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Jia X, Ma Y, Zhang X, Shen Z, Wang M, Jiang L, Wei X, Li C, Zhang M, Yang T. A preliminary study of calcium channel-associated mRNA and miRNA networks in post-traumatic epileptic rats. Sci Rep 2023; 13:13103. [PMID: 37567882 PMCID: PMC10421957 DOI: 10.1038/s41598-023-39485-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The calcium channels are the main pathogenesis and therapeutic target for post-traumatic epilepsy (PTE). However, differentially expressed miRNAs (DEMs) and mRNAs associated with calcium channels in PTE and their interactions are poorly understood. We produced a PTE model in rats and conducted RNA-seq in PTE rats. Gene annotation was used to verify differentially expressed mRNAs related to calcium channels. RNAhybrid, PITA, and Miranda prediction were used to build the miRNA-mRNA pairs. Furthermore, Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were used for the functional enrichment analysis of DEMs. The quantification changes of mRNA and miRNA were verified by RT-qPCR. There were 431 identified differentially expressed genes (DEGs) in PTE rats compared with the sham group, of which five mRNAs and 7 miRNAs were related to calcium channels. The miRNA-mRNA network suggested a negative correlation between 11 pairs of miRNA-mRNA involved in the p53 signaling pathway, HIF-1 signaling pathway. RT-qPCR verified three upregulated mRNAs in PTE rats, associated with 7 DEMs negatively related to them, respectively. This study has revealed the changes in miRNA-mRNA pairs associated with calcium channels in PTE, which might contribute to the further interpretation of potential underlying molecular mechanisms of PTE and the discovery of promising diagnostics.
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Affiliation(s)
- Xiao Jia
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
- State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy, Nankai University, Tianjin, 300350, China
| | - Yixun Ma
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
- College of Biological Science, China Agricultural University, Beijing, 100193, China
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Xiaoyuan Zhang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
| | - Zefang Shen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
| | - Min Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
| | - Lufang Jiang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
| | - Xuan Wei
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
| | - Chang Li
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China
| | - Mengzhou Zhang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China.
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China.
| | - Tiantong Yang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, No. 25 Xitucheng Road, Haidian District, Beijing, 100088, China.
- Collaborative Innovation Center of Judicial Civilization, Beijing, 100088, China.
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102
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Zhuang XX, Liu T, Wei LB, Gao JR. Construction of chronic glomerulonephritis‑related lncRNA‑mRNA regulatory network and lncRNA‑-miRNA‑mRNA ceRNA network by bioinformatics analysis. Exp Ther Med 2023; 26:403. [PMID: 37522060 PMCID: PMC10375445 DOI: 10.3892/etm.2023.12102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 06/16/2023] [Indexed: 08/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are ncRNA transcripts >200 nucleotides that are important genetic regulators. LncRNAs can directly regulate mRNA through a lncRNA-mRNA regulatory mode and can also regulate mRNA through competitive binding to micro (mi)RNA, which is generally known as the competitive endogenous RNA (ceRNA) network. The present study evaluated the functional roles and regulatory networks of lncRNAs in chronic glomerulonephritis (CGN). The proliferative ability of mouse glomerular mesangial cells (GMCs) induced by different concentrations of lipopolysaccharide (LPS) was assessed using the Cell Counting Kit-8 assay, and RNA sequencing (RNA-seq) was performed to identify differentially expressed lncRNAs in LPS-induced GMCs. Based on the sequencing results, six lncRNAs were selected for validation using reverse transcription-quantitative PCR (RT-qPCR). Furthermore, the lncRNA-mRNA regulatory network and the lncRNA-miRNA-mRNA ceRNA network were constructed to assess the role and mechanism of CGN-related lncRNAs. To elucidate the biological functions of lncRNAs, Gene Ontology (GO) biological process term enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed on all mRNAs involved in the lncRNA-mRNA regulatory network and in the ceRNA network. A total of 1,532 differentially expressed lncRNAs, including 594 upregulated lncRNAs and 938 downregulated lncRNAs, were identified using RNA-seq. The results of RT-qPCR validation were consistent with RNA-seq results. An lncRNA-mRNA regulatory network, including 236 lncRNAs and 556 mRNAs, and a ceRNA network, including 6 lncRNAs, 18 miRNAs and 419 mRNAs, were successfully constructed. The GO biological process term enrichment and KEGG pathway enrichment analyses demonstrated that those lncRNAs were often related to inflammatory response and substance metabolism. The present study identified key CGN-related lncRNAs in LPS-induced GMCs, and further demonstrated a global view of the lncRNA-mRNA regulatory network and ceRNA network involved in CGN. These results offered novel insights into the roles of lncRNAs in the pathogenesis of CGN and identified potential diagnostic biomarkers.
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Affiliation(s)
- Xing-Xing Zhuang
- Department of Pharmacy, Chaohu Hospital of Anhui Medical University, Chaohu, Anhui 238000, P.R. China
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Tao Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Liang-Bing Wei
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
| | - Jia-Rong Gao
- Department of Pharmacy, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui 230012, P.R. China
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103
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Zhang X, Li X, Wang C, Wang S, Zhuang Y, Liu B, Lian X. Identification of markers for predicting prognosis and endocrine metabolism in nasopharyngeal carcinoma by miRNA-mRNA network mining and machine learning. Front Endocrinol (Lausanne) 2023; 14:1174911. [PMID: 37538797 PMCID: PMC10396331 DOI: 10.3389/fendo.2023.1174911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/21/2023] [Indexed: 08/05/2023] Open
Abstract
Background Nasopharyngeal cancer (NPC) has a high incidence in Southern China and Asia, and its survival is extremely poor in advanced patients. MiRNAs play critical roles in regulating gene expression and serve as therapeutic targets in cancer. This study sought to disclose key miRNAs and target genes responsible for NPC prognosis and endocrine metabolism. Materials and methods Three datasets (GSE32960, GSE70970, and GSE102349) of NPC samples came from Gene Expression Omnibus (GEO). Limma and WGCNA were applied to identify key prognostic miRNAs. There were 12 types of miRNA tools implemented to study potential target genes (mRNAs) of miRNAs. Univariate Cox regression and stepAIC were introduced to construct risk models. Pearson analysis was conducted to analyze the correlation between endocrine metabolism and RiskScore. Single-sample gene set enrichment analysis (ssGSEA), MCP-counter, and ESTIMATE were performed for immune analysis. The response to immunotherapy was predicted by TIDE and SubMap analyses. Results Two key miRNAs (miR-142-3p and miR-93) were closely involved in NPC prognosis. The expression of the two miRNAs was dysregulated in NPC cell lines. A total of 125 potential target genes of the key miRNAs were screened, and they were enriched in autophagy and mitophagy pathways. Five target genes (E2F1, KCNJ8, SUCO, HECTD1, and KIF23) were identified to construct a prognostic model, which was used to divide patients into high group and low group. RiskScore was negatively correlated with most endocrine-related genes and pathways. The low-risk group manifested higher immune infiltration, anticancer response, more activated immune-related pathways, and higher response to immunotherapy than the high-risk group. Conclusions This study revealed two key miRNAs that were highly contributable to NPC prognosis. We delineated the specific links between key miRNAs and prognostic mRNAs with miRNA-mRNA networks. The effectiveness of the five-gene model in predicting NPC prognosis as well as endocrine metabolism provided a guidance for personalized immunotherapy in NPC patients.
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Affiliation(s)
- Xixia Zhang
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiao Li
- Department Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Caixia Wang
- Department Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shuang Wang
- Department Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yuan Zhuang
- Department Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Bing Liu
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xin Lian
- Department of Otolaryngology Head and Neck Surgery, Shengjing Hospital of China Medical University, Shenyang, China
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Aldabbas R, Shaker OG, Ismail MF, Fathy N. miRNA-559 and MTDH as possible diagnostic markers of psoriasis: Role of PTEN/AKT/FOXO pathway in disease pathogenesis. Mol Cell Biochem 2023; 478:1427-1438. [PMID: 36348199 PMCID: PMC10209283 DOI: 10.1007/s11010-022-04599-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 10/24/2022] [Indexed: 11/09/2022]
Abstract
Psoriasis is a persistent, inflammatory, autoimmune skin disorder which can be elicited by genetic and environmental factors. Several microRNAs (miRNAs) that are abnormally expressed in psoriasis have emerged as an interesting candidate in psoriasis pathogenesis. However, the expression profile and function of miRNA-559, and its direct target metadherin (MTDH), in psoriasis need to be further illuminated. This study intended to assess miRNA-559 and MTDH levels in skin and sera of psoriatic patients and to investigate their clinical significance in an attempt for developing novel distinct tools for early diagnosis of psoriasis. Moreover, this study aimed at exploring participation of miRNA-559 in regulating MTDH/PTEN/AKT pathway in psoriasis. Expression levels of miRNA-559, AKT, FOXO1 and PTEN were measured by real-time qRT-PCR, whereas MTDH and p27 levels were assessed by ELISA in lesional, non-lesional tissues and serum of 20 psoriatic patients and 20 matching controls. Correlation study was conducted between different parameters. The diagnostic performance of miRNA-559 and MTDH in psoriasis was estimated by receiver operating characteristic (ROC) curve analysis. Expression of miRNA-559 in psoriatic patients was significantly downregulated in both lesional tissues and serum as compared to controls. Conversely, MTDH protein level showed significant increase in both tissues and serum of psoriatic patients and was inversely correlated with miRNA-559 level. Meanwhile, levels of PTEN, AKT and FOXO1 were dramatically changed in psoriatic patients compared to controls. Furthermore, serum miRNA-559 and MTDH displayed comparable diagnostic accuracy in discriminating psoriatic patients from controls. Yet, miRNA-559 demonstrated superior diagnostic performance than MTDH in psoriasis diagnosis. Together, the current findings provide the first suggestion of a new mechanism by which downregulation of miRNA-559 might induce proliferation in psoriasis through modulating PTEN/AKT/FOXO1 pathway by positive regulation of MTDH. Thus, miRNA-559 and MTDH might be proposed as promising diagnostic biomarkers of psoriasis.
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Affiliation(s)
- Rana Aldabbas
- PHD Student at Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Olfat G. Shaker
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Cairo University, Cairo, 11562 Egypt
| | - Manal F. Ismail
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562 Egypt
| | - Nevine Fathy
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Kasr El-Aini Street, Cairo, 11562 Egypt
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105
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Liu Y, Liu X, Wang M, Chen C, Li X, Liang Z, Shan Y, Yin Y, Sun F, Li Z, Li H. Characterizations of microRNAs involved in the molecular mechanisms underlying the therapeutic effects of noni ( Morinda citrifolia L.) fruit juice on hyperuricemia in mice. Front Nutr 2023; 10:1121734. [PMID: 37426193 PMCID: PMC10324520 DOI: 10.3389/fnut.2023.1121734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 06/06/2023] [Indexed: 07/11/2023] Open
Abstract
Background Hyperuricemia is generally defined as the high level of serum uric acid and is well known as an important risk factor for the development of various medical disorders. However, the medicinal treatment of hyperuricemia is frequently associated with multiple side-effects. Methods The therapeutic effect of noni (Morinda citrifolia L.) fruit juice on hyperuricemia and the underlying molecular mechanisms were investigated in mouse model of hyperuricemia induced by potassium oxonate using biochemical and high-throughput RNA sequencing analyses. Results The levels of serum uric acid (UA) and xanthine oxidase (XOD) in mice treated with noni fruit juice were significantly decreased, suggesting that the noni fruit juice could alleviate hyperuricemia by inhibiting the XOD activity and reducing the level of serum UA. The contents of both serum creatinine and blood urine nitrogen of the noni fruit juice group were significantly lower than those of the model group, suggesting that noni fruit juice promoted the excretion of UA without causing deleterious effect on the renal functions in mice. The differentially expressed microRNAs involved in the pathogenesis of hyperuricemia in mice were identified by RNA sequencing with their target genes further annotated based on both Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases to explore the metabolic pathways and molecular mechanisms underlying the therapeutic effect on hyperuricemia by noni fruit juice. Conclusion Our study provided strong experimental evidence to support the further investigations of the potential application of noni fruit juice in the treatment of hyperuricemia.
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Affiliation(s)
- Yue Liu
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Xianjun Liu
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Mengyuan Wang
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Changwu Chen
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Xiaohong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Zhiyong Liang
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
- Qingdao Haoda Marine Biotechnology Co., Ltd., Qingdao, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
- Key Laboratory for Molecular Enzymology and Engineering, Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Yuhe Yin
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, United States
| | - Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Hao Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
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106
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Bi Y, Liu X, Liu Y, Wang M, Shan Y, Yin Y, Meng X, Sun F, Li H, Li Z. Molecular and biochemical investigations of the anti-fatigue effects of tea polyphenols and fruit extracts of Lycium ruthenicum Murr. on mice with exercise-induced fatigue. Front Mol Biosci 2023; 10:1223411. [PMID: 37416624 PMCID: PMC10319583 DOI: 10.3389/fmolb.2023.1223411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/13/2023] [Indexed: 07/08/2023] Open
Abstract
Background: The molecular mechanisms regulating the therapeutic effects of plant-based ingredients on the exercise-induced fatigue (EIF) remain unclear. The therapeutic effects of both tea polyphenols (TP) and fruit extracts of Lycium ruthenicum (LR) on mouse model of EIF were investigated. Methods: The variations in the fatigue-related biochemical factors, i.e., lactate dehydrogenase (LDH), superoxide dismutase (SOD), tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), interleukin-2 (IL-2), and interleukin-6 (IL-6), in mouse models of EIF treated with TP and LR were determined. The microRNAs involved in the therapeutic effects of TP and LR on the treatment of mice with EIF were identified using the next-generation sequencing technology. Results: Our results revealed that both TP and LR showed evident anti-inflammatory effect and reduced oxidative stress. In comparison with the control groups, the contents of LDH, TNF-α, IL-6, IL-1β, and IL-2 were significantly decreased and the contents of SOD were significantly increased in the experimental groups treated with either TP or LR. A total of 23 microRNAs (21 upregulated and 2 downregulated) identified for the first time by the high-throughput RNA sequencing were involved in the molecular response to EIF in mice treated with TP and LR. The regulatory functions of these microRNAs in the pathogenesis of EIF in mice were further explored based on Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses with a total of over 20,000-30,000 target genes annotated and 44 metabolic pathways enriched in the experimental groups based on GO and KEGG databases, respectively. Conclusion: Our study revealed the therapeutic effects of TP and LR and identified the microRNAs involved in the molecular mechanisms regulating the EIF in mice, providing strong experimental evidence to support further agricultural development of LR as well as the investigations and applications of TP and LR in the treatment of EIF in humans, including the professional athletes.
