scholarly journals RNA-sequencing of human post-mortem hypothalamus and nucleus accumbens identifies expression profiles associated with obesity.

2022 ◽  
Author(s):  
Christian Wake ◽  
Julie A. Schneider ◽  
Thor D. Stein ◽  
Joli Bregu ◽  
Adam Labadorf ◽  
...  
Keyword(s):  
Immune System ◽  
Nucleus Accumbens ◽  
Rna Sequencing ◽  
Small Rna ◽  
Brain Region ◽  
Expression Profiles ◽  
Cytokine Signaling ◽  
Small Rna Sequencing ◽  
Increased Risk ◽  
Sequencing Studies

Obesity, the accumulation of body fat to excess, may cause serious negative health effects, including increased risk of heart disease, type 2 diabetes, stroke and certain cancers. The biology of obesity is complex and not well understood, involving both environmental and genetic factors and affecting metabolic and endocrine mechanisms in tissues of the gut, adipose, and brain. Previous RNA sequencing studies have identified transcripts associated with obesity and body mass index in blood and fat, often using animal models, but RNA sequencing studies in human brain tissue related to obesity have not been previously undertaken. We conducted both large and small RNA sequencing of hypothalamus (207 samples) and nucleus accumbens (276 samples) from individuals defined as consistently obese (124 samples), consistently normal weight as controls (148 samples) or selected without respect to BMI and falling within neither case nor control definition (211 samples), based on longitudinal BMI measures. The samples were provided by three cohort studies with brain donation programs; the Framingham Heart Study (FHS), the Religious Orders Study (ROS) and the Rush Memory and Aging Project (MAP). For each brain region and large/small RNA sequencing set, differential expression of obesity, BMI, brain region and sex was performed. Analyses were done transcriptome-wide as well as with a priori defined sets of obesity or BMI-associated mRNAs and microRNAs (miRNAs). There are sixteen mRNAs and five microRNAs that are differentially expressed (adjusted p < 0.05) by obesity or BMI in these tissues, several of which were validated with qPCR data. The results include many that are BMI-associated, such as APOBR and CES1, as well as many associated with the immune system and some with addiction, such as the gene sets 'cytokine signaling in immune system' and 'opioid signaling'. In spite of the relatively large number of samples, our study was likely under-powered to detect other transcripts or miRNA with relevant but smaller effects.

scholarly journals Comprehensive analysis of human small RNA sequencing data provides insights into expression profiles and miRNA editing

RNA Biology ◽  
2014 ◽  
Vol 11 (11) ◽  
pp. 1375-1385 ◽  
Author(s):  
Jing Gong ◽  
Yuliang Wu ◽  
Xiantong Zhang ◽  
Yifang Liao ◽  
Vusumuzi Leroy Sibanda ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Expression Profiles ◽  
Comprehensive Analysis ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Mirna Editing

scholarly journals Small RNA sequencing revealed aberrant piRNA expression profiles in deciduas of recurrent spontaneous abortion patients

BIOCELL ◽  
2022 ◽  
Vol 46 (4) ◽  
pp. 1013-1023
Author(s):  
JIABAO WU ◽  
XIAOHUA LIU ◽  
LU HAN ◽  
HUA NIE ◽  
YUAN TANG ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Spontaneous Abortion ◽  
Small Rna ◽  
Expression Profiles ◽  
Recurrent Spontaneous Abortion ◽  
Small Rna Sequencing

scholarly journals sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression

2019 ◽  
Vol 47 (W1) ◽  
pp. W530-W535 ◽  
Author(s):  
Ernesto Aparicio-Puerta ◽  
Ricardo Lebrón ◽  
Antonio Rueda ◽  
Cristina Gómez-Martín ◽  
Stavros Giannoukakos ◽  
...  
Keyword(s):  
Differential Expression ◽  
Rna Sequencing ◽  
Small Rna ◽  
Pcr Amplification ◽  
Small Rna Sequencing ◽  
User Friendliness ◽  
Rna Profiling ◽  
Sequencing Studies ◽  
Microrna Sequencing ◽  
Downstream Analysis

