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miRNA prediction

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https://www.readbyqxmd.com/read/28329018/a-unique-microrna-profile-in-end-stage-heart-failure-indicates-alterations-in-specific-cardiovascular-signaling-networks
#1
Sathyamangla V Naga Prasad, Manveen K Gupta, Zhong-Hui Duan, Venkata Suresh K Surampudi, Chang-Gong Liu, Ashwin Kotwal, Christine S Moravec, Randall C Starling, Dianne M Perez, Subha Sen, Qingyu Wu, Edward F Plow, Sadashiva Karnik
It is well established that the gene expression patterns are substantially altered in cardiac hypertrophy and heart failure, however, less is known about the reasons behind such global differences. MicroRNAs (miRNAs) are short non-coding RNAs that can target multiple molecules to regulate wide array of proteins in diverse pathways. The goal of the study was to profile alterations in miRNA expression using end-stage human heart failure samples with an aim to build signaling network pathways using predicted targets for the altered miRNA and to determine nodal molecules regulating individual networks...
2017: PloS One
https://www.readbyqxmd.com/read/28325277/reverse-expression-of-aging-associated-molecules-through-transfection-of-mirnas-to-aged-mice
#2
Jung-Hee Kim, Bo-Ram Lee, Eun-Sook Choi, Kyeong-Min Lee, Seong-Kyoon Choi, Jung Hoon Cho, Won Bae Jeon, Eunjoo Kim
Molecular changes during aging have been studied to understand the mechanism of aging progress. Herein, changes in microRNA (miRNA) expression in the whole blood of mice were studied to systemically reverse aging and propose them as non-invasive biomarkers. Through next-generation sequencing analysis, we selected 27 differentially expressed miRNAs during aging. The most recognized function involved was liver steatosis, a type of non-alcoholic fatty liver disease (NAFLD). Among 27 miRNAs, six were predicted to be involved in NAFLD, miR-16-5p, miR-17-5p, miR-21a-5p, miR-30c-5p, miR-103-3p, and miR-130a-3p; alterations in their blood and liver levels were confirmed by real-time qPCR...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28324890/regulation-of-itga3-by-the-dual-stranded-microrna-199-family-as-a-potential-prognostic-marker-in-bladder-cancer
#3
Takashi Sakaguchi, Hirofumi Yoshino, Masaya Yonemori, Kazutaka Miyamoto, Satoshi Sugita, Ryosuke Matsushita, Toshihiko Itesako, Shuichi Tatarano, Masayuki Nakagawa, Hideki Enokida
BACKGROUND: Based on the microRNA (miRNA) signature of bladder cancer (BC) by deep sequencing, we recently found that several double-stranded mature miRNAs derived from the same pre-miRNAs were sufficiently expressed and acted as tumour suppressors by regulating common target genes in BC. Our deep-sequencing signature of BC showed that all miR-199 family members (miR-199a-3p/-5p and miR-199b-3p/-5p) were also downregulated. We hypothesised that these miRNAs may function as tumour suppressors by regulating common target genes...
March 21, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28323040/-machine-learning-based-identification-of-endogenous-cellular-microrna-sponges-against-viral-micrornas
#4
Soowon Kang, Seunghyun Park, Sungroh Yoon, Hyeyoung Min
A "miRNA sponge" is an artificial oligonucleotide-based miRNA inhibitor containing multiple binding sites for a specific miRNA. Each miRNA sponge can bind and sequester several miRNA copies, thereby decreasing the cellular levels of the target miRNA. In addition to developing artificial miRNA sponges, scientists have sought endogenous RNA transcripts and found that long non-coding RNAs, competing endogenous RNAs, pseudogenes, circular RNAs, and coding RNAs could act as miRNA sponges under precise conditions...
March 17, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28321518/identification-and-characterization-of-durum-wheat-micrornas-in-leaf-and-root-tissues
#5
Veronica Fileccia, Edoardo Bertolini, Paolo Ruisi, Dario Giambalvo, Alfonso Salvatore Frenda, Gina Cannarozzi, Zerihun Tadele, Cristina Crosatti, Federico Martinelli
MicroRNAs are a class of post-transcriptional regulators of plant developmental and physiological processes and responses to environmental stresses. Here, we present the study regarding the annotation and characterization of MIR genes conducted in durum wheat. We characterized the miRNAome of leaf and root tissues at tillering stage under two environmental conditions: irrigated with 100% (control) and 55% of evapotranspiration (early water stress). In total, 90 microRNAs were identified, of which 32 were classified as putative novel and species-specific miRNAs...