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Affiliation(s)
- Yingxin Bi
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Xianjun Liu
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Yue Liu
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Mengyuan Wang
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Yaming Shan
- National Engineering Laboratory for AIDS Vaccine, School of Life Sciences, Jilin University, Changchun, China
- Key Laboratory for Molecular Enzymology and Engineering, The Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Yuhe Yin
- School of Chemistry and Life Science, Changchun University of Technology, Changchun, China
| | - Xianglong Meng
- Department of Burns Surgery, The First Hospital of Jilin University, Changchun, China
| | - Fengjie Sun
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA, United States
| | - Hao Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
| | - Zhandong Li
- College of Biological and Food Engineering, Jilin Engineering Normal University, Changchun, China
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107
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Wang X, Lin DH, Yan Y, Wang AH, Liao J, Meng Q, Yang WQ, Zuo H, Hua MM, Zhang F, Zhu H, Zhou H, Huang TY, He R, Li G, Tan YQ, Shi HJ, Gou LT, Li D, Wu L, Zheng Y, Fu XD, Li J, Liu R, Li GH, Liu MF. The PIWI-specific insertion module helps load longer piRNAs for translational activation essential for male fertility. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-023-2390-5. [PMID: 37335463 DOI: 10.1007/s11427-023-2390-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]
Abstract
PIWI-clade proteins harness piRNAs of 24-33 nt in length. Of great puzzles are how PIWI-clade proteins incorporate piRNAs of different sizes and whether the size matters to PIWI/piRNA function. Here we report that a PIWI-Ins module unique in PIWI-clade proteins helps define the length of piRNAs. Deletion of PIWI-Ins in Miwi shifts MIWI to load with shorter piRNAs and causes spermiogenic failure in mice, demonstrating the functional importance of this regulatory module. Mechanistically, we show that longer piRNAs provide additional complementarity to target mRNAs, thereby enhancing the assembly of the MIWI/eIF3f/HuR super-complex for translational activation. Importantly, we identify a c.1108C>T (p.R370W) mutation of HIWI (human PIWIL1) in infertile men and demonstrate in Miwi knock-in mice that this genetic mutation impairs male fertility by altering the property of PIWI-Ins in selecting longer piRNAs. These findings reveal a critical role of PIWI-Ins-ensured longer piRNAs in fine-tuning MIWI/piRNA targeting capacity, proven essential for spermatid development and male fertility.
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Affiliation(s)
- Xin Wang
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Di-Hang Lin
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yue Yan
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - An-Hui Wang
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China
| | - Jiaoyang Liao
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qian Meng
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Wen-Qing Yang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Heng Zuo
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Min-Min Hua
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China
| | - Fengjuan Zhang
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hongwen Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Tian-Yu Huang
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Rui He
- Key Laboratory of Fertility Preservation and Maintenance of Ministry of Education, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, 750004, China
| | - Guangyong Li
- Department of Urology, General Hospital of Ningxia Medical University, Ningxia Medical University, Yinchuan, 750004, China
| | - Yue-Qiu Tan
- Institute of Reproductive and Stem Cell Engineering, College of Basic of Medicine, Central South University, Changsha, 410000, China
| | - Hui-Juan Shi
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China
| | - Lan-Tao Gou
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dangsheng Li
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Ligang Wu
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yonggang Zheng
- Department of Physiology, Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Xiang-Dong Fu
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, 310024, China
| | - Jinsong Li
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Rujuan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Guo-Hui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, China.
| | - Mo-Fang Liu
- Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310024, China.
- State Key Laboratory of Molecular Biology, State Key Laboratory of Cell Biology, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Chen CY, Chao YM, Cho CC, Chen CS, Lin WY, Chen YH, Cassar M, Lu CS, Yang JL, Chan JYH, Juo SHH. Cerebral Semaphorin3D is a novel risk factor for age-associated cognitive impairment. Cell Commun Signal 2023; 21:140. [PMID: 37316917 DOI: 10.1186/s12964-023-01158-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 05/02/2023] [Indexed: 06/16/2023] Open
Abstract
BACKGROUND We previously reported that miR-195 exerts neuroprotection by inhibiting Sema3A and cerebral miR-195 levels decreased with age, both of which urged us to explore the role of miR-195 and miR-195-regulated Sema3 family members in age-associated dementia. METHODS miR-195a KO mice were used to assess the effect of miR-195 on aging and cognitive functions. Sema3D was predicted as a miR-195 target by TargetScan and then verified by luciferase reporter assay, while effects of Sema3D and miR-195 on neural senescence were assessed by beta-galactosidase and dendritic spine density. Cerebral Sema3D was over-expressed by lentivirus and suppressed by si-RNA, and effects of over-expression of Sema3D and knockdown of miR-195 on cognitive functions were assessed by Morris Water Maze, Y-maze, and open field test. The effect of Sema3D on lifespan was assessed in Drosophila. Sema3D inhibitor was developed using homology modeling and virtual screening. One-way and two-way repeated measures ANOVA were applied to assess longitudinal data on mouse cognitive tests. RESULTS Cognitive impairment and reduced density of dendritic spine were observed in miR-195a knockout mice. Sema3D was identified to be a direct target of miR-195 and a possible contributor to age-associated neurodegeneration as Sema3D levels showed age-dependent increase in rodent brains. Injection of Sema3D-expressing lentivirus caused significant memory deficits while silencing hippocampal Sema3D improved cognition. Repeated injections of Sema3D-expressing lentivirus to elevate cerebral Sema3D for 10 weeks revealed a time-dependent decline of working memory. More importantly, analysis of the data on the Gene Expression Omnibus database showed that Sema3D levels were significantly higher in dementia patients than normal controls (p < 0.001). Over-expression of homolog Sema3D gene in the nervous system of Drosophila reduced locomotor activity and lifespan by 25%. Mechanistically, Sema3D might reduce stemness and number of neural stem cells and potentially disrupt neuronal autophagy. Rapamycin restored density of dendritic spines in the hippocampus from mice injected with Sema3D lentivirus. Our novel small molecule increased viability of Sema3D-treated neurons and might improve autophagy efficiency, which suggested Sema3D could be a potential drug target. Video Abstract CONCLUSION: Our results highlight the importance of Sema3D in age-associated dementia. Sema3D could be a novel drug target for dementia treatment.
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Affiliation(s)
- Chien-Yuan Chen
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yung-Mei Chao
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Ching-Chang Cho
- Institute of Translational Medicine and New Drug Development, China Medical University, Taichung, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Cheng-Sheng Chen
- Department of Psychiatry, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Department of Psychiatry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wei-Yong Lin
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan
- Brain Diseases Research Center, China Medical University, Taichung, Taiwan
| | - Yi-Hung Chen
- Graduate Institute of Acupuncture Science, China Medical University, Taichung, Taiwan
- Chinese Medicine Research Center, China Medical University, Taichung, Taiwan
| | - Marlène Cassar
- Formation and Regulation of Neuronal Connectivity Research Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Institut du Cerveau Et de La Moelle Epinière (ICM)-Sorbonne, UniversitéInserm, CNRS, Hôpital Pitié-Salpêtrière, Paris, France
| | - Cecilia S Lu
- Formation and Regulation of Neuronal Connectivity Research Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Jenq-Lin Yang
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Julie Y H Chan
- Institute for Translational Research in Biomedicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Suh-Hang H Juo
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan.
- Institute of Translational Medicine and New Drug Development, China Medical University, Taichung, Taiwan.
- Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
- Drug Development Center, China Medical University, Taichung, Taiwan.
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Morya VK, Lee HW, Park CW, Park CW, Hyun JT, Noh KC. Computational Analysis of miR-140 and miR-135 as Potential Targets to Develop Combinatorial Therapeutics for Degenerative Tendinopathy. Clin Orthop Surg 2023; 15:463-476. [PMID: 37274502 PMCID: PMC10232305 DOI: 10.4055/cios22237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/10/2022] [Accepted: 11/10/2022] [Indexed: 06/06/2023] Open
Abstract
Background Degenerative tendinopathy, a condition causing movement restriction due to high pain, highly impacts productivity and quality of life. The healing process is a complex phenomenon and involves a series of intra-cellular and inter-cellular processes. Proliferation and differentiation of the tenocyte is a major and essential process to heal degenerative tendinopathy. The recent development in microRNA (miRNA)-mediated reprogramming of the cellular function through specific pathways opened door for the development of new regenerative therapeutics. Based on information about gene expression and regulation of tendon injury and healing, we attempted to evaluate the combinatorial effect of selected miRNAs for better healing of degenerative tendinopathy. Methods The present study was designed to evaluate the combinatorial effect of two miRNAs (has-miR-140 and has-miR-135) in the healing process of the tendon. Publicly available information/data were retrieved from appropriate platforms such as PubMed. Only molecular data, directly associated with tendinopathies, including genes/proteins and miRNAs, were used in this study. The miRNAs involved in tendinopathy were analyzed by a Bioinformatics tools (e.g., TargetScan, miRDB, and the RNA22v2). Interactive involvement of the miRNAs with key proteins involved in tendinopathy was predicted by the Insilco approach. Results Based on information available in the public domain, tendon healing-associated miRNAs were predicted to explore their therapeutic potentials. Based on computation analysis, focusing on the potential regulatory effect on tendon healing, the miR-135 and miR-140 were selected for this study. These miRNAs were found as key players in tendon healing through Rho-associated coiled-coil containing protein kinase 1 (ROCK1), IGF-1/PI3K/Akt, PIN, and Wnt signaling pathways. It was also predicted that these miRNAs may reprogram the cells to induce proliferation and differentiation activity. Many miRNAs are likely to regulate genes important for the tendinopathy healing process, and the result of this study allows an approach for miRNA-mediated regeneration of the tenocyte for tendon healing. Based on computational analysis, the role of these miRNAs in different pathways was established, and the results provided insights into the combinatorial approach of miRNA-mediated cell reprogramming. Conclusions In this study, the association between miRNAs and the disease was evaluated to correlate the tendinopathy genes and the relevant role of different miRNAs in their regulation. Through this study, it was established that the synergistic effect of more than one miRNA on directed reprogramming of the cell could be helpful in the regeneration of damaged tissue. It is anticipated that this study will be helpful for the design of miRNA cocktails for the orchestration of cellular reprogramming events.
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Affiliation(s)
- Vivek Kumar Morya
- Department of Orthopaedics, Kangnam Sacred Heart Hospital, Hallym University School of Medicine, Seoul, Korea
| | - Ho-Won Lee
- Department of Orthopaedics, Kangnam Sacred Heart Hospital, Hallym University School of Medicine, Seoul, Korea
| | - Chang-Wook Park
- Department of Orthopaedics, Kangnam Sacred Heart Hospital, Hallym University School of Medicine, Seoul, Korea
| | - Chang-Won Park
- Department of Orthopaedics, Kangnam Sacred Heart Hospital, Hallym University School of Medicine, Seoul, Korea
| | - Jin Tak Hyun
- Department of Orthopaedics, Kangnam Sacred Heart Hospital, Hallym University School of Medicine, Seoul, Korea
| | - Kyu-Cheol Noh
- Department of Orthopaedics, Kangnam Sacred Heart Hospital, Hallym University School of Medicine, Seoul, Korea
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Zhu D, Feng T, Mo N, Han R, Lu W, Cui Z. Eriocheir sinensis feminization-1c ( Fem-1c) and Its Predicted miRNAs Involved in Sexual Development and Regulation. Animals (Basel) 2023; 13:1813. [PMID: 37889731 PMCID: PMC10251896 DOI: 10.3390/ani13111813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 10/29/2023] Open
Abstract
Feminization-1c (Fem-1c) is important for sex differentiation in the model organism Caenorhabditis elegans. In our previous study, the basic molecular characteristics of the Fem-1c gene (EsFem-1c) in Eriocheir sinensis (Henri Milne Edwards, 1854) were cloned to determine the relationship with sex differentiation. In this study, the genomic sequence of EsFem-1c contained five exons and four introns, with an exceptionally long 3'UTR sequence. The qRT-PCR results of EsFem-1c demonstrated lower tissue expression in the androgenic gland of the intersex crab than the normal male crab, implying that EsFem-1c plays a role in crab AG development. RNA interference experiments and morphological observations of juvenile and mature crabs indicated that EsFem-1c influences sexual development in E. sinensis. A dual-luciferase reporter assay disclosed that tcf-miR-315-5p effectively inhibits the translation of the EsFem-1c gene, influencing male development. An intriguing finding was that miRNA tcf-miR-307 could increase EsFem-1c expression by binding to the alternative splicing region with a length of 248 bp (ASR-248) in the 3'UTR sequence. The present research contributes to a better understanding of the molecular regulation mechanism of EsFem-1c and provides a resource for future studies of the miRNA-mediated regulation of sexual development and regulation in E. sinensis.
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Affiliation(s)
- Dandan Zhu
- School of Marine Sciences, Ningbo University, Ningbo 315020, China; (D.Z.)
| | - Tianyi Feng
- School of Marine Sciences, Ningbo University, Ningbo 315020, China; (D.Z.)
| | - Nan Mo
- School of Marine Sciences, Ningbo University, Ningbo 315020, China; (D.Z.)
| | - Rui Han
- School of Marine Sciences, Ningbo University, Ningbo 315020, China; (D.Z.)
| | - Wentao Lu
- School of Marine Sciences, Ningbo University, Ningbo 315020, China; (D.Z.)
| | - Zhaoxia Cui
- School of Marine Sciences, Ningbo University, Ningbo 315020, China; (D.Z.)
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266071, China
- DECAPODA Biology Science and Technology Co., Ltd. (Lianyungang), Lianyungang 222000, China
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111
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Lin BC, Katneni U, Jankowska KI, Meyer D, Kimchi-Sarfaty C. In silico methods for predicting functional synonymous variants. Genome Biol 2023; 24:126. [PMID: 37217943 PMCID: PMC10204308 DOI: 10.1186/s13059-023-02966-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be "silent," but mounting evidence has revealed that these variants can cause RNA and protein changes and are implicated in over 85 human diseases and cancers. Recent improvements in computational platforms have led to the development of numerous machine-learning tools, which can be used to advance synonymous SNV research. In this review, we discuss tools that should be used to investigate synonymous variants. We provide supportive examples from seminal studies that demonstrate how these tools have driven new discoveries of functional synonymous SNVs.
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Affiliation(s)
- Brian C Lin
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Katarzyna I Jankowska
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA.
