Comprehensive analysis of differentially expressed lncRNAs and associated ceRNA networks in Patau syndrome

Abstract Objective: LncRNAs are a class of competing for endogenous RNAs (ceRNAs) with no coding ability and have miRNA binding sites that competitively bind to miRNAs and inhibit miRNA-mediated regulation of target genes. In recent years, an increasing number of studies have recognized the biological functions of lncRNAs.Methods: Illumina RNA-Seq technology was used to analyze the cord blood with Patau syndrome (PS) fetal and the peripheral blood of pregnant women to obtain differential expression profiles of lncRNAs, miRNAs, and mRNAs. Further, Combined with bioinformatics analysis of the biological functions of differentially expressed lncRNAs (DElncRNAs). Results: The results showed that 467 DElncRNAs, 8512 differentially expressed mRNAs (DEmRNAs), and 18 differentially expressed miRNAs (DEmiRNAs) were found to be co-expressed in cord blood and peripheral blood. The hsa-miR-15a-5p is located on chromosome 13. We constructed the ceRNA network with hsa-miR-15a-5p, lncRNAs as the bait, and mRNAs as the targe. Conclusion: We consider that the DElncRNAs may indirectly regulate the target gene CLASRP or KARS by binding hsa-miR-15a-5p to participate in the occurrence of PS.

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Effect of miR-27b-5p on apoptosis of human vascular endothelial cells induced by simulated microgravity

APOPTOSIS ◽

10.1007/s10495-019-01580-6 ◽

2019 ◽

Vol 25 (1-2) ◽

pp. 73-91 ◽

Cited By ~ 1

Author(s):

Yi-Kai Pan ◽

Cheng-Fei Li ◽

Yuan Gao ◽

Yong-Chun Wang ◽

Xi-Qing Sun

Keyword(s):

Endothelial Cells ◽

Western Blot ◽

Target Gene ◽

Simulated Microgravity ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Luciferase Assay ◽

Qrt Pcr ◽

Differentially Expressed Mirnas

AbstractWeightlessness-induced cardiovascular dysfunction can lead to physiological and pathological consequences. It has been shown that spaceflight or simulated microgravity can alter expression profiles of some microRNAs (miRNAs). Here, we attempt to identify the role of miRNAs in human umbilical vein endothelial cells (HUVECs) apoptosis under simulated microgravity. RNA-sequencing and quantitative real-time PCR (qRT-PCR) assays were used to identify differentially expressed miRNAs in HUVECs under simulated microgravity. Then we obtained the target genes of these miRNAs through target analysis software. Moreover, GO and KEGG enrichment analysis were performed. The effects of these miRNAs on HUVECs apoptosis were evaluated by flow cytometry, Western blot and Hoechst staining. Furthermore, we obtained the target gene of miR-27b-5p by luciferase assay, qRT-PCR and Western blot. Finally, we investigated the relationship between this target gene and miR-27b-5p in HUVECs apoptosis under normal gravity or simulated microgravity. We found 29 differentially expressed miRNAs in HUVECs under simulated microgravity. Of them, the expressions of 3 miRNAs were validated by qRT-PCR. We demonstrated that miR-27b-5p affected HUVECs apoptosis by inhibiting zinc fingers and homeoboxes 1 (ZHX1). Our results reported here demonstrate for the first time that simulated microgravity can alter the expression of some miRNAs in HUVECs and miR-27b-5p may protect HUVECs from apoptosis under simulated microgravity by targeting ZHX1.

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Identification and Characterization of New Microrna Biomarkers and Target Genes in Drug-Insensitive CD34+ CML Stem/Progenitor Cells Using Global Comparative RNA-Seq Analyses

Blood ◽

10.1182/blood.v126.23.1567.1567 ◽

2015 ◽

Vol 126 (23) ◽

pp. 1567-1567

Author(s):

Hanyang Lin ◽

Jonathan Zeng ◽

Katharina Rothe ◽

Jens Ruschmann ◽

Oleh Petriv ◽

...

