Identification of New miRNA-mRNA Networks in the Development of Non-syndromic Cleft Lip With or Without Cleft Palate

Objective: To identify new microRNA (miRNA)-mRNA networks in non-syndromic cleft lip with or without cleft palate (NSCL/P).Materials and Methods: Overlapping differentially expressed miRNAs (DEMs) were selected from cleft palate patients (GSE47939) and murine embryonic orofacial tissues (GSE20880). Next, the target genes of DEMs were predicted by Targetscan, miRDB, and FUNRICH, and further filtered through differentially expressed genes (DEGs) from NSCL/P patients and controls (GSE42589), MGI, MalaCards, and DECIPHER databases. The results were then confirmed by in vitro experiments. NSCL/P lip tissues were obtained to explore the expression of miRNAs and their target genes.Results: Let-7c-5p and miR-193a-3p were identified as DEMs, and their overexpression inhibited cell proliferation and promoted cell apoptosis. PIGA and TGFB2 were confirmed as targets of let-7c-5p and miR-193a-3p, respectively, and were involved in craniofacial development in mice. Negative correlation between miRNA and mRNA expression was detected in the NSCL/P lip tissues. They were also associated with the occurrence of NSCL/P based on the MGI, MalaCards, and DECIPHER databases.Conclusions: Let-7c-5p-PIGA and miR-193a-3p-TGFB2 networks may be involved in the development of NSCL/P.

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Dysregulation of autophagy-associated microRNAs in condyloma acuminatum

10.21203/rs.3.rs-15974/v1 ◽

2020 ◽

Author(s):

Shi Wu ◽

Dan Lu ◽

Xinkai Zheng ◽

Jin Xu ◽

Zhen Li ◽

...

Keyword(s):

Cell Proliferation ◽

Light Chain ◽

Target Genes ◽

Condyloma Acuminatum ◽

Differentially Expressed ◽

Control Group ◽

Healthy Controls ◽

Related Protein ◽

Ki 67 ◽

Differentially Expressed Mirnas

Abstract Objectives This study was designed to investigate the miRNAs that regulate the cell proliferation of condyloma acuminatum (CA) lesions and their targets.Methods The expression of Ki-67 in 26 CA patients compared with 10 healthy controls was assessed by immunohistochemistry. And the different miRNAs in 4 CA patients and 4 control cases were analyzed by bioinformatics. PCR was used to validate the expression of screened miRNA and its corresponding target genes.Results The expression of Ki-67 was abnormally increased in CA compared with healthy controls ( P <0.05). The comparison of the control group with the CA group revealed 81 differentially expressed miRNAs, of which 56 were downregulated and 25 were upregulated. Two of the differentially expressed miRNAs, miR-30a-5p and miR-514a-3p, are associated with cell proliferation and their target genes are autophagy-related protein (Atg) 5 and Atg12, and Atg3 and Atg12, respectively. PCR results showed that the expression levels of miR-30a-5p and miR-514a-3p were decreased in CA patients compared with healthy controls ( P <0.05), whereas the expression of Atg5, Atg12 and Atg3 was increased ( P <0.05). The expression of the autophagy proteins microtubule-associated protein 1 light chain 3 (LC3) and P62/SQSTM1 (P62) was abnormally increased in the local lesion tissue of the 26 patients with CA compared with the 10 healthy controls, as assessed by immunohistochemistry ( P <0.05).Conclusions Our results suggest that autophagy levels may be modulated by has-miRNA30a-5p and has-miRNA514a-3p in CA patients, leading to dysregulated cell proliferation.

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MicroRNA-124-3p Plays a Crucial Role in Cleft Palate Induced by Retinoic Acid

Frontiers in Cell and Developmental Biology ◽

10.3389/fcell.2021.621045 ◽

2021 ◽

Vol 9 ◽

Author(s):

Hiroki Yoshioka ◽

Yurie Mikami ◽

Sai Shankar Ramakrishnan ◽

Akiko Suzuki ◽

Junichi Iwata

Keyword(s):