Abstract Since the original publication of sRNAtoolbox in 2015, small RNA research experienced notable advances in different directions. New protocols for small RNA sequencing have become available to address important issues such as adapter ligation bias, PCR amplification artefacts or to include internal controls such as spike-in sequences. New microRNA reference databases were developed with different foci, either prioritizing accuracy (low number of false positives) or completeness (low number of false negatives). Additionally, other small RNA molecules as well as microRNA sequence and length variants (isomiRs) have continued to gain importance. Finally, the number of microRNA sequencing studies deposited in GEO nearly triplicated from 2014 (280) to 2018 (764). These developments imply that fast and easy-to-use tools for expression profiling and subsequent downstream analysis of miRNA-seq data are essential to many researchers. Key features in this sRNAtoolbox release include addition of all major RNA library preparation protocols to sRNAbench and improvements in sRNAde, a tool that summarizes several aspects of small RNA sequencing studies including the detection of consensus differential expression. A special emphasis was put on the user-friendliness of the tools, for instance sRNAbench now supports parallel launching of several jobs to improve reproducibility and user time efficiency.

scholarly journals Differential miRNA Expression Profiles in Cumulus and Mural Granulosa Cells from Human Pre-ovulatory Follicles

MicroRNA ◽  
2018 ◽  
Vol 8 (1) ◽  
pp. 61-67 ◽  
Author(s):  
Daniela Andrei ◽  
Roland A. Nagy ◽  
Aafke van Montfoort ◽  
Uwe Tietge ◽  
Martijn Terpstra ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Granulosa Cells ◽  
Small Rna ◽  
Mirna Expression ◽  
Target Gene ◽  
Expression Profiles ◽  
Cell Types ◽  
Small Rna Sequencing ◽  
Gene Sets ◽  
Mirna Expression Profiles

Background: Mural Granulosa Cells (MGCs) and Cumulus Cells (CCs) are two specialized cell types that differentiate from a common progenitor during folliculogenesis. Although these two cell types have specialized functions and gene expression profiles, little is known about their microRNA (miRNA) expression patterns. Objective: To describe the miRNA profile of mural and cumulus granulosa cells from human preovulatory follicles. </P><P> Methods: Using small RNA sequencing, we defined the miRNA expression profiles of human primary MGCs and CCs, isolated from healthy women undergoing ovum pick-up for in vitro Fertilization (IVF). Results: Small RNA sequencing revealed the expression of several hundreds of miRNAs in MGCs and CCs with 53 miRNAs being significantly differentially expressed between MGCs and CCs. We validated the differential expression of miR-146a-5p, miR-149-5p, miR-509-3p and miR-182-5p by RT-qPCR. Analysis of proven targets revealed 37 targets for miR-146a-5p, 43 for miR-182-5p, 2 for miR-509-3p and 9 for miR-149-5p. Gene Ontology (GO) analysis for these 4 target gene sets revealed enrichment of 12 GO terms for miR-146a-5p and 10 for miR-182-5p. The GO term ubiquitin-like protein conjugation was enriched within both miRNA target gene sets. We generated miRNA expression profiles for MGCs and CCs and identified several differentially expressed miRNAs.

scholarly journals Small RNA Sequencing Reveals Transfer RNA-derived Small RNA Expression Profiles in Retinal Neovascularization

2020 ◽  
Vol 17 (12) ◽  
pp. 1713-1722
Author(s):  
Yingqian Peng ◽  
Jingling Zou ◽  
Jiang-Hui Wang ◽  
Huilan Zeng ◽  
Wei Tan ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Expression Profiles ◽  
Transfer Rna ◽  
Retinal Neovascularization ◽  
Small Rna Sequencing ◽  
Rna Expression

scholarly journals Small RNA sequencing revealed aberrant piRNA expression profiles in colorectal cancer

2019 ◽  
Author(s):  
Jie Yin ◽  
Wei Qi ◽  
Chen‑Guang Ji ◽  
Dong‑Xuan Zhang ◽  
Xiao‑Li Xie ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Rna Sequencing ◽  
Small Rna ◽  
Expression Profiles ◽  
Small Rna Sequencing

