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Integrated analysis of hepatic miRNA and mRNA expression profiles in the spontaneous recovery of liver fibrosis [miRNA]

ABSTRACT: Liver fibrosis, results from the imbalance between extracellular matrix (ECM) production and degradation, is a common pathological consequence of various chronic liver diseases. Although a large number of miRNAs have been reported in liver fibrosis progression, miRNA-mRNA interactions involved in its reversal process remain to be fully elucidated. In the current study, we performed an integrated analysis of miRNA and mRNA expression profiles in a hepatic fibrosis recovery mouse model induced by thioacetamide. A total of 102 miRNA and 2,845 mRNAs showed significant differential expression in recovery mice compared to fibrotic mice. Moreover, 3,769 putative negatively correlated miRNA-mRNA pairs were revealed to be potentially implicated in the biological function regulation of small molecule metabolism and ECM organization. By integrating miRNA-mRNA regulatory networks, mmu-miR-1843a-5p, mmu-miR-193a-5p, mmu-miR-194-2-3p and mmu-miR-30c-2-3p were identified as lysyl oxidase-specific miRNAs that were associated with the pathogenesis of fibrosis recovery. Our results provide potential novel biomarkers and candidate targets for the treatment of liver fibrosis.

ORGANISM(S): Mus musculus

PROVIDER: GSE173456 | GEO | 2022/04/26

REPOSITORIES: GEO

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Integrated analysis of hepatic miRNA and mRNA expression profiles in the spontaneous recovery of liver fibrosis [mRNA]

Project description:Liver fibrosis, results from the imbalance between extracellular matrix (ECM) production and degradation, is a common pathological consequence of various chronic liver diseases. Although a large number of miRNAs have been reported in liver fibrosis progression, miRNA-mRNA interactions involved in its reversal process remain to be fully elucidated. In the current study, we performed an integrated analysis of miRNA and mRNA expression profiles in a hepatic fibrosis recovery mouse model induced by thioacetamide. A total of 102 miRNA and 2,845 mRNAs showed significant differential expression in recovery mice compared to fibrotic mice. Moreover, 3,769 putative negatively correlated miRNA-mRNA pairs were revealed to be potentially implicated in the biological function regulation of small molecule metabolism and ECM organization. By integrating miRNA-mRNA regulatory networks, mmu-miR-1843a-5p, mmu-miR-193a-5p, mmu-miR-194-2-3p and mmu-miR-30c-2-3p were identified as lysyl oxidase-specific miRNAs that were associated with the pathogenesis of fibrosis recovery. Our results provide potential novel biomarkers and candidate targets for the treatment of liver fibrosis.

2022-04-26 | GSE173961 | GEO

Identification of miRNAs as biomarkers of drug response of Pien Tze Huang in Hepatic Fibrosis Treatments

Project description:Pien Tze Huang (PZH) is herbal traditional Chinese medicine which was widely utilized in Asia for hepatic diseases. We constructed two groups hepatic fibrosis mice model using CCl4, one group using PZH treatment and another group replacing PZH with double distilled water. All 12 mice were fed for 8 weeks and then killed to have their liver tissue taken out. Small RNA-seq were used to identify miRNAs of PZH medicine effect for hepatic fibrosis. We found the expression of these miRNAs (mmu-miR-205-5p, mmu-miR-3064-5p, mmu-miR-205-5p, mmu-miR-370-3p, mmu-miR-665-3p) were changed in PZH medicine treatment for hepatic fibrosis study. Furthermore, Hmga2 and Fgf9, miRNAs corresponding target genes (Sp4, Slc2a6, Tln2, Hmga2, Ank3, Pax9, Fgf9), have been reported association with hepatic fibrosis.

2021-06-28 | GSE137100 | GEO

Maternal Circulating miRNAs Contribute to Negative Pregnancy Outcomes by Altering Placental Transcriptome and Fetal Vascular Dynamics

Project description:We performed RNA sequencing on the fetal portion of murine placentas isolated at gestational day (GD) 18, 8 days after dams are exposed to a single intravascular administration of either pooled murine-conserved HEamiRNAs (50 μg of pooled equimolar quantities of mmu-miR-222-5p, mmu-miR-187-5p, mmu-mir-299a, mmu-miR-491-3p, miR-760-3p, mmu-miR-671-3p, mmu-miR-449a-5p and mmu-miR-204-5p mimics) or control scrambled miRNAs.