Cell Proliferation ◽

Retinoic Acid ◽

Cleft Palate ◽

Cleft Lip ◽

Specific Inhibitor ◽

Mouse Embryos ◽

Congenital Birth Defects ◽

Excessive Intake

Cleft lip with/without cleft palate (CL/P) is one of the most common congenital birth defects, showing the complexity of both genetic and environmental contributions [e.g., maternal exposure to alcohol, cigarette, and retinoic acid (RA)] in humans. Recent studies suggest that epigenetic factors, including microRNAs (miRs), are altered by various environmental factors. In this study, to investigate whether and how miRs are involved in cleft palate (CP) induced by excessive intake of all-trans RA (atRA), we evaluated top 10 candidate miRs, which were selected through our bioinformatic analyses, in mouse embryonic palatal mesenchymal (MEPM) cells as well as in mouse embryos treated with atRA. Among them, overexpression of miR-27a-3p, miR-27b-3p, and miR-124-3p resulted in the significant reduction of cell proliferation in MEPM cells through the downregulation of CP-associated genes. Notably, we found that excessive atRA upregulated the expression of miR-124-3p, but not of miR-27a-3p and miR-27b-3p, in both in vivo and in vitro. Importantly, treatment with a specific inhibitor for miR-124-3p restored decreased cell proliferation through the normalization of target gene expression in atRA-treated MEPM cells and atRA-exposed mouse embryos, resulting in the rescue of CP in mice. Taken together, our results indicate that atRA causes CP through the induction of miR-124-3p in mice.

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The high expression of miR-564 in patients with systemic lupus erythematosus promotes differentiation and maturation of DC cells by negatively regulating TP53 expression in vitro

Lupus ◽

10.1177/09612033211020367 ◽

2021 ◽

pp. 096120332110203

Author(s):

Ziyue Teng ◽

Xiaoying Lin ◽

Chunyan Luan ◽

Yixuan Sun ◽

Xiaolan Li

Keyword(s):

Systemic Lupus Erythematosus ◽

Dendritic Cells ◽

Lupus Erythematosus ◽

Target Genes ◽

Differentially Expressed ◽

Systemic Lupus ◽

Differentially Expressed Mirnas ◽

And Migration ◽

Si Rna

Background miRNA is involved in the occurrence and progression of systemic lupus erythematosus (SLE), but the regulatory effect of miRNA on dendritic cells in SLE patients is still unclear. Material and methods Bioinformatics methods were used to analyze the differentially expressed miRNA and its target genes in SLE patients. In vitro experiments were conducted to explore the effects and mechanisms of differentially expressed miRNAs in SLE patients on the differentiation and maturation of monocyte-derived dendritic cells. Results Bioinformatics analysis showed that miR-564 was up-regulated in SLE patients, and TP53 was the core target gene of miR-564. The expression level of miR-564 showed a rising trend during the differentiation and maturation of monocytes into Mo-DC cells. The differentiation, maturation and proliferation of Mo-DC cells were significantly inhibited by transfection with miR-564 antagomir. The expression of TP53 is negatively regulated by miR-564. In rescue experiments, the proliferation and migration of DC cells were significantly restored by co-transfection of miR-564 antagomir and TP53 si-RNA. Conclusion Highly expressed miR-564 promotes the maturation, proliferation of Mo-DC cells by negatively regulating the expression of TP53.

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A combined microRNA and target protein-based panel for predicting the probability and severity of uraemic vascular calcification: a translational study

Cardiovascular Research ◽

10.1093/cvr/cvaa255 ◽

2020 ◽

Cited By ~ 2

Author(s):

Chia-Ter Chao ◽

Hsiang-Yuan Yeh ◽

You-Tien Tsai ◽

Chih-Kang Chiang ◽

Huei-Wen Chen

Keyword(s):