March 20, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28320521/differential-mirna-expression-analysis-during-late-stage-terminal-hindgut-development-in-fetal-rats
#6
Shuguang Jin, Junxiang Wang, Hong Chen, Bo Xiang
BACKGROUND: Terminal hindgut deformity is the leading digestive tract malformation, however, the etiology and pathogenesis remained unknown. To date, gene expression abnormalities were considered the primary cause of these diseases. miRNAs have been found to play an important role in regulating the expression of genes. METHODS: A total of 24 pregnant rats were randomly divided into two groups. The experimental group (n=12) received 1% ethylenethiourea (125mg/kg) by gavage on gestational day 11, while the control group (n=12) received the same volume of distilled water...
March 12, 2017: Journal of Pediatric Surgery
https://www.readbyqxmd.com/read/28320388/exploring-the-fgfr3-related-oncogenic-mechanism-in-bladder-cancer-using-bioinformatics-strategy
#7
Wei Cao, Enguang Ma, Li Zhou, Tan Yuan, Chunying Zhang
BACKGROUND: Aberrant activation of fibroblast growth factor receptor 3 (FGFR3) is frequently observed in bladder cancer, but how it involved in carcinogenesis is not well understood. The current study was aimed to investigate the underlying mechanism on the progression of bladder cancer. METHODS: The GSE41035 dataset downloaded from Gene Expression Omnibus was used to identify the differentially expressed genes (DEGs) between bladder cancer cell line RT112 with or without depletion of FGFR3, and gene ontology enrichment analysis was performed...
March 20, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28320379/mirnas-associated-with-prostate-cancer-risk-and-progression
#8
REVIEW
Hung N Luu, Hui-Yi Lin, Karina Dalsgaard Sørensen, Olorunseun O Ogunwobi, Nagi Kumar, Ganna Chornokur, Catherine Phelan, Dominique Jones, LaCreis Kidd, Jyotsna Batra, Kosj Yamoah, Anders Berglund, Robert J Rounbehler, Mihi Yang, Sang Haak Lee, Nahyeon Kang, Seung Joon Kim, Jong Y Park, Giuliano Di Pietro
Prostate cancer is the most common malignancy among men in the US. Though considerable improvement in the diagnosis of prostate cancer has been achieved in the past decade, predicting disease outcome remains a major clinical challenge. Recent expression profiling studies in prostate cancer suggest microRNAs (miRNAs) may serve as potential biomarkers for prostate cancer risk and disease progression. miRNAs comprise a large family of about 22-nucleotide-long non-protein coding RNAs, regulate gene expression post-transcriptionally and participate in the regulation of numerous cellular processes...
March 20, 2017: BMC Urology
https://www.readbyqxmd.com/read/28320202/identification-and-expression-of-equine-mer-derived-mirnas
#9
Jeong-An Gim, Heui-Soo Kim
MicroRNAs (miRNAs) are single-stranded, small RNAs (21-23 nucleotides) that function in gene silencing and translational inhibition via the RNA interference mechanism. Most miRNAs originate from host genomic regions, such as intergenic regions, introns, exons, and transposable elements (TEs). Here, we focused on the palindromic structure of medium reiteration frequencies (MERs), which are similar to precursor miRNAs. Five MER consensus sequences (MER5A1, MER53, MER81, MER91C, and MER117) were matched with paralogous transcripts predicted to be precursor miRNAs in the horse genome (equCab2) and located in either intergenic regions or introns...
March 21, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28319645/the-atypical-genesis-and-bioavailability-of-the-plant-based-small-rna-mir2911-bulking-up-while-breaking-down
#10
Jian Yang, Natee Kongchan, Cecilia Primo Planta, Joel R Neilson, Kendal D Hirschi
SCOPE: The uptake of dietary plant small RNAs (sRNAs) in consumers remains controversial, which is mainly due to low dietary content in combination with poor fractional absorption. MIR2911, among all the plant sRNAs including microRNAs, has been shown to be one of the most robustly absorbed sRNAs. Here we analyze the unusual abundance and unique genesis of MIR2911 during vegetable processing. METHODS AND RESULTS: Using qRT-PCR, the abundance of MIR2911 increased dramatically in macerated tissues while other microRNAs degraded...
