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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/28649807/microrna-196-regulates-hox-gene-expression-in-human-gluteal-adipose-tissue
#1
Adeline Divoux, Hui Xie, Jian-Liang Li, Kalypso Karastergiou, Ranjan J Perera, R Jeffrey Chang, Susan K Fried, Steven R Smith
OBJECTIVE: Lower body fat is associated with diminishing cardiometabolic risk. Physiological differences between gluteofemoral and abdominal subcutaneous adipocyte functions are known, but the molecular basis for depot differences in adipocyte function is poorly understood. The objective of this study was to identify depot differences in microRNA (miRNA) expression in human abdominal and gluteofemoral subcutaneous adipose tissues and their implication in gene regulation. METHODS: Abdominal and gluteofemoral adipose tissue aspirates obtained from 18 participants (9 male and 9 female, age 30 ± 1...
June 25, 2017: Obesity
https://www.readbyqxmd.com/read/28643865/characterization-and-biological-function-of-milk-derived-mirnas
#2
Regina Golan-Gerstl, Yaffa Elbaum Shiff, Vardit Lavi-Moshayoff, Daniel Schecter Dena Leshkowitz, Shimon Reif
SCOPE: Breastfeeding is associated with reduced risk of infection, immune mediated disorders, obesity and even cancer. Recently it was found that breast milk contains a variety of microRNAs (miRNAs) in the skim and fat layer that can be transferred to infants, and appear to play important roles in those biological functions. METHODS AND RESULTS: This study applied Next Generation Sequencing and quantitative real time PCR analysis to determine the miRNA expression profile of the skim and fat fraction of human, goat, and bovine milk as well as infant formulas...
June 23, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28641312/impact-of-novel-mir-145-3p-regulatory-networks-on-survival-in-patients-with-castration-resistant-prostate-cancer
#3
Yusuke Goto, Akira Kurozumi, Takayuki Arai, Nijiro Nohata, Satoko Kojima, Atsushi Okato, Mayuko Kato, Kazuto Yamazaki, Yasuo Ishida, Yukio Naya, Tomohiko Ichikawa, Naohiko Seki
BACKGROUND: Despite recent advancements, metastatic castration-resistant prostate cancer (CRPC) is not considered curative. Novel approaches for identification of therapeutic targets of CRPC are needed. METHODS: Next-generation sequencing revealed 945-1248 miRNAs from each lethal mCRPC sample. We constructed miRNA expression signatures of CRPC by comparing the expression of miRNAs between CRPC and normal prostate tissue or hormone-sensitive prostate cancer (HSPC)...
June 22, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28626163/lower-serum-levels-of-mir-29c-3p-and-mir-19b-3p-as-biomarkers-for-alzheimer-s-disease
#4
Yuquan Wu, Juan Xu, Jing Xu, Jun Cheng, Demin Jiao, Chun Zhou, Yi Dai, Qingyong Chen
MicroRNAs (miRNAs) are short noncoding RNA that participate in posttranscriptional gene regulation. However, little is understood about the roles of miRNAs in Alzheimer's disease (AD). In this study, we used next-generation sequencing on RNA extracted from the serum samples of 20 AD patients and 20 controls, yielding a total of 72 miRNAs with significantly changed expression levels. Among these candidates, we selected 9 miRNAs with most significant alteration in disease, and validated their expression levels using RT-qPCR analysis on serum samples from 45 AD patients and 40 control subjects...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28611354/chronic-low-dose-exposure-to-a-mixture-of-environmental-endocrine-disruptors-induces-micrornas-isomirs-deregulation-in-mouse-concomitant-with-intratesticular-estradiol-reduction
#5
Julio Buñay, Eduardo Larriba, Ricardo D Moreno, Jesús Del Mazo
Humans are environmentally exposed not only to single endocrine-disrupting chemicals (EDCs) but to mixtures that affect their reproductive health. In reproductive tissues, microRNAs (miRNAs) are emerging as key targets of EDCs. Here, we analysed changes in the testis "miRNome" (and their biogenesis mechanism) in chronically exposed adult mice to a cocktail of five EDCs containing 0.3 mg/kg-body weight (BW)/day of each phthalate (DEHP, DBP, BBP) and 0.05 mg/kg-BW/day of each alkylphenol (NP, OP), from conception to adulthood...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28606918/evaluation-of-tumor-derived-exosomal-mirna-as-potential-diagnostic-biomarkers-for-early-stage-non-small-cell-lung-cancer-using-next-generation-sequencing
#6
Xiance Jin, Yanfan Chen, Hanbin Chen, Shaoran Fei, Didi Chen, Xiaona Cai, Linger Liu, Baochai Lin, Huafang Su, Lihao Zhao, Meng Su, Huanle Pan, Lanxiao Shen, Deyao Xie, Congying Xie
<br />To identify tumor-derived exosomal biomarkers that are able to discriminate between adenocarcinoma (AC) and squamous cell carcinoma (SCC) as a non-invasive method in the early diagnosis of non-small-cell lung cancer (NSCLC). <br /><br />Experimental Design: <br />Tumor-derived exosomes from the plasma of early stage NSCLC patients were isolated. Exosomal miRNA profiling of 46 stage I NSCLC patients and 42 healthy individuals was performed using miRNA-seq to identify and validate AC- and SCC-specific miRNAs...
