Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis
Chronic epididymitis (CE) refers to a long-lasting inflammatory condition of the epididymis, which is considered the most common site of intrascrotal inflammation and an important aetiological factor of male infertility. Recent studies demonstrate that small RNAs secreted from epididymal epithelium...
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| Format: | Article |
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Frontiers Media S.A.
2022-05-01
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| Series: | Frontiers in Immunology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fimmu.2022.883803/full |
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| author | Jialei Gong Jialei Gong Peng Wang Jin-Chuan Liu Jin-Chuan Liu Jianlin Li Jianlin Li Qun-Xiong Zeng Qun-Xiong Zeng Chen Yang Yanfeng Li Di Yu Dandan Cao Yong-Gang Duan |
| author_facet | Jialei Gong Jialei Gong Peng Wang Jin-Chuan Liu Jin-Chuan Liu Jianlin Li Jianlin Li Qun-Xiong Zeng Qun-Xiong Zeng Chen Yang Yanfeng Li Di Yu Dandan Cao Yong-Gang Duan |
| author_sort | Jialei Gong |
| collection | DOAJ |
| description | Chronic epididymitis (CE) refers to a long-lasting inflammatory condition of the epididymis, which is considered the most common site of intrascrotal inflammation and an important aetiological factor of male infertility. Recent studies demonstrate that small RNAs secreted from epididymal epithelium modulate embryo development and offspring phenotypes via sperm transmission, and the resulting modifications may lead to transgenerational inheritance. However, to date, the genome-wide analysis of small RNA together with the transcriptomic expression profiles of human epididymis and CE is still lacking. In this study, we facilitated next-generation sequencing and bioinformatics to comprehensively analyze the small RNA and mRNA in an integrative way and identified signatures associated with CE. Both of the small RNA and mRNA expression data demonstrated relatively larger molecular differences among the segmental region of the epididymides, including caput, corpus, and cauda, than that of the inflammatory conditions. By comparing the inflamed caputs to the controls, a total of 1727 genes (1220 upregulated and 507 downregulated; 42 most significant genes, adjusted P <0.05) and 34 miRNAs (23 upregulated and 11 downregulated) were identified as differentially expressed. In silico functional enrichment analysis showed their roles in regulating different biological activities, including leukocyte chemotaxis, extracellular milieu reconstruction, ion channel and transporter-related processes, and nervous system development. Integrative analysis of miRNA and mRNA identified a regulatory network consisting of 22 miRNAs and 31 genes (miRNA-mRNA) which are strong candidates for CE. In addition, analysis about other species of small RNA, including (miRNA), piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA), Y RNA, and rsRNA identified the distinct expression pattern of tsRNA in CE. In summary, our study performed small RNA and miRNA profiling and integrative analysis in human CE. The findings will help to understand the role of miRNA-mRNA in the pathogenesis of CE and provide molecular candidates for the development of potential biomarkers for human CE. |
| first_indexed | 2024-04-13T09:04:42Z |
| format | Article |
| id | doaj.art-a1e4a421dcbc408bb60a55d9e70e7c34 |
| institution | Directory Open Access Journal |
| issn | 1664-3224 |
| language | English |
| last_indexed | 2024-04-13T09:04:42Z |
| publishDate | 2022-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Immunology |
| spelling | doaj.art-a1e4a421dcbc408bb60a55d9e70e7c342022-12-22T02:53:01ZengFrontiers Media S.A.Frontiers in Immunology1664-32242022-05-011310.3389/fimmu.2022.883803883803Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic EpididymitisJialei Gong0Jialei Gong1Peng Wang2Jin-Chuan Liu3Jin-Chuan Liu4Jianlin Li5Jianlin Li6Qun-Xiong Zeng7Qun-Xiong Zeng8Chen Yang9Yanfeng Li10Di Yu11Dandan Cao12Yong-Gang Duan13Shenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong – Shenzhen Hospital, Shenzhen, ChinaThe University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, AustraliaDepartment of Urology, Daping Hospital, Army Medical University, Chongqing, ChinaShenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong – Shenzhen