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Next Generation Sequencing of miRNA profile in HFD-induced diabetic ICR liver tissue treated by a Chinese formula

Project description:Objective: To investigate the impact of JTXK granule on the miRNA expression profiles in hepatic tissue of diabetic mice, and to explore the molecular targets and associated signaling pathways of JTXK granule in its anti-diabetic effect. Methods: High fat diet was used to induce diabetic model, and mice were subsequently divided into JTXK-treated group and model group. After 8 weeks’ intervention we screened the differentially expressed miRNAs between the two groups using microRNA sequencing analysis (3 mice in each group). Finally, miRNA target gene prediction, GO and KEGG analysis were applied to explore the function of DEMs. Results: A total of 33 significantly differentiated miRNAs were detected in comparison between the two groups (|log2(fold change) |＞0.3, P<0.05). MiRNA-mRNA analysis showed that mmu-miR-30a-5p, mmu-miR-23b-5p, mmu-miR-199a-5p, mmu-miR-425-5p and mmu-miR-214-3p are closely related to inflammatory response, histological changes and insulin signal transduction in liver. In addition, KEGG analysis showed that the DEMs were closely related to Ras and insulin signaling pathway. Conclusion: JTXK granule exerts anti-diabetic effect in hepatic tissue of diabetic mice by modulating miRNAs and mRNAs network.

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miRNA information of Yiqi-Bushen-Tiaozhi Recipe against NASH

Project description:MicroRNAs (miRNAs) have emerged as potential therapeutic targets for non-alcoholic fatty liver disease/non-alcoholic steatohepatitis (NAFLD/NASH). Traditional Chineses Medicine (TCM) plays an important role in the prevention or treatment of NAFLD/NASH. However, miRNA targets of TCM against NASH still remain largely unknown. Here, we showed that Yiqi-Bushen-Tiaozhi (YBT) recipe effectively attenuated diet-induced NASH in C57BL/6 mice. To identify the miRNA targets of YBT and understand the potential underlying mechanisms, we performed network pharmacology using miRNA and mRNA deep sequencing data combined with Ingenuity Pathway Analysis (IPA). Mmu-let-7a-5p, mmu-let-7b-5p, mmu-let-7g-3p and mmu-miR-106b-3p were screened as the main targets of YBT. Our results suggested that YBT might alleviate NASH by regulating the expression of these miRNAs that potentially modulate inflammation/immunity and oxidative stress. This study provides useful information for guiding future studies on the mechanism of YBT against NASH by regulating miRNAs.

2020-12-07 | GSE144721 | GEO

RNA-seq expression analysis of mouse liver treated with locked nucleic acids (LNAs) that inhibit mmu-miR-802-5p and mmu-miR-1948-5p

Project description:Total RNA-seq analysis of mouse liver following LNA treatment in vivo to identify mRNA targets of mmu-miR-802-5p and mmu-miR-1948-5p.

2018-01-25 | GSE103880 | GEO

Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes

Project description:Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound healing support, oral therapies, and anti-tumour treatments. While its applications shown promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus applied non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (5 time points spanning 2 hours), we compared the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, miR-223-3p also exhibited an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single blood cell sequencing revealed the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.

2023-07-12 | GSE236801 | GEO

Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes

2023-07-12 | GSE236788 | GEO

Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes

Project description:This SuperSeries is composed of the SubSeries listed below. Non-thermal plasma, a partially ionized gas, holds significant potential for clinical applications, including wound-healing support, oral therapies, and anti-tumour treatments. While its applications showed promising outcomes, the underlying molecular mechanisms remain incompletely understood. We thus apply non-thermal plasma to mouse auricular skin and conducted non-coding RNA sequencing, as well as single-cell blood sequencing. In a time-series analysis (five timepoints spanning 2 hours), we compare the expression of microRNAs in the plasma-treated left ears to the unexposed right ears of the same mice as well as to the ears of unexposed control mice. Our findings indicate specific effects in the treated ears for a set of five miRNAs: mmu-miR-144-5p, mmu-miR-144-3p, mmu-miR-142a-5p, mmu-miR-223-3p, and mmu-miR-451a. Interestingly, mmu-miR-223-3p also exhibits an increase over time in the right non-treated ear of the exposed mice, suggesting systemic effects. Notably, this miRNA, along with mmu-miR-142a-5p and mmu-miR-144-3p, regulates genes and pathways associated with wound healing and tissue regeneration (namely ErbB, FoxO, Hippo, and PI3K-Akt signalling). This co-regulation is particularly remarkable considering the significant seed dissimilarities among the miRNAs. Finally, single-cell sequencing of PBMCs reveals the downregulation of 12 from 15 target genes in B-cells, Cd4+ and Cd8+ T-cells. Collectively, our data provide evidence for a systemic effect of non-thermal plasma.

2023-07-12 | GSE236802 | GEO

5b763f6e-2031-4d46-913d-ee7491e7e50c - samples

Project description:iPSC-derived neurons were treated with mimics and inhibitors of the miRNAs miR-150-5p, hsa-mir-193a-3p and hsa-miR-19b-3p. RNA-sequencing was then performed to examine the effects of miRNA up-regulation and inhibition.

| EGAD00001006844 | EGA

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