June 12, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28599301/a-functional-variant-in-grem1-confers-risk-for-colorectal-cancer-by-disrupting-a-hsa-mir-185-3p-binding-site
#7
Jiaoyuan Li, Hui Liu, Li Zou, Juntao Ke, Yi Zhang, Ying Zhu, Yang Yang, Yajie Gong, Jianbo Tian, Danyi Zou, Xiating Peng, Jing Gong, Rong Zhong, Kun Huang, Jiang Chang, Xiaoping Miao
The transforming growth factor beta (TGF-β) pathway has been implicated in carcinogenesis of intestinal canal. Except for common variants indentified by genome-wide association studies, variants with lower frequency can also explain a part of the disease heritability, especially those in gene regulatory regions. In this study, we searched for colorectal cancer (CRC) related functional low-frequency variants (minor allele frequency 1-5%) in untranslated regions (UTR) involved in the TGF-β signaling using a next-generation sequencing based approach...
May 23, 2017: Oncotarget
https://www.readbyqxmd.com/read/28596526/mechanistic-roles-of-micrornas-in-hepatocarcinogenesis-a-study-of-thioacetamide-with-multiple-doses-and-time-points-of-rats
#8
Harsh Dweep, Yuji Morikawa, Binsheng Gong, Jian Yan, Zhichao Liu, Tao Chen, Halil Bisgin, Wen Zou, Huixiao Hong, Tieliu Shi, Ping Gong, Christina Castro, Takeki Uehara, Yuping Wang, Weida Tong
Environmental chemicals exposure is one of the primary factors for liver toxicity and hepatocarcinoma. Thioacetamide (TAA) is a well-known hepatotoxicant and could be a liver carcinogen in humans. The discovery of early and sensitive microRNA (miRNA) biomarkers in liver injury and tumor progression could improve cancer diagnosis, prognosis, and management. To study this, we performed next generation sequencing of the livers of Sprague-Dawley rats treated with TAA at three doses (4.5, 15 and 45 mg/kg) and four time points (3-, 7-, 14- and 28-days)...
June 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28587571/expression-profiling-of-lncrnas-mirnas-and-mrnas-and-their-differential-expression-in-leiomyoma-using-next-generation-rna-sequencing
#9
Tsai-Der Chuang, Omid Khorram
The objective of this study was to identify the expression profile of long noncoding RNAs (lncRNAs) with concurrent assessment of microRNA (miRNA) and messenger RNA (mRNA) profiles in leiomyomas and paired myometrium using next-generation RNA sequencing and assembly of RNA transcripts. Total RNA was isolated from leiomyoma and paired myometrium (N = 8) and samples from 3 pairs were subjected to RNA sequencing. Normalized assembly of over 48 000 lncRNAs resulted in identification of 45 936 lncRNAs. Of these lncRNAs, 22 148 representing overlapping, intergenic, intronic, and antisense subtypes were expressed in all paired tissues, with 5941 (2813 up- and 3128 downregulated at ≥1...
January 1, 2017: Reproductive Sciences
https://www.readbyqxmd.com/read/28586912/comparison-of-microrna-expression-in-aqueous-humor-of-normal-and-primary-open-angle-glaucoma-patients-using-pcr-arrays-a-pilot-study
#10
Hari Jayaram, Jay I Phillips, Diana C Lozano, Tiffany E Choe, William O Cepurna, Elaine C Johnson, John C Morrison, Devin M Gattey, Julie A Saugstad, Kate E Keller
Purpose: MicroRNAs (miRNAs) are small, endogenous noncoding RNAs that have been detected in human aqueous humor (AH). Prior studies have pooled samples to obtain sufficient quantities for analysis or used next-generation sequencing. Here, we used PCR arrays with preamplification to identify and compare miRNAs from individual AH samples between patients with primary open-angle glaucoma (POAG) and normal controls. Methods: AH was collected before cataract surgery from six stable, medically treated POAG patients and eight age-matched controls...