Vascular Calcification ◽

Target Genes ◽

Ex Vivo ◽

Target Protein ◽

Functional Enrichment ◽

Differentially Expressed ◽

Target Proteins ◽

Differentially Expressed Mirnas

Abstract Aims Vascular calcification (VC) increases the future risk of cardiovascular events in uraemic patients, but effective therapies are still unavailable. Accurate identification of those at risk of developing VC using pathogenesis-based biomarkers is of particular interest and may facilitate individualized risk stratification. We aimed to uncover microRNA (miRNA)-target protein-based biomarker panels for evaluating uraemic VC probability and severity. Methods and results We created a three-tiered in vitro VC model and an in vivo uraemic rat model receiving high phosphate diet to mimic uraemic VC. RNAs from the three-tiered in vitro and in vivo uraemic VC models underwent miRNA and mRNA microarray, with results screened for differentially expressed miRNAs and their target genes as biomarkers. Findings were validated in original models and additionally in an ex vivo VC model and human cells, followed by functional assays of identified miRNAs and target proteins, and tests of sera from end-stage renal disease (ESRD) and non-dialysis-dependent chronic kidney disease (CKD) patients without and with VC. Totally 122 down-regulated and 119 up-regulated miRNAs during calcification progression were identified initially; further list narrowing based on miRNA–mRNA pairing, anti-correlation, and functional enrichment left 16 and 14 differentially expressed miRNAs and mRNAs. Levels of four miRNAs (miR-10b-5p, miR-195, miR-125b-2-3p, and miR-378a-3p) were shown to decrease throughout all models tested, while one mRNA (SULF1, a potential target of miR-378a-3p) exhibited the opposite trend concurrently. Among 96 ESRD (70.8% with VC) and 59 CKD patients (61% with VC), serum miR-125b2-3p and miR-378a-3p decreased with greater VC severity, while serum SULF1 levels increased. Adding serum miR-125b-2-3p, miR-378a-3p, and SULF1 into regression models for VC substantially improved performance compared to using clinical variables alone. Conclusion Using a translational approach, we discovered a novel panel of biomarkers for gauging the probability/severity of uraemic VC based on miRNAs/target proteins, which improved the diagnostic accuracy.

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Identification of the TF-miRNA-mRNA Co-regulatory Networks Involved in Sepsis

10.21203/rs.3.rs-801025/v1 ◽

2021 ◽

Author(s):

Xiaoqian Luo ◽

Weina Lu ◽

Jianfeng Zhao ◽

Jun Hu ◽

Enjiang Chen ◽

...

Keyword(s):

Expression Analysis ◽

Regulatory Network ◽

Regulatory Networks ◽

Mirna Target ◽

Target Genes ◽

Medical Condition ◽

Differentially Expressed ◽

Biological Targets ◽

Differentially Expressed Mirnas

Abstract BackgroundSepsis is a life-threatening medical condition caused by a dysregulated host response to infection. Recent studies have found that the expression of miRNAs is associated with the pathogenesis of sepsis and septic shock. Our study aimed to reveal which miRNAs may be involved in the dysregulated immune response in sepsis and how these miRNAs interact with transcription factors (TFs) using a computational approach with in vitro validation studies. MethodsTo determine the network of TFs, miRNAs and target genes involved in sepsis, GEO datasets GSE94717 and GSE131761 were used to identify differentially expressed miRNAs and DEGs. TargetScan and miRWalk databases were used to predict biological targets that overlap with the identified DEGs of differentially expressed miRNAs. The TransmiR database was used to predict the differential miRNA TFs that overlap with the identified DEGs. The TF-miRNA-mRNA network was constructed and visualized. Finally, qRT-PCR was used to verify the expression of TFs and miRNA in HUVECs. ResultBetween the healthy and sepsis groups, there were 146 upregulated and 98 downregulated DEGs in the GSE131761 dataset, and there were 1 upregulated and 183 downregulated DEMs in the GSE94717 dataset. A regulatory network of the TF-miRNA-target genes was established. According to the experimental results, RUNX3 was found to be downregulated while MAPK14 was upregulated, which corroborates the result of the computational expression analysis. In a HUVECs model, miR-19b-1-5p and miR-5009-5p were found to be significantly downregulated. Other TFs and miRNAs did not correlate with our bioinformatics expression analysis. ConclusionWe constructed a TF-miRNA-target gene regulatory network and identified potential treatment targets RUNX3, MAPK14, miR-19b-1-5p and miR-5009-5p. This information provides an initial basis for understanding the complex sepsis regulatory mechanisms.

