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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/28098890/characterization-of-the-microrna-profile-in-early-stage-cervical-squamous-cell-carcinoma-by-next-generation-sequencing
#1
Wansong Lin, Mei Feng, Guilin Chen, Zhifeng Zhou, Jieyu Li, Yunbin Ye
Squamous cell carcinoma (SCC) is histologically the most prominent type of cervical cancer. There is accumulating evidence suggesting that microRNAs (miRNAs) play important regulatory roles in the biological processes of cervical squamous cell carcinoma (CSCC). Deciphering the miRNA regulatory network in CSCC could deepen our understanding at the molecular level of CSCC initiation and progression. In the present study, we performed next‑generation sequencing (NGS) to profile miRNA expression in 3 pairs of early-stage CSCC samples...
January 16, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28079885/mirna182-regulates-percentage-of-myeloid-and-erythroid-cells-in-chronic-myeloid-leukemia
#2
Deepak Arya, Sasikala P Sachithanandan, Cecil Ross, Dasaradhi Palakodeti, Shang Li, Sudhir Krishna
The deregulation of lineage control programs is often associated with the progression of haematological malignancies. The molecular regulators of lineage choices in the context of tyrosine kinase inhibitor (TKI) resistance remain poorly understood in chronic myeloid leukemia (CML). To find a potential molecular regulator contributing to lineage distribution and TKI resistance, we undertook an RNA-sequencing approach for identifying microRNAs (miRNAs). Following an unbiased screen, elevated miRNA182-5p levels were detected in Bcr-Abl-inhibited K562 cells (CML blast crisis cell line) and in a panel of CML patients...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28077310/zebrafish-let-7b-acts-downstream-of-hypoxia-inducible-factor-1%C3%AE-to-assist-in-hypoxia-mediated-cell-proliferation-and-cell-cycle-regulation
#3
Chun-Xiao Huang, Nan Chen, Xin-Jie Wu, Yan He, Cui-Hong Huang, Hong Liu, Wei-Min Wang, Huan-Ling Wang
AIMS: Hypoxia-inducible factor-1α (HIF-1α) is a transcriptional regulator of cellular responses to hypoxic stress. MicroRNAs (miRNAs) play an essential role in hypoxia-mediated cellular responses. Previous studies have identified some let-7 family members as hypoxia-regulated miRNAs (HRMs). In the present study, we aimed to investigate whether zebrafish let-7b/7f contribute cellular hypoxic response in a Hif-1α-dependent manner. MAIN METHODS: Stable suppression of zebrafish hif-1α was achieved by microinjection of an optimized short-hairpin RNA (shRNA) expression vector...
January 8, 2017: Life Sciences
https://www.readbyqxmd.com/read/28074869/urinary-exosome-derived-micrornas-reflecting-the-changes-of-renal-function-and-histopathology-in-dogs
#4
Osamu Ichii, Hiroshi Ohta, Taro Horino, Teppei Nakamura, Marina Hosotani, Tatsuya Mizoguchi, Keitaro Morishita, Kensuke Nakamura, Yuki Hoshino, Satoshi Takagi, Noboru Sasaki, Mitsuyoshi Takiguchi, Ryo Sato, Kazuhisa Oyamada, Yasuhiro Kon
MicroRNAs act as post-transcriptional regulators, and urinary exosome (UExo)-derived microRNAs may be used as biomarkers. Herein, we screened for UExo-derived microRNAs reflecting kidney disease (KD) status in dogs. Examined dogs were divided into healthy kidney control (HC) and KD groups according to renal dysfunction. We confirmed the appearance of UExo having irregular globe-shapes in a dog by immunoblot detection of the exosome markers, TSG101 and CD9. Based on our previous data using KD model mice and the data obtained herein by next generation sequencing of UExo-derived microRNAs in dogs, miR-26a, miR-146a, miR-486, miR-21a, and miR-10a/b were selected as candidate microRNAs...
