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Ghahramani Almanghadim H, Karimi B, Valizadeh S, Ghaedi K. Biological functions and affected signaling pathways by Long Non-Coding RNAs in the immune system. Noncoding RNA Res 2025; 10:70-90. [PMID: 39315339 PMCID: PMC11417496 DOI: 10.1016/j.ncrna.2024.09.001] [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: 04/14/2024] [Revised: 08/14/2024] [Accepted: 09/01/2024] [Indexed: 09/25/2024] Open
Abstract
Recently, the various regulative functions of long non-coding RNAs (LncRNAs) have been well determined. Recently, the vital role of LncRNAs as gene regulators has been identified in the immune system, especially in the inflammatory response. All cells of the immune system are governed by a complex and ever-changing gene expression program that is regulated through both transcriptional and post-transcriptional processes. LncRNAs regulate gene expression within the cell nucleus by influencing transcription or through post-transcriptional processes that affect the splicing, stability, or translation of messenger RNAs (mRNAs). Recent studies in immunology have revealed substantial alterations in the expression of lncRNAs during the activation of the innate immune system as well as the development, differentiation, and activation of T cells. These lncRNAs regulate key aspects of immune function, including the manufacturing of inflammatory molecules, cellular distinction, and cell movement. They do this by modulating protein-protein interactions or through base pairing with RNA and DNA. Here we review the current understanding of the mechanism of action of lncRNAs as novel immune-related regulators and their impact on physiological and pathological processes related to the immune system, including autoimmune diseases. We also highlight the emerging pattern of gene expression control in important research areas at the intersection between immunology and lncRNA biology.
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Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Sepehr Valizadeh
- Department of Internal Medicine, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
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Arshi A, Mahmoudi E, Raeisi F, Dehghan Tezerjani M, Bahramian E, Ahmed Y, Peng C. Exploring potential roles of long non-coding RNAs in cancer immunotherapy: a comprehensive review. Front Immunol 2024; 15:1446937. [PMID: 39257589 PMCID: PMC11384988 DOI: 10.3389/fimmu.2024.1446937] [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: 06/10/2024] [Accepted: 08/05/2024] [Indexed: 09/12/2024] Open
Abstract
Cancer treatment has long been fraught with challenges, including drug resistance, metastasis, and recurrence, making it one of the most difficult diseases to treat effectively. Traditional therapeutic approaches often fall short due to their inability to target cancer stem cells and the complex genetic and epigenetic landscape of tumors. In recent years, cancer immunotherapy has revolutionized the field, offering new hope and viable alternatives to conventional treatments. A particularly promising area of research focuses on non-coding RNAs (ncRNAs), especially long non-coding RNAs (lncRNAs), and their role in cancer resistance and the modulation of signaling pathways. To address these challenges, we performed a comprehensive review of recent studies on lncRNAs and their impact on cancer immunotherapy. Our review highlights the crucial roles that lncRNAs play in affecting both innate and adaptive immunity, thereby influencing the outcomes of cancer treatments. Key observations from our review indicate that lncRNAs can modify the tumor immune microenvironment, enhance immune cell infiltration, and regulate cytokine production, all of which contribute to tumor growth and resistance to therapies. These insights suggest that lncRNAs could serve as potential targets for precision medicine, opening up new avenues for developing more effective cancer immunotherapies. By compiling recent research on lncRNAs across various cancers, this review aims to shed light on their mechanisms within the tumor immune microenvironment.
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Affiliation(s)
- Asghar Arshi
- Department of Biology, York University, Toronto, ON, Canada
| | - Esmaeil Mahmoudi
- Young Researchers and Elite Club, Islamic Azad University, Shahrekord, Iran
| | | | - Masoud Dehghan Tezerjani
- Department of bioinformatics, School of Advanced Medical Technologies, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Elham Bahramian
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Yeasin Ahmed
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, United States
| | - Chun Peng
- Department of Biology, York University, Toronto, ON, Canada
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Maqbool M, Hussain MS, Shaikh NK, Sultana A, Bisht AS, Agrawal M. Noncoding RNAs in the COVID-19 Saga: An Untold Story. Viral Immunol 2024; 37:269-286. [PMID: 38968365 DOI: 10.1089/vim.2024.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2024] Open
Affiliation(s)
- Mudasir Maqbool
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, India
| | - Md