAs were obtained in cattle vs...
May 11, 2018: Reproduction in Domestic Animals, Zuchthygiene
Jansen Fernandes, Andre Schwambach Vieira, Juliana Carlota Kramer-Soares, Eduardo Alves Da Silva, Kil Sun Lee, Iscia Lopes-Cendes, Ricardo Mario Arida
BACKGROUND: It is widely known that physical activity positively affects the overall health and brain function. Recently, microRNAs (miRNAs) have emerged as potential regulators of numerous biological processes within the brain. These molecules modulate gene expression post-transcriptionally by inducing mRNA degradation and inhibiting the translation of target mRNAs. METHODS: To verify whether the procognitive effects of physical exercise are accompanied by changes in the activity of miRNA-mRNA network in the brain, differential expression analysis was performed in the hippocampus of control (CTL) and exercised (Ex) rats subjected to 4 weeks of treadmill exercise...
May 7, 2018: Biochimica et Biophysica Acta
Gabriella Guelfi, Giovanni Cochetti, Valentina Stefanetti, Danilo Zampini, Silvana Diverio, Andrea Boni, Ettore Mearini
There is emerging evidence that microRNAs (miRNAs) dysregulation is involved in the genesis and the progression of Prostate Cancer (PCa), thus potentially increasing their use in urological clinical practice. This is the first pilot study which utilizes Illumina Deep Sequencing to examine the entire miRNAs spectrum existent in urine exfoliated prostate cells (UEPCs) of PCa patients. A total of 11 male patients with histological diagnosis of PCa were enrolled in the present study. First-catch urine (30 mL) was collected following a prostate massage...
May 8, 2018: Scientific Reports
Sara De Iudicibus, Marianna Lucafò, Nicola Vitulo, Stefano Martelossi, Rosanna Zimbello, Fabio De Pascale, Claudio Forcato, Samuele Naviglio, Alessia Di Silvestre, Marco Gerdol, Gabriele Stocco, Giorgio Valle, Alessandro Ventura, Matteo Bramuzzo, Giuliana Decorti
The aim of this research was the identification of novel pharmacogenomic biomarkers for better understanding the complex gene regulation mechanisms underpinning glucocorticoid (GC) action in paediatric inflammatory bowel disease (IBD). This goal was achieved by evaluating high-throughput microRNA (miRNA) profiles during GC treatment, integrated with the assessment of expression changes in GC receptor (GR) heterocomplex genes. Furthermore, we tested the hypothesis that differentially expressed miRNAs could be directly regulated by GCs through investigating the presence of GC responsive elements (GREs) in their gene promoters...
May 8, 2018: International Journal of Molecular Sciences
Ye Liu, Zhongqi Chen, Kun Xu, Zhengxia Wang, Chaojie Wu, Zhixiao Sun, Ningfei Ji, Mao Huang, Mingshun Zhang
AIM: To explore the miRNAs profile of CD4+ T lymphocytes in asthma via next generation sequencing. METHODS: In the murine model of acute asthma, spleen CD4+ T lymphocytes were sorted, in which small RNAs were extracted and sequenced. Novel miRNAs were measured with real time quantitative reverse transcription polymerase chain reaction (qRT-PCR). RESULTS: A total of 127 miRNAs were found to exhibit at least twofold change. In the 262 predicted novel miRNAs, 14 novel miRNAs were measured in qRT-PCR in the sorted CD4+ T cells or in the differentiated Th1/Th2 cells and novel miR-11 (xxx-m0228-3p) was significantly decreased in the sorted CD4+ T cells from the murine model of asthma and in the Th2 cells...
May 8, 2018: Epigenomics
Anna Janaszak-Jasiecka, Anna Siekierzycka, Sylwia Bartoszewska, Marcin Serocki, Lawrence W Dobrucki, James F Collawn, Leszek Kalinowski, Rafal Bartoszewski
The nitric oxide (NO) secreted by vascular endothelium is required for the maintenance of cardiovascular homeostasis. Diminished release of NO generated by endothelial NO synthase contributes to endothelial dysfunction. Hypoxia and ischemia reduce endothelial eNOS expression via posttranscriptional mechanisms that result in NOS3 transcript destabilization. Here, we examine whether microRNAs contribute to this mechanism. We followed the kinetics of hypoxia-induced changes in NOS3 mRNA and eNOS protein levels in primary human umbilical vein endothelial cells (HUVECs)...
