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Sharifi S, Pakdel A, Pakdel MH, Tabashiri R, Bakhtiarizadeh MR, Tahmasebi A. Integrated co-expression analysis of regulatory elements (miRNA, lncRNA, and TFs) in bovine monocytes induced by Str. uberis. Sci Rep 2023; 13:15076. [PMID: 37699972 PMCID: PMC10497586 DOI: 10.1038/s41598-023-42067-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
Non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), together with transcription factors, are critical pre-, co-, and post-transcriptional regulators. In addition to their criteria as ideal biomarkers, they have great potential in disease prognosis, diagnosis, and treatment of complex diseases. Investigation of regulatory mechanisms in the context of bovine mastitis, as most common and economic disease in the dairy industry, to identify elements influencing the expression of candidate genes as key regulators of the mammary immune response is not yet fully understood. Transcriptome profiles (50 RNA-Seq and 50 miRNA-Seq samples) of bovine monocytes induced by Str. uberis were used for co-expression module detection and preservation analysis using the weighted gene co-expression network analysis (WGCNA) approach. Assigned mi-, lnc-, and m-modules used to construct the integrated regulatory networks and miRNA-lncRNA-mRNA regulatory sub-networks. Remarkably, we have identified 18 miRNAs, five lncRNAs, and seven TFs as key regulators of str. uberis-induced mastitis. Most of the genes introduced here, mainly involved in immune response, inflammation, and apoptosis, were new to mastitis. These findings may help to further elucidate the underlying mechanisms of bovine mastitis, and the discovered genes may serve as signatures for early diagnosis and treatment of the disease.
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Affiliation(s)
- Somayeh Sharifi
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Islamic Republic of Iran.
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111, Islamic Republic of Iran.
| | - Mohammad Hossein Pakdel
- Department of Plant Molecular Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Islamic Republic of Iran
| | - Raana Tabashiri
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Islamic Republic of Iran
| | - Mohammad Reza Bakhtiarizadeh
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, 3391653755, Islamic Republic of Iran
| | - Ahmad Tahmasebi
- Institute of Biotechnology, Shiraz University, Shiraz, 71946-84334, Islamic Republic of Iran
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Chen JG, Liu SC, Nie Q, Du YT, Lv YY, He LP, Chen G. Exosome-derived long noncoding RNAs: Mediators of host-Plasmodium parasite communication. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1808. [PMID: 37553236 DOI: 10.1002/wrna.1808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/21/2023] [Accepted: 06/27/2023] [Indexed: 08/10/2023]
Abstract
Overcoming challenges associated with malaria eradication proves to be a formidable task due to the complicated life cycle exhibited by the malaria parasite and the lack of safe and enduring vaccines against malaria. Investigating the interplay between Plasmodium parasites and their mammalian hosts is crucial for the development of novel vaccines. Long noncoding RNAs (lncRNAs) derived from Plasmodium parasites or host cells have emerged as potential signaling molecules involved in the trafficking of proteins, RNA (mRNAs, miRNAs, and ncRNAs), and DNA. These lncRNAs facilitate the interaction between hosts and parasites, impacting normal physiology or pathology in malaria-infected individuals. Moreover, they possess the capacity to regulate immune responses and associated signaling pathways, thus potentially influencing chromatin organization, epigenetic modifications, mRNA processing, splicing, and translation. However, the functional role of exosomal lncRNAs in malaria remains poorly understood. This review offers a comprehensive analysis of lncRNA and exosomal lncRNA profiles during malaria infection. It presents an overview of recent progress in elucidating the involvement of exosomal lncRNAs in host-parasite interactions. Additionally, potential exosomal lncRNAs linked to the domains of innate and adaptive immunity in the context of malaria are proposed. These findings may contribute to the discovery of new diagnostic and therapeutic strategies for malaria. Furthermore, the need for additional research was highlighted that aimed to elucidate the mechanisms underlying lncRNA transportation into host cells and their targeting of specific genes to regulate the host's immune response. This knowledge gap presents an opportunity for future investigations, offering innovative approaches to enhance malarial control. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Jin-Guang Chen
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, China
| | - Shuang-Chun Liu
- Municipal Hospital Affiliated to Medical School of Taizhou University, Taizhou, China
| | - Qing Nie
- Weifang Centers for Disease Control and Prevention, Weifang, Shandong Province, China
| | - Yun-Ting Du
- Department of Laboratory Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Yin-Yi Lv
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, China
| | - Lian-Ping He
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, China
| | - Guang Chen
- Taizhou Central Hospital (Taizhou University Hospital), Taizhou University, Taizhou, China
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Feng F, Jiao P, Wang J, Li Y, Bao B, Luoreng Z, Wang X. Role of Long Noncoding RNAs in the Regulation of Cellular Immune Response and Inflammatory Diseases. Cells 2022; 11:cells11223642. [PMID: 36429069 PMCID: PMC9688074 DOI: 10.3390/cells11223642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/12/2022] [Accepted: 11/14/2022] [Indexed: 11/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are recently discovered genetic regulatory molecules that regulate immune responses and are closely associated with the occurrence and development of various diseases, including inflammation, in humans and animals. Under specific physiological conditions, lncRNA expression varies at the cell or tissue level, and lncRNAs can bind to specific miRNAs, target mRNAs, and target proteins to participate in certain processes, such as cell differentiation and inflammatory responses, via the corresponding signaling pathways. This review article summarizes the regulatory role of lncRNAs in macrophage polarization, dendritic cell differentiation, T cell differentiation, and endothelial and epithelial inflammation. In addition, it describes the molecular mechanism of lncRNAs in acute kidney injury, hepatitis, inflammatory injury of the lung, osteoarthritis, mastitis, and neuroinflammation to provide a reference for the molecular regulatory network as well as the genetic diagnosis and treatment of inflammatory diseases in humans and animals.
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Affiliation(s)
- Fen Feng
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Peng Jiao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jinpeng Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Yanxia Li
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Binwu Bao
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
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