Hospital, Shenzhen, ChinaDepartment of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, Hong Kong SAR, ChinaShenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong – Shenzhen Hospital, Shenzhen, ChinaDepartment of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, Hong Kong SAR, ChinaShenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong – Shenzhen Hospital, Shenzhen, ChinaDepartment of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong, Hong Kong SAR, ChinaShenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong – Shenzhen Hospital, Shenzhen, ChinaDepartment of Urology, Daping Hospital, Army Medical University, Chongqing, ChinaThe University of Queensland Diamantina Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, QLD, AustraliaShenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong – Shenzhen Hospital, Shenzhen, ChinaShenzhen Key Laboratory of Fertility Regulation, Center of Assisted Reproduction and Embryology, The University of Hong Kong – Shenzhen Hospital, Shenzhen, ChinaChronic epididymitis (CE) refers to a long-lasting inflammatory condition of the epididymis, which is considered the most common site of intrascrotal inflammation and an important aetiological factor of male infertility. Recent studies demonstrate that small RNAs secreted from epididymal epithelium modulate embryo development and offspring phenotypes via sperm transmission, and the resulting modifications may lead to transgenerational inheritance. However, to date, the genome-wide analysis of small RNA together with the transcriptomic expression profiles of human epididymis and CE is still lacking. In this study, we facilitated next-generation sequencing and bioinformatics to comprehensively analyze the small RNA and mRNA in an integrative way and identified signatures associated with CE. Both of the small RNA and mRNA expression data demonstrated relatively larger molecular differences among the segmental region of the epididymides, including caput, corpus, and cauda, than that of the inflammatory conditions. By comparing the inflamed caputs to the controls, a total of 1727 genes (1220 upregulated and 507 downregulated; 42 most significant genes, adjusted P <0.05) and 34 miRNAs (23 upregulated and 11 downregulated) were identified as differentially expressed. In silico functional enrichment analysis showed their roles in regulating different biological activities, including leukocyte chemotaxis, extracellular milieu reconstruction, ion channel and transporter-related processes, and nervous system development. Integrative analysis of miRNA and mRNA identified a regulatory network consisting of 22 miRNAs and 31 genes (miRNA-mRNA) which are strong candidates for CE. In addition, analysis about other species of small RNA, including (miRNA), piwi-interacting RNA (piRNA), tRNA-derived small RNA (tsRNA), Y RNA, and rsRNA identified the distinct expression pattern of tsRNA in CE. In summary, our study performed small RNA and miRNA profiling and integrative analysis in human CE. The findings will help to understand the role of miRNA-mRNA in the pathogenesis of CE and provide molecular candidates for the development of potential biomarkers for human CE.https://www.frontiersin.org/articles/10.3389/fimmu.2022.883803/fullmulti-omicssmall RNAsmicroRNAtsRNAmRNAintegrative analysis |
| spellingShingle | Jialei Gong Jialei Gong Peng Wang Jin-Chuan Liu Jin-Chuan Liu Jianlin Li Jianlin Li Qun-Xiong Zeng Qun-Xiong Zeng Chen Yang Yanfeng Li Di Yu Dandan Cao Yong-Gang Duan Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis Frontiers in Immunology multi-omics small RNAs microRNA tsRNA mRNA integrative analysis |
| title | Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis |
| title_full | Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis |
| title_fullStr | Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis |
| title_full_unstemmed | Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis |
| title_short | Integrative Analysis of Small RNA and mRNA Expression Profiles Identifies Signatures Associated With Chronic Epididymitis |
| title_sort | integrative analysis of small rna and mrna expression profiles identifies signatures associated with chronic epididymitis |
| topic | multi-omics small RNAs microRNA tsRNA mRNA integrative analysis |
| url | https://www.frontiersin.org/articles/10.3389/fimmu.2022.883803/full |
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