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112
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Zhuang X, Xie F, Lin Z, Luo J, Chen T, Xi Q, Zhang Y, Sun J. Effect of miR-493-5p on proliferation and differentiation of myoblast by targeting ANKRD17. Cell Tissue Res 2023:10.1007/s00441-023-03777-3. [PMID: 37178193 DOI: 10.1007/s00441-023-03777-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
The hypertrophy and conversion of postnatal muscle fibers largely determine the yield and quality of meat, which is closely related to the economic value of pigs. MicroRNA (miRNA), as a kind of endogenous noncoding RNA molecule, is widely involved in myogenesis of livestock and poultry. The longissimus dorsi tissues of Lantang pigs at 1 and 90 days (LT1D and LT90D) were collected and profiled by miRNA-seq. We found 1871 and 1729 miRNA candidates in LT1D and LT90D samples, and 794 miRNAs were shared. We identified 16 differentially expressed miRNAs between two tested groups and explored the function of miR-493-5p inmyogenesis. The miR-493-5p promoted the proliferation and inhibited the differentiation of myoblasts. Using GO and KEGG analyses of 164 target genes of miR-493-5p, we found that ATP2A2, PPP3CA, KLF15, MED28, and ANKRD17 genes were related to muscle development. RT-qPCR detection showed that the expression level of ANKRD17 was highly expressed in LT1D libraries, and the double luciferase report test preliminarily proved that miR-493-5p and ANKRD17 have a directly targeting relationship. We established miRNA profiles for the longissimus dorsi tissues of 1-day-old and 90-day-old Lantang pigs and found that miR-493-5p was differentially expressed and associated with myogenesis by targeting ANKRD17 gene. Our results should serve as a reference for future studies on pork quality.
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Affiliation(s)
- Xiaona Zhuang
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Fang Xie
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Zekun Lin
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Junyi Luo
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Ting Chen
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Qianyun Xi
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China
| | - Yongliang Zhang
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
| | - Jiajie Sun
- College of Animal Science, Guangdong Provincial Key Laboratory of Animal Nutrition Control, National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou, 510642, Guangdong, China.
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Choi D, Kim J, Yang JW, Kim JH, Park S, Shin JI. Dysregulated MicroRNAs in the Pathogenesis of Systemic Lupus Erythematosus: A Comprehensive Review. Int J Biol Sci 2023; 19:2495-2514. [PMID: 37215992 PMCID: PMC10197884 DOI: 10.7150/ijbs.74315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 12/11/2022] [Indexed: 05/24/2023] Open
Abstract
Systemic lupus erythematosus is a chronic autoimmune disease of which clinical presentation is vastly heterogeneous, ranging from mild skin rashes to severe renal diseases. Treatment goal of this illness is to minimize disease activity and prevent further organ damage. In recent years, much research has been done on the epigenetic aspects of SLE pathogenesis, for among the various factors known to contribute to the pathogenic process, epigenetic factors, especially microRNAs, bear the most therapeutic potential that can be altered unlike congenital genetic factors. This article reviews and updates what has been discovered so far about the pathogenesis of lupus, while focusing on the dysregulation of microRNAs in lupus patients in comparison to healthy controls along with the potentially pathogenic roles of the microRNAs commonly reported to be either upregulated or downregulated. Furthermore, this review includes microRNAs of which results are controversial, suggesting possible explanations for such discrepancies and directions for future research. Moreover, we aimed to emphasize the point that had been overlooked so far in studies regarding microRNA expression levels; that is, which specimen was used to assess the dysregulation of microRNAs. To our surprise, a vast number of studies have not considered this factor and have analyzed the potential role of microRNAs in general. Despite extensive investigations done on microRNA levels, their significance and potential role remain a mystery, which calls for further studies on this particular subject in regard of which specimen is used for assessment.
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Affiliation(s)
- Daeun Choi
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jimin Kim
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Won Yang
- Department of Nephrology, Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Ji Hong Kim
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Seoyeon Park
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
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Dong Y, Gao Q, Chen Y, Zhang Z, Du Y, Liu Y, Zhang G, Li S, Wang G, Chen X, Liu H, Han L, Ye Y. Identification of CircRNA signature associated with tumor immune infiltration to predict therapeutic efficacy of immunotherapy. Nat Commun 2023; 14:2540. [PMID: 37137884 PMCID: PMC10156742 DOI: 10.1038/s41467-023-38232-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Circular RNAs (circRNAs) play important roles in the regulation of cancer. However, the clinical implications and regulatory networks of circRNAs in cancer patients receiving immune checkpoint blockades (ICB) have not been fully elucidated. Here, we characterize circRNA expression profiles in two independent cohorts of 157 ICB-treated advanced melanoma patients and reveal overall overexpression of circRNAs in ICB non-responders in both pre-treatment and early during therapy. Then, we construct circRNA-miRNA-mRNA regulatory networks to reveal circRNA-related signaling pathways in the context of ICB treatment. Further, we construct an ICB-related circRNA signature (ICBcircSig) score model based on progression-free survival-related circRNAs to predict immunotherapy efficacy. Mechanistically, the overexpression of ICBcircSig circTMTC3 and circFAM117B could increase PD-L1 expression via the miR-142-5p/PD-L1 axis, thus reducing T cell activity and leading to immune escape. Overall, our study characterizes circRNA profiles and regulatory networks in ICB-treated patients, and highlights the clinical utility of circRNAs as predictive biomarkers of immunotherapy.
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Affiliation(s)
- Yu Dong
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Furong Laboratory, Changsha, Hunan, 410008, P. R. China
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Lin Gang Laboratory, Shanghai, 200025, China
| | - Qian Gao
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Furong Laboratory, Changsha, Hunan, 410008, P. R. China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, 410008, P. R. China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yong Chen
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, P. R. China
| | - Zhao Zhang
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- MOE Key Laboratory of Metabolism and Molecular Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200433, P. R. China
| | - Yanhua Du
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yuan Liu
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Guangxiong Zhang
- Lin Gang Laboratory, Shanghai, 200025, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, 410008, P. R. China
| | - Shengli Li
- Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, 201620, China
| | - Gaoyang Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xiang Chen
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Furong Laboratory, Changsha, Hunan, 410008, P. R. China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, 410008, P. R. China.
| | - Hong Liu
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Furong Laboratory, Changsha, Hunan, 410008, P. R. China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, 410008, P. R. China.
| | - Leng Han
- Department of Biochemistry and Molecular Biology, McGovern Medical School at The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX, 77030, USA.
- Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX, 77030, USA.
| | - Youqiong Ye
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China.
- Shanghai Institute of Immunology, State Key Laboratory of Oncogenes and Related Genes, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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Vaddi PK, Osborne DG, Nicklawsky A, Williams NK, Menon DR, Smith D, Mayer J, Reid A, Domenico J, Nguyen GH, Robinson WA, Ziman M, Gao D, Zhai Z, Fujita M. CTLA4 mRNA is downregulated by miR-155 in regulatory T cells, and reduced blood CTLA4 levels are associated with poor prognosis in metastatic melanoma patients. Front Immunol 2023; 14:1173035. [PMID: 37197667 PMCID: PMC10183574 DOI: 10.3389/fimmu.2023.1173035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/17/2023] [Indexed: 05/19/2023] Open
Abstract
Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4) is an immune checkpoint expressed in regulatory T (Treg) cells and activated T lymphocytes. Despite its potential as a treatment strategy for melanoma, CTLA-4 inhibition has limited efficacy. Using data from The Cancer Genome Atlas (TCGA) melanoma database and another dataset, we found that decreased CTLA4 mRNA was associated with a poorer prognosis in metastatic melanoma. To investigate further, we measured blood CTLA4 mRNA in 273 whole-blood samples from an Australian cohort and found that it was lower in metastatic melanoma than in healthy controls and associated with worse patient survival. We confirmed these findings using Cox proportional hazards model analysis and another cohort from the US. Fractionated blood analysis revealed that Treg cells were responsible for the downregulated CTLA4 in metastatic melanoma patients, which was confirmed by further analysis of published data showing downregulated CTLA-4 surface protein expression in Treg cells of metastatic melanoma compared to healthy donors. Mechanistically, we found that secretomes from human metastatic melanoma cells downregulate CTLA4 mRNA at the post-transcriptional level through miR-155 while upregulating FOXP3 expression in human Treg cells. Functionally, we demonstrated that CTLA4 expression inhibits the proliferation and suppressive function of human Treg cells. Finally, miR-155 was found to be upregulated in Treg cells from metastatic melanoma patients compared to healthy donors. Our study provides new insights into the underlying mechanisms of reduced CTLA4 expression observed in melanoma patients, demonstrating that post-transcriptional silencing of CTLA4 by miRNA-155 in Treg cells may play a critical role. Since CTLA-4 expression is downregulated in non-responder melanoma patients to anti-PD-1 immunotherapy, targeting miRNA-155 or other factors involved in regulating CTLA4 expression in Treg cells without affecting T cells could be a potential strategy to improve the efficacy of immunotherapy in melanoma. Further research is needed to understand the molecular mechanisms regulating CTLA4 expression in Treg cells and identify potential therapeutic targets for enhancing immune-based therapies.
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Affiliation(s)
- Prasanna Kumar Vaddi
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Douglas Grant Osborne
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Andrew Nicklawsky
- University of Colorado Cancer Center Biostatistics Core, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Nazanin K. Williams
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Dinoop Ravindran Menon
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Derek Smith
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jonathan Mayer
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Anna Reid
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Joanne Domenico
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Giang Huong Nguyen
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - William A. Robinson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melanie Ziman
- School of Medical and Health Sciences, Edith Cowan University, Perth, WA, Australia
- School of Biomedical Science, University of Western Australia, Perth, WA, Australia
| | - Dexiang Gao
- University of Colorado Cancer Center Biostatistics Core, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Zili Zhai
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Mayumi Fujita
- Department of Dermatology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Immunology, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Veterans Affairs Medical Center, VA Eastern Colorado Health Care System, Aurora, CO, United States
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116
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Zhao L, Zhang G, Tang A, Huang B, Mi D. Microgravity alters the expressions of DNA repair genes and their regulatory miRNAs in space-flown Caenorhabditis elegans. LIFE SCIENCES IN SPACE RESEARCH 2023; 37:25-38. [PMID: 37087176 DOI: 10.1016/j.lssr.2023.02.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 05/03/2023]
Abstract
During spaceflight, multiple unique hazardous factors, particularly microgravity and space radiation, can induce different types of DNA damage, which pose a constant threat to genomic integrity and stability of living organisms. Although organisms have evolved different kinds of conserved DNA repair pathways to eliminate this DNA damage on Earth, the impact of space microgravity on the expressions of these DNA repair genes and their regulatory miRNAs has not been fully explored. In this study, we integrated all existing datasets, including both transcriptional and miRNA microarrays in wild-type (WT) Caenorhabditis elegans that were exposed to the treatments of spaceflight (SF), spaceflight control with a 1g centrifugal device (SC), and ground control (GC) in three space experiments with the periods of 4, 8 and 16.5 days. The results of principal component analysis showed the gene expression patterns for five major DNA repair pathways (i.e., non-homologous end joining (NHEJ), homologous recombination (HR), mismatch repair (MMR), nucleotide excision repair (NER), and base excision repair (BER)) were well separated and clustered between SF/GC and SC/GC treatments after three spaceflights. In the 16.5-days space experiment, we also selected the datasets of dys-1 mutant and ced-1 mutant of C. elegans, which respectively presented microgravity-insensitivity and radiosensitivity. Compared to the WT C. elegans flown in the 16.5-days spaceflight, the separation distances between SF and SC samples were significantly reduced in the dys-1 mutant, while greatly enhanced in the ced-1 mutant for five DNA repair pathways. By comparing the results of differential expression analysis in SF/GC versus SC/GC samples, we found the DNA repair genes annotated in the pathways of BER and NER were prominently down-regulated under microgravity during both the 4- and 8-days spaceflights. While, under microgravity, the genes annotated in MMR were dominatingly up-regulated during the 4-days spaceflight, and those annotated in HR were mainly up-regulated during the 8-days spaceflight. And, most of the DNA repair genes annotated in the pathways of BER, NER, MMR, and HR were up-regulated under microgravity during the 16.5-days spaceflight. Using miRNA-mRNA integrated analysis, we determined the regulatory networks of differentially expressed DNA repair genes and their regulatory miRNAs in WT C. elegans after three spaceflights. Compared to GC conditions, the differentially expressed miRNAs were analyzed under SF and SC treatments of three spaceflights, and some altered miRNAs that responded to SF and SC could regulate the expressions of corresponding DNA repair genes annotated in different DNA repair pathways. In summary, these findings indicate that microgravity can significantly alter the expression patterns of DNA repair genes and their regulatory miRNAs in space-flown C. elegans. The alterations of the expressions of DNA repair genes and the dominating DNA repair pathways under microgravity are possibly related to the spaceflight period. In addition, the key miRNAs are identified as the post-transcriptional regulators to regulate the expressions of various DNA repair genes under microgravity. These altered miRNAs that responded to microgravity can be implicated in regulating diverse DNA repair processes in space-flown C. elegans.
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Affiliation(s)
- Lei Zhao
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China.
| | - Ge Zhang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Aiping Tang
- College of Science, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Baohang Huang
- Institute of Environmental Systems Biology, College of Environmental Science and Engineering, Dalian Maritime University, Dalian 116026, Liaoning, China
| | - Dong Mi
- College of Science, Dalian Maritime University, Dalian 116026, Liaoning, China
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117
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Su D, Swearson S, Krongbaramee T, Sun H, Hong L, Amendt BA. Exploring microRNAs in craniofacial regenerative medicine. Biochem Soc Trans 2023; 51:841-854. [PMID: 37073783 PMCID: PMC11244734 DOI: 10.1042/bst20221448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/20/2023]
Abstract
microRNAs (miRs) have been reported over the decades as important regulators in bone development and bone regeneration. They play important roles in maintaining the stem cell signature as well as regulating stem cell fate decisions. Thus, delivering miRs and miR inhibitors to the defect site is a potential treatment towards craniofacial bone defects. However, there are challenges in translation of basic research to clinics, including the efficiency, specificity, and efficacy of miR manipulation methods and the safety of miR delivery systems. In this review, we will compare miR oligonucleotides, mimics and antagomirs as therapeutic reagents to treat disease and regenerate tissues. Newer technology will be discussed as well as the efficiency and efficacy of using these technologies to express or inhibit miRs in treating and repairing oral tissues. Delivery of these molecules using extracellular vesicles and nanoparticles can achieve different results and depending on their composition will elicit specific effects. We will highlight the specificity, toxicity, stability, and effectiveness of several miR systems in regenerative medicine.
