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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/28335433/evaluation-and-adaptation-of-a-laboratory-based-cdna-library-preparation-protocol-for-retrospective-sequencing-of-archived-micrornas-from-up-to-35-year-old-clinical-ffpe-specimens
#1
Olivier Loudig, Tao Wang, Kenny Ye, Juan Lin, Yihong Wang, Andrew Ramnauth, Christina Liu, Azadeh Stark, Dhananjay Chitale, Robert Greenlee, Deborah Multerer, Stacey Honda, Yihe Daida, Heather Spencer Feigelson, Andrew Glass, Fergus J Couch, Thomas Rohan, Iddo Z Ben-Dov
Formalin-fixed paraffin-embedded (FFPE) specimens, when used in conjunction with patient clinical data history, represent an invaluable resource for molecular studies of cancer. Even though nucleic acids extracted from archived FFPE tissues are degraded, their molecular analysis has become possible. In this study, we optimized a laboratory-based next-generation sequencing barcoded cDNA library preparation protocol for analysis of small RNAs recovered from archived FFPE tissues. Using matched fresh and FFPE specimens, we evaluated the robustness and reproducibility of our optimized approach, as well as its applicability to archived clinical specimens stored for up to 35 years...
March 14, 2017: International Journal of Molecular Sciences
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/28314265/next-generation-sequencing-for-microrna-profiling-microrna-21-3p-promotes-oral-cancer-metastasis
#3
Hui-Hwa Tseng, Yu-Kai Tseng, Jyun-Jie You, Bor-Hwang Kang, Tsung-Han Wang, Cheng-Mei Yang, Hung-Chih Chen, Huei-Han Liou, Pei-Feng Liu, Luo-Ping Ger, Kuo-Wang Tsai
Dysfunctional microRNAs (miRNAs) play a crucial role in oral squamous cell carcinoma (OSCC) progression. In the present study, we performed next-generation sequencing for miRNA profiling of the OSCC tissues and corresponding adjacent normal tissues in two patients with OSCC. We observed that 45 miRNAs were substantially up-regulated and 17 miRNAs were down-regulated in OSCC tissues. Since information on the biological role of miR-21-3p (passenger strand) in OSCC is limited, the expression levels of miR-21-3p were further evaluated in 95 OSCC tissue samples by a stem-loop real-time polymerase chain reaction...
March 2017: Anticancer Research
https://www.readbyqxmd.com/read/28303893/changes-in-mirna-in-the-lung-and-whole-blood-after-whole-thorax-irradiation-in-rats
#4
Feng Gao, Pengyuan Liu, Jayashree Narayanan, Meiying Yang, Brian L Fish, Yong Liu, Mingyu Liang, Elizabeth R Jacobs, Meetha Medhora
We used a rat model of whole thorax x-ray irradiation to profile the microRNA (miRNA) in lung and blood up to 4 weeks after radiation. MiRNA from normal and irradiated Wistar rat lungs and whole blood were analyzed by next-generation sequencing and the changes by radiation were identified by differential deRNA-seq 1, 2, 3 and 4 weeks after irradiation. The average total reads/library was 2,703,137 with a mean of 88% mapping to the rat genome. Detailed profiles of 100 of the most abundant miRNA in rat blood and lung are described...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302568/mutational-profile-from-targeted-ngs-predicts-survival-in-ldct-screening-detected-lung-cancers
#5
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/28300211/als-along-the-axons-expression-of-coding-and-noncoding-rna-differs-in-axons-of-als-models
#6
Nimrod Rotem, Iddo Magen, Ariel Ionescu, Noga Gershoni-Emek, Topaz Altman, Christopher J Costa, Tal Gradus, Metsada Pasmanik-Chor, Dianna E Willis, Iddo Z Ben-Dov, Eran Hornstein, Eran Perlson
Amyotrophic lateral sclerosis (ALS) is a multifactorial lethal motor neuron disease with no known treatment. Although the basic mechanism of its degenerative pathogenesis remains poorly understood, a subcellular spatial alteration in RNA metabolism is thought to play a key role. The nature of these RNAs remains elusive, and a comprehensive characterization of the axonal RNAs involved in maintaining neuronal health has yet to be described. Here, using cultured spinal cord (SC) neurons grown using a compartmented platform followed by next-generation sequencing (NGS) technology, we find that RNA expression differs between the somatic and axonal compartments of the neuron, for both mRNA and microRNA (miRNA)...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28292266/microrna-categorization-using-sequence-motifs-and-k-mers
#7
Malik Yousef, Waleed Khalifa, İlhan Erkin Acar, Jens Allmer
BACKGROUND: Post-transcriptional gene dysregulation can be a hallmark of diseases like cancer and microRNAs (miRNAs) play a key role in the modulation of translation efficiency. Known pre-miRNAs are listed in miRBase, and they have been discovered in a variety of organisms ranging from viruses and microbes to eukaryotic organisms. The computational detection of pre-miRNAs is of great interest, and such approaches usually employ machine learning to discriminate between miRNAs and other sequences...