Keyword(s):

Progenitor Cells ◽

Mirna Target ◽

Target Genes ◽

Expression Profiles ◽

Therapeutic Targets ◽

Mapk Signaling ◽

Differentially Expressed ◽

Rna Seq ◽

Cd34 Cells ◽

Differentially Expressed Mirnas

Abstract Therapeutic targeting of BCR-ABL with selective ABL tyrosine kinase inhibitors (TKIs) has led to a significant survival benefit for early phase CML. However, TKI monotherapies are rarely curative, with persistence of leukemic stem cells, emergence of resistance and relapses remaining as challenges. To identify differentially expressed and new miRNAs in CD34+ CML stem/progenitor cells that might serve as potential biomarkers and/or therapeutic targets, we have performed Illumina Deep Sequencing to obtain absolute miRNA expression profiles of highly purified CD34+ cells obtained at newly diagnosed stage from six CML patients. Three of the patients were classified retrospectively, after imatinib (IM) therapy, as IM-responders and three as IM-nonresponders. CD34+ cells isolated from five normal bone marrow (NBM) samples were similarly analyzed as controls. Bioconductor DESeq2 analysis revealed 63 differentially expressed miRNAs between CML and NBM samples (adjusted P<0.05). Most differentially expressed miRNAs identified were down-regulated in CML compared to NBM, while 17 were up-regulated. Interestingly, 12 miRNAs were found to be differentially expressed between the IM-responders and IM-nonresponders. In addition, 34 novel miRNAs were identified in the CD34+ CML stem/progenitor cells. We next validated the sequencing data in a larger cohort of samples. CD34+ cells from IM-responders (n=12), IM-nonresponders (n=10) and normal individuals (n=11) were analyzed using a high-throughput qPCR microfluidics device. These studies confirmed the differential expression in CD34+ CML cells of 32 of the 63 miRNAs (adjusted P<0.05), including an increased level of oncomirs miR-155 and miR-17-92, and a decreased level of tumor suppressors miR-145, miR-151, and miR-452. Importantly, significant changes in some of these miRNAs were detected in CD34+ cells from CML patients (n=60) after three months of nilotinib (NL) treatment compared to the same patient samples before the treatment: expression of 18 miRNAs were normalized after NL therapy, whereas 10 showed little change. To further identify potential miRNA target genes, RNA-seq analysis was performed on the same RNA samples to correlate miRNA profiles with corresponding mRNA expression changes. Bioconductor RmiR analysis was performed to match miRNA target genes whose expression was inversely correlated with the expression of deregulated miRNAs based on three of six prediction algorithms (mirBase, TargetScan, miRanda, tarBase, mirTarget2, and PicTar). We have identified 1,210 differentially expressed mRNAs that are predicted targets of the deregulated miRNAs in the comparison of CML and NBM data. Interestingly, only seven differentially expressed genes were predicted targets of the deregulated miRNAs identified in a comparison of IM-responders and IM-nonresponders. Most of the predicted target genes are involved in cell cycle regulation, MAPK signaling and TGF-beta signaling pathways according to DAVID Bioinformatics Resources analysis, which clusters predicted target genes to known KEGG pathways. To elucidate the biological significance of the differentially expressed miRNAs in TKI-insensitive CML stem/progenitor cells, a number of functional assays were performed. An initial screen of eight miRNAs, selected for their novelty and CML-related potential target genes, was performed by transiently transfecting CML cells with miRNA mimics or inhibitors, and chemically synthesized RNAs which mimic or inhibit mature endogenous miRNAs. Four of the eight miRNA mimics/inhibitors transfected cells displayed significant growth disadvantages and enhanced sensitivity to TKI treatments based on trypan-blue exclusion, thymidine incorporation, apoptosis, and colony-forming cell assays. Q-RT-PCR analysis further showed reduced expression of their predicted target genes in cells transfected with miRNA mimics. Taken together, we have identified aberrant, differentially expressed miRNAs and their target genes in TKI-insensitive CML stem/progenitor cells that may serve as useful biomarkers to predict clinical response of CML patients to TKI therapy and ultimately lead to identification of new therapeutic targets for improved treatment options in CML. Disclosures No relevant conflicts of interest to declare.

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Small RNA sequencing evaluation of renal microRNA biomarkers in dogs with X-linked hereditary nephropathy

Scientific Reports ◽

10.1038/s41598-021-96870-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Candice P. Chu ◽

Shiguang Liu ◽

Wenping Song ◽

Ethan Y. Xu ◽

Mary B. Nabity

Keyword(s):

