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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/28940437/analysis-of-argonaute-2-microrna-complexes-in-ex-vivo-stored-red-blood-cells
#1
Long Vu, Viswanath Ragupathy, Sandhya Kulkarni, Chintamani Atreya
BACKGROUND: Human enucleated mature red blood cells (RBCs) contain both mature microRNAs (miRNAs) and mRNAs, and we have previously correlated RBC storage lesion processes such as eryptosis, adenosine 5'-triphosphate loss, and RBC indices with differentially expressed miRNAs. Here we have characterized Argonaute 2 (AGO2)-miRNA complexes in stored mature RBCs as a first step toward understanding their role, if any. STUDY DESIGN AND METHODS: In this report AGO2-bound miRNAs in mature RBCs isolated from RBCs collected from three different healthy donors and stored for 24 hours at 4 to 6°C were identified by anti-AGO2 immunoprecipitation (IP) followed by next-generation sequencing of the RNA isolated from the IP...
September 20, 2017: Transfusion
https://www.readbyqxmd.com/read/28939056/ectopic-overexpression-of-mcpip1-impairs-adipogenesis-by-modulating-micrornas
#2
Magdalena Losko, Agata Lichawska-Cieslar, Maria Kulecka, Agnieszka Paziewska, Izabela Rumienczyk, Michal Mikula, Jolanta Jura
Adipogenesis is a process of preadipocyte differentiation that requires action of numerous factors. Monocyte chemoattractant protein-1-induced protein 1 (MCPIP1) possesses the N-terminus of the PilT protein (PilT N-terminus or PIN domain) that has RNase properties. This protein degrades transcripts coding for inflammation and differentiation - related proteins. Moreover, MCPIP1 is a broad suppressor of the miRNA biogenesis. We previously found that MCPIP1 degrades transcript encoding CCAAT/Enhancer Binding Protein Beta (C/EBPβ) and influences adipogenesis...
September 19, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28928862/discovering-the-mir-26a-5p-targetome-in-prostate-cancer-cells
#3
Milena Rizzo, Gabriele Berti, Francesco Russo, Sofia Fazio, Monica Evangelista, Romina D'Aurizio, Marco Pellegrini, Giuseppe Rainaldi
Purpose. miR-26a-5p is a tumor suppressor (TS) miRNA often downregulated in several tumor tissues and tumor cell lines. In this work, we performed the re-expression of the miR-26a-5p in DU-145 prostate cancer cells to collect genes interacting with miR-26a-5p and analyzed their integration in the tumorigenesis related pathways. Methods. The transfection of DU-145 prostate cancer cells with miR-26a-5p was done using nucleofection. The biological effects induced by miR-26a-5p re-expression were detected with routine assays for cell proliferation, cell cycle, survival, apoptosis and cell migration...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28927254/integrated-analysis-of-microrna-and-mrna-expression-in-peripheral-blood-leukocytes-of-warmblood-horses-before-and-after-exercise
#4
Hang-Ah Kim, Myung-Chul Kim, Na-Yon Kim, Doug-Young Ryu, Hong-Seok Lee, Yongbaek Kim
Exercise capacity is a valuable trait in horses, and it has been used as one of their selection criteria. Although exercise affects molecular homeostasis and adaptation in horses, the mechanisms underlying these effects are not fully understood. This study was carried out to identify changes in the blood profiles of microRNAs (miRNAs) and mRNAs induced by exercise in horse leukocytes. Total RNAs isolated from the peripheral blood leukocytes of four Warmblood horses before and after exercise were subjected to next-generation sequencing (NGS) and microarray analyses to determine the miRNA and mRNA expression profiles, respectively...