May 8, 2018: Angiogenesis
M D Morin, D Lang-Ouellette, P J Lyons, N Crapoulet, P Morin
BACKGROUND: Mammalian hibernation is a fascinating phenomenon that involves multiple molecular and biochemical changes to proceed. While the molecular picture associated with torpor has become clearer in recent years, the function of non-coding RNAs, and especially of microRNAs, solicited during this process is not well understood. OBJECTIVE: To better characterize a signature of cold torpor-associated miRNAs in the hibernating thirteen-lined ground squirrel Ictidomys tridecemlineatus...
July 2017: Cryo Letters
Simon Andreasen, Tina Klitmøller Agander, Kristine Bjørndal, Daiva Erentaite, Steffen Heegaard, Stine R Larsen, Linea Cecilie Melchior, Qihua Tan, Benedicte Parm Ulhøi, Irene Wessel, Preben Homøe
Adenoid cystic carcinoma (ACC) is among the most common salivary gland malignancies, and is notorious for its unpredictable clinical course with frequent local recurrences and metastatic spread. However, the molecular mechanisms for metastatic spread are poorly understood. This malignancy is known to frequently harbor gene fusions involving MYB , MYBL1 , and NFIB , and to have a low mutational burden. Most studies have focused on primary tumors to understand the biology of ACC, but this has not revealed a genetic cause for metastatic dissemination in the majority of cases...
April 13, 2018: Oncotarget
Wenfeng Chen, Guosheng Lin, Yizhou Yao, Jishen Chen, Hanli Shui, Qinghai Yang, Xiaoya Wang, Xiaoyuan Weng, Ling Sun, Fei Chen, Sheng Yang, Yufeng Yang, Yongjian Zhou
MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression that target mRNAs for translational repression or cleavage. The present study was conducted to identify differentially expressed miRNAs in primary tumor tissues of rectal carcinoma (RC) that may be associated with heterochrony hepatic metastasis (HHM). Samples were collected exclusively from patients with RC but not colon cancer (CC); Next-generation high-throughput sequencing technology and bioinformatics tools were used to profile and analyze small RNAs and their corresponding targets in primary tumor tissues with HHM (n=2) or without metastases (non-metastatic, NM; n=2)...
May 2018: Oncology Letters
Robert K Nam, Tania Benatar, Yutaka Amemiya, Christopher J D Wallis, Joan Miguel Romero, Melina Tsagaris, Christopher Sherman, Linda Sugar, Arun Seth
MicroRNAs (miRNAs) are small noncoding RNA molecules that post-transcriptionally regulate gene expression. Dysregulation of miRNAs is frequently associated with disease and, in particular, is involved in prostate cancer progression. Next generation miRNA sequencing identified a panel of five miRNAs associated with prostate cancer recurrence and metastasis. High expression of one of these five miRNAs, miR-652, correlated significantly with an increased rate of prostate cancer biochemical recurrence. Overexpression of miR-652 in prostate cancer cells, PC3 and LNCaP, resulted in increased growth, migration and invasion...
April 10, 2018: Oncotarget
Azliana Mohamad Yusof, Rahman Jamal, Rohaizak Muhammad, Shahrun Niza Abdullah Suhaimi, Isa Mohamed Rose, Sazuita Saidin, Nurul-Syakima Ab Mutalib
The incidence rate of papillary thyroid carcinoma (PTC) has rapidly increased in the recent decades, and the microRNA (miRNA) is one of the potential biomarkers in this cancer. Despite good prognosis, certain features such as lymph node metastasis (LNM) and BRAF V600E mutation are associated with a poor outcome. More than 50% of PTC patients present with LNM and BRAF V600E is the most common mutation identified in this cancer. The molecular mechanisms underlying these features are yet to be elucidated. This study aims to elucidate miRNA-genes interaction networks in PTC with or without LNM and to determine the association of BRAF V600E mutation with miRNAs and genes expression profiles...
2018: Frontiers in Endocrinology
Xiancheng Qu, Menghong Hu, Yueyong Shang, Lisha Pan, Peixuan Jia, Chunxue Fu, Qigen Liu, Youji Wang
Next-generation sequencing was used to analyze the effects of toxic microcystin-LR (MC-LR) on silver carp ( Hypophthalmichthys molitrix ). Silver carps were intraperitoneally injected with MC-LR, and RNA-seq and miRNA-seq in the liver were analyzed at 0.25, 0.5, and 1 h. The expression of glutathione S-transferase (GST), which acts as a marker gene for MC-LR, was tested to determine the earliest time point at which GST transcription was initiated in the liver tissues of the MC-LR-treated silver carps. Hepatic RNA-seq/miRNA-seq analysis and data integration analysis were conducted with reference to the identified time point...