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Affiliation(s)
- Dan Su
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, U.S.A
- Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA, U.S.A
| | - Samuel Swearson
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, U.S.A
| | - Tadkamol Krongbaramee
- Iowa Institute for Oral Health Research, The University of Iowa, Iowa City, IA, U.S.A
- Division of Endodontics, Department of Restorative Dentistry & Periodontology, Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
| | - Hongli Sun
- Iowa Institute for Oral Health Research, The University of Iowa, Iowa City, IA, U.S.A
| | - Liu Hong
- Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA, U.S.A
- Iowa Institute for Oral Health Research, The University of Iowa, Iowa City, IA, U.S.A
| | - Brad A Amendt
- Department of Anatomy and Cell Biology, The University of Iowa, Iowa City, IA, U.S.A
- Craniofacial Anomalies Research Center, The University of Iowa, Iowa City, IA, U.S.A
- Iowa Institute for Oral Health Research, The University of Iowa, Iowa City, IA, U.S.A
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118
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Liang X, Zhang Y, Jiao Y, Mai J, Deng Y, Du X. Identification and comparative analysis of miRNA transcriptomes after allograft and xenograft transplantation in Pinctada fucata martensii. FISH & SHELLFISH IMMUNOLOGY 2023; 137:108752. [PMID: 37080325 DOI: 10.1016/j.fsi.2023.108752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 05/03/2023]
Abstract
Effective immune regulation after transplantation during pearl production is crucial for the cultivation of high-quality pearls. MicroRNAs (miRNAs) play an important role in a variety of physiological processes. To understand the regulatory rules of miRNAs after transplantation in Pinctada funcata martensii, we constructed 13 miRNA transcriptomes, including the control group (Con), allograft (Al), and xenograft (Xe) transplantation at six time points (6, 12, and 24 h and 3, 6, and 12 days), in which the xenografted mantle tissue was from Pinctada maxima. We identified 159 differentially expressed miRNAs (DEMs) and found that these DEMs showed high expression at 12 h, 24 h, and 3 days after transplantation. A total of 130 DEMs, such as Let-7, were present in the Al and Xe groups; miR-34 and 16 other DEMs were specifically present in the Al group; miR-216b and 13 other DEMs were specifically present in the Xe group. Compared with the Con group, the target genes of DEMs in the Al group were significantly enriched in protein complex, cytoskeleton, and macromolecular complex, and the Xe group was significantly enriched in ribonucleoside metabolic process, nucleoside binding, and cell division. Compared with the Al group, the target genes in the Xe group were significantly enriched in response to DNA damage stimulation. Overall, multiple pathways associated with cellular activity were enriched in higher numbers of genes in the Xe group than in the Al group. These findings enriched the information on immune regulatory mechanisms at the expression level of miRNAs in P. f. martensii after transplantation.
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Affiliation(s)
- Xueru Liang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuting Zhang
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yu Jiao
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China.
| | - Jieni Mai
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China
| | - Yuewen Deng
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China; Guangdong Provincial Key Laboratory of Pathogenic Biology and Epidemiology for Aquatic Economic Animals, Zhanjiang, 524088, China
| | - Xiaodong Du
- Fishery College, Guangdong Ocean University, Zhanjiang, 524025, China; Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province, Zhanjiang, 524088, China; Guangdong Science and Innovation Center for Pearl Culture, Zhanjiang, 524088, China
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119
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Wang X, Huang P, Lei M, Ma Y, Chen H, Sun J, Hu Y, Shi J. Global expression and functional analysis of human piRNAs during HSV-1 infection. Virus Res 2023; 328:199087. [PMID: 36894069 DOI: 10.1016/j.virusres.2023.199087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/18/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are a class of non-coding RNAs that play a key role in spermatogenesis. However, little is known about their expression characterization and role in somatic cells infected with herpes simplex virus type 1 (HSV-1). In this study, we systematically investigated the cellular piRNA expression profiles of HSV-1-infected human lung fibroblasts. Compared with the control group, 69 differentially expressed piRNAs were identified in the infection group, among which 52 were up-regulated and 17 were down-regulated. The changes in the expression of 8 piRNAs were further verified by RT-qPCR with a similar expression trend. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the target genes of piRNAs were mainly involved in antiviral immunity and various human disease-related signaling pathways. Furthermore, we tested the effects of four up-regulated piRNAs on viral replication by transfecting piRNA mimics. The results showed that the virus titers of the group transfected with piRNA-hsa-28,382 (alias piR-36,233) mimic decreased significantly, and that of the group transfected piRNA-hsa-28,190 (alias piR-36,041) mimic significantly increased. Overall, our results revealed the expression characteristics of piRNAs in HSV-1-infected cells. We also screened two piRNAs that potentially regulate HSV-1 replication. These results may promote a better understanding of the regulatory mechanism of pathophysiological changes induced by HSV-1 infection.
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Affiliation(s)
- Xu Wang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Pu Huang
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Mengyue Lei
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Ying Ma
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China
| | - Hongli Chen
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China; Kunming Medical University, Kunming, Yunnan, China
| | - Jing Sun
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Yunzhang Hu
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
| | - Jiandong Shi
- Yunnan Provincial Key Laboratory of Vector-borne Diseases Control and Research, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan, China.
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120
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Zhang C, Liu P, Sun L, Cao C. Integration of miRNA and mRNA expression profiles in Asian spongy moth Lymantria dispar in response to cyantraniliprole. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105364. [PMID: 36963953 DOI: 10.1016/j.pestbp.2023.105364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 06/18/2023]
Abstract
The Asian spongy moth, Lymantria dispar, is a worldwide forest pest that damages >500 plant species. Nowadays, chemical control is the most widely used method because of its rapidity and effectiveness, but the insecticide resistance is a growing concern for spongy moth. As important post-transcriptional regulators of gene expression, whether microRNAs (miRNAs) are involved in insecticide tolerance is little known in spongy moth. Therefore, an integrated analysis of miRNA and mRNA was performed on L. dispar larvae treated with cyantraniliprole. Compared to the control group, a total of 432 differentially expressed genes (DEGs) and 23 differentially expressed miRNAs (DEMs) were identified in L. dispar larvae under cyantraniliprole exposure. Among them, twelve DEGs encoding detoxification enzymes/proteins were further analyzed. Twenty-one genes related to insecticide tolerance were predicted by 11 DEMs, of which 25 miRNA-mRNA interactions were identified. In the miRNA-mRNA network, novel-miR-4 and mmu-miR-3475-3p were involved in the response of L. dispar to cyantraniliprole stress by regulating five genes associated with detoxification, respectively. The P450 gene CYP4C1 (c34384.graph_c0) was the only DEG related to detoxification in the network, which was regulated by novel-miR-4. The expression levels of ten DEMs were confirmed by quantitative reverse transcription PCR (RT-qPCR) and the trends were consistent with miRNA-seq. This study identified some candidate miRNAs and mRNAs related to cyantraniliprole tolerance in L. dispar, which provides valuable transcriptomic information for revealing the molecular mechanisms of insect tolerance and developing novel insecticides.
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Affiliation(s)
- Chenshu Zhang
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, PR China
| | - Peng Liu
- Jinan State-Owned Liubu Forest Farms, Jinan 250100, PR China
| | - Lili Sun
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, PR China.
| | - Chuanwang Cao
- Key Laboratory of Sustainable Forest Ecosystem Management-Ministry of Education, Northeast Forestry University, Harbin 150040, PR China.
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121
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Tang X, Fu J, Yao Y, Xu M. Identification and characterization of immune-related microRNAs in hybrid snakehead(Channa maculata♀ × Channa argus♂)after treated by Echinacea purpurea (Linn.) Moench. FISH & SHELLFISH IMMUNOLOGY 2023; 135:108653. [PMID: 36868540 DOI: 10.1016/j.fsi.2023.108653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Echinacea purpurea (Linn.) Moench (EP) is a globally popular herbal medicine, which showed effects on growth promotion, antioxidant and immunomodulatory activities in fish culture world widely. However, there are few studies about the effects on miRNAs by EP in fish. The hybrid snakehead fish (Channa maculate♀ × Channa argus ♂) was new important economic specie of freshwater aquaculture in China with high market value and demand while there were only a few reports about its miRNAs. To overview immune-related miRNAs of the hybrid snakehead fish and to further understand the immune regulating mechanism of EP, we herein constructed and analyzed three small RNA libraries of immune tissues including liver, spleen and head kidney of the fish with or without EP treatment via Illumina high-throughput sequencing technology. Results showed that EP can affect the immune activities of fish by the miRNA-regulated ways. Totally, 67 (47 up and 20 down) miRNAs in liver, 138 (55 up and 83 down) miRNAs in spleen, and 251 (15 up and 236 down) miRNAs in spleen were detected, as well as 30, 60, 139 kinds of immune-related miRNAs belonging to 22, 35 and 66 families of the three tissues respectively. The expressions of 8 immune-related miRNA family members were found in all the three tissues, including miR-10, miR-133, miR-22 and etc. Some miRNAs have been identified involved in the innate and adaptive immune responses, such as the miR-125, miR-138, and miR-181 family. Ten miRNA families with antioxidant target genes were also discovered, including miR-125, miR-1306, and miR-138, etc. Results from Gene Ontology (GO) and KEGG pathway analysis further confirmed there are a majority immune response targets of the miRNAs involved in the EP treatment process. Our study deepened understanding roles of miRNAs in fish immune system and provides new ideas for the study of immune mechanism of EP.
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Affiliation(s)
- Xuelian Tang
- School of Biological Science and Technology, University of Jinan, Jinan, 250022, China.
| | - Jinghua Fu
- College of Marine Science, South China Agricultural University, Guangzhou, 510642, China
| | - Ya Yao
- College of Marine Science, South China Agricultural University, Guangzhou, 510642, China
| | - Minjun Xu
- College of Marine Science, South China Agricultural University, Guangzhou, 510642, China; State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China.
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122
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Liu X, Dou B, Tang W, Yang H, Chen K, Wang Y, Qin J, Yang F. Cardioprotective effects of circ_0002612 in myocardial ischemia/reperfusion injury correlate with disruption of miR-30a-5p-dependent Ppargc1a inhibition. Int Immunopharmacol 2023; 117:110006. [PMID: 37012879 DOI: 10.1016/j.intimp.2023.110006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 02/19/2023] [Accepted: 03/06/2023] [Indexed: 03/14/2023]
Abstract
INTRODUCTION Novel mechanistic insights into the effects of circular RNAs (circRNAs) on the physiology and pathology of cardiovascular diseases are under increasingly active investigation. This study defined the cardioprotective role and mechanistic actions of circ_0002612 in myocardial ischemia/reperfusion injury (MI/RI). METHODS MI/RI was induced in mice by ligation of the left anterior descending (LAD) artery followed by reperfusion, and the in vitro model was established in cultured cardiomyocytes under hypoxia/reoxygenation (H/R) conditions. Interaction among circ_0002612, miR-30a-5p, Ppargc1a, and NLRP3 was predicted by bioinformatics analysis and further experimentally identified. Gain- and loss-of-function experiments were performed to evaluate the effect of the circ_0002612/miR-30a-5p/Ppargc1a/NLRP3 axis on the cardiac function and myocardial infarction of I/R-injured mice, as well as viability and apoptosis of H/R-challenged cardiomyocytes. RESULTS In the myocardial tissues of MI/RI mice, miR-30a-5p was negatively correlated with circ_0002612 or Ppargc1a, but circ_0002612 was positively correlated with the expression of Ppargc1a. circ_0002612 competitively bound to miR-30a-5p to release expression of its target gene Ppargc1a. circ_0002612 promoted cardiomyocyte viability while suppressing the apoptosis by impairing the miR-30a-5p-mediated inhibition of Ppargc1a. Additionally, Ppargc1a inhibited the expression of NLRP3 and consequently facilitated cardiomyocyte proliferation while suppressing cell apoptosis. By inhibiting the expression of NLRP3, circ_0002612 protected mice from MI/RI. CONCLUSION Overall, this study demonstrates the cardioprotective role of circ_0002612 against MI/RI, which may be a viable target for MI/RI.
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Liu Y, Xing K, Ao H, Zhang F, Zhao X, Liu H, Shi Y, Yu Y, Wang C. Competing endogenous RNA network construction based on long non-coding RNAs, microRNAs, and mRNAs related to fat deposition in Songliao black swine. Anim Genet 2023; 54:132-143. [PMID: 36596449 DOI: 10.1111/age.13283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 10/19/2022] [Accepted: 11/24/2022] [Indexed: 01/05/2023]
Abstract
China has a long history of pig breeding and a number of local breeds. The Songliao Black pig, bred in China in 2009, shows high variation in backfat thickness and therefore is well-suited to fat deposition research. Fat deposition is a complex trait, and the underlying regulatory factors are not fully characterized. In this study, the molecular basis of fat deposition traits was evaluated by comparisons between three individuals with extremely high-backfat thickness and three with extremely low-backfat thickness selected from 53 gilts. Subcutaneous adipose tissues of the back were collected for strand-specific library RNA sequencing (RNA-seq) and small RNA-seq. We identified 13 184 mRNAs, 2046 long non-coding (lnc)RNAs, and 494 micro (mi)RNAs by high-throughput sequencing. Furthermore, we detected 150 differentially expressed mRNAs, 66 differentially expressed lncRNAs, and eight differentially expressed miRNAs. A functional enrichment analysis indicated that these genes are involved in multiple fat metabolism-related pathways, including positive regulation of fat cell differentiation, and fat digestion and absorption. We used various algorithms (miRanda, TargetScan, and RNAhybrid) to predict targeting relationships and constructed a competing endogenous RNA network containing seven lncRNAs, three miRNAs, and six mRNAs. All these genes were differentially expressed between the extremely high and low backfat thickness groups or enriched in pathways related to fat metabolism. Our results provide insight into the regulatory mechanisms by which non-coding RNAs and their target genes influence backfat deposition in pigs. Furthermore, our newly constructed competing endogenous RNA (lncRNA-miRNA-mRNA) network provides a basis for further exploration of fat deposition traits and non-coding RNA functions.
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Affiliation(s)
- Yibing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kai Xing
- Animal Science and Technology College, Beijing University of Agriculture, Beijing, China
| | - Hong Ao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fengxia Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xitong Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Huatao Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yong Shi
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chuduan Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Zhu MX, Zhao TY, Li Y. Insight into the mechanism of DNA methylation and miRNA-mRNA regulatory network in ischemic stroke. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:10264-10283. [PMID: 37322932 DOI: 10.3934/mbe.2023450] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Epigenetic changes, such as DNA methylation and miRNA-target gene mechanisms, have recently emerged as key provokers in Ischemic stroke (IS) onset. However, cellular and molecular events harboring these epigenetic alterations are poorly understood. Therefore, the present study aimed to explore the potential biomarkers and therapeutic targets for IS. METHODS miRNAs, mRNAs and DNA methylation datasets of IS were derived from the GEO database and normalized by PCA sample analysis. Differentially expressed genes (DEGs) were identified, and GO and KEGG enrichment analyses were performed. The overlapped genes were utilized to construct a protein-protein interaction network (PPI). Meanwhile, differentially expressed mRNAs and miRNAs interaction pairs were obtained from the miRDB, TargetScan, miRanda, miRMap and miTarBase databases. We constructed differential miRNA-target gene regulatory networks based on mRNA-miRNA interactions. RESULTS A total of 27 up-regulated and 15 down-regulated differential miRNAs were identified. Dataset analysis identified 1053 and 132 up-regulated and 1294 and 9068 down-regulated differentially expressed genes in the GSE16561 and GSE140275 datasets, respectively. Moreover, 9301 hypermethylated and 3356 hypomethylated differentially methylated sites were also identified. Moreover, DEGs were enriched in terms related to translation, peptide biosynthesis, gene expression, autophagy, Th1 and Th2 cell differentiation, primary immunodeficiency, oxidative phosphorylation and T cell receptor signaling pathway. MRPS9, MRPL22, MRPL32 and RPS15 were identified as hub genes. Finally, a differential miRNA-target gene regulatory network was constructed. CONCLUSIONS RPS15, along with hsa-miR-363-3p and hsa-miR-320e have been identified in the differential DNA methylation protein interaction network and miRNA-target gene regulatory network, respectively. These findings strongly posit the differentially expressed miRNAs as potential biomarkers to improve ischemic stroke diagnosis and prognosis.
