Multiple functions and regulatory network of miR-150 in B lymphocyte-related diseases

Hu, Yue-Zi; Li, Qiao; Wang, Pengfei; Li, Xueping; Hu, Zhao‐Lan

doi:10.3389/fonc.2023.1140813

Cited by 10 publications

(2 citation statements)

References 155 publications

(204 reference statements)

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“…CD3D, CD3E, CD2, SIT1 ) were enriched in pathways related to T cell and lymphocyte activation (see the Supplementary Material ). dCCA identified miR-150, a miRNA that plays critical roles in lymphocyte development and is significantly associated with RCC survival [ 23 , 24 ]. It was found to be strongly co-expressed with these genes in the chRCC subtype but weakly in the ccRCC and pRCC subtypes.…”

Section: Resultsmentioning

confidence: 99%

dCCA: detecting differential covariation patterns between two types of high-throughput omics data

Lee,

Ma,

et al. 2024

Briefings in Bioinformatics

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Motivation The advent of multimodal omics data has provided an unprecedented opportunity to systematically investigate underlying biological mechanisms from distinct yet complementary angles. However, the joint analysis of multi-omics data remains challenging because it requires modeling interactions between multiple sets of high-throughput variables. Furthermore, these interaction patterns may vary across different clinical groups, reflecting disease-related biological processes. Results We propose a novel approach called Differential Canonical Correlation Analysis (dCCA) to capture differential covariation patterns between two multivariate vectors across clinical groups. Unlike classical Canonical Correlation Analysis, which maximizes the correlation between two multivariate vectors, dCCA aims to maximally recover differentially expressed multivariate-to-multivariate covariation patterns between groups. We have developed computational algorithms and a toolkit to sparsely select paired subsets of variables from two sets of multivariate variables while maximizing the differential covariation. Extensive simulation analyses demonstrate the superior performance of dCCA in selecting variables of interest and recovering differential correlations. We applied dCCA to the Pan-Kidney cohort from the Cancer Genome Atlas Program database and identified differentially expressed covariations between noncoding RNAs and gene expressions. Availability and Implementation The R package that implements dCCA is available at https://github.com/hwiyoungstat/dCCA.

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Section: Resultsmentioning

confidence: 99%

dCCA: detecting differential covariation patterns between two types of high-throughput omics data

Lee,

Ma,

et al. 2024

Briefings in Bioinformatics

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“…The role of microRNAs has been confirmed in both B-cell differentiation and B-cell tolerance [30]. miR-150 was found to be a critical regulator of proliferation, differentiation, metabolism and apoptosis of B-cells, and altered expression of which was established as a diagnostic biomarker of various autoimmune diseases [31]. miR-130b is involved in the molecular regulation of B-cell activation through modulating the NFκB pathway by targeting the lysine deubiquitinase CYLD gene [32].…”

Section: B Lymphocytementioning

confidence: 99%

Role of microRNAs in Immune Regulation with Translational and Clinical Applications

Gaál

2024

IJMS

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MicroRNAs (miRNAs) are 19–23 nucleotide long, evolutionarily conserved noncoding RNA molecules that regulate gene expression at the post-transcriptional level. In this review, involvement of miRNAs is summarized in the differentiation and function of immune cells, in anti-infective immune responses, immunodeficiencies and autoimmune diseases. Roles of miRNAs in anticancer immunity and in the transplantation of solid organs and hematopoietic stem cells are also discussed. Major focus is put on the translational clinical applications of miRNAs, including the establishment of noninvasive biomarkers for differential diagnosis and prediction of prognosis. Patient selection and response prediction to biological therapy is one of the most promising fields of application. Replacement or inhibition of miRNAs has enormous therapeutic potential, with constantly expanding possibilities. Although important challenges still await solutions, evaluation of miRNA fingerprints may contribute to an increasingly personalized management of immune dysregulation with a remarkable reduction in toxicity and treatment side effects. More detailed knowledge of the molecular effects of physical exercise and nutrition on the immune system may facilitate self-tailored lifestyle recommendations and advances in prevention.

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Choice of blood collection methods influences extracellular vesicles counts and miRNA profiling

Tran,

Oliveira‐Jr,

Chidester

et al. 2024

J of Extracellular Bio

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Circulating RNAs have been investigated systematically for over 20 years, both as constituents of circulating extracellular vesicles (EVs) or, more recently, non‐EV RNA carriers, such as exomeres and supermeres. The high level of variability and low reproducibility rate of EV/extracellular RNA (exRNA) results generated even on the same biofluids promoted several efforts to limit pre‐analytical variability by standardizing sample collection and sample preparation, along with instrument validation, setup and calibration. Anticoagulants (ACs) are often chosen based on the initial goal of the study and not necessarily for the later EV and/or exRNA analyses. We show the effects of blood collection on EV size, abundance, and antigenic composition, as well on the miRNAs. Our focus of this work was on the effect of ACs on the number and antigenic composition of circulating EVs and on a set of circulating miRNA species, which were shown to be relevant as disease markers in several cancers and Alzheimer's disease. Results show that while the number of plasma EVs, their relative size, and post‐fluorescence labeling profile varied with each AC, their overall antigenic composition, with few exceptions, did not change significantly. However, the number of EVs expressing platelet and platelet‐activation markers increased in serum samples. For overall miRNA expression levels, EDTA was a better AC, although this may have been associated with stimulation of cells in the blood collection tube. Citrate and serum rendered better results for a set of miRNAs that were described as circulating markers for Alzheimer's disease, colon, and papillary thyroid cancers.

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Multiple functions and regulatory network of miR-150 in B lymphocyte-related diseases

Cited by 10 publications

References 155 publications

dCCA: detecting differential covariation patterns between two types of high-throughput omics data

dCCA: detecting differential covariation patterns between two types of high-throughput omics data

Role of microRNAs in Immune Regulation with Translational and Clinical Applications

Choice of blood collection methods influences extracellular vesicles counts and miRNA profiling

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