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miRNA next generation sequencing

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https://www.readbyqxmd.com/read/28439834/an-assessment-of-the-next-generation-of-animal-mirna-target-prediction-algorithms
#1
Thomas Bradley, Simon Moxon
The advent of genome-wide next-generation sequencing technologies has revolutionized the genomic and transcriptomic fields. New technologies also present an opportunity for greater discovery and understanding of post-transcriptional processes, in particular, translational inhibition of transcripts by miRBP (microRNA-RNA binding protein) complexes. Not only have novel methodologies been developed for the direct sequencing of RBP-bound RNA, but a new class of miRNA (microRNA) target prediction algorithms trained on this data has emerged...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28439832/computational-and-experimental-identification-of-tissue-specific-microrna-targets
#2
Raheleh Amirkhah, Hojjat Naderi Meshkin, Ali Farazmand, John E J Rasko, Ulf Schmitz
In this chapter we discuss computational methods for the prediction of microRNA (miRNA) targets. More specifically, we consider machine learning-based approaches and explain why these methods have been relatively unsuccessful in reducing the number of false positive predictions. Further we suggest approaches designed to improve their performance by considering tissue-specific target regulation. We argue that the miRNA targetome differs depending on the tissue type and introduce a novel algorithm that predicts miRNA targets specifically for colorectal cancer...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28435243/peripheral-leukocyte-micrornas-as-novel-biomarkers-for-copd
#3
Ruiying Wang, Jianying Xu, Hu Liu, Zhiping Zhao
COPD is a multifactorial disease caused by environmental determinants as well as genetic risk factors. The prevalence and mortality of COPD continue to increase, and underdiagnosis of COPD remains a critical issue. Previous reports investigated promising microRNAs (miRNAs) to reveal the molecular mechanism for the development of COPD; however, diagnostic and therapeutic markers for COPD have not yet been found. For this study, 20 representative COPD patients were separated into four groups based on increasing severity (A, B, C, and D) and compared to six healthy controls...
2017: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/28423960/the-role-of-molecular-diagnostic-testing-in-the-management-of-thyroid-nodules
#4
Maureen D Moore, Suraj Panjwani, Katherine D Gray, Brendan M Finnerty, Rasa Zarnegar, Thomas J Fahey
Fine needle aspiration (FNA) with cytologic examination remains the standard of care for investigation of thyroid nodules. However, as many as 30% of FNA samples are cytologically indeterminate for malignancy, which confounds clinical management. To reduce the burden of repeat diagnostic testing and unnecessary surgery, there has been extensive investigation into molecular markers that can be detected on FNA specimens to more accurately stratify a patient's risk of malignancy. Areas Covered: In this review, the authors discuss recent evidence and progress in molecular markers used in the diagnosis of thyroid cancer highlighting somatic gene alterations, molecular technologies and microRNA analysis...
April 19, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28423361/next-generation-sequencing-reveals-microrna-markers-of-adrenocortical-tumors-malignancy
#5
Łukasz Koperski, Marta Kotlarek, Michał Świerniak, Monika Kolanowska, Anna Kubiak, Barbara Górnicka, Krystian Jażdżewski, Anna Wójcicka
BACKGROUND: Adrenocortical carcinoma is a rare finding among common adrenocortical tumors, but it is highly aggressive and requires early detection and treatment. Still, the differential diagnosis between benign and malignant lesions is difficult even for experienced pathologists and there is a significant need for novel diagnostic methods. In this study we aimed to reveal a complete set of microRNAs expressed in the adrenal gland and to identify easily detectable, stable and objective biomarkers of adrenocortical malignancy...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28420619/analysis-of-variants-in-upstream-open-reading-frames-of-human-globin-related-genes
#6
Ye Yuhua, Zhang Qianqian, Zhong Jianmei, Li Yihong, Zhang Li, Yu Qiuxia, Xu Xiangmin
β-thalassemia is an autosomal recessive monogenic disease that is caused by defects in the production of β-like globin chains. Activation of γ-globin gene and the increase in fetal hemoglobin expression have been demonstrated as one of the most important factors to ameliorate the clinical outcome of β-thalassemia patients. In this study, 202 genes or miRNAs associated with human hemoglobin gene expression from 1802 β-thalassemia patients were analyzed with target capture and next generation sequencing strategies in terms of functional variants that might affect hemoglobin gene expression...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28413835/mirna-signatures-can-predict-acute-liver-failure-in-hepatitis-e-infected-pregnant-females
#7
Nirupma Trehanpati, Rashi Sehgal, Sharda Patra, Ashish Vyas, Madavan Vasudevan, Ritu Khosla, Arshi Khanam, Guresh Kumar, Rakhi Maiwall, Gayatri Ramakrishna, Shyam Kottilil, Shiv Kumar Sarin
BACKGROUND: Acute viral hepatitis E (AVH-E) can often result in acute liver failure (ALF) during pregnancy. microRNAs serve as mediators in drug induced liver failure. We investigated their role as a biomarker in predicting ALF due to HEV (ALF-E). METHODS: We performed next generation sequencing and subsequent validation studies in PBMCs of pregnant (P) self limiting AVH-E, ALF due to HEV (ALF-E) and compared with AVH-E in non-pregnant (NP) females and healthy controls...