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Affiliation(s)
- Ming-Xi Zhu
- Department of Anatomy, School of Basic Medicine and Life Science, Hainan Medical University, 3 College Road, Hainan 571199, China
| | - Tian-Yang Zhao
- Department of Anesthesia, The 4th Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Harbin 150001, China
| | - Yan Li
- Department of Anesthesia, The 4th Affiliated Hospital of Harbin Medical University, 37 Yiyuan Street, Harbin 150001, China
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Prabhu SR, Ware AP, Umakanth S, Hande M, Mahabala C, Saadi AV, Satyamoorthy K. Erythrocyte miRNA-92a-3p interactions with PfEMP1 as determinants of clinical malaria. Funct Integr Genomics 2023; 23:93. [PMID: 36941394 PMCID: PMC10027640 DOI: 10.1007/s10142-023-01028-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/06/2023] [Accepted: 03/13/2023] [Indexed: 03/22/2023]
Abstract
Based on the recently added high throughput analysis data on small noncoding RNAs in modulating disease pathophysiology of malaria, we performed an integrative computational analysis for exploring the role of human-host erythrocytic microRNAs (miRNAs) and their influence on parasite survival and host homeostasis. An in silico analysis was performed on transcriptomic datasets accessed from PlasmoDB and Gene Expression Omnibus (GEO) repositories analyzed using miRanda, miRTarBase, mirDIP, and miRDB to identify the candidate miRNAs that were further subjected to network analysis using MCODE and DAVID. This was followed by immune infiltration analysis and screening for RNA degradation mechanisms. Seven erythrocytic miRNAs, miR-451a, miR-92a-3p, miR-16-5p, miR-142-3p, miR-15b-5p, miR-19b-3p, and miR-223-3p showed favourable interactions with parasite genes expressed during blood stage infection. The miR-92a-3p that targeted the virulence gene PfEMP1 showed drastic reduction during infection. Performing pathway analysis for the human-host gene targets for the miRNA identified TOB1, TOB2, CNOT4, and XRN1 genes that are associated to RNA degradation processes, with the exoribonuclease XRN1, highly enriched in the malarial samples. On evaluating the role of exoribonucleases in miRNA degradation further, the pattern of Plasmodium falciparum_XRN1 showed increased levels during infection thus suggesting a defensive role for parasite survival. This study identifies miR-92a-3p, a member of C13orf25/ miR-17-92 cluster, as a novel miRNA inhibitor of the crucial parasite genes responsible for symptomatic malaria. Evidence for a plausible link to chromosome 13q31.3 loci controlling the epigenetic disease regulation is also suggested.
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Affiliation(s)
- Sowmya R Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Akshay Pramod Ware
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Shashikiran Umakanth
- Department of Medicine, Dr. TMA Pai Hospital, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Manjunath Hande
- Department of Medicine, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Chakrapani Mahabala
- Department of Medicine, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Abdul Vahab Saadi
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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126
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Fei X, Jin M, Yuan Z, Li T, Lu Z, Wang H, Lu J, Quan K, Yang J, He M, Wang T, Wang Y, Wei C. MiRNA-Seq reveals key MicroRNAs involved in fat metabolism of sheep liver. Front Genet 2023; 14:985764. [PMID: 36968587 PMCID: PMC10035661 DOI: 10.3389/fgene.2023.985764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 02/27/2023] [Indexed: 03/11/2023] Open
Abstract
There is a genetic difference between Hu sheep (short/fat-tailed sheep) and Tibetan sheep (short/thin-tailed sheep) in tail type, because of fat metabolism. Previous studies have mainly focused directly on sheep tail fat, which is not the main organ of fat metabolism. The function of miRNAs in sheep liver fat metabolism has not been thoroughly elucidated. In this study, miRNA-Seq was used to identify miRNAs in the liver tissue of three Hu sheep (short/fat-tailed sheep) and three Tibetan sheep (short/thin-tailed sheep) to characterize the differences in fat metabolism of sheep. In our study, Hu sheep was in a control group, we identified 11 differentially expressed miRNAs (DE miRNAs), including six up-regulated miRNAs and five down-regulated miRNAs. Miranda and RNAhybrid were used to predict the target genes of DE miRNAs, obtaining 3,404 target genes. A total of 115 and 67 GO terms as well as 54 and 5 KEGG pathways were significantly (padj < 0.05) enriched for predicted 3,109 target genes of up-regulated and 295 target genes of down-regulated miRNAs, respectively. oar-miR-432 was one of the most up-regulated miRNAs between Hu sheep and Tibetan sheep. And SIRT1 is one of the potential target genes of oar-miR-432. Furthermore, functional validation using the dual-luciferase reporter assay indicated that the up-regulated miRNA; oar-miR-432 potentially targeted sirtuin 1 (SIRT1) expression. Then, the oar-miR-432 mimic transfected into preadipocytes resulted in inhibited expression of SIRT1. This is the first time reported that the expression of SIRT1 gene was regulated by oar-miR-432 in fat metabolism of sheep liver. These results could provide a meaningful theoretical basis for studying the fat metabolism of sheep.
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Affiliation(s)
- Xiaojuan Fei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Meilin Jin
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Taotao Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Huihua Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jian Lu
- National Animal Husbandry Service, Beijing, China
| | - Kai Quan
- College of Animals Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Junxiang Yang
- Gansu Institute of Animal Husbandry and Veterinary Medicine, Pingliang, China
| | - Maochang He
- Gansu Institute of Animal Husbandry and Veterinary Medicine, Pingliang, China
| | - Tingpu Wang
- College of Bioengineering and Biotechnology, TianShui Normal University, Tianshui, China
| | - Yuqin Wang
- College of Animals Science and Technology, Henan University of Science and Technology, Luoyang, China
- *Correspondence: Caihong Wei, ; Yuqin Wang,
| | - Caihong Wei
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Caihong Wei, ; Yuqin Wang,
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127
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Homberg N, Galvão Ferrarini M, Gaspin C, Sagot MF. MicroRNA Target Identification: Revisiting Accessibility and Seed Anchoring. Genes (Basel) 2023; 14:genes14030664. [PMID: 36980936 PMCID: PMC10048102 DOI: 10.3390/genes14030664] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/23/2023] [Accepted: 03/04/2023] [Indexed: 03/09/2023] Open
Abstract
By pairing to messenger RNAs (mRNAs for short), microRNAs (miRNAs) regulate gene expression in animals and plants. Accurately identifying which mRNAs interact with a given miRNA and the precise location of the interaction sites is crucial to reaching a more complete view of the regulatory network of an organism. Only a few experimental approaches, however, allow the identification of both within a single experiment. Computational predictions of miRNA–mRNA interactions thus remain generally the first step used, despite their drawback of a high rate of false-positive predictions. The major computational approaches available rely on a diversity of features, among which anchoring the miRNA seed and measuring mRNA accessibility are the key ones, with the first being universally used, while the use of the second remains controversial. Revisiting the importance of each is the aim of this paper, which uses Cross-Linking, Ligation, And Sequencing of Hybrids (CLASH) datasets to achieve this goal. Contrary to what might be expected, the results are more ambiguous regarding the use of the seed match as a feature, while accessibility appears to be a feature worth considering, indicating that, at least under some conditions, it may favour anchoring by miRNAs.
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Affiliation(s)
- Nicolas Homberg
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, 69622 Villeurbanne, France
- INRIA Lyon Centre, 69100 Villeurbanne, France
- UR0875 MIAT, INRAE, Université de Toulouse, 31326 Castanet-Tolosan, France
| | - Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, 69622 Villeurbanne, France
- INRIA Lyon Centre, 69100 Villeurbanne, France
| | - Christine Gaspin
- UR0875 MIAT, INRAE, Université de Toulouse, 31326 Castanet-Tolosan, France
- Correspondence: (C.G.); (M.-F.S.)
| | - Marie-France Sagot
- Laboratoire de Biométrie et Biologie Evolutive, Université de Lyon, CNRS, UMR5558, 69622 Villeurbanne, France
- INRIA Lyon Centre, 69100 Villeurbanne, France
- Correspondence: (C.G.); (M.-F.S.)
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128
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Fan R, Hilfinger A. The effect of microRNA on protein variability and gene expression fidelity. Biophys J 2023; 122:905-923. [PMID: 36698314 PMCID: PMC10027439 DOI: 10.1016/j.bpj.2023.01.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 12/23/2022] [Accepted: 01/20/2023] [Indexed: 01/27/2023] Open
Abstract
Small regulatory RNA molecules such as microRNA modulate gene expression through inhibiting the translation of messenger RNA (mRNA). Such posttranscriptional regulation has been recently hypothesized to reduce the stochastic variability of gene expression around average levels. Here, we quantify noise in stochastic gene expression models with and without such regulation. Our results suggest that silencing mRNA posttranscriptionally will always increase, rather than decrease, gene expression noise when the silencing of mRNA also increases its degradation, as is expected for microRNA interactions with mRNA. In that regime, we also find that silencing mRNA generally reduces the fidelity of signal transmission from deterministically varying upstream factors to protein levels. These findings suggest that microRNA binding to mRNA does not generically confer precision to protein expression.
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Affiliation(s)
- Raymond Fan
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical & Physical Sciences, University of Toronto, Mississauga, Ontario, Canada.
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, Ontario, Canada; Department of Chemical & Physical Sciences, University of Toronto, Mississauga, Ontario, Canada; Department of Cell & Systems Biology, University of Toronto, , Toronto, Ontario, Canada; Department of Mathematics, University of Toronto, Toronto, Ontario, Canada
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Luo YM, Yang SD, Wen MY, Wang B, Liu JH, Li ST, Li YY, Cheng H, Zhao LL, Li SM, Jiang JJ. Insights into the mechanisms of triptolide nephrotoxicity through network pharmacology-based analysis and RNA-seq. FRONTIERS IN PLANT SCIENCE 2023; 14:1144583. [PMID: 36959927 PMCID: PMC10027700 DOI: 10.3389/fpls.2023.1144583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Triptolide (TPL) is a promising plant-derived compound for clinical therapy of multiple human diseases; however, its application was limited considering its toxicity. METHODS To explore the underlying molecular mechanism of TPL nephrotoxicity, a network pharmacology based approach was utilized to predict candidate targets related with TPL toxicity, followed by deep RNA-seq analysis to characterize the features of three transcriptional elements include protein coding genes (PCGs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs) as well as their associations with nephrotoxicity in rats with TPL treatment. RESULTS & DISCUSSION Although the deeper mechanisms of TPL nephrotoxcity remain further exploration, our results suggested that c-Jun is a potential target of TPL and Per1 related circadian rhythm signaling is involved in TPL induced renal toxicity.
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Affiliation(s)
- Yue-Ming Luo
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Shu-Dong Yang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Miao-Yu Wen
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Bing Wang
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Jia-Hui Liu
- Department of Nephrology, Shenzhen Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Si-Ting Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yu-Yan Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Hong Cheng
- Department of Geriatrics, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Li-Li Zhao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Graduate school of Clinical Medicine, Anhui Medical University, Hefei, China
| | - Shun-Min Li
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Jian-Jun Jiang
- Department of Nephrology, Shenzhen Traditional Chinese Medicine Hospital, The Fourth Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
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130
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Rayford KJ, Cooley A, Strode AW, Osi I, Arun A, Lima MF, Misra S, Pratap S, Nde PN. Trypanosoma cruzi dysregulates expression profile of piRNAs in primary human cardiac fibroblasts during early infection phase. Front Cell Infect Microbiol 2023; 13:1083379. [PMID: 36936778 PMCID: PMC10017870 DOI: 10.3389/fcimb.2023.1083379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/13/2023] [Indexed: 03/06/2023] Open
Abstract
Trypanosoma cruzi, the etiological agent of Chagas Disease, causes severe morbidity, mortality, and economic burden worldwide. Though originally endemic to Central and South America, globalization has led to increased parasite presence in most industrialized countries. About 40% of infected individuals will develop cardiovascular, neurological, and/or gastrointestinal pathologies. Accumulating evidence suggests that the parasite induces alterations in host gene expression profiles in order to facilitate infection and pathogenesis. The role of regulatory gene expression machinery during T. cruzi infection, particularly small noncoding RNAs, has yet to be elucidated. In this study, we aim to evaluate dysregulation of a class of sncRNAs called piRNAs during early phase of T. cruzi infection in primary human cardiac fibroblasts by RNA-Seq. We subsequently performed in silico analysis to predict piRNA-mRNA interactions. We validated the expression of these selected piRNAs and their targets during early parasite infection phase by stem loop qPCR and qPCR, respectively. We found about 26,496,863 clean reads (92.72%) which mapped to the human reference genome. During parasite challenge, 441 unique piRNAs were differentially expressed. Of these differentially expressed piRNAs, 29 were known and 412 were novel. In silico analysis showed several of these piRNAs were computationally predicted to target and potentially regulate expression of genes including SMAD2, EGR1, ICAM1, CX3CL1, and CXCR2, which have been implicated in parasite infection, pathogenesis, and various cardiomyopathies. Further evaluation of the function of these individual piRNAs in gene regulation and expression will enhance our understanding of early molecular mechanisms contributing to infection and pathogenesis. Our findings here suggest that piRNAs play important roles in infectious disease pathogenesis and can serve as potential biomarkers and therapeutic targets.