March 14, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28289279/next-gen-sequencing-identifies-non-coding-variation-disrupting-mirna-binding-sites-in-neurological-disorders
#8
P Devanna, X S Chen, J Ho, D Gajewski, S D Smith, A Gialluisi, C Francks, S E Fisher, D F Newbury, S C Vernes
Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes...
March 14, 2017: Molecular Psychiatry
https://www.readbyqxmd.com/read/28289238/stroke-and-circulating-extracellular-rnas
#9
Eric Mick, Ravi Shah, Kahraman Tanriverdi, Venkatesh Murthy, Mark Gerstein, Joel Rozowsky, Robert Kitchen, Martin G Larson, Daniel Levy, Jane E Freedman
BACKGROUND AND PURPOSE: There is increasing interest in extracellular RNAs (ex-RNAs), with numerous reports of associations between selected microRNAs (miRNAs) and a variety of cardiovascular disease phenotypes. Previous studies of ex-RNAs in relation to risk for cardiovascular disease have investigated small numbers of patients and assayed only candidate miRNAs. No human studies have investigated links between novel ex-RNAs and stroke. METHODS: We conducted unbiased next-generation sequencing using plasma from 40 participants of the FHS (Framingham Heart Study; Offspring Cohort Exam 8) followed by high-throughput polymerase chain reaction of 471 ex-RNAs...
March 13, 2017: Stroke; a Journal of Cerebral Circulation
https://www.readbyqxmd.com/read/28277545/mir-377-induces-senescence-in-human-skin-fibroblasts-by-targeting-dna-methyltransferase-1
#10
Hong-Fu Xie, Ying-Zi Liu, Rui Du, Ben Wang, Meng-Ting Chen, Yi-Ya Zhang, Zhi-Li Deng, Ji Li
Skin aging is a complicated physiological process and epigenetic feature, including microRNA-mediated regulation and DNA methylation, have been shown to contribute to this process. DNA methylation is regulated by DNA methyltransferase, of which DNA methyltransferase 1 (DNMT1) is the most abundantly known. But evidence supporting its role in skin aging remains scarce, and no report regards its specifical upstream-regulating molecules in the process of skin aging so far. Here, we found that DNMT1 expression was markedly higher in young human skin fibroblasts (HSFs) than that in passage-aged HSFs, and DNMT1 knockdown significantly induced the senescence phenotype in young HSFs...
March 9, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28265491/fuchs-towards-full-circular-rna-characterization-using-rnaseq
#11
Franziska Metge, Lisa F Czaja-Hasse, Richard Reinhardt, Chistoph Dieterich
Circular RNAs (circRNAs) belong to a recently re-discovered species of RNA that emerge during RNA maturation through a process called back-splicing. A downstream 5' splice site is linked to an upstream 3' splice site to form a circular transcript instead of a canonical linear transcript. Recent advances in next-generation sequencing (NGS) have brought circRNAs back into the focus of many scientists. Since then, several studies reported that circRNAs are differentially expressed across tissue types and developmental stages, implying that they are actively regulated and not merely a by-product of splicing...