September 20, 2017: Journal of Veterinary Science
https://www.readbyqxmd.com/read/28925390/alterations-of-micrornas-throughout-the-malignant-evolution-of-cutaneous-squamous-cell-carcinoma-the-role-of-mir-497-in-epithelial-to-mesenchymal-transition-of-keratinocytes
#5
A Mizrahi, A Barzilai, D Gur-Wahnon, I Z Ben-Dov, S Glassberg, T Meningher, E Elharar, M Masalha, J Jacob-Hirsch, H Tabibian-Keissar, I Barshack, J Roszik, R Leibowitz-Amit, Y Sidi, D Avni
Skin carcinogenesis is known to be a multi-step process with several stages along its malignant evolution. We hypothesized that transformation of normal epidermis to cutaneous squamous cell carcinoma (cSCC) is causally linked to alterations in microRNAs (miRNA) expression. For this end we decided to evaluate their alterations in the pathologic states ending in cSCC. Total RNA was extracted from formalin fixed paraffin embedded biopsies of five stages along the malignant evolution of keratinocytes towards cSCC: Normal epidermis, solar elastosis, actinic keratosis KIN1-2, advanced actinic keratosis KIN3 and well-differentiated cSCC...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28915579/microrna-profiling-associated-with-non-small-cell-lung-cancer-next-generation-sequencing-detection-experimental-validation-and-prognostic-value
#6
Sandra Gallach, Eloisa Jantus-Lewintre, Silvia Calabuig-Fariñas, David Montaner, Sergio Alonso, Rafael Sirera, Ana Blasco, Marta Usó, Ricardo Guijarro, Miguel Martorell, Carlos Camps
BACKGROUND: The average five-year survival for non-small cell lung cancer (NSCLC) patients is approximately 15%. Emerging evidence indicates that microRNAs (miRNAs) constitute a new class of gene regulators in humans that may play an important role in tumorigenesis. Hence, there is growing interest in studying their role as possible new biomarkers whose expression is aberrant in cancer. Therefore, in this study we identified dysregulated miRNAs by next generation sequencing (NGS) and analyzed their prognostic value...
August 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28903026/differential-expression-of-genes-in-fetal-brain-as-a-consequence-of-maternal-protein-deficiency-and-nematode-infection
#7
Manjurul Haque, Lisa M Starr, Kristine G Koski, Marilyn E Scott
Maternal dietary protein deficiency and gastrointestinal nematode infection during early pregnancy have negative impacts on both maternal placental gene expression and fetal growth in the mouse. Here we used next-generation RNA sequencing to test our hypothesis that maternal protein deficiency and/or nematode infection also alter the expression of genes in the developing fetal brain. Outbred pregnant CD1 mice were used in a 2×2 design with two levels of dietary protein (24% versus 6%) and two levels of infection (repeated sham versus Heligmosomoides bakeri beginning at gestation day 5)...
September 10, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28892169/a-global-survey-of-alternative-splicing-in-allopolyploid-cotton-landscape-complexity-and-regulation
#8
Maojun Wang, Pengcheng Wang, Fan Liang, Zhengxiu Ye, Jianying Li, Chao Shen, Liuling Pei, Feng Wang, Jiang Hu, Lili Tu, Keith Lindsey, Daohua He, Xianlong Zhang
Alternative splicing (AS) is a crucial regulatory mechanism in eukaryotes, which acts by greatly increasing transcriptome diversity. The extent and complexity of AS has been revealed in model plants using high-throughput next-generation sequencing. However, this technique is less effective in accurately identifying transcript isoforms in polyploid species because of the high sequence similarity between coexisting subgenomes. Here we characterize AS in the polyploid species cotton. Using Pacific Biosciences single-molecule long-read isoform sequencing (Iso-Seq), we developed an integrated pipeline for Iso-Seq transcriptome data analysis (https://github...
September 11, 2017: New Phytologist
https://www.readbyqxmd.com/read/28884089/splenic-microrna-expression-profiles-and-integration-analyses-involved-in-host-responses-to-salmonella-enteritidis-infection-in-chickens
#9
Peng Li, Wenlei Fan, Qinghe Li, Jie Wang, Ranran Liu, Nadia Everaert, Jie Liu, Yonghong Zhang, Maiqing Zheng, Huanxian Cui, Guiping Zhao, Jie Wen
To understand the role of miRNAs in regulating genes involved in the host response to Salmonella enteritidis (SE) infection, next generation sequencing was applied to explore the altered splenic expression of microRNAs (miRNAs) and deregulated genes in specific-pathogen-free chickens. Birds were either infected or not (controls, C) and those challenged with SE were evaluated 24 h later and separated into two groups on the basis of the severity of clinical symptoms and blood load of SE: resistant (R, SE challenged-slight clinical symptoms and <10(5) cfu / 10 μL), and susceptible (S, SE challenged-severe clinical symptoms and >10(7) cfu/10 μL)...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28862265/anaplastic-sarcomas-of-the-kidney-are-characterized-by-dicer1-mutations
#10
Mona K Wu, Gordan M Vujanic, Somayyeh Fahiminiya, Noriko Watanabe, Paul S Thorner, Maureen J O'Sullivan, Marc R Fabian, William D Foulkes
Anaplastic sarcoma of the kidney is a rare tumor (≤25 reported cases) characterized by the presence of cysts, and solid areas composed of bundles of undifferentiated spindle cells, showing marked cellular anaplasia (usually accompanied by TP53 overexpression). These tumors often feature prominent areas of cartilage or chondroid material. Germline mutations in DICER1, encoding the microRNA (miRNA) processor DICER1, cause an eponymous syndrome. Recent reports suggest that anaplastic sarcoma of the kidney should be included in DICER1 syndrome as germline DICER1 mutations are associated with the occurrence of such tumors...