January 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28060806/high-throughput-sequencing-of-extracellular-rna-from-human-plasma
#5
Kirsty M Danielson, Renee Rubio, Fieda Abderazzaq, Saumya Das, Yaoyu E Wang
The presence and relative stability of extracellular RNAs (exRNAs) in biofluids has led to an emerging recognition of their promise as 'liquid biopsies' for diseases. Most prior studies on discovery of exRNAs as disease-specific biomarkers have focused on microRNAs (miRNAs) using technologies such as qRT-PCR and microarrays. The recent application of next-generation sequencing to discovery of exRNA biomarkers has revealed the presence of potential novel miRNAs as well as other RNA species such as tRNAs, snoRNAs, piRNAs and lncRNAs in biofluids...
2017: PloS One
https://www.readbyqxmd.com/read/28058815/small-rnaome-profiling-from-human-skeletal-muscle-novel-mirnas-and-their-targets-associated-with-cancer-cachexia
#6
Ashok Narasimhan, Sunita Ghosh, Cynthia Stretch, Russell Greiner, Oliver F Bathe, Vickie Baracos, Sambasivarao Damaraju
BACKGROUND: MicroRNAs (miRs) are small non-coding RNAs that regulate gene (mRNA) expression. Although the pathological role of miRs have been studied in muscle wasting conditions such as myotonic and muscular dystrophy, their roles in cancer cachexia (CC) are still emerging. OBJECTIVES: The objectives are (i) to profile human skeletal muscle expressed miRs; (ii) to identify differentially expressed (DE) miRs between cachectic and non-cachectic cancer patients; (iii) to identify mRNA targets for the DE miRs to gain mechanistic insights; and (iv) to investigate if miRs show potential prognostic and predictive value...
January 6, 2017: Journal of Cachexia, Sarcopenia and Muscle
https://www.readbyqxmd.com/read/28049410/tcga2bed-extracting-extending-integrating-and-querying-the-cancer-genome-atlas
#7
Fabio Cumbo, Giulia Fiscon, Stefano Ceri, Marco Masseroli, Emanuel Weitschek
BACKGROUND: Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types. RESULTS: We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration...
January 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28030794/circulating-mirnas-as-biomarkers-for-oral-squamous-cell-carcinoma-recurrence-in-operated-patients
#8
Yan Yan, Xuan Wang, Morten T Venø, Vivi Bakholdt, Jens A Sørensen, Annelise Krogdahl, Zheng Sun, Shan Gao, Jørgen Kjems
MicroRNAs (miRNAs) are small regulatory non-coding RNAs for which altered expression in cancers can serve as potential biomarkers for diseases. We here investigated whether circulating miRNAs can serve as biomarkers for predicting post-operational recurrence of oral squamous cell carcinoma (OSCC) in patients. Plasma samples from 8 Danish OSCC patients were collected before, and one year after surgical operation, as well as from 3 Danish healthy controls and subjected to miRNA profiling by next generation sequencing...
December 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/28025711/differential-expression-of-mirnas-and-associated-gene-targets-in-grapevine-leafroll-associated-virus-3-infected-plants
#9
Rachelle Bester, Johan T Burger, Hans J Maree
MicroRNAs (miRNAs) are a class of endogenous small non-coding RNAs (sRNA) that play an essential role in the regulation of target mRNAs expressed during plant development and in response to stress. MicroRNA expression profiling has helped to identify miRNAs that regulate a range of processes, including the plant's defence response to pathogens. In this study, differential miRNA expression in own-rooted Vitis vinifera cv. Cabernet Sauvignon plants infected with grapevine leafroll-associated virus 3 was investigated with microarrays and next-generation sequencing (NGS) of sRNA and mRNA...
December 26, 2016: Archives of Virology
https://www.readbyqxmd.com/read/28005467/defining-the-purity-of-exosomes-required-for-diagnostic-profiling-of-small-rna-suitable-for-biomarker-discovery
#10
Camelia Quek, Shayne A Bellingham, Chol-Hee Jung, Benjamin J Scicluna, Mitch C Shambrook, Robyn A Sharples, Lesley Cheng, Andrew F Hill
Small non-coding RNAs (ncRNA), including microRNAs (miRNA), enclosed in exosomes are being utilised for biomarker discovery in disease. Two common exosome isolation methods involve differential ultracentrifugation or differential ultracentrifugation coupled with Optiprep gradient fractionation. Generally, the incorporation of an Optiprep gradient provides better separation and increased purity of exosomes. The question of whether increased purity of exosomes is required for small ncRNA profiling, particularly in diagnostic and biomarker purposes, has not been addressed and highly debated...