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Pro-Angiogenic Activity of Monocytic-Type Myeloid-Derived Suppressor Cells from Balb/C Mice Infected with Echinococcus Granulosus and the Regulatory Role of miRNAs

Cellular Physiology and Biochemistry ◽

10.1159/000495498 ◽

2018 ◽

Vol 51 (3) ◽

pp. 1207-1220 ◽

Cited By ~ 2

Author(s):

Jian-hai Yin ◽

Cong-shan Liu ◽

Ai-ping Yu ◽

Jia-qing Yao ◽

Yu-juan Shen ◽

...

Keyword(s):

Quantitative Pcr ◽

Echinococcus Granulosus ◽

Protein Transport ◽

Target Genes ◽

Suppressor Cells ◽

Differentially Expressed ◽

Signalling Pathways ◽

Myeloid Derived Suppressor Cells ◽

Differentially Expressed Mirnas

Background/Aims: This study aims to predict the pro-angiogenic functions of monocytic-type myeloid-derived suppressor cells (M-MDSCs) derived from mice infected with Echinococcus granulosus. Methods: M-MDSCs were collected from Balb/c mice infected with E. granulosus and normal mice (control) and cultured in vitro. Human umbilical vein endothelial cells (HUVECs) were stimulated with the cell supernatant, and angiogenesis was investigated and analysed by the Angiogenesis module of the software NIH Image J. RNA was extracted from fresh isolated M-MDSCs and analysed with miRNA microarray; differentially expressed miRNAs and their potential functions were analysed through several bioinformatics tools. Finally, quantitative PCR was used to confirm the results of microarray analysis. Results: M-MDSCs from mice infected with E. granulosus could promote the formation of tubes from HUVECs in vitro. Moreover, vascular endothelial growth factor (VEGF) showed significantly high expression, whereas soluble fms-like tyrosine kinase-1 (sFlt-1) showed low expression at the transcriptional level in M-MDSCs from mice infected with E. granulosus. Microarray analysis of miRNAs showed that 28 miRNAs were differentially expressed in M-MDSCs from the two experimental mice groups, and 272 target genes were predicted using the microRNA databases TargetScan, PITA and microRNAorg. These target genes were mainly involved in the biological processes of intracellular protein transport, protein targeting to the lysosome and protein transport, and mainly located in the cytoplasm, neuronal cell body and membrane. Moreover, they were mainly involved in the molecular functions of protein binding, metal ion binding and SH3 domain binding. Further, the differentially expressed miRNAs were mainly enriched in the endocytosis, Wnt and axon guidance pathways, as well as the MAPK, focal adhesion, PI3K-Akt, cAMP, mTOR and TGF-β signalling pathways, which are linked to immunoregulation and angiogenesis based on the results of bioinformatics analysis with DIANA-miRPath 3.0. In addition, the expression of eight miRNAs was randomly verified by quantitative PCR independently in three mice infected with E. granulosus and three normal mice. Conclusion: M-MDSCs have a potential angiogenic role during E. granulosus infection, and miRNAs may play a role in the immune response and angiogenesis functions of M-MDSCs through regulation of the identified signalling pathways.

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Downregulation of Hsa-miR-3616-3p in Triple-Negative Breast Cancer is Associated with Cell Migration and Invasion

10.21203/rs.3.rs-824447/v1 ◽

2021 ◽

Author(s):

Keqian Wu ◽

Rui Peng ◽

Zheng Zhang ◽

Handeng Liu ◽

Yan Sun

Keyword(s):