June 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28586032/a-sketch-of-known-and-novel-mycn-associated-mirna-networks-in-neuroblastoma
#11
Francesca Megiorni, Moreno Colaiacovo, Samantha Cialfi, Heather P McDowell, Alessandro Guffanti, Simona Camero, Armando Felsani, Paul D Losty, Barry Pizer, Rajeev Shukla, Carlo Cappelli, Eva Ferrara, Antonio Pizzuti, Anna Moles, Carlo Dominici
Neuroblastoma (NB) originates from neural crest-derived precursors and represents the most common childhood extracranial solid tumour. MicroRNAs (miRNAs), a class of small non-coding RNAs that participate in a wide variety of biological processes by regulating gene expression, appear to play an essential role within the NB context. High-throughput next generation sequencing (NGS) was applied to study the miRNA transcriptome in a cohort of NB tumours with and without MYCN-amplification (MNA and MNnA, respectively) and in dorsal root ganglia (DRG), as a control...
June 6, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28574862/the-role-of-micrornas-in-the-therapeutic-action-of-d-cycloserine-in-a-post-traumatic-stress-disorder-animal-model-an-exploratory-study
#12
Stefanie Malan-Müller, Lorren Fairbairn, Stephanie Hart, Willie M U Daniels, Mahjoubeh Jalali Sefid Dashti, Martin Kidd, Soraya Seedat, Junaid Gamieldien, Sîan M J Hemmings
OBJECTIVES: Post-traumatic stress disorder is characterized by impaired fear extinction and excessive anxiety. D-Cycloserine (DCS) has previously been shown to facilitate fear extinction and decrease anxiety in animal and human studies. This study utilized a contextual fear-conditioning animal model to investigate the involvement of microRNAs (miRNAs) in fear extinction and the reduction of anxiety, as mediated by the co-administration of DCS and behavioural fear extinction. METHODS: Fear conditioning consisted of an electric foot shock; fear extinction consisted of behavioural fear extinction co-administered with either DCS or saline...
June 1, 2017: Psychiatric Genetics
https://www.readbyqxmd.com/read/28574782/rna-based-ovarian-cancer-research-from-a-gene-to-systems-biomedicine-perspective
#13
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer remains the leading cause of death from a gynecologic malignancy, and treatment of this disease is harder than any other type of female reproductive cancer. Improvements in the diagnosis and development of novel and effective treatment strategies for complex pathophysiologies, such as ovarian cancer, require a better understanding of disease emergence and mechanisms of progression through systems medicine approaches. RNA-level analyses generate new information that can help in understanding the mechanisms behind disease pathogenesis, to identify new biomarkers and therapeutic targets and in new drug discovery...
August 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28560166/small-rna-seq-analysis-in-response-to-methyl-jasmonate-and-abscisic-acid-treatment-in-persicaria-minor
#14
Nazaruddin Nazaruddin, Abdul Fatah A Samad, Muhammad Sajad, Jaeyres Jani, Zamri Zainal, Ismanizan Ismail
Persicaria minor (Kesum) is an important medicinal plant with high level of secondary metabolite contents, especially, terpenoids and flavonoids. Previous studies have revealed that application of exogenous phytohormone could increase secondary metabolite contents of the plant. MicroRNAs (miRNAs) are small RNAs that play important regulatory roles in various biological processes. In order to explore the possible role of miRNA in the regulation of these phytohormones signaling pathway and uncovering their potential correlation, we, for the first time, have generated the smallRNA library of Kesum plant...
June 2017: Genomics Data
https://www.readbyqxmd.com/read/28546527/effect-of-necrosis-on-the-mirna-mrna-regulatory-network-in-crt-mg-human-astroglioma-cells
#15
So-Hee Ahn, Jung-Hyuck Ahn, Dong-Ryeol Ryu, Jisoo Lee, Min-Sun Cho, Youn-Hee Choi
Purpose: Glioblastoma multiforme (GBM) is the most common adult primary intracranial tumor. The remarkable features of GBM include central necrosis. MicroRNAs (miRNAs) have been considered as diagnostic/prognostic biomarkers for many cancers, including glioblastoma. However, the effect of necrosis on the miRNA expression profile and predicted miRNA-mRNA regulatory information remain unclear. The purpose of this study is to examine the effect of necrotic cells on the modulation of miRNA and mRNA expression profiles and miRNA-mRNA network in CRT-MG cells...