Small Rna ◽

Target Genes ◽

Differentially Expressed ◽

Small Rna Sequencing ◽

Rna Seq ◽

Ckd Progression ◽

Critical Pathways ◽

Qrt Pcr ◽

Hereditary Nephropathy ◽

Differentially Expressed Mirnas

AbstractDogs with X-linked hereditary nephropathy (XLHN) are an animal model for Alport syndrome in humans and progressive chronic kidney disease (CKD). Using mRNA sequencing (mRNA-seq), we have characterized the gene expression profile affecting the progression of XLHN; however, the microRNA (miRNA, miR) expression remains unknown. With small RNA-seq and quantitative RT-PCR (qRT-PCR), we used 3 small RNA-seq analysis tools (QIAGEN OmicSoft Studio, miRDeep2, and CPSS 2.0) to profile differentially expressed renal miRNAs, top-ranked miRNA target genes, and enriched biological processes and pathways in CKD progression. Twenty-three kidney biopsies were collected from 5 dogs with XLHN and 4 age-matched, unaffected littermates at 3 clinical time points (T1: onset of proteinuria, T2: onset of azotemia, and T3: advanced azotemia). We identified up to 23 differentially expressed miRNAs at each clinical time point. Five miRNAs (miR-21, miR-146b, miR-802, miR-142, miR-147) were consistently upregulated in affected dogs. We identified miR-186 and miR-26b as effective reference miRNAs for qRT-PCR. This study applied small RNA-seq to identify differentially expressed miRNAs that might regulate critical pathways contributing to CKD progression in dogs with XLHN.

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RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype

Animals ◽

10.3390/ani10091565 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1565

Author(s):

Zhiyun Hao ◽

Yuzhu Luo ◽

Jiqing Wang ◽

Jiang Hu ◽

Xiu Liu ◽

...

Keyword(s):

Mammary Gland ◽

Signaling Pathway ◽

Target Genes ◽

Mammary Epithelial Cells ◽

Expression Profiles ◽

Wnt Signaling Pathway ◽

Mammary Epithelial ◽

Differentially Expressed ◽

Rna Seq ◽

Non Coding Rnas

Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA with >200 nucleotides in length. Some lncRNAs have been proven to have clear regulatory functions in many biological processes of mammals. However, there have been no reports on the roles of lncRNAs in ovine mammary gland tissues. In the study, the expression profiles of lncRNAs were studied using RNA-Seq in mammary gland tissues from lactating Small-Tailed Han (STH) ewes and Gansu Alpine Merino (GAM) ewes with different milk yield and ingredients. A total of 1894 lncRNAs were found to be expressed. Compared with the GAM ewes, the expression levels of 31 lncRNAs were significantly up-regulated in the mammary gland tissues of STH ewes, while 37 lncRNAs were remarkably down-regulated. Gene Ontogeny (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the target genes of differentially expressed lncRNAs were enriched in the development and proliferation of mammary epithelial cells, morphogenesis of mammary gland, ErbB signaling pathway, and Wnt signaling pathway. Some miRNA sponges of differentially expressed lncRNAs, reported to be associated with lactation and mammary gland morphogenesis, were found in a lncRNA-miRNA network. This study reveals comprehensive lncRNAs expression profiles in ovine mammary gland tissues, thereby providing a further understanding of the functions of lncRNAs in the lactation and mammary gland development of sheep.

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Construction of miRNA-target networks using microRNA profiles of CVB3-infected HeLa cells

Scientific Reports ◽

10.1038/s41598-019-54188-w ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Hai Lan Yao ◽

Mi Liu ◽

Wen Jun Wang ◽

Xin Ling Wang ◽

Juan Song ◽

...

Keyword(s):

Hela Cells ◽

Regulatory Networks ◽

Cellular Differentiation ◽

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Differentially Expressed ◽

Mirna Regulation ◽

Cvb3 Infection ◽

Differentially Expressed Mirnas

AbstractMicroRNAs (miRNAs) play an important role in regulating gene expression in multiple biological processes and diseases. Thus, to understand changes in miRNA during CVB3 infection, specific miRNA expression profiles were investigated at 3 h, 6 h, and 9 h postinfection in HeLa cells by small-RNA high-throughput sequencing. Biological implications of 68 differentially expressed miRNAs were analyzed through GO and KEGG pathways. Interaction networks between 34 known highly differentially expressed miRNAs and targets were constructed by mirDIP and Navigator. The predicted targets showed that FAM135A, IKZF2, PLAG1, ZNF148, PHC3, LCOR and DYRK1A, which are associated with cellular differentiation and transcriptional regulation, were recognized by 8 miRNAs or 9 miRNAs through interactional regulatory networks. Seven target genes were confirmed by RT-qPCR. The results showed that the expression of DYRK1A, FAM135A, PLAG1, ZNF148, and PHC3 were obviously inhibited at 3 h, 6 h, and 9 h postinfection. The expression of LCOR did not show a significant change, and the expression of IKZF2 increased gradually with prolonged infection time. Our findings improve the understanding of the pathogenic mechanism of CVB3 infection on cellular differentiation and development through miRNA regulation, which has implications for interventional approaches to CVB3-infection therapy. Our results also provide a new method for screening target genes of microRNA regulation in virus-infected cells.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