Breast Cancer ◽

Triple Negative Breast Cancer ◽

Target Genes ◽

Triple Negative ◽

Micro Rna ◽

Differentially Expressed ◽

Migration And Invasion ◽

Candidate Mirnas ◽

Differentially Expressed Mirnas

Abstract Background: Micro RNA (miRNA), a class of endogenous small RNAs with a length of about 20-24 nucleotides, have been played a variety of important regulatory roles in cells and have attracted the attention of researchers because involvement of initiation and progression of diverse kinds of human diseases, especially cancer. However, the regulatory role of miRNA in triple negative breast cancer (TNBC), its clinical significance and potential mechanism are still largely unknown.Methods: In this study, the differentially expressed miRNAs were analyzed using GEO2R from GSE57897 and GSE97811 of the Gene Expression Omnibus (GEO). Then, we performed the overall survival (OS) analysis of four candidate miRNAs. And the expressions of four candidate miRNAs in TNBC and non-TNBC tissues were tested by Quantitative real-time PCR. We determined the level and prognostic values of hsa-miR-3616-3p in TNBC patients. Then, TNBC cells migration and invasion were studied in vitro with hsa-miR-3616-3p by using wounding heal assays and transwell assays. Next, target genes and transcription factors of hsa-miR-3616-3p enrichment analysis, were performed by the Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway.Results: Based on GSE57897 and GSE97811, we found 962 differentially expressed miRNAs including 943 up-regulated miRNAs and 19 down-regulated miRNAs. We selected top2 up-regulated miRNAs as hsa-miR-4428 and hsa-miR-575, and top2 down-regulated miRNAs as hsa-miR-3616-3p and hsa-miR-3909, and then we found that low expression of 4 candidated miRNAs had a worse prognosis in TNBC subtype. Next, we verified that the expression of hsa-miR-3616-3p was the most downregulated in TNBC tissues compared with matched surrounding tissues by qRT-PCR. Moerover, our results showed that overexpression of hsa-miR-3616-3p inhibited TNBC cells migration, and invasion in vitro.Conclusions: Our study might reveal important roles of hsa-miR-3616-3p plays in TNBC migration and invasion.

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Bioinformatics Analysis Reveals Functions of MicroRNAs in Rice Under the Drought Stress

Current Bioinformatics ◽

10.2174/1574893615666200207092410 ◽

2021 ◽

Vol 15 (8) ◽

pp. 927-936 ◽

Cited By ~ 3

Author(s):

Yan Peng ◽

Yuewu Liu ◽

Xinbo Chen

Keyword(s):

Drought Stress ◽

Target Genes ◽

Hot Spot ◽

Interaction Network ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Protein Protein Interaction ◽

Promising Tool ◽

Differentially Expressed Mirnas ◽

Aba Biosynthesis

Background: Drought is one of the most damaging and widespread abiotic stresses that can severely limit the rice production. MicroRNAs (miRNAs) act as a promising tool for improving the drought tolerance of rice and have become a hot spot in recent years. Objective: In order to further extend the understanding of miRNAs, the functions of miRNAs in rice under drought stress are analyzed by bioinformatics. Method: In this study, we integrated miRNAs and genes transcriptome data of rice under the drought stress. Some bioinformatics methods were used to reveal the functions of miRNAs in rice under drought stress. These methods included target genes identification, differentially expressed miRNAs screening, enrichment analysis of DEGs, network constructions for miRNA-target and target-target proteins interaction. Results: (1) A total of 229 miRNAs with differential expression in rice under the drought stress, corresponding to 73 rice miRNAs families, were identiﬁed. (2) 1035 differentially expressed genes (DEGs) were identified, which included 357 up-regulated genes, 542 down-regulated genes and 136 up/down-regulated genes. (3) The network of regulatory relationships between 73 rice miRNAs families and 1035 DEGs was constructed. (4) 25 UP_KEYWORDS terms of DEGs, 125 GO terms and 7 pathways were obtained. (5) The protein-protein interaction network of 1035 DEGs was constructed. Conclusion: (1) MiRNA-regulated targets in rice might mainly involve in a series of basic biological processes and pathways under drought conditions. (2) MiRNAs in rice might play critical roles in Lignin degradation and ABA biosynthesis. (3) MiRNAs in rice might play an important role in drought signal perceiving and transduction.

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LncRNA UCA1 promotes development of gastric cancer via the miR-145/MYO6 axis

Cellular & Molecular Biology Letters ◽

10.1186/s11658-021-00275-8 ◽

2021 ◽

Vol 26 (1) ◽

Author(s):

An Yang ◽

Xin Liu ◽

Ping Liu ◽

Yunzhang Feng ◽

Hongbo Liu ◽

...