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Affiliation(s)
- Kayla J. Rayford
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Ayorinde Cooley
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Anthony W. Strode
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Inmar Osi
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Ashutosh Arun
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
| | - Maria F. Lima
- Biomedical Sciences, School of Medicine, City College of New York, New York, NY, United States
| | - Smita Misra
- School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, United States
| | - Siddharth Pratap
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
- Bioinformatics Core, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, United States
| | - Pius N. Nde
- Department of Microbiology, Immunology, and Physiology, Meharry Medical College, Nashville, TN, United States
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131
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Xu H, Zhu Y, Hsiao AWT, Xu J, Tong W, Chang L, Zhang X, Chen YF, Li J, Chen W, Zhang Y, Chan HF, Lee CW. Bioactive glass-elicited stem cell-derived extracellular vesicles regulate M2 macrophage polarization and angiogenesis to improve tendon regeneration and functional recovery. Biomaterials 2023; 294:121998. [PMID: 36641814 DOI: 10.1016/j.biomaterials.2023.121998] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/31/2022] [Accepted: 01/08/2023] [Indexed: 01/11/2023]
Abstract
Effective countermeasures for tendon injury remains unsatisfactory. Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs)-based therapy via regulation of Mφ-mediated angiogenesis has emerged as a promising strategy for tissue regeneration. Still, approaches to tailor the functions of EVs to treat tendon injuries have been limited. We reported a novel strategy by applying MSC-EVs boosted with bioactive glasses (BG). BG-elicited EVs (EVB) showed up-regulation of medicinal miRNAs, including miR-199b-3p and miR-125a-5p, which play a pivotal role in M2 Mφ-mediated angiogenesis. EVB accelerated angiogenesis via the reprogrammed anti-inflammatory M2 Mφs compared with naïve MSC-EVs (EVN). In rodent Achilles tendon rupture model, EVB local administration activated anti-inflammatory responses via M2 polarization and led to a spatial correlation between M2 Mφs and newly formed blood vessels. Our results showed that EVB outperformed EVN in promoting tenogenesis and in reducing detrimental morphological changes without causing heterotopic ossification. Biomechanical test revealed that EVB significantly improved ultimate load, stiffness, and tensile modulus of the repaired tendon, along with a positive correlation between M2/M1 ratio and biomechanical properties. On the basis of the boosted nature to reprogram regenerative microenvironment, EVB holds considerable potential to be developed as a next-generation therapeutic modality for enhancing functional regeneration to achieve satisfying tendon regeneration.
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Affiliation(s)
- Hongtao Xu
- Department of Orthopedics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China; Musculoskeletal Research Laboratory, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, China; Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Yanlun Zhu
- Institute for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Allen Wei-Ting Hsiao
- Musculoskeletal Research Laboratory, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jiankun Xu
- Musculoskeletal Research Laboratory, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, China; Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Wenxue Tong
- Musculoskeletal Research Laboratory, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, China; Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Liang Chang
- Musculoskeletal Research Laboratory, Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Hong Kong SAR, China; Innovative Orthopaedic Biomaterial and Drug Translational Research Laboratory, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Xuerao Zhang
- Institute for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China.
| | - Yi-Fan Chen
- The Ph.D. Program for Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; International Ph.D. Program for Translational Science, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan; Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Jie Li
- Division of Spine Surgery, Department of Orthopedic Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
| | - Wei Chen
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Yingze Zhang
- Department of Orthopedic Surgery, The Third Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Hon Fai Chan
- Institute for Tissue Engineering and Regenerative Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Key Laboratory for Regenerative Medicine of the Ministry of Education of China, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China; Center for Neuromusculoskeletal Restorative Medicine, Hong Kong SAR, China.
| | - Chien-Wei Lee
- Center for Translational Genomics & Regenerative Medicine Research, China Medical University Hospital, China Medical University, Taichung, Taiwan.
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Xu F, Hu L, Wang S, Shen Y, Liu H, Wang Y, Zhu L. Microarray profiling of circular RNAs in LPS-induced Beas-2B cells and identification of circ_2979 as a potential biomarker for ARDS. Cell Signal 2023; 103:110561. [PMID: 36528242 DOI: 10.1016/j.cellsig.2022.110561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Acute respiratory distress syndrome (ARDS) is a major cause of high mortality and morbidity in critically ill patients. Circular RNAs (CircRNAs) are widely expressed in numerous tissues and are associated with various diseases. However, the role of circRNAs in ARDS remains unclear. In this study, we found that cell viability and proliferation were reduced in lipopolysaccharide (LPS)-induced Beas-2B cells. Microarray analysis identified 1131 differentially expressed circRNAs in LPS-treated Beas-2B cells, with 623 circRNAs significantly upregulated and 508 circRNAs strongly downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed significant enrichment and indicated potential functions and pathways of differentially expressed circRNAs. Reverse transcription-polymerase chain reaction (RT-PCR) analysis confirmed that expression of circ_2979, circ_5438, circ_4557 and circ_2066 in LPS-induced Beas-2B cells was consistent with the results obtained by RNA sequencing (RNA-seq). Additionally, we recruited 17 patients with ARDS and 13 healthy volunteers and found that expression of circ_2979 in serum was significantly increased in the patients with ARDS compared with healthy volunteers. Spearman's analyses indicated that circ_2979 was correlated with partial pressure of carbon dioxide in arterial blood (PaCO2), the ratio of partial pressure of arterial oxygen to the fraction of inspired oxygen (PaO2/FiO2), interleukin 2 receptor (IL-2R) and fibrinogen (FIB). The results suggested that circRNAs may play an important role in the progression of ARDS, and that circ_2979 may serve as a diagnosis and prognosis biomarker for ARDS.
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Affiliation(s)
- Fan Xu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, 180 Feng Lin Road, Shanghai 200032, PR China.
| | - Lijuan Hu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, 180 Feng Lin Road, Shanghai 200032, PR China.
| | - Sijiao Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, 180 Feng Lin Road, Shanghai 200032, PR China
| | - Yue Shen
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, 180 Feng Lin Road, Shanghai 200032, PR China.
| | - Hanhan Liu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, 180 Feng Lin Road, Shanghai 200032, PR China
| | - Yali Wang
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, 180 Feng Lin Road, Shanghai 200032, PR China.
| | - Lei Zhu
- Department of Pulmonary Medicine, Zhongshan Hospital, Fudan University, 180 Feng Lin Road, Shanghai 200032, PR China; Department of Pulmonary and Critical Care Medicine, Huadong Hospital affiliated to Fudan University, 221 Yan An Road, Shanghai 200040, PR China.
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U A, Viswam P, Kattupalli D, Eppurathu Vasudevan S. Elucidation of transfer RNAs as stress regulating agents and the experimental strategies to conceive the functional role of tRNA-derived fragments in plants. Crit Rev Biotechnol 2023; 43:275-292. [PMID: 35382663 DOI: 10.1080/07388551.2022.2026288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In plants, the transfer RNAs (tRNAs) exhibit their profound influence in orchestrating diverse physiological activities like cell growth, development, and response to several surrounding stimuli. The tRNAs, which were known to restrict their function solely in deciphering the codons, are now emerging as frontline defenders in stress biology. The plants that are constantly confronted with a huge panoply of stresses rely on tRNA-mediated stress regulation by altering the tRNA abundance, curbing the transport of tRNAs, fragmenting the mature tRNAs during stress. Among them, the studies on the generation of transfer RNA-derived fragments (tRFs) and their biological implication in stress response have attained huge interest. In plants, the tRFs hold stable expression patterns and regulate biological functions under diverse environmental conditions. In this review, we discuss the fate of plant tRNAs upon stress and thereafter how the tRFs are metamorphosed into sharp ammunition to wrestle with stress. We also address the various methods developed to date for uncovering the role of tRFs and their function in plants.
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Affiliation(s)
- Aswathi U
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Pooja Viswam
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
| | - Divya Kattupalli
- Rajiv Gandhi Centre for Biotechnology, Transdisciplinary Biology Laboratory, Thiruvananthapuram, India
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Chen WT, Yang MJ, Tsuei YW, Su TC, Siao AC, Kuo YC, Huang LR, Chen Y, Chen SJ, Chen PC, Cheng CF, Ku HC, Kao YH. Green Tea Epigallocatechin Gallate Inhibits Preadipocyte Growth via the microRNA-let-7a/HMGA2 Signaling Pathway. Mol Nutr Food Res 2023; 67:e2200336. [PMID: 36825504 DOI: 10.1002/mnfr.202200336] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 01/19/2023] [Indexed: 02/25/2023]
Abstract
SCOPE This study investigates the effect of epigallocatechin gallate (EGCG) on white and beige preadipocyte growth and explores the involvement of the miR-let-7a/HMGA2 pathway. METHODS AND RESULTS 3T3-L1 and D12 cells are treated with EGCG. The effect of EGCG on cell proliferation and viability is evaluated, as well as microRNA (miRNA)-related signaling pathways. EGCG inhibits 3T3-L1 and D12 preadipocyte growth, upregulates miR-let-7a expression, and downregulates high-mobility group AT-hook 2 (HMGA2) mRNA and protein levels in a time- and dose-dependent manner. In addition, overexpression of miR-let-7a significantly inhibits the growth of 3T3-L1 and D12 cells and decreases HMGA2 mRNA and protein levels. MiR-let-7a inhibitor antagonizes the inhibitory effects of EGCG on the number and viability of 3T3-L1 and D12 cells. Furthermore, miR-let-7a inhibitor reverses the EGCG-induced increase in miR-let-7a expression levels and decrease in HMGA2 mRNA and protein levels. HMGA2 overexpression induces an increase in cell number and viability and antagonizes EGCG-suppressed cell growth and HMGA2 expression in 3T3-L1 and D12 preadipocytes. CONCLUSION EGCG inhibits the growth of 3T3-L1 and D12 preadipocytes by modulating the miR-let-7a and HMGA2 pathways.
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Affiliation(s)
- Wen-Ting Chen
- Department of Life Sciences, National Central University, Taoyuan, 320, Taiwan
| | - Meei-Ju Yang
- Tea Research and Extension Station, Council of Agriculture, Executive Yuan Number 324 Chung-Hsing RD., Taoyuan, 326, Taiwan
| | - Yi-Wei Tsuei
- Department of Emergency Medicine, Taoyuan Armed Forces General Hospital, Taoyuan, 325, Taiwan
| | - Tsung-Chen Su
- Tea Research and Extension Station, Council of Agriculture, Executive Yuan Number 324 Chung-Hsing RD., Taoyuan, 326, Taiwan
| | - An-Ci Siao
- Department of Life Sciences, National Central University, Taoyuan, 320, Taiwan
| | - Yow-Chii Kuo
- Department of Gastroenterology, Landseed Hospital, Taoyuan, 324, Taiwan
| | - Ling-Ru Huang
- Department of Life Sciences, National Central University, Taoyuan, 320, Taiwan
| | - Yi Chen
- Department of Life Sciences, National Central University, Taoyuan, 320, Taiwan
| | - Sy-Jou Chen
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Po-Chuan Chen
- Department of Emergency Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Ching-Feng Cheng
- Department of Pediatrics, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, 23142, Taiwan.,Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Department of Pediatrics, Tzu Chi University, Hualien, 97004, Taiwan
| | - Hui-Chen Ku
- Department of Pediatrics, Taipei Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, New Taipei City, 23142, Taiwan
| | - Yung-Hsi Kao
- Department of Life Sciences, National Central University, Taoyuan, 320, Taiwan
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Tripodi L, Sasso E, Feola S, Coluccino L, Vitale M, Leoni G, Szomolay B, Pastore L, Cerullo V. Systems Biology Approaches for the Improvement of Oncolytic Virus-Based Immunotherapies. Cancers (Basel) 2023; 15:1297. [PMID: 36831638 PMCID: PMC9954314 DOI: 10.3390/cancers15041297] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/22/2023] Open
Abstract
Oncolytic virus (OV)-based immunotherapy is mainly dependent on establishing an efficient cell-mediated antitumor immunity. OV-mediated antitumor immunity elicits a renewed antitumor reactivity, stimulating a T-cell response against tumor-associated antigens (TAAs) and recruiting natural killer cells within the tumor microenvironment (TME). Despite the fact that OVs are unspecific cancer vaccine platforms, to further enhance antitumor immunity, it is crucial to identify the potentially immunogenic T-cell restricted TAAs, the main key orchestrators in evoking a specific and durable cytotoxic T-cell response. Today, innovative approaches derived from systems biology are exploited to improve target discovery in several types of cancer and to identify the MHC-I and II restricted peptide repertoire recognized by T-cells. Using specific computation pipelines, it is possible to select the best tumor peptide candidates that can be efficiently vectorized and delivered by numerous OV-based platforms, in order to reinforce anticancer immune responses. Beyond the identification of TAAs, system biology can also support the engineering of OVs with improved oncotropism to reduce toxicity and maintain a sufficient portion of the wild-type virus virulence. Finally, these technologies can also pave the way towards a more rational design of armed OVs where a transgene of interest can be delivered to TME to develop an intratumoral gene therapy to enhance specific immune stimuli.
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Affiliation(s)
- Lorella Tripodi
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Emanuele Sasso
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Sara Feola
- Laboratory of Immunovirotherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00100 Helsinki, Finland
- Translational Immunology Research Program (TRIMM), University of Helsinki, 00100 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00100 Helsinki, Finland
| | - Ludovica Coluccino
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Maria Vitale
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Guido Leoni
- Nouscom Srl, via Castel Romano 100, 00128 Rome, Italy
| | - Barbara Szomolay
- Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff CF14 4YS, UK
| | - Lucio Pastore
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80138 Naples, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, 80131 Naples, Italy
| | - Vincenzo Cerullo
- Laboratory of Immunovirotherapy, Drug Research Program, Faculty of Pharmacy, University of Helsinki, 00100 Helsinki, Finland
- Translational Immunology Research Program (TRIMM), University of Helsinki, 00100 Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, 00100 Helsinki, Finland
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136
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In Silico Identification of Cassava Genome-Encoded MicroRNAs with Predicted Potential for Targeting the ICMV-Kerala Begomoviral Pathogen of Cassava. Viruses 2023; 15:v15020486. [PMID: 36851701 PMCID: PMC9963618 DOI: 10.3390/v15020486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Cassava mosaic disease (CMD) is caused by several divergent species belonging to the genus Begomovirus (Geminiviridae) transmitted by the whitefly Bemisia tabaci cryptic species group. In India and other parts of Asia, the Indian cassava mosaic virus-Kerala (ICMV-Ker) is an emergent begomovirus of cassava causing damage that results in reduced yield loss and tuber quality. Double-stranded RNA-mediated interference (RNAi) is an evolutionary conserved mechanism in eukaryotes and highly effective, innate defense system to inhibit plant viral replication and/or translation. The objective of this study was to identify and characterize cassava genome-encoded microRNAs (mes-miRNA) that are predicted to target ICMV-Ker ssDNA-encoded mRNAs, based on four in silico algorithms: miRanda, RNA22, Tapirhybrid, and psRNA. The goal is to deploy the predicted miRNAs to trigger RNAi and develop cassava plants with resistance to ICMV-Ker. Experimentally validated mature cassava miRNA sequences (n = 175) were downloaded from the miRBase biological database and aligned with the ICMV-Ker genome. The miRNAs were evaluated for base-pairing with the cassava miRNA seed regions and to complementary binding sites within target viral mRNAs. Among the 175 locus-derived mes-miRNAs evaluated, one cassava miRNA homolog, mes-miR1446a, was identified to have a predicted miRNA target binding site, at position 2053 of the ICMV-Ker genome. To predict whether the cassava miRNA might bind predicted ICMV-Ker mRNA target(s) that could disrupt viral infection of cassava plants, a cassava locus-derived miRNA-mRNA regulatory network was constructed using Circos software. The in silico-predicted cassava locus-derived mes-miRNA-mRNA network corroborated interactions between cassava mature miRNAs and the ICMV-Ker genome that warrant in vivo analysis, which could lead to the development of ICMV-Ker resistant cassava plants.