10.21203/rs.2.15327/v1 ◽

2019 ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan Zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background: MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results: In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-165 mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 ( PLCβ1) gene was verified to be a target of ssc-mir-423-5p . Conclusions: This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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Integrated analysis of sex-biased mRNA and miRNA expression profiles in the gonad of the discus fish (Symphysodon aequifasciatus)

10.1101/492264 ◽

2018 ◽

Cited By ~ 1

Author(s):

yuanshuai Fu ◽

Zhe Xu ◽

Zaizhong Chen ◽

Bin Wen ◽

Jianzhong Gao

Keyword(s):

Molecular Mechanisms ◽

Target Genes ◽

High Efficiency ◽

Expression Profiles ◽

Gonad Development ◽

Differentially Expressed ◽

Cdna Libraries ◽

Integrated Analysis ◽

Illumina Hiseq ◽

Differentially Expressed Mirnas

The discus fish (Symphysodon aequifasciatus) is an ornamental fish that is well-known around the world. Phenotype investigation indicated that there are no significant differences in appearance between males and females of the discus fish. To better understand the sexual development mechanisms and obtain a high efficiency sex identification method in the artificial reproduction process of the discus fish, we constructed six cDNA libraries from three adult testes and three adult ovaries, and perform RNA-sequencing for identifying sex-biased candidate genes, microRNA (miRNA), and metabolic pathway using the Illumina Hiseq 4000. A total of 50,082 non-redundant genes (unigenes) were identified, of which 18,570 unigenes were significantly overexpressed in testes, and 11,182 unigenes were significantly overexpressed in ovaries, and 8 differentially expressed unigenes were validated by quantitative Real-Time PCR (qPCR). A total of 551 miRNAs were identified, of which 47 miRNAs were differentially expressed between testes and ovaries, and 7 differentially expressed miRNAs and one non-differential miRNA were validated by qPCR. Twenty-four of these differentially expressed miRNAs and their 15 predicted target genes constituted 41 important miRNA-mRNA interaction pairs, which may be important candidates for sex-related miRNAs and sex-related genes in the discus fish. Some of vital sex-related metabolic pathways were also identified that may play key roles in regulating gonad development of the discus fish. These results can provide important insights to better understand molecular mechanisms for sexual dimorphism in gonads development.

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Integrated analysis of miRNA and mRNA expression profiles in testes of Duroc and Meishan boars

BMC Genomics ◽

10.1186/s12864-020-07096-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Haisheng Ding ◽

Min Liu ◽

Changfan Zhou ◽

Xiangbin You ◽

Tao Su ◽

...

Keyword(s):

High Throughput Sequencing ◽

Target Genes ◽

Expression Profiles ◽

Male Gamete ◽

Mirna Expression Profile ◽

Mapk Signaling ◽

Differentially Expressed ◽

Integrated Analysis ◽

Testis Development ◽

Differentially Expressed Mirnas

Abstract Background MicroRNAs (miRNAs) are small non-coding RNAs playing vital roles in regulating posttranscriptional gene expression. Elucidating the expression regulation of miRNAs underlying pig testis development will contribute to a better understanding of boar fertility and spermatogenesis. Results In this study, miRNA expression profile was investigated in testes of Duroc and Meishan boars at 20, 75, and 270 days of age by high-throughput sequencing. Forty-five differentially expressed miRNAs were identified from testes of Duroc and Meishan boars before and after puberty. Integrated analysis of miRNA and mRNA profiles predicted many miRNA-mRNA pairs. Gene ontology and biological pathway analyses revealed that predicted target genes of ssc-mir-423-5p, ssc-mir-34c, ssc-mir-107, ssc-mir-196b-5p, ssc-mir-92a, ssc-mir-320, ssc-mir-10a-5p, and ssc-mir-181b were involved in sexual reproduction, male gamete generation, and spermatogenesis, and GnRH, Wnt, and MAPK signaling pathway. Four significantly differentially expressed miRNAs and their predicted target genes were validated by quantitative real-time polymerase chain reaction, and phospholipase C beta 1 (PLCβ1) gene was verified to be a target of ssc-mir-423-5p. Conclusions This study provides an insight into the functional roles of miRNAs in testis development and spermatogenesis and offers useful resources for understanding differences in sexual function development caused by the change in miRNAs expression between Duroc and Meishan boars.