December 22, 2016: RNA Biology
https://www.readbyqxmd.com/read/28000891/expression-of-mir%C3%A2-26a-exhibits-a-negative-correlation-with-hmga1-and-regulates-cancer-progression-by-targeting-hmga1-in-lung-adenocarcinoma-cells
#11
Noboru Sekimoto, Ayako Suzuki, Yutaka Suzuki, Sumio Sugano
Lung cancer is the most common cause of cancer‑associated mortality worldwide, and the number of cases is increasing annually. Several studies have shown that microRNAs (miRNAs) control proliferation, differentiation, and apoptosis in various cell types, and increasing evidence indicates the presence of aberrant miRNA expression profiles and unique miRNA signaling pathways in several types of cancer. The present study aimed to identify miRNAs, which correlated specifically with the progression of lung cancer through the analysis of 57,100 transcripts and 1,341 small RNA expression profiles in 26 lung adenocarcinoma cell lines using next‑generation sequencing...
February 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/27993935/mirna-profiling-of-human-naive-cd4-t-cells-links-mir-34c-5p-to-cell-activation-and-hiv-replication
#12
Andreia J Amaral, Jorge Andrade, Russell B Foxall, Paula Matoso, Ana M Matos, Rui S Soares, Cheila Rocha, Christian G Ramos, Rita Tendeiro, Ana Serra-Caetano, José A Guerra-Assunção, Mariana Santa-Marta, João Gonçalves, Margarida Gama-Carvalho, Ana E Sousa
Cell activation is a vital step for T-cell memory/effector differentiation as well as for productive HIV infection. To identify novel regulators of this process, we used next-generation sequencing to profile changes in microRNA expression occurring in purified human naive CD4 T cells in response to TCR stimulation and/or HIV infection. Our results demonstrate, for the first time, the transcriptional up-regulation of miR-34c-5p in response to TCR stimulation in naive CD4 T cells. The induction of this miR was further consistently found to be reduced by both HIV-1 and HIV-2 infections...
December 19, 2016: EMBO Journal
https://www.readbyqxmd.com/read/27989132/dietary-phytochemicals-and-cancer-chemoprevention-a-perspective-on-oxidative-stress-inflammation-and-epigenetics
#13
Wenji Li, Yue Guo, Chengyue Zhang, Renyi Wu, Anne Yuqing Yang, John Gaspar, Ah-Ng Tony Kong
Oxidative stress occurs when cellular reactive oxygen species levels exceed the self-antioxidant capacity of the body. Oxidative stress induces many pathological changes, including inflammation and cancer. Chronic inflammation is believed to be strongly associated with the major stages of carcinogenesis. The nuclear factor erythroid 2-related factor 2 (Nrf2) pathway plays a crucial role in regulating oxidative stress and inflammation by manipulating key antioxidant and detoxification enzyme genes via the antioxidant response element...
December 19, 2016: Chemical Research in Toxicology
https://www.readbyqxmd.com/read/27935861/microrna-203-predicts-human-survival-after-resection-of-colorectal-liver-metastasis
#14
T Peter Kingham, Hoang C B Nguyen, Jian Zheng, Ioannis T Konstantinidis, Eran Sadot, Jinru Shia, Deborah Kuk, Steven Zhang, Leonard Saltz, Michael I D'Angelica, William R Jarnagin, Hani Goodarzi, Sohail F Tavazoie
BACKGROUND: Resection of colorectal liver metastasis (CRLM) can be curative. Predicting which patients may benefit from resection, however, remains challenging. Some microRNAs (miRNAs) become deregulated in cancers and contribute to cancer progression. We hypothesized that miRNA expression can serve as a prognostic marker of survival after CRLM resection. RESULTS: MiR-203 was significantly overexpressed in tumors of short-term survivors compared to long-term survivors...