Keyword(s):

Gastric Cancer ◽

Cell Proliferation ◽

Cancer Cells ◽

Cell Apoptosis ◽

Gastric Cancer Cell ◽

Gastric Cancer Cells ◽

Gastric Cancer Cell Lines ◽

Development Of Gastric Cancer

Abstract Background Long noncoding RNA (lncRNA), urothelial carcinoma-associated 1 (UCA1) is aberrantly expressed in multiple cancers and has been verified as an oncogene. However, the underlying mechanism of UCA1 in the development of gastric cancer is not fully understood. In the present study, we aimed to identify how UCA1 promotes gastric cancer development. Methods The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) data were used to analyze UCA1 and myosin VI (MYO6) expression in gastric cancer. Western blot and quantitative real-time PCR (QPCR) were performed to test the expression level of the UCA1/miR-145/MYO6 axis in gastric cancer cell lines and tissues. The roles of the UCA1/miR-145/MYO6 axis in gastric cancer in vitro and in vivo were investigated by CCK-8 assay, flow cytometry, siRNAs, immunohistochemistry, and a mouse xenograft model. The targeted relationship among UCA1, miR-145, and MYO6 was predicted using LncBase Predicted v.2 and TargetScan online software, and then verified by luciferase activity assay and RNA immunoprecipitation. Results UCA1 expression was higher but miR-145 expression was lower in gastric cancer cell lines or tissues, compared to the adjacent normal cell line or normal tissues. Function analysis verified that UCA1 promoted cell proliferation and inhibited cell apoptosis in the gastric cancer cells in vitro and in vivo. Mechanistically, UCA1 could bind directly to miR-145, and MYO6 was found to be a downstream target gene of miR-145. miR-145 mimics or MYO6 siRNAs could partly reverse the effect of UCA1 on gastric cancer cells. Conclusions UCA1 accelerated cell proliferation and inhibited cell apoptosis through sponging miR-145 to upregulate MYO6 expression in gastric cancer, indicating that the UCA1/miR-145/MYO6 axis may serve as a potential therapeutic target for gastric cancer.

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Sevoflurane inhibits malignant progression of colorectal cancer via hsa_circ_0000231-mediated miR-622

Journal of Biological Research-Thessaloniki ◽

10.1186/s40709-021-00145-6 ◽

2021 ◽

Vol 28 (1) ◽

Author(s):

Jingpeng Wang ◽

Shuyuan Li ◽

Gaofeng Zhang ◽

Huihua Han

Keyword(s):

Colorectal Cancer ◽

Cell Proliferation ◽

Cell Apoptosis ◽

Volatile Anesthetic ◽

Tumor Formation ◽

Luciferase Reporter ◽

Migration And Invasion ◽

Circular Rnas

Abstract Background Sevoflurane (Sev), a commonly used volatile anesthetic, has been reported to inhibit the process of colorectal cancer (CRC). Circular RNAs (circRNAs) are revealed to participate in the pathogenesis of CRC. This study aims to reveal the mechanism of hsa_circ_0000231 in Sev-mediated CRC progression. Methods The expression of hsa_circ_0000231 and microRNA-622 (miR-622) was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Protein level was determined by western blot analysis. Cell proliferation was investigated by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), cell colony formation and DNA content quantitation assays. Cell apoptosis was detected by Annexin V-fluorescein isothiocyanate and propidium iodide double staining and caspase 3 activity assays. Cell migration and invasion were investigated by wound-healing and transwell invasion assays, respectively. The putative relationship between hsa_circ_0000231 and miR-622 was predicted by circular RNA Interactome online database, and identified by dual-luciferase reporter and RNA immunoprecipitation assays. The impacts of hsa_circ_0000231 on Sev-mediated tumor formation in vivo were presented by in vivo assay. Results Hsa_circ_0000231 expression was upregulated, while miR-622 was downregulated in CRC tissues and cells compared with control groups. Sev treatment decreased hsa_circ_0000231 expression, but increased miR-622 expression in CRC cells. Sev treatment suppressed cell proliferation, migration and invasion, and induced cell apoptosis. Hsa_circ_0000231 overexpression restored Sev-mediated CRC progression in vitro. Additionally, hsa_circ_0000231 acted as a sponge of miR-622, and miR-622 inhibitors reversed the impacts of hsa_circ_0000231 silencing on CRC process. Furthermore, Sev treatment inhibited tumor growth by regulating hsa_circ_0000231 in vivo. Conclusion Hsa_circ_0000231 attenuated Sev-aroused repression impacts on CRC development by sponging miR-622. This findings may provide an appropriate anesthetic protocol for CRC sufferers undergoing surgery.

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