March 20, 2017: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/28317889/mirnas-novel-regulators-of-autoimmunity-mediated-pancreatic-%C3%AE-cell-destruction-in-type-1-diabetes
#11
REVIEW
Ying Zheng, Zhen Wang, Zhiguang Zhou
MicroRNAs (miRNAs) are a series of conserved, short, non-coding RNAs that modulate gene expression in a posttranscriptional manner. miRNAs are involved in almost every physiological and pathological process. Type 1 diabetes (T1D) is an autoimmune disease that is the result of selective destruction of pancreatic β-cells driven by the immune system. miRNAs are also important participants in T1D pathogenesis. Herein, we review the most recent data on the potential involvement of miRNAs in T1D. Specifically, we focus on two aspects: the roles of miRNAs in maintaining immune homeostasis and regulating β-cell survival and/or functions in T1D...
March 20, 2017: Cellular & Molecular Immunology
https://www.readbyqxmd.com/read/28317323/a-functional-snp-regulated-by-mir-196a-3p-in-the-3-utr-of-fgf2-is-associated-with-bone-mineral-density-in-the-chinese-population
#12
Dong-Li Zhu, Yan Guo, Yan Zhang, Shan-Shan Dong, Wen Xu, Ruo-Han Hao, Xiao-Feng Chen, Han Yan, Shui-Yun Yang, Tie-Lin Yang
Previous studies have identified FGF2 as a susceptibility gene for osteoporosis in Caucasians. Evaluating the genetic associations in different ethnicities is necessary. Moreover, elucidating the functional mechanism for the susceptibility loci is important to offer new targets for therapeutic studies. Here, we genotyped ten SNPs in FGF2 and tested for associations with bone mineral density (BMD) in a discovery sample of 1300 Chinese subjects. Nominally significant results were subjected to replication in another sample of 1039 Chinese subjects...
March 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28314792/comparative-profiling-of-small-rnas-of-pig-seminal-plasma-and-ejaculated-and-epididymal-sperm
#13
Cai Chen, Han Wu, Dan Shen, Saisai Wang, Li Zhang, Xiaoyan Wang, Bo Gao, Tianwen Wu, Bichun Li, Kui Li, Chengyi Song
The similarities and differences of small RNAs in seminal plasma, epididymal sperm and ejaculated sperm remain largely undefined. We conducted a systematic comparative analysis of small RNA profiles in pig ejaculated sperm, epididymal sperm and seminal plasma and found that the diversity distribution of small RNA species was generally similar, whereas the abundance of small RNAs is dramatically different across the three libraries; miRNAs and small RNAs derived from rRNA, tRNA, small nuclear RNA, 7SK RNA, NRON RNA and cis-regulatory RNA were enriched in the three libraries, but piRNA was absent...
March 17, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28314270/global-microrna-expression-profiling-identifies-unique-microrna-pattern-of-radioresistant-glioblastoma-cells
#14
Jakub Ondracek, Pavel Fadrus, Jiri Sana, Andrej Besse, Tomas Loja, Marek Vecera, Lenka Radova, Martin Smrcka, Pavel Slampa, Ondrej Slaby
Glioblastoma multiforme (GBM) is the most aggressive intracranial tumor characterized with infaust prognosis. Despite advances in neurosurgical and radiotherapeutic techniques and chemotherapy, the median overall survival ranges between 12-15 months from diagnosis. The main cause of treatment failure is considered the presence of tumor cells resistant to conventional therapy, mainly radiotherapy. MicroRNAs (miRNAs) are small, non-coding RNAs that function as post-transcriptional regulators of gene expression and have been repeatedly proven to play important roles in pathogenesis and biological features of many cancers, including GBM and its radioresistant phenotype...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28303124/identification-and-characterization-of-mirnas-in-response-to-leishmania-donovani-infection-delineation-of-their-roles-in-macrophage-dysfunction
#15
Neeraj Tiwari, Vinod Kumar, Mallikarjuna Rao Gedda, Ashish K Singh, Vijay K Singh, Sreenivas Gannavaram, Surya P Singh, Rakesh K Singh
The outcome of Leishmania infection depends on parasite abilities to evade host immune response and its survival in hostile environment of host macrophages. Despite a wealth of gained crucial information, parasite strategies by which it dampens host macrophage functions remain poorly understood. Micro RNAs (miRNAs) are evolutionarily conserved class of endogenous 22-nucleotide small non-coding RNA gene products, described to participate in the regulation of almost every cellular process investigated so far...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28302568/mutational-profile-from-targeted-ngs-predicts-survival-in-ldct-screening-detected-lung-cancers
#16
Carla Verri, Cristina Borzi, Todd Holscher, Matteo Dugo, Andrea Devecchi, Katherine Drake, Stefano Sestini, Paola Suatoni, Elisa Romeo, Gabriella Sozzi, Ugo Pastorino, Mattia Boeri
BACKGROUND: The issue of overdiagnosis in low-dose computed tomography (LDCT)-screening trials could be addressed by the development of complementary biomarkers able to improve detection of aggressive disease. The mutation profile of LDCT screening-detected lung tumours is currently unknown. METHODS: Targeted next-generation sequencing was performed in 94 LDCT screening-detected lung tumours. Associations with clinicopathologic features, survival and the risk profile of a plasma microRNA signature classifier (MSC) were analyzed...