May 22, 2017: Cancer Research and Treatment: Official Journal of Korean Cancer Association
https://www.readbyqxmd.com/read/28545106/serum-microrna-signatures-as-liquid-biopsies-for-interrogating-hepatotoxic-mechanisms-and-liver-pathogenesis-in-human
#16
Julian Krauskopf, Theo M de Kok, Shelli J Schomaker, Mark Gosink, Deborah A Burt, Patricia Chandler, Roscoe L Warner, Kent J Johnson, Florian Caiment, Jos C Kleinjans, Jiri Aubrecht
MicroRNAs (miRNAs) released into the peripheral circulation upon cellular injury have shown a promise as a new class of tissue-specific biomarkers. We were first to demonstrate that next-generation sequencing analysis of serum from human subjects with acetaminophen-induced liver injury revealed a specific signature of circulating miRNAs. We consequently hypothesized that different types of hepatic liver impairments might feature distinct signatures of circulating miRNAs and that this approach might be useful as minimally invasive diagnostic "liquid biopsies" enabling the interrogation of underlying molecular mechanisms of injury in distant tissues...
2017: PloS One
https://www.readbyqxmd.com/read/28543398/interdigital-tissue-remodelling-in-the-embryonic-limb-involves-dynamic-regulation-of-the-mirna-profiles
#17
Beatriz Garcia-Riart, Carlos I Lorda-Diez, Jessica C Marin-Llera, Juan A Garcia-Porrero, Juan M Hurle, Juan A Montero
Next-generation sequencing in combination with quantitative polymerase chain reaction analysis revealed a dynamic miRNA signature in the interdigital mesoderm of the chick embryonic hinlimb in the course of interdigit remodelling. During this period, 612 previously known chicken miRNAs (gga-miRNAs) and 401 non-identified sequences were expressed in the interdigital mesoderm. Thirty-six microRNAs, represented by more than 750 reads per million, displayed differential expression between stages HH29 (6 id) and HH32 (7...
May 24, 2017: Journal of Anatomy
https://www.readbyqxmd.com/read/28540684/next-generation-sequencing-for-microrna-expression-profile
#18
Yue Hu, Wenjun Lan, Daniel Miller
Sequencing technologies have made considerable advancements. From the Sanger sequencing method to the next-generation sequencing (NGS) methods, and from the NGS methods to the third-generation sequencing methods, we can see the development thread of the sequencing technology. Currently, NGS is the main contender in the sequencing market. NGS technologies provide an opportunity to research the microRNA (miRNA) expression profiles in detail. The NGS platforms have their own special characteristics, but share some main ideas...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28531200/discovery-of-micrornas-during-early-spermatogenesis-in-chicken
#19
Lu Xu, Qixin Guo, Guobin Chang, Lingling Qiu, Xiangping Liu, Yulin Bi, Yu Zhang, Hongzhi Wang, Wei Lu, Lichen Ren, Ying Chen, Yang Zhang, Qi Xu, Guohong Chen
Spermatogenesis is a complex process that involves many elements. However, until now, little is known at the molecular level about spermatogenesis in poultry. Here we investigated microRNAs and their target genes that may be involved in germ cell development and spermatogonial in chicken. We used next-generation sequencing to analyze miRNA expression profiles in three types of germline cells: primordial germ cells (PGCs), spermatogonial stem cells (SSCs), and spermatogonia (Sp) during early stage of spermatogenesis...
2017: PloS One
https://www.readbyqxmd.com/read/28529949/microrna-expression-varies-according-to-glucose-tolerance-measurement-platform-and-biological-source
#20
S Dias, S Hemmings, C Muller, J Louw, C Pheiffer
Dysregulated microRNA (miRNA) expression is observed during type 2 diabetes (T2D), although the consistency of miRNA expression across measurement platform and biological source is uncertain. Here we report miRNA profiling in the whole blood and serum of South African women with different levels of glucose tolerance, using next generation sequencing (NGS) and quantitative real time PCR (qRT-PCR). Whole blood-derived miRNAs from women with newly diagnosed T2D (n = 4), impaired glucose tolerance (IGT) (n = 4), and normal glucose tolerance (NGT) (n = 4) were subjected to NGS, whereafter transcript levels of selected miRNAs were quantified in the whole blood and serum of these women using qRT-PCR...
2017: BioMed Research International
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