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Baig MS, Deepanshu, Prakash P, Alam P, Krishnan A. In silico analysis reveals hypoxia-induced miR-210-3p specifically targets SARS-CoV-2 RNA. J Biomol Struct Dyn 2023; 41:12305-12327. [PMID: 36752331 DOI: 10.1080/07391102.2023.2175255] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 01/01/2023] [Indexed: 02/09/2023]
Abstract
Human coronaviruses (HCoVs) until the emergence of SARS in 2003 were associated with mild cold and upper respiratory tract infections. The ongoing pandemic caused by SARS-CoV-2 has enhanced the potential for infection and transmission as compared to other known members of this family. MicroRNAs (miRNA) are 21-25 nucleotides long non-coding RNA that bind to 3' UTR of genes and regulate almost every aspect of cellular function. Several human miRNAs have been known to target viral genomes, mostly to downregulate their expression and sometimes to upregulate also. In some cases, host miRNAs could be sequestered by the viral genome to create a condition for favourable virus existence. The ongoing SARS CoV-2 pandemic is unique based on its transmissibility and severity and we hypothesised that there could be a unique mechanism for its pathogenesis. In this study, we exploited in silico approach to identify human respiratory system-specific miRNAs targeting the viral genome of three highly pathogenic HCoVs (SARS-CoV-2 Wuhan strain, SARS-CoV, and MERS-CoV) and three low pathogenic HCoVs (OC43, NL63, and HKU1). We identified ten common microRNAs that target all HCoVs studied here. In addition, we identified unique miRNAs which targeted specifically one particular HCoV. miR-210-3p was the single unique lung-specific miRNA, which was found to target the NSP3, NSP4, and NSP13 genes of SARS-CoV-2. Further miR-210-NSP3, miR-210-NSP4, and miR-210-NSP13 SARS-CoV-2 duplexes were docked with the hAGO2 protein (PDB ID 4F3T) which showed Z-score values of -1.9, -1.7, and -1.6, respectively. The role of miR-210-3p as master hypoxia regulator and inflammation regulation may be important for SARS-CoV-2 pathogenesis. Overall, this analysis advocates that miR-210-3p be investigated experimentally in SARS-CoV-2 infection.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Deepanshu
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Prem Prakash
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
| | - Pravej Alam
- Department of Biology, College of Science and Humanities in Al-Kharj, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Anuja Krishnan
- Department of Molecular Medicine, Jamia Hamdard, New Delhi, India
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138
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Long noncoding RNA TARL promotes antibacterial activity and prevents bacterial escape in Miichthys miiuy through suppression of TAK1 downregulation. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2254-6. [PMID: 36738431 DOI: 10.1007/s11427-022-2254-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 12/07/2022] [Indexed: 02/05/2023]
Abstract
Noncoding RNA (ncRNA) is an important regulatory factor that plays a major role in innate immunity. However, most studies on ncRNA have focused on mammals, resulting in a knowledge gap on ncRNA in lower vertebrates such as teleost fish. In this study, we identified a new long noncoding RNA (lncRNA), termed TAK1-related lncRNA (TARL), which can play a positive role in the antibacterial immunity of Miichthys miiuy to Vibrio anguillarum and V. harveyi. We also found a novel microRNA miR-2188-3p that could target TAK1 and inhibit the host antibacterial response and promote bacterial escape. We further found that the antibacterial effect inhibited by miR-2188-3p could be reversed with TARL. Moreover, V. anguillarum and V. harveyi are the two most susceptible Gram-negative pathogens of aquaculture fish, and the economic losses caused by these two bacteria are immeasurable every year. This study is the first to report on the ability of lncRNA to prevent the escape of V. anguillarum and V. harveyi in fish through the competing endogenous RNA (ceRNA) mechanism. Our results not only elucidate the ceRNA mechanism of the lncRNA in antibacterial immune responses but also provide new insights into the impact of lncRNA on host immunity and bacterial escape.
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139
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Uterine Flushing Fluid-Derived Let-7b Targets CXCL10 to Regulate Uterine Receptivity in Goats during Embryo Implantation. Int J Mol Sci 2023; 24:ijms24032799. [PMID: 36769111 PMCID: PMC9917504 DOI: 10.3390/ijms24032799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
Exosomes have the ability to carry a wide range of chemicals, convey them to target cells or target regions, and act as "messengers." For the purpose of investigating embryo attachment, it is helpful to comprehend the range of exosomal mRNAs and miRNAs derived from the uterine flushing fluid before and after embryo attachment. In this study, we recovered exosomes from goat uterine rinsing fluid at 5, 15, and 18 days of gestation and used RNA-Seq to identify the mRNA and miRNA profiles of exosomes obtained from uterine rinsing fluid before and after embryo implantation. In total, 91 differently expressed miRNAs and 27,487 differentially expressed mRNAs were found. The target genes predicted by the differentially expressed miRNAs and the differentially expressed mRNAs were mainly membrane-related organelles with catalytic activity, binding activity, transcriptional regulation activity, and involved in metabolism, biological regulation, development, and other processes. This was revealed by GO analysis. Furthermore, KEGG analysis revealed that they were abundant in signaling pathways associated with embryo implantation, including the "PI3K-Akt signaling pathway," "Toll-like receptor signaling pathway," "TGF-beta signaling route," "Notch signaling pathway," and others. Moreover, our research has demonstrated, for the first time, that chi-let-7b-5p specifically targets the 3'UTR of CXCL10. Our research offers a fresh viewpoint on the mechanics of embryo attachment.
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140
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Nayak R, Chattopadhyay T, Gupta P, Mallick B. Integrative analysis of small non-coding RNAs predicts a piRNA/miRNA-CCND1/BRAF/HRH1/ATXN3 regulatory circuit that drives oncogenesis in glioblastoma. Mol Omics 2023; 19:252-261. [PMID: 36688618 DOI: 10.1039/d2mo00245k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The high-grade astrocytoma, glioblastoma multiforme (GBM), is the most common primary tumour of the brain, known for being aggressive and developing drug resistance. The non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), have critical functions in tumorigenesis and cancer drug resistance. Hence, we profiled miRNAs, piRNAs, and genes in U-87 MG GBM cells by next-generation sequencing and performed target prediction, pathway enrichment, protein-protein interaction, co-expression studies, and qRT-PCR validations to predict their possible roles in the malignancy. The study identified 335 miRNAs, 665 piRNAs, and 4286 genes differentially expressed (DE) in GBM. Among them 128 DE genes (DEGs) were targeted by both miRNAs and piRNAs, while 1817 and 192 were targeted solely by miRNAs or piRNAs, respectively. Interestingly, all the DEG targets enriched in cancer processes were overexpressed in GBM. Among these, BRAF was solely targeted by two piRNAs and this was found to be co-expressed with 19 sole targets of 5 miRNAs, including CCND1, and both were found to regulate cell proliferation in cancer. We conjectured that upregulated HRH1 and ATXN3 were targeted by both piRNAs and miRNAs, and along with BRAF and CCND1 might induce cell proliferation in GBM through G-protein-coupled receptor or Akt signalling pathways due to downregulation of the respective targeting small RNAs. These targets were also linked to the progression and overall survival of GBM patients, suggesting that they could be used as biomarkers. Overall, this study has identified a few novel ncRNA targets, which might aid in a better understanding of GBM pathogenesis.
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Affiliation(s)
- Rojalin Nayak
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Trisha Chattopadhyay
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Pooja Gupta
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
| | - Bibekanand Mallick
- RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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141
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Yin M, Wang J, Zhang J, Wang W, Lu W, Xu F, Ma X, Lyu S, Chen L, Zhang L, Dong Z, Xiao Y. Transcription analyses of differentially expressed mRNAs, lncRNAs, circRNAs, and miRNAs in the growth plate of rats with glucocorticoid-induced growth retardation. PeerJ 2023; 11:e14603. [PMID: 36684670 PMCID: PMC9851049 DOI: 10.7717/peerj.14603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/29/2022] [Indexed: 01/17/2023] Open
Abstract
Background Glucocorticoids (GCs) are commonly used to treat autoimmune diseases and malignancies in children and adolescents. Growth retardation is a common adverse effect of GC treatment in pediatric patients. Accumulating evidence indicates that non-coding RNAs (ncRNAs) are involved in the pathogenesis of glucocorticoid-induced growth retardation (GIGR), but the roles of specific ncRNAs in growth remain largely unknown. Methods In this study, 2-week-old male Sprague-Dawley rats had been treated with 2 mg/kg/d of dexamethasone for 7 or 14 days, after which the growth plate tissues were collected for high-throughput RNA sequencing to identify differentially expressed mRNAs, lncRNAs, circRNAs, and miRNAs in GIGR rats. Results Transcriptomic analysis identified 1,718 mRNAs, 896 lncRNAs, 60 circRNAs, and 72 miRNAs with different expression levels in the 7d group. In the 14d group, 1,515 mRNAs, 880 lncRNAs, 46 circRNAs, and 55 miRNAs with differential expression were identified. Four mRNAs and four miRNAs that may be closely associated with the development of GIGR were further validated by real-time quantitative fluorescence PCR. Function enrichment analysis indicated that the PI3K-Akt signaling pathway, NF-kappa B signaling pathway, and TGF-β signaling pathway participated in the development of the GIGR. Moreover, the constructed ceRNA networks suggested that several miRNAs (including miR-140-3p and miR-127-3p) might play an important role in the pathogenesis of GIGR. Conclusions These results provide new insights and important clues for exploring the molecular mechanisms underlying GIGR.
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Affiliation(s)
- Mingyue Yin
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Junqi Wang
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Juanjuan Zhang
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Wei Wang
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Wenli Lu
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Fei Xu
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China,Department of Pediatrics, Liqun Hospital, Putuo District, Shanghai, China
| | - Xiaoyu Ma
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Sheng Lyu
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Lifen Chen
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Lidan Zhang
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Zhiya Dong
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Yuan Xiao
- Department of Pediatrics, Ruijin Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
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Altered miRNA Expression Profiles in the Serum of Beagle Dogs Experimentally Infected with Toxocara canis. Animals (Basel) 2023; 13:ani13020299. [PMID: 36670839 PMCID: PMC9854737 DOI: 10.3390/ani13020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Toxocara canis is a neglected roundworm, which can cause debilitating disease in dogs and humans worldwide. Serum is an excellent material for monitoring the occurrence of many diseases. However, no information is available on the expression of microRNAs (miRNAs) in the serum of dogs infected with T. canis. In this study, RNA-seq analysis was performed to identify the serum miRNA profiles in Beagle dogs infected with T. canis at different stages of infection. A total of 3, 25 and 25 differently expressed miRNAs (DEmiRNAs) were identified in dog serum at 24 h post-infection (hpi), 10 days post-infection (dpi) and 36 dpi, respectively, such as cfa-let-7g, cfa-miR-16, cfa-miR-92b, cfa-miR-93, cfa-miR-122, cfa-miR-485 and cfa-miR-451. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these miRNAs could regulate the pathways related to parasitic infectious diseases and immune system, such as amoebiasis, toxoplasmosis, platelet activation, IL-17 signaling pathway and chemokine signaling pathway. These results provide a foundation to explore the underlying regulatory role of miRNAs in definitive hosts after T. canis infection.
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143
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Tarhriz V, Abkhooie L, Sarabi MM. Regulation of HIF-1 by MicroRNAs in Various Cardiovascular Diseases. Curr Cardiol Rev 2023; 19:51-56. [PMID: 37005512 PMCID: PMC10518879 DOI: 10.2174/1573403x19666230330105259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 01/04/2023] [Accepted: 02/07/2023] [Indexed: 04/04/2023] Open
Abstract
Today, we see an increase in death due to cardiovascular diseases all over the world, which has a lot to do with the regulation of oxygen homeostasis. Also, hypoxia-inducing factor 1 (HIF-1) is considered a vital factor in hypoxia and its physiological and pathological changes. HIF- 1 is involved in cellular activities, including proliferation, differentiation, and cell death in endothelial cells (ECs) and cardiomyocytes. Similar to HIF-1α, which acts as a protective element against various diseases in the cardiovascular system, the protective role of microRNAs (miRNAs) has also been proved using animal models. The number of miRNAs identified in the regulation of gene expression responsive to hypoxia and the importance of investigating the involvement of the non-coding genome in cardiovascular diseases is increasing, which shows the issue's importance. In this study, the molecular regulation of HIF-1 by miRNAs is considered to improve therapeutic approaches in clinical diagnoses of cardiovascular diseases.
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Affiliation(s)
- Vahideh Tarhriz
- Molecular Medicine Research Center, Biomedicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Abkhooie
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
- Department of Medical Biotechnology, Faculty of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Mostafa Moradi Sarabi
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran
- Department of Biochemistry and Genetics, School of Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
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Li Y, Chen L, Li Y, Deng P, Yang C, Li Y, Liao L, Zhu Z, Wang Y, Huang R. miR-2188-5p promotes GCRV replication by the targeted degradation of klf2a in Ctenopharyngodon idellus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104516. [PMID: 36084755 DOI: 10.1016/j.dci.2022.104516] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Studies on host immunity evasion by aquatic viruses have largely focused on coding genes. There is accumulating evidence for the important biological functions of non-coding miRNAs in virus-host interactions. The regulatory functions of non-coding miRNAs in fish reovirus-host interactions remain unknown. Here, miR-2188-5p in grass carp (Ctenopharyngodon idellus), a miRNA specific to teleosts, was predicted to target the 3' UTR of the transcription factor klf2a. A correlation analysis and dual-luciferase reporter assay revealed that miR-2188-5p could induce the degradation of klf2a. The expression of miR-2188-5p induced the degradation of klf2a in a dose-dependent manner, suppressing the type I interferon response and promoting grass carp reovirus (GCRV) replication. As determined by a co-expression analysis, klf2a inhibited viral infection when miR-2188-5p was overexpressed. The targeted degradation of klf2a by miR-2188-5p could inhibit the type I interferon response and promote the replication of GCRV; however, this targeted degradation ability was insufficient to fully inhibit GCRV infection. These results provide novel insights into the regulatory effects and biological functions of non-coding miRNAs in fish-virus interactions.