September 1, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28857182/altered-mir-193a-5p-expression-in-children-with-cow-s-milk-allergy
#11
Valeria D'Argenio, Valentina Del Monaco, Lorella Paparo, Fatima Domenica Elisa De Palma, Rita Nocerino, Francesca D'Alessio, Feliciano Visconte, Valentina Discepolo, Luigi Del Vecchio, Francesco Salvatore, Roberto Berni Canani
BACKGROUND: Cow's milk allergy (CMA) is one of the most common food allergies in children. Epigenetic mechanisms have been suggested to play a role in CMA pathogenesis. We shown that DNA methylation of Th1/Th2 cytokine genes and FoxP3 affects CMA disease course. Preliminary evidence suggest that also the miRNome could be implicated in the pathogenesis of allergy. Main study outcome was to comparatively evaluate miRNome in children with CMA and in healthy controls. METHODS: Peripheral blood mononuclear cells were obtained from children aged 4-18 months: 10 CMA patients, 9 CMA patients who outgrew CMA, and 11 healthy controls...
August 30, 2017: Allergy
https://www.readbyqxmd.com/read/28838324/microbial-regulation-of-microrna-expression-in-the-amygdala-and-prefrontal-cortex
#12
Alan E Hoban, Roman M Stilling, Gerard M Moloney, Rachel D Moloney, Fergus Shanahan, Timothy G Dinan, John F Cryan, Gerard Clarke
BACKGROUND: There is growing evidence for a role of the gut microbiome in shaping behaviour relevant to many psychiatric and neurological disorders. Preclinical studies using germ-free (GF) animals have been essential in contributing to our current understanding of the potential importance of the host microbiome for neurodevelopment and behaviour. In particular, it has been repeatedly demonstrated that manipulation of the gut microbiome modulates anxiety-like behaviours. The neural circuits that underlie anxiety- and fear-related behaviours are complex and heavily depend on functional communication between the amygdala and prefrontal cortex (PFC)...
August 25, 2017: Microbiome
https://www.readbyqxmd.com/read/28832679/a-comprehensive-simulation-study-on-classification-of-rna-seq-data
#13
Gökmen Zararsız, Dincer Goksuluk, Selcuk Korkmaz, Vahap Eldem, Gozde Erturk Zararsiz, Izzet Parug Duru, Ahmet Ozturk
RNA sequencing (RNA-Seq) is a powerful technique for the gene-expression profiling of organisms that uses the capabilities of next-generation sequencing technologies. Developing gene-expression-based classification algorithms is an emerging powerful method for diagnosis, disease classification and monitoring at molecular level, as well as providing potential markers of diseases. Most of the statistical methods proposed for the classification of gene-expression data are either based on a continuous scale (eg...
2017: PloS One
https://www.readbyqxmd.com/read/28829370/mir-30a-5p-inhibits-epithelial-to-mesenchymal-transition-and-upregulates-expression-of-tight-junction-protein-claudin-5-in-human-upper-tract-urothelial-carcinoma-cells
#14
Yueh-Hua Chung, Sung-Chou Li, Ying-Hsien Kao, Hao-Lun Luo, Yuan-Tso Cheng, Pey-Ru Lin, Ming-Hong Tai, Po-Hui Chiang
The involvement of microRNAs (miRNAs) in cancer development and their potential as prognostic biomarkers are becoming increasingly known. However, the signature of miRNAs and their regulatory roles in tumorigenesis of upper tract urothelial carcinoma (UTUC) remain to be elucidated. This study aimed to profile the miRNA expression pattern in UTUC tumor tissues and identify candidate miRNAs with prognostic and/or therapeutic functions. METHODS AND RESULTS: We collected 22 UTUC tissue and adjacent normal tissues samples from patients who underwent nephroureterectomy...