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A systemic study of indoxacarb resistance in Spodoptera litura revealed complex expression profiles and regulatory mechanism

Scientific Reports ◽

10.1038/s41598-019-51234-5 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 5

Author(s):

Li Shi ◽

Yao Shi ◽

Ya Zhang ◽

Xiaolan Liao

Keyword(s):

Spodoptera Litura ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Resistance Mechanisms ◽

Differentially Expressed ◽

Glutathione S Transferase ◽

Differentially Expressed Mirnas ◽

Important Pest ◽

Resistant Strains

Abstract The tobacco cutworm, Spodoptera litura, is an important pest of crop and vegetable plants worldwide, and its resistance to insecticides have quickly developed. However, the resistance mechanisms of this pest are still unclear. In this study, the change in mRNA and miRNA profiles in the susceptible, indoxacarb-resistant and field indoxacarb-resistant strains of S. litura were characterized. Nine hundred and ten co-up-regulated and 737 co-down-regulated genes were identified in the resistant strains. Further analysis showed that 126 co-differentially expressed genes (co-DEGs) (cytochrome P450, carboxy/cholinesterase, glutathione S-transferase, ATP-binding cassette transporter, UDP-glucuronosyl transferase, aminopeptidase N, sialin, serine protease and cuticle protein) may play important roles in indoxacarb resistance in S. litura. In addition, a total of 91 known and 52 novel miRNAs were identified, and 10 miRNAs were co-differentially expressed in the resistant strains of S. litura. Furthermore, 10 co-differentially expressed miRNAs (co-DEmiRNAs) had predicted co-DEGs according to the expected miRNA-mRNA negative regulation pattern and 37 indoxacarb resistance-related co-DEGs were predicted to be the target genes. These results not only broadened our understanding of molecular mechanisms of insecticide resistance by revealing complicated profiles, but also provide important clues for further study on the mechanisms of miRNAs involved in indoxacarb resistance in S. litura.

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Potential Diagnostic and Therapeutic Targets for Hepatocellular Carcinoma Based on Exosome-Derived Competitive Endogenous RNA Network

10.21203/rs.3.rs-487982/v1 ◽

2021 ◽

Author(s):

Yuan Tian ◽

Dongliang Yang ◽

Tieshan Wang ◽

He Bu ◽

JinBao Wu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Target Genes ◽

Immune Escape ◽

Malignant Tumors ◽

Expression Profiles ◽

Therapeutic Targets ◽

Differentially Expressed ◽

Cerna Network ◽

Differentially Expressed Mirnas ◽

Competitive Endogenous Rna

Abstract Background: Hepatocellular carcinoma (HCC) is one of the most malignant tumors in the world. The pathogenesis of HCC is complex and closely related to chronic uncontrollable inflammation. As a bridge between inflammation and cancer, circulating exosomes play a vital role in early tumorigenesis, metastasis, and immune escape. Studies have shown that exosomes containing specific RNAs may be potential diagnostic and therapeutic targets for HCC. Purpose The current research investigated key circRNA through exosome-derived competitive endogenous RNA network based on the ExoRBase database. Methods: The circRNA, lncRNA, and mRNA expression profiles of human blood samples were downloaded from the ExoRBase database. At the standard of P<0.05 and log FC>0, differentially expressed genes (DEGs) were further identified between normal human and HCC patients. The co-expressed pairs of DEGs were predicted by TargetScan, miRcode, and StarBase databases. The ceRNA network was constructed by Cytoscape software. Subsequently, target genes corresponding to circRNA in the ceRNA network were annotated and analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG). The potential transcription factors were screened by FunRich database. Results: At the criterion of P<0.05 and log FC>0, 13 differentially expressed circRNAs(DECs) were identified with 9 up-regulated and 4 down-regulated. The co-expressed differentially expressed miRNAs-mRNAs (DEMis-DEMs) (620 pairs), differentially expressed miRNAs- LncRNAs (DEMis-DElncRNA) (684 pairs) and DEMis-DECs (53 pairs) were finally predicted to construct the ceRNA network. The GO analysis indicated that target genes in the ceRNA network were mainly enriched in the molecular function of protein serine/threonine kinase activity. KEGG pathway analysis suggested target genes were enriched in two pathways of MAPK and central carbon metabolism. Conclusion: The study provides a valuable reference for HCC through the ceRNA network in exosomes. Besides, hsa_circ_0000284 may be potential diagnostic markers of HCC.

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