December 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27928969/new-candidate-genes-for-lack-of-sensitivity-to-therapy-in-pediatric-leukemias
#15
Weronika Bereza, Joanna Szczepanek, Joanna Laskowska, Andrzej Tretyn
In recent years, significant development of molecular genetics has contributed to the better understanding of leukemogenesis and classification of the different leukemia subtypes. Patients diagnosed with acute leukemia usually undergo chemotherapy, which involves the induction of remission, consolidation of remission and maintenance therapy. Patients are still vulnerable to relapse due to differences in the sensitivity of leukemia cells to the chemotherapeutic agent, because of the active drugs removal from the cells, improving the repair of DNA damage or abnormalities in the apoptotic pathway...
December 8, 2016: Current Cancer Drug Targets
https://www.readbyqxmd.com/read/27908722/unexpected-regulation-of-mirna-abundance-during-adaptation-of-early-somite-mouse-embryos-to-diabetic-pregnancy
#16
J Zhao, T B M Hakvoort, A Jongejan, J M Ruijter, A H C van Kampen, W H Lamers
Maternal diabetes is one of major causes of congenital malformations in offspring, but the underlying mechanism is still unclear. MiRNAs play an important role in transcriptional and post-transcriptional regulation of gene expression. However, no miRNA expression profiling of hyperglycemic offspring are thus far available. Female mice were made diabetic with streptozotocin, treated with slow-release insulin tablets, and mated. MiRNA expression profiling with Next Generation Sequencing on the SOLiD5 platform was performed on 8 control and 5 hyperglycemic embryonic day (ED)8...
January 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27908684/identification-and-profiling-of-mirnas-in-overwintering-lissorhoptrus-oryzophilus-via-next-generation-sequencing
#17
Shuang Yang, Juhong Zhang, Shang Wang, Xinxin Zhang, Yan Liu, Jinghui Xi
MicroRNAs (miRNAs) are important regulators of various biological processes in organisms. Insects subjected to abiotic stress can regulate gene expression post-transcriptionally through the use of microRNAs. However, the role of miRNAs in response to cold stress in Lissorhoptrus oryzophilus Kuschel remains unknown. The rice water weevil, L. oryzophilus, is an invasive insect that is able to survive cold winters. To characterize changes in miRNAs in response to overwintering in L. oryzophilus, a comprehensive comparative analysis of microRNAs was performed involving an overwintering and a normal adult...
November 29, 2016: Cryobiology
https://www.readbyqxmd.com/read/27899663/large-scale-analysis-of-microrna-expression-epi-transcriptomic-features-and-biogenesis
#18
Dimitrios M Vitsios, Matthew P Davis, Stijn van Dongen, Anton J Enright
MicroRNAs are important genetic regulators in both animals and plants. They have a range of functions spanning development, differentiation, growth, metabolism and disease. The advent of next-generation sequencing technologies has made it a relatively straightforward task to detect these molecules and their relative expression via sequencing. There are a large number of published studies with deposited datasets. However, there are currently few resources that capitalize on these data to better understand the features, distribution and biogenesis of miRNAs...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27895664/application-of-genomic-technologies-to-the-breeding-of-trees
#19
REVIEW
Maria L Badenes, Angel Fernández I Martí, Gabino Ríos, María J Rubio-Cabetas
The recent introduction of next generation sequencing (NGS) technologies represents a major revolution in providing new tools for identifying the genes and/or genomic intervals controlling important traits for selection in breeding programs. In perennial fruit trees with long generation times and large sizes of adult plants, the impact of these techniques is even more important. High-throughput DNA sequencing technologies have provided complete annotated sequences in many important tree species. Most of the high-throughput genotyping platforms described are being used for studies of genetic diversity and population structure...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27882772/mirnas-differentially-expressed-by-next-generation-sequencing-in-cord-blood-buffy-coat-samples-of-boys-and-girls
#20
Daneida Lizarraga, Karen Huen, Mary Combs, Maria Escudero-Fung, Brenda Eskenazi, Nina Holland
AIM: Differences in children's development and susceptibility to diseases and exposures have been observed by sex, yet human studies of sex differences in miRNAs are limited. MATERIALS & METHODS: The genome-wide miRNA expression was characterized by sequencing-based EdgeSeq assay in cord blood buffy coats from 89 newborns, and 564 miRNAs were further analyzed. RESULTS: Differential expression of most miRNAs was higher in boys. Neurodevelopment, RNA metabolism and metabolic ontology terms were enriched among miRNA targets...
December 2016: Epigenomics
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