April 2017: Heliyon
https://www.readbyqxmd.com/read/28411393/global-exosome-transcriptome-profiling-reveals-biomarkers-for-multiple-sclerosis
#8
Igor Selmaj, Maria Cichalewska, Magdalena Namiecinska, Grazyna Galazka, Wojciech Horzelski, Krzysztof W Selmaj, Marcin P Mycko
OBJECTIVE: Accumulating evidence supports a role for exosomes in immune regulation. In this study, we investigated the total circulating exosome transcriptome in relapsing-remitting multiple sclerosis patients (RRMS) and healthy controls (HC). METHODS: Next generation sequencing (NGS) was used to define the global RNA profile of serum exosomes in 19 RRMS patients (9 in relapse, 10 in remission) and 10 HC. We analyzed 5 million reads and over 50,000 transcripts per sample, including a detailed analysis of microRNA (miRNA) differentially expressed in RRMS...
April 15, 2017: Annals of Neurology
https://www.readbyqxmd.com/read/28407097/mircat2-accurate-prediction-of-plant-and-animal-micrornas-from-next-generation-sequencing-datasets
#9
Claudia Paicu, Irina Mohorianu, Matthew Stocks, Ping Xu, Aurore Coince, Martina Billmeier, Tamas Dalmay, Vincent Moulton, Simon Moxon
Motivation: MicroRNAs are a class of _21-22 nucleotide small RNAs which are excised from a stable hairpin-like secondary structure. They have important gene regulatory functions and are involved in many pathways including developmental timing, organogenesis and development in eukaryotes. There are several computational tools for miRNA detection from next-generation sequencing (NGS) datasets. However, many of these tools suffer from high false positive and false negative rates. Here we present a novel miRNA prediction algorithm, miRCat2...
April 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28402935/mirna-profiling-of-gastrointestinal-stromal-tumors-by-next-generation-sequencing
#10
Ugne Gyvyte, Simonas Juzenas, Violeta Salteniene, Juozas Kupcinskas, Lina Poskiene, Laimutis Kucinskas, Sonata Jarmalaite, Kristina Stuopelyte, Ruta Steponaitiene, Georg Hemmrich-Stanisak, Matthias Hübenthal, Alexander Link, Sabine Franke, Andre Franke, Dalia Pangonyte, Vaiva Lesauskaite, Limas Kupcinskas, Jurgita Skieceviciene
Deregulation of miRNAs has been observed virtually in all major types of cancer, whereas the miRNA signature in GIST is not well characterized yet. In this study the first high-throughput miRNA profiling of 15 paired GIST and adjacent normal tissue samples was performed using small RNA-seq approach and differentially expressed miRNAs as well as isomiRNAs were defined. Highly significantly deregulated miRNAs were selected for validation by Taq-Man low-density array in replication group of 40 paired samples. Validated miRNAs were further subjected to enrichment analysis, which revealed significantly enriched KEGG pathways in the main GIST associated pathways...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28382754/cellular-and-extracellular-mirnas-are-blood-compartment-specific-diagnostic-targets-in-sepsis
#11
Marlene Reithmair, Dominik Buschmann, Melanie Märte, Benedikt Kirchner, Daniel Hagl, Ines Kaufmann, Martina Pfob, Alexander Chouker, Ortrud K Steinlein, Michael W Pfaffl, Gustav Schelling
Septic shock is a common medical condition with a mortality approaching 50% where early diagnosis and treatment are of particular importance for patient survival. Novel biomarkers that serve as prompt indicators of sepsis are urgently needed. High-throughput technologies assessing circulating microRNAs represent an important tool for biomarker identification, but the blood-compartment specificity of these miRNAs has not yet been investigated. We characterized miRNA profiles from serum exosomes, total serum and blood cells (leukocytes, erythrocytes, platelets) of sepsis patients by next-generation sequencing and RT-qPCR (n = 3 × 22) and established differences in miRNA expression between blood compartments...