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Affiliation(s)
- Yangyu Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liangming Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yangyang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Deng
- Wuhan Academy of Agricultural Sciences, Wuhan, 430207, China
| | - Cheng Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yongming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Lanjie Liao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zuoyan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yaping Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Rong Huang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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Cao Y, Li R, Du Y, Jin N, Fang T, Ma F, Jin P. miR-92b-5p negatively regulates IKK through targeting its ORF region in the innate immune responses of amphioxus (Branchiostoma belcheri). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 138:104556. [PMID: 36167145 DOI: 10.1016/j.dci.2022.104556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Cephalochordate (Amphioxus), situated at a key phylogenetic position in the phylum Chordata, serves as a model organism for studying the origin and evolution of the vertebrate innate immune. In this study, five members of precursor miR-92 family (miR-92a-1, miR-92a-2, miR-92b, miR-92c and miR-92d) are identified in Branchiostoma belcheri, and their evolutionary conservation and potential molecular functions in innate immunity are analyzed. Among them, miR-92b-5p was validated in HEK293 cells to target the coding region but not classic 3'UTR of IKK (inhibitor of nuclear factor kappa-B kinase) mRNA, one integral component of MAPK and TLR4 immune signaling. Furthermore, the spatiotemporal expression patterns of miR-92b-5p and IKK were examined in different tissues or different time points (2 h, 4 h, 8 h, 12 h, 24 h and 48 h) post LPS stimulation at RNA and protein level in vivo. The seemingly inverse expression pattern between miR-92b-5p and IKK supports the involvement of miR-92b-5p in Branchiostoma belcheri innate immune response. In conclusion, our work not only illustrates the evolutionary pattern of Branchiostoma belcheri miR-92 family across chordates, but also reveals that miR-92b-5p could target IKK expression to regulate innate immune response.
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Affiliation(s)
- Yunpeng Cao
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Ranting Li
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Yongxin Du
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Na Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Tao Fang
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Fei Ma
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
| | - Ping Jin
- Laboratory for Comparative Genomics and Bioinformatics & Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Science, Nanjing Normal University, Nanjing, 210046, China.
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146
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Ye S, Xiong F, He X, Yuan Y, Li D, Ye D, Shi L, Lin Z, Zhao M, Feng S, Zhou B, Weng H, Hong L, Ye H, Gao S. DNA hypermethylation-induced miR-182 silence targets BCL2 and HOXA9 to facilitate the self-renewal of leukemia stem cell, accelerate acute myeloid leukemia progression, and determine the sensitivity of BCL2 inhibitor venetoclax. Theranostics 2023; 13:77-94. [PMID: 36593968 PMCID: PMC9800726 DOI: 10.7150/thno.77404] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 11/10/2022] [Indexed: 12/02/2022] Open
Abstract
Rationale: microRNAs (miRNAs) are frequently deregulated and play important roles in the pathogenesis and progression of acute myeloid leukemia (AML). miR-182 functions as an onco-miRNA or tumor suppressor miRNA in the context of different cancers. However, whether miR-182 affects the self-renewal of leukemia stem cells (LSCs) and normal hematopoietic stem progenitor cells (HSPCs) is unknown. Methods: Bisulfite sequencing was used to analyze the methylation status at pri-miR-182 promoter. Lineage-negative HSPCs were isolated from miR-182 knockout (182KO) and wild-type (182WT) mice to construct MLL-AF9-transformed AML model. The effects of miR-182 depletion on the overall survival and function of LSC were analyzed in this mouse model in vivo. Results: miR-182-5p (miR-182) expression was lower in AML blasts than normal controls (NCs) with hypermethylation observed at putative pri-miR-182 promoter in AML blasts but unmethylation in NCs. Overexpression of miR-182 inhibited proliferation, reduced colony formation, and induced apoptosis in leukemic cells. In addition, depletion of miR-182 accelerated the development and shortened the overall survival (OS) in MLL-AF9-transformed murine AML through increasing LSC frequency and self-renewal ability. Consistently, overexpression of miR-182 attenuated AML development and extended the OS in the murine AML model. Most importantly, miR-182 was likely dispensable for normal hematopoiesis. Mechanistically, we identified BCL2 and HOXA9 as two key targets of miR-182 in this context. Most importantly, AML patients with miR-182 unmethylation had high expression of miR-182 followed by low protein expression of BCL2 and resistance to BCL2 inhibitor venetoclax (Ven) in vitro. Conclusions: Our results suggest that miR-182 is a potential therapeutic target for AML patients through attenuating the self-renewal of LSC but not HSPC. miR-182 promoter methylation could determine the sensitivity of Ven treatment and provide a potential biomarker for it.
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Affiliation(s)
- Sisi Ye
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Fang Xiong
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Xiaofei He
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Yigang Yuan
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Danyang Li
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Daijiao Ye
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Liuzhi Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Zihan Lin
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Min Zhao
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Shuya Feng
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Bin Zhou
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China
| | - Huachun Weng
- The College of Medical Technology, Shanghai University of Medicine& Health Sciences; 279 ZhouZhuGong Street, Pudong District, Shanghai, China
| | - Lili Hong
- Department of Hematology, The First Affiliated Hospital of Zhejiang Chinese Medical University, 54 Post Road, Hangzhou, Zhejiang Province, China
| | - Haige Ye
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China.,✉ Corresponding authors: Dr. Haige Ye, E-mail: , Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China. Tel: +86-577-55579127; Fax: +86-577-55579127. Dr. Shenmeng Gao, E-mail: , Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China. Tel.: +86-577-55578080; Fax: +86-577-55578080
| | - Shenmeng Gao
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, Zhejiang Province, China.,✉ Corresponding authors: Dr. Haige Ye, E-mail: , Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China. Tel: +86-577-55579127; Fax: +86-577-55579127. Dr. Shenmeng Gao, E-mail: , Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, 1 Xuefubei Street, Ouhai District, Wenzhou, 325000, Zhejiang Province, China. Tel.: +86-577-55578080; Fax: +86-577-55578080
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147
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Huo D, Su F, Yang H, Sun L. Exosomal microRNAs regulate the heat stress response in sea cucumber Apostichopus japonicus. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 249:114419. [PMID: 36527848 DOI: 10.1016/j.ecoenv.2022.114419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 12/08/2022] [Accepted: 12/10/2022] [Indexed: 06/17/2023]
Abstract
Exosomes are small extracellular vesicles that contain nucleic acids such as microRNAs and may participate in important biological processes. We made the initial report of exosomes from sea cucumber Apostichopus japonicus, that were classically cup-shaped and had an average size of 74.65 nm, and identified specific exosome biomarkers (HSP70, TSG101, and CD9). We explored changes in the global expression of microRNAs in exosomes from the commercially important A. japonicus under normal conditions and heat-stressed conditions for 3 and 7 d. We found that heat stress increased exosome production and modified the expression profiles of the microRNAs that they contained. Novel_mir31, novel_mir132, novel_mir26, miR-92_1, and novel_mir27 were commonly found to be differentially expressed in three comparison groups, indicating their importance in the heat stress response. The microRNA expression levels were validated by qPCR. Function analysis of the target genes of these microRNAs indicated they were involved mainly in replication and repair in the initial response of A. japonicus to heat stress exposure. Conversely, during acclimation to the high temperature conditions, the target genes of the differentially expressed microRNAs were primarily involved in metabolism adjustments. Our results will contribute to a better understanding of the regulatory roles of exosomes in sea cucumber, and provide insights into the functions of sea cucumber exosome-shuttled microRNAs against environmental stresses exacerbated by global warming.
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Affiliation(s)
- Da Huo
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Fang Su
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China
| | - Hongsheng Yang
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China; The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan 430071, China
| | - Lina Sun
- CAS Key Laboratory of Marine Ecology and Environmental Sciences, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; Laboratory for Marine Ecology and Environmental Science, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao 266071, China; CAS Engineering Laboratory for Marine Ranching, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shandong Province Key Laboratory of Experimental Marine Biology, Qingdao 266071, China.
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148
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Xie SC, Zhou CX, Zhai BT, Zheng WB, Liu GH, Zhu XQ. A combined miRNA-piRNA signature in the serum and urine of rabbits infected with Toxoplasma gondii oocysts. Parasit Vectors 2022; 15:490. [PMID: 36572911 PMCID: PMC9793633 DOI: 10.1186/s13071-022-05620-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/15/2022] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Increasing evidence has shown that non-coding RNA (ncRNA) molecules play fundamental roles in cells, and many are stable in body fluids as circulating RNAs. Study on these ncRNAs will provide insights into toxoplasmosis pathophysiology and/or help reveal diagnostic biomarkers. METHODS We performed a high-throughput RNA-Seq study to comprehensively profile the microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) in rabbit serum and urine after infection with Toxoplasma gondii oocysts during the whole infection process. RESULTS Total RNA extracted from serum and urine samples of acutely infected [8 days post-infection (DPI)], chronically infected (70 DPI) and uninfected rabbits were subjected to genome-wide small RNA sequencing. We identified 2089 miRNAs and 2224 novel piRNAs from the rabbit sera associated with T. gondii infection. Meanwhile, a total of 518 miRNAs and 4182 novel piRNAs were identified in the rabbit urine associated with T. gondii infection. Of these identified small ncRNAs, 1178 and 1317 serum miRNAs and 311 and 294 urine miRNAs were identified as differentially expressed (DE) miRNAs in the acute and chronic stages of infections, respectively. A total of 1748 and 1814 serum piRNAs and 597 and 708 urine piRNAs were found in the acute and chronic infection stages, respectively. Of these dysregulated ncRNAs, a total of 88 common DE miRNAs and 120 DE novel piRNAs were found in both serum and urine samples of infected rabbits. CONCLUSIONS These findings provide valuable data for revealing the physiology of herbivore toxoplasmosis caused by oocyst infection. Circulating ncRNAs identified in this study are potential novel diagnostic biomarkers for the detection/diagnosis of toxoplasmosis in herbivorous animals.
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Affiliation(s)
- Shi-Chen Xie
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan Province People’s Republic of China ,grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province People’s Republic of China
| | - Chun-Xue Zhou
- grid.27255.370000 0004 1761 1174Department of Pathogen Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012 Shandong Province People’s Republic of China
| | - Bin-Tao Zhai
- grid.410727.70000 0001 0526 1937Key Laboratory of Veterinary Pharmaceutical Development, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Ministry of Agriculture, Lanzhou, 730050 Gansu Province People’s Republic of China ,grid.410727.70000 0001 0526 1937State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046 Gansu Province People’s Republic of China
| | - Wen-Bin Zheng
- grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province People’s Republic of China
| | - Guo-Hua Liu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan Province People’s Republic of China
| | - Xing-Quan Zhu
- grid.257160.70000 0004 1761 0331Research Center for Parasites and Vectors, College of Veterinary Medicine, Hunan Agricultural University, Changsha, 410128 Hunan Province People’s Republic of China ,grid.412545.30000 0004 1798 1300Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801 Shanxi Province People’s Republic of China
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Identification of Circular RNAs of Testis and Caput Epididymis and Prediction of Their Potential Functional Roles in Donkeys. Genes (Basel) 2022; 14:genes14010066. [PMID: 36672807 PMCID: PMC9858477 DOI: 10.3390/genes14010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with a covalently closed loop. Studies have demonstrated that circRNA can function as microRNA (miRNA) sponges or competing endogenous RNAs. Although circRNA has been explored in some species and tissues, the genetic basis of testis development and spermatogenesis in donkeys remain unknown. We performed RNA-seq to detect circRNA expression profiles of adult donkey testes. Length distribution and other characteristics were shown a total of 1971 circRNAs were differentially expressed and 12,648 and 6261 circRNAs were detected from the testis and caput epididymis, respectively. Among these circRNAs, 1472 circRNAs were downregulated and 499 circRNAs were upregulated in the testis. Moreover, KEGG pathway analyses and Gene Ontology were performed for host genes of circRNAs. A total of 39 upregulated circRNA host genes were annotated in spermatogenesis terms, including PIWIL2, CATSPERD, CATSPERB, SPATA6, and SYCP1. Other host genes were annotated in the focal adhesion, Rap1 signaling pathway. Downregulated expressed circRNA host genes participated in the TGF-β signaling pathway, GnRH signaling pathway, estrogen signaling pathway, and calcium signaling pathway. Our discoveries provide a solid foundation for identifying and characterizing critical circRNAs involved in testis development or spermatogenesis.
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150
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Vasiliev GV, Ovchinnikov VY, Lisachev PD, Bondar NP, Grinkevich LN. The Expression of miRNAs Involved in Long-Term Memory Formation in the CNS of the Mollusk Helix lucorum. Int J Mol Sci 2022; 24:ijms24010301. [PMID: 36613744 PMCID: PMC9820140 DOI: 10.3390/ijms24010301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/15/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
Mollusks are unique animals with a relatively simple central nervous system (CNS) containing giant neurons with identified functions. With such simple CNS, mollusks yet display sufficiently complex behavior, thus ideal for various studies of behavioral processes, including long-term memory (LTM) formation. For our research, we use the formation of the fear avoidance reflex in the terrestrial mollusk Helix lucorum as a learning model. We have shown previously that LTM formation in Helix requires epigenetic modifications of histones leading to both activation and inactivation of the specific genes. It is known that microRNAs (miRNAs) negatively regulate the expression of genes; however, the role of miRNAs in behavioral regulation has been poorly investigated. Currently, there is no miRNAs sequencing data being published on Helix lucorum, which makes it impossible to investigate the role of miRNAs in the memory formation of this mollusk. In this study, we have performed sequencing and comparative bioinformatics analysis of the miRNAs from the CNS of Helix lucorum. We have identified 95 different microRNAs, including microRNAs belonging to the MIR-9, MIR-10, MIR-22, MIR-124, MIR-137, and MIR-153 families, known to be involved in various CNS processes of vertebrates and other species, particularly, in the fear behavior and LTM. We have shown that in the CNS of Helix lucorum MIR-10 family (26 miRNAs) is the most representative one, including Hlu-Mir-10-S5-5p and Hlu-Mir-10-S9-5p as top hits. Moreover, we have shown the involvement of the MIR-10 family in LTM formation in Helix. The expression of 17 representatives of MIR-10 differentially changes during different periods of LTM consolidation in the CNS of Helix. In addition, using comparative analysis of microRNA expression upon learning in normal snails and snails with deficient learning abilities with dysfunction of the serotonergic system, we identified a number of microRNAs from several families, including MIR-10, which expression changes only in normal animals. The obtained data can be used for further fundamental and applied behavioral research.
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Affiliation(s)
- Gennady V. Vasiliev
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Vladimir Y. Ovchinnikov
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Pavel D. Lisachev
- Federal Research Center for Information and Computational Technologies, 6 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Natalia P. Bondar
- The Federal Research Center Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Larisa N. Grinkevich
- The Federal State Budget Scientific Institution Pavlov Institute of Physiology, Russian Academy of Sciences, 6 nab. Makarova, St. Petersburg 199034, Russia
- Correspondence:
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