Small RNA Sequencing to Discover Circulating MicroRNA Biomarkers of Testicular Toxicity in Dogs

2020 ◽  
pp. 109158182096151
Author(s):  
Jennifer C. Shing ◽  
Kai Schaefer ◽  
Shaun E. Grosskurth ◽  
Andy H. Vo ◽  
Tatiana Sharapova ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
Exploratory Study ◽  
Quantitative Polymerase Chain Reaction ◽  
Small Rna Sequencing ◽  
Circulating Microrna ◽  
Testicular Toxicity ◽  
Potential Candidate ◽  
Drug Induced ◽  
Organ Systems

Predictive indicators of testicular toxicity could improve drug development by allowing early in-life screening for this adverse effect before it becomes severe. We hypothesized that circulating microRNAs (miRNAs) could serve as testicular toxicity biomarkers in dogs. Herein, we describe the results of an exploratory study conducted to discover biomarkers of drug-induced testicular injury. Following a dose-selection study using the testicular toxicant ethylene glycol monomethyl ether (EGME), we chose a dose of 50 mg/kg/d EGME to avoid systemic toxicity and treated 2 groups of dogs (castrated, non-castrated) for 14 to 28 days. Castrated animals were used as negative controls to identify biomarkers specific for testicular toxicity because EGME can cause toxicity to organ systems in addition to the testis. Blood was collected daily during the dosing period, followed by recovery for 29 to 43 days with less frequent sampling. Dosing was well tolerated, resulting in mild-to-moderate degeneration in testes and epididymides. Global profiling of serum miRNAs at selected dosing and recovery time points was completed by small RNA sequencing. Bioinformatics data analysis using linear modeling demonstrated several circulating miRNAs that were differentially abundant during the dosing period compared with baseline and/or castrated control samples. Confirmatory reverse transcription quantitative polymerase chain reaction data in these animals was unable to detect sustained alterations of miRNAs in serum, except for 1 potential candidate cfa-miR-146b. Taken together, we report the results of a comprehensive exploratory study and suggest future directions for follow-up research to address the challenge of developing diagnostic biomarkers of testicular toxicity.

scholarly journals Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis

Diagnostics ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 964
Author(s):  
Sarka Benesova ◽  
Mikael Kubista ◽  
Lukas Valihrach
Keyword(s):  
Rna Sequencing ◽  
Small Rna ◽  
High Sensitivity ◽  
Small Rna Sequencing ◽  
Rna Seq ◽  
Liquid Biopsies ◽  
Comprehensive Overview ◽  
Rna Molecules ◽  
Novel Mirna ◽  
The Many

MicroRNAs (miRNAs) are a class of small RNA molecules that have an important regulatory role in multiple physiological and pathological processes. Their disease-specific profiles and presence in biofluids are properties that enable miRNAs to be employed as non-invasive biomarkers. In the past decades, several methods have been developed for miRNA analysis, including small RNA sequencing (RNA-seq). Small RNA-seq enables genome-wide profiling and analysis of known, as well as novel, miRNA variants. Moreover, its high sensitivity allows for profiling of low input samples such as liquid biopsies, which have now found applications in diagnostics and prognostics. Still, due to technical bias and the limited ability to capture the true miRNA representation, its potential remains unfulfilled. The introduction of many new small RNA-seq approaches that tried to minimize this bias, has led to the existence of the many small RNA-seq protocols seen today. Here, we review all current approaches to cDNA library construction used during the small RNA-seq workflow, with particular focus on their implementation in commercially available protocols. We provide an overview of each protocol and discuss their applicability. We also review recent benchmarking studies comparing each protocol’s performance and summarize the major conclusions that can be gathered from their usage. The result documents variable performance of the protocols and highlights their different applications in miRNA research. Taken together, our review provides a comprehensive overview of all the current small RNA-seq approaches, summarizes their strengths and weaknesses, and provides guidelines for their applications in miRNA research.

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