2017: PeerJ
https://www.readbyqxmd.com/read/28262816/effect-of-age-on-pro-inflammatory-mirnas-contained-in-mesenchymal-stem-cell-derived-extracellular-vesicles
#12
J Fafián-Labora, I Lesende-Rodriguez, P Fernández-Pernas, S Sangiao-Alvarellos, L Monserrat, O J Arntz, F J Van de Loo, J Mateos, M C Arufe
Stem cells possess significant age-dependent differences in their immune-response profile. These differences were analysed by Next-Generation Sequencing of six age groups from bone marrow mesenchymal stem cells. A total of 9,628 genes presenting differential expression between age groups were grouped into metabolic pathways. We focused our research on young, pre-pubertal and adult groups, which presented the highest amount of differentially expressed genes related to inflammation mediated by chemokine and cytokine signalling pathways compared with the newborn group, which was used as a control...
March 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28259757/comprehensive-characteristics-of-microrna-expression-profile-of-equine-sarcoids
#13
Klaudia Pawlina, Artur Gurgul, Tomasz Szmatoła, Christoph Koch, Kathrin Mählmann, Maciej Witkowski, Monika Bugno-Poniewierska
Equine sarcoids are the most common neoplasms occurring in horses. Despite frequent occurrence, they are still not well described at the molecular level. Thus, in the present study, we performed a comprehensive comparative analysis of sarcoid miRNAome profile to identify aberrantly expressed microRNAs, along with their structural variants, potentially useful as biomarkers and, in a wider perspective, broaden the knowledge about this tumor and underlying mechanisms. To this end, we conducted next generation sequencing and as a result we identified both known and potentially novel miRNAs...
March 1, 2017: Biochimie
https://www.readbyqxmd.com/read/28257601/mir181b-3p-and-its-target-importin-%C3%AE-5-regulate-tlr4-signaling-in-kupffer-cells-and-liver-injury-in-mice-in-response-to-ethanol
#14
Paramananda Saikia, Damien Bellos, Megan R McMullen, Katherine A Pollard, Carol de la Motte, Laura E Nagy
Increased inflammatory signaling by Kupffer cells contributes to alcoholic liver disease (ALD). Here we investigated the impact of small-specific sized hyaluronic acid of ∼35kD (HA35) on ethanol-induced sensitization of Kupffer cells, as well as ethanol-induced liver injury in mice. Un-biased analysis of microRNA (miRNA) expression in Kupffer cells identified miRNAs regulated by both ethanol and HA35. TLR4-mediated signaling was assessed in primary cultures of Kupffer cells from ethanol- and pair-fed rats after treatment with HA35...
March 3, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28235734/a-novel-electrochemiluminescence-biosensor-for-the-detection-of-micrornas-based-on-a-dna-functionalized-nitrogen-doped-carbon-quantum-dots-as-signal-enhancers
#15
Qiao Liu, Cheng Ma, Xing-Pei Liu, Yu-Pin Wei, Chang-Jie Mao, Jun-Jie Zhu
An ultrasensitive electrochemiluminescence (ECL) biosensor for the detection of microRNA was developed based on nicking enzymes Nb.BbvCI mediated signal amplification (NESA). First, the hairpin probe1-N-CQDs with assistant probe and microRNA (miRNA) formed Y junction structure which was cleaved with the addition of nicking enzymes Nb.BbvCI to release miRNA and assistant probe. Subsequently, the released miRNA and assistant probe can initiate the next recycling process. The generation of numerous intermediate sequences nitrogen doped carbon quantum dots-DNA (N-CQDs-DNA) can further hybridize with hairpin probe2 immobilized on GO/Au composite modified electrode surface, the initial ECL intensity was enhanced...
June 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28229383/mirna-based-heavy-metal-homeostasis-and-plant-growth
#16
Ali Noman, Muhammad Aqeel
Plants have been naturally gifted with mechanisms to adjust under very high or low nutrient concentrations. Heavy metal toxicity is considered as a major growth and yield-limiting factor for plants. This stress includes essential as well as non-essential metals. MicroRNAs (miRNAs) are known for mediating post-transcriptional regulation by cleaving transcripts or translational inhibition. It is commonly agreed that an extensive understanding of plant miRNAs will significantly help in the induction of tolerance against environmental stresses...