2018: Frontiers in Physiology
Nicole Ludwig, Tobias Fehlmann, Valentina Galata, Andre Franke, Christina Backes, Eckart Meese, Andreas Keller
BACKGROUND: Although mature miRNAs are relatively stable in vivo, RNA degradation can have a substantial influence on small noncoding RNA (sncRNA) profiles. METHODS: Using different tissue storage conditions and RNA isolation procedures, we analyzed the integrity and quality of RNA isolates from human lung and heart tissues. We sequenced a total of 64 RNA samples and quantified the effect of RNA degradation, DNA contamination, and other confounding factors on the sncRNA-seq data...
April 24, 2018: Clinical Chemistry
Yong Chen, Zhili Li, Yi Shi, Guangfu Huang, Longyi Chen, Haibin Tan, Zhenyu Wang, Cheng Yin, Junting Hu
BACKGROUND: The deregulation of circulating microRNAs (miRNAs) is always associated with development and progression of human diseases. We are aimed to assess whether brain arteriovenous malformations (BAVMs) patients present a distinct miRNA signature compared with healthy subjects. METHODS: Three unruptured BAVMs patients and three normal controls were recruited as case and normal groups. Peripheral blood was collected and miRNA signature was obtained by next-generation sequencing, followed by comparative, functional, and network analyses...
April 21, 2018: World Neurosurgery
Feng Li, Karolina Elżbieta Kaczor-Urbanowicz, Jie Sun, Blanca Majem, Hsien-Chun Lo, Yong Kim, Kikuye Koyano, Shannon Liu Rao, So Young Kang, Su Mi Kim, Kyoung-Mee Kim, Sung Kim, David Chia, David Elashoff, Tristan R Grogan, Xinshu Xiao, David T W Wong
BACKGROUND: It was recently discovered that abundant and stable extracellular RNA (exRNA) species exist in bodily fluids. Saliva is an emerging biofluid for biomarker development for noninvasive detection and screening of local and systemic diseases. Use of RNA-Sequencing (RNA-Seq) to profile exRNA is rapidly growing; however, no single preparation and analysis protocol can be used for all biofluids. Specifically, RNA-Seq of saliva is particularly challenging owing to high abundance of bacterial contents and low abundance of salivary exRNA...
April 23, 2018: Clinical Chemistry
Jie Ma, Shanshan Shang, Jihan Wang, Tianbu Zhang, Fayi Nie, Xiaobin Song, Heping Zhao, Chunhui Zhu, Rui Zhang, Dingjun Hao
MicroRNAs (miRNAs) are a class of endogenous and non-coding single-stranded RNAs with length of about 22 nucleotides, and many are evolutionarily conserved. Although postmortem brain samples provide direct evidence of miRNA dysregulation within the brain, peripheral tissue samples can be obtained from living subjects and have the potential to yield biomarkers that could be used as diagnostic tools. To verify and detect additional miRNAs differentially expressed in peripheral blood and further explore their diagnostic value and function for schizophrenia, we performed a next-generation sequencing approach in combination with a literature search to select appropriate miRNAs...
April 7, 2018: Psychiatry Research
Havjin Jacob, Luka Stanisavljevic, Kristian Eeg Storli, Kjersti E Hestetun, Olav Dahl, Mette P Myklebust
About 20 percent of TNM-stage II colon cancer patients who are treated by surgical resection develop recurrence, and adjuvant chemotherapy in this group is still debated among researchers and clinicians. Currently, adverse histopathological and clinical factors are used to select patients for adjuvant chemotherapy following surgery. However, additional biomarkers to classify patients at risk of recurrence are needed. We have conducted a study using fresh frozen tumor tissue from 54 TNM-stage II colon cancer patients and performed microRNA profiling using next-generation sequencing...
April 18, 2018: Scientific Reports
Federico Martinelli, Gina Cannarozzi, Bipin Balan, Fredy Siegrist, Annett Weichert, Regula Blösch, Zerihun Tadele
Tef [Eragrostis tef (Zucc.) Trotter], a staple food crop in the Horn of Africa and particularly in Ethiopia, has several beneficial agronomical and nutritional properties, including waterlogging and drought tolerance. In this study, we performed microRNA profiling of tef using the Illumina HiSeq 2500 platform, analyzing both shoots and roots of two tef genotypes, one drought-tolerant (Tsedey) and one drought-susceptible (Alba). We obtained more than 10 million filtered reads for each of the 24 sequenced small cDNA libraries...
March 29, 2018: Journal of Plant Physiology
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