August 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28821885/the-expression-profiles-of-mirna-mrna-of-early-response-in-genetically-improved-farmed-tilapia-oreochromis-niloticus-liver-by-acute-heat-stress
#15
Jun Qiang, Wen J Bao, Fan Y Tao, Jie He, Xia H Li, Pao Xu, Lan Y Sun
Genetically improved farmed tilapia (GIFT, Oreochromis niloticus) are commercially important fish that are cultured in China. GIFT are highly susceptible to diseases when exposed to high temperatures in summer. Better understanding the GIFT regulatory response to heat stress will not only help in determining the relationship between heat stress signalling pathways and adaption mechanisms, but will also contribute to breeding new high-temperature tolerant strains of GIFT. In this study, we built control (28 °C) and heat-treated (37...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821725/interplay-between-maternal-slc6a4-mutation-and-prenatal-stress-a-possible-mechanism-for-autistic-behavior-development
#16
Calvin P Sjaarda, Patrick Hecht, Amy J M McNaughton, Audrina Zhou, Melissa L Hudson, Matt J Will, Garth Smith, Muhammad Ayub, Ping Liang, Nansheng Chen, David Beversdorf, Xudong Liu
The low activity allele of the maternal polymorphism, 5HTTLPR, in the serotonin transporter, SLC6A4, coupled with prenatal stress is reported to increase the risk for children to develop autism spectrum disorder (ASD). Similarly, maternal Slc6a4 knock-out and prenatal stress in rodents results in offspring demonstrating ASD-like characteristics. The present study uses an integrative genomics approach to explore mechanistic changes in early brain development in mouse embryos exposed to this maternal gene-environment phenomenon...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28815576/microrna-and-mesial-temporal-lobe-epilepsy-with-hippocampal-sclerosis-whole-mirnome-profiling-of-human-hippocampus
#17
Petra Bencurova, Jiri Baloun, Katerina Musilova, Lenka Radova, Boris Tichy, Martin Pail, Martin Zeman, Eva Brichtova, Marketa Hermanova, Sarka Pospisilova, Marek Mraz, Milan Brazdil
OBJECTIVE: Mesial temporal lobe epilepsy (mTLE) is a severe neurological disorder characterized by recurrent seizures. mTLE is frequently accompanied by neurodegeneration in the hippocampus resulting in hippocampal sclerosis (HS), the most common morphological correlate of drug resistance in mTLE patients. Incomplete knowledge of pathological changes in mTLE+HS complicates its therapy. The pathological mechanism underlying mTLE+HS may involve abnormal gene expression regulation, including posttranscriptional networks involving microRNAs (miRNAs)...
August 16, 2017: Epilepsia
https://www.readbyqxmd.com/read/28811555/identification-of-novel-micrornas-in-the-sheep-heart-and-their-regulation-in-heart-failure
#18
Lee Lee Wong, Miriam T Rademaker, Eng Leng Saw, Kar Sheng Lew, Leigh J Ellmers, Christopher J Charles, Arthur Mark Richards, Peipei Wang
Study of microRNA (miRNAs) using sheep models is limited due to lack of miRNA information. We therefore investigated oar-miRNAs and their regulation in an ovine model of heart failure (HF). Left ventricular (LV) tissue was collected from normal (Cont), HF (LV pacing @ ~220bpm for 13-days) and HF-recovery sheep (HF-R, 26-days after pacing cessation). MiRNA expression was profiled using next-generation sequencing (NGS) and miRNA array, and validated by stem-loop qPCR. Detected sequences were mapped against the ovine genome (Oar v4...
August 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798252/pollen-induced-oxidative-dna-damage-response-regulates-mirnas-controlling-allergic-inflammation
#19
Leopoldo Aguilera-Aguirre, Wenjing Hao, Lang Pan, Xiaoxue Li, Alfredo Saavedra-Molina, Attila Bacsi, Zsolt Radak, Sanjiv Sur, Allan R Brasier, Xueqing Ba, Istvan Boldogh
A mucosal oxidative burst is a hallmark response to pollen exposure that promotes allergic inflammatory responses. Reactive species constituents of oxidative stress signal via the modification of cellular molecules including nucleic acids. One of the most abundant oxidative genomic base damage is 8-oxo-7,8-dihydroguanine (8-oxoG), which is removed from DNA by 8-oxoguanine DNA glycosylase1 (OGG1). OGG1 in complex with 8-oxoG acts as a GDP-GTP exchange factor and induces acute inflammation; however, the mechanism(s) by which OGG1 signaling regulates allergic airway inflammation is not known...
August 10, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28791028/trna-derived-smallrnas-smallrnas-repertoire-has-yet-to-be-decoded-in-plants
#20
Gaurav Sablok, Kun Yang, Rui Chen, Xiaopeng Wen
Among several smallRNAs classes, microRNAs play an important role in controlling the post-transcriptional events. Next generation sequencing has played a major role in extending the landscape of miRNAs and revealing their spatio-temporal roles in development and abiotic stress. Lateral evolution of these smallRNAs classes have widely been seen with the recently emerging knowledge on tRNA derived smallRNAs. In the present perspective, we discussed classification, identification and roles of tRNA derived smallRNAs across plants and their potential involvement in abiotic and biotic stresses...
2017: Frontiers in Plant Science
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