February 22, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28218741/identification-of-micrornas-associated-with-invasive-and-aggressive-phenotype-in-cutaneous-melanoma-by-next-generation-sequencing
#17
Sankhiros Babapoor, Rong Wu, James Kozubek, Donna Auidi, Jane M Grant-Kels, Soheil S Dadras
A comprehensive repertoire of human microRNAs (miRNAs) that could be involved in early melanoma invasion into the dermis remains unknown. To this end, we sequenced small RNAs (18-30 nucleotides) isolated from an annotated series of invasive melanomas (average invasive depth, 2.0 mm), common melanocytic nevi, and matched normal skin (n=28). Our previously established bioinformatics pipeline identified 765 distinct mature known miRNAs and defined a set of top 40 list that clearly segregated melanomas into thin (0...
February 20, 2017: Laboratory Investigation; a Journal of Technical Methods and Pathology
https://www.readbyqxmd.com/read/28218475/profound-changes-in-mirna-expression-during-cancer-initiation-by-aflatoxin-b1-and-their-abrogation-by-the-chemopreventive-triterpenoid-cddo-im
#18
Merricka C Livingstone, Natalie M Johnson, Bill D Roebuck, Thomas W Kensler, John D Groopman
Aflatoxin B1 (AFB1 ) is a potent human and animal hepatocarcinogen. To investigate the effects of aflatoxin on miRNA expression during the initiation phase of carcinogenesis, next-generation sequencing was used to analyze liver tissues from F344 rats exposed to 200 µg/kg per day AFB1 for 4 weeks. A panel of miRNAs was identified that was upregulated with AFB1 treatment compared to controls: rno-miR-434-3p, rno-miR-411-5p, rno-miR-221-3p, rno-miR-127-3p, rno-miR-205, rno-miR-429, rno-miR-34a-5p, rno-miR-181c-3p, rno-miR-200b-3p, and rno-miR-541-5p...
February 20, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28207805/unraveling-the-microrna-of-caragana-korshinskii-along-a-precipitation-gradient-on-the-loess-plateau-china-using-high-throughput-sequencing
#19
Pengbo Ning, Yulu Zhou, Lifang Gao, Yingying Sun, Wenfei Zhou, Furong Liu, Zhenye Yao, Lifang Xie, Junhui Wang, Chunmei Gong
Drought remains one of the main factors that negatively affect plant growth and development. Caragana korshinskii is widely distributed on the Loess Plateau, China, where it mediates soil and water loss and helps prevent desertification. However, little is known about the stress response mechanisms of C. korshinskii in water-starved environments. MicroRNAs (miRNAs) have been implicated in the regulation of plant responses to several types of biotic and abiotic stress. Here, we describe the miRNAs of wild C...
2017: PloS One
https://www.readbyqxmd.com/read/28194813/microrna-191-acts-as-a-tumor-promoter-by-modulating-the-tet1-p53-pathway-in-intrahepatic-cholangiocarcinoma
#20
Hao Li, Zun-Qiang Zhou, Zhang-Ru Yang, Da-Nian Tong, Jiao Guan, Bao-Jie Shi, Jia Nie, Xian-Ting Ding, Bin Li, Guang-Wen Zhou, Zheng-Yun Zhang
Current treatment of intrahepatic cholangiocarcinoma (ICC) remains ineffective because knowledge of ICC carcinogenesis is unclear. Increasing evidence suggests that microRNAs (miRNAs), including miRNA-191, play an important role in tumorigenesis, but expression and biological functions of miRNA-191 in ICC remain to be established. This study aimed to investigate the functions and underlying mechanisms of miRNA-191 in ICC. ICC miRNA profiles were generated in 5 pairs of ICC and matched to normal bile duct tissues by next-generation sequencing technology; ICC miRNA profiles were verified in 18 pairs of ICC tissues and normal bile duct tissues by quantitative reverse transcription PCR (qRT-PCR)...
February 14, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
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