March 13, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28302473/quantitative-relationship-between-chemical-properties-and-bioactivities-of-anti-microrna-oligonucleotides-targeted-to-tumor-associated-microrna-21
#17
Koji Nagahama, Kenta Iseda, Daichi Kawano, Junji Kawakami
Synthetic anti-microRNA oligonucleotides (AMOs) are promising drug candidates to inactivate disease-related microRNAs because of their sequence-specific binding to their targets and the variety of chemical modifications available. Over the last decade, the qualitative relationships between the chemical properties of AMOs and bioactivity (inactivation of their target miRNAs) have been studied to enhance their bioactivity. On the other hand, in real-world drug development, drugs must be designed case-by-case, taking many factors into account...
March 13, 2017: Biochimie
https://www.readbyqxmd.com/read/28302149/identification-and-interaction-analysis-of-key-genes-and-micrornas-in-hepatocellular-carcinoma-by-bioinformatics-analysis
#18
Tong Mou, Di Zhu, Xufu Wei, Tingting Li, Daofeng Zheng, Junliang Pu, Zhen Guo, Zhongjun Wu
BACKGROUND: Hepatocellular carcinoma (HCC) is the most common liver malignancy worldwide. However, present studies of its multiple gene interaction and cellular pathways still could not explain the initiation and development of HCC perfectly. To find the key genes and miRNAs as well as their potential molecular mechanisms in HCC, microarray data GSE22058, GSE25097, and GSE57958 were analyzed. METHODS: The microarray datasets GSE22058, GSE25097, and GSE57958, including mRNA and miRNA profiles, were downloaded from the GEO database and were analyzed using GEO2R...
March 16, 2017: World Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28302134/microrna-142-regulates-inflammation-and-t-cell-differentiation-in-an-animal-model-of-multiple-sclerosis
#19
Farideh Talebi, Samira Ghorbani, Wing Fuk Chan, Roobina Boghozian, Farimah Masoumi, Sedigheh Ghasemi, Mohammed Vojgani, Christopher Power, Farshid Noorbakhsh
BACKGROUND: MicroRNAs have emerged as an important class of modulators of gene expression. These molecules influence protein synthesis through translational repression or degradation of mRNA transcripts. Herein, we investigated the potential role of miR-142a isoforms, miR-142a-3p and miR-142a-5p, in the context of autoimmune neuroinflammation. METHODS: The expression levels of two mature isoforms of miR-142 were measured in the brains of patients with multiple sclerosis (MS) and the CNS tissues from mice with experimental autoimmune encephalomyelitis (EAE), an animal model of MS...
March 16, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/28301325/circulating-mirnas-as-biomarkers-of-gait-speed-responses-to-aerobic-exercise-training-in-obese-older-adults
#20
Tan Zhang, Tina E Brinkley, Keqin Liu, Xin Feng, Anthony P Marsh, Stephen Kritchevsky, Xiaobo Zhou, Barbara J Nicklas
Gait speed is a useful predictor of adverse outcomes, including incident mobility disability and mortality in older adults. While aerobic exercise training (AEX) is generally an effective therapy to improve gait speed, individual responses are highly variable. Circulating microRNAs (miRNAs) may contribute to inter-individual changes in gait speed with AEX. We examined whether plasma miRNAs are associated with gait speed changes (dGaitSp) in 33 obese older adults (age: 69.3±3.6 years, BMI: 34.0±3.1 kg/m(2), 85% white, 73% women) who performed treadmill walking, 4 days/week for 5 months...
March 15, 2017: Aging
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