April 6, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28370207/micrornas-based-imaging-techniques-in-cancer-diagnosis-and-therapy
#12
Maryam Keshavarzi, Mohammad Jafar Rezaie, Saba Sorayayi, Mohsen Mohammadi, Amir Ghaderi, Ayoob Rostamzadeh, Aria Masoudifar, Hamed Mirzaei
Cancer is one of the most serious global health concerns in different populations. Several studies indicated that there are many potentially promising cellular and molecular targets for cancer therapy within cancer cells and their microenvironment. Among different cellular and molecular targets involved in cancer pathogenesis, microRNAs (miRNAs) are well known as key targets for cancer therapy. miRNAs are one of main classes of non-coding RNAs. These molecules play important roles in different critical processes of cancer pathogenesis...
March 29, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28358390/microrna-exocytosis-by-large-dense-core-vesicle-fusion
#13
Alican Gümürdü, Ramazan Yildiz, Erden Eren, Gökhan Karakülah, Turgay Ünver, Şermin Genç, Yongsoo Park
Neurotransmitters and peptide hormones are secreted into outside the cell by a vesicle fusion process. Although non-coding RNA (ncRNA) that include microRNA (miRNA) regulates gene expression inside the cell where they are transcribed, extracellular miRNA has been recently discovered outside the cells, proposing that miRNA might be released to participate in cell-to-cell communication. Despite its importance of extracellular miRNA, the molecular mechanisms by which miRNA can be stored in vesicles and released by vesicle fusion remain enigmatic...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28348640/exploration-of-small-rna-seq-data-for-small-non-coding-rnas-in-human-colorectal-cancer
#14
Srinivas V Koduru, Amit K Tiwari, Sprague W Hazard, Milind Mahajan, Dino J Ravnic
Background: Improved healthcare and recent breakthroughs in technology have substantially reduced cancer mortality rates worldwide. Recent advancements in next-generation sequencing (NGS) have allowed genomic analysis of the human transcriptome. Now, using NGS we can further look into small non-coding regions of RNAs (sncRNAs) such as microRNAs (miRNAs), Piwi-interacting-RNAs (piRNAs), long non-coding RNAs (lncRNAs), and small nuclear/nucleolar RNAs (sn/snoRNAs) among others. Recent studies looking at sncRNAs indicate their role in important biological processes such as cancer progression and predict their role as biomarkers for disease diagnosis, prognosis, and therapy...
2017: Journal of Genomics
https://www.readbyqxmd.com/read/28339495/microrna-expression-profiles-identify-disease-specific-alterations-in-systemic-lupus-erythematosus-and-primary-sj%C3%A3-gren-s-syndrome
#15
Ji-Qing Chen, Gábor Papp, Szilárd Póliska, Krisztina Szabó, Tünde Tarr, Bálint László Bálint, Péter Szodoray, Margit Zeher
The discovery of microRNAs (miRNAs) and their critical role in genetic control opened new avenues in understanding of various biological processes including immune cell lineage commitment, differentiation, proliferation and apoptosis. However, a given miRNA may have hundreds of different mRNA targets and a target might be regulated by multiple miRNAs, thus the characterisation of dysregulated miRNA expression profiles could give a better insight into the development of immunological disturbances in autoimmune diseases...
2017: PloS One
https://www.readbyqxmd.com/read/28338918/integrated-mirna-and-mrna-expression-profiling-reveals-the-response-regulators-of-a-susceptible-tomato-cultivar-to-early-blight-disease
#16
Deepti Sarkar, Ranjan Kumar Maji, Sayani Dey, Arijita Sarkar, Zhumur Ghosh, Pallob Kundu
Early blight, caused by the fungus Alternaria solani, is a devastating foliar disease of tomatoes, causes massive yield loss each year worldwide. Molecular basis of the compatible host-pathogen interaction was elusive. We adopted next generation sequencing approach to decipher miRNAs and mRNAs that are differentially expressed during Alternaria-stress in tomato. Some of the interesting findings were also validated by alternative techniques. Our analysis revealed 181 known-miRNAs, belonging to 121 miRNA families, of which 67 miRNAs showed at least 2-fold change in expression level with the majority being downregulated...
March 3, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
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
#17
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
#18
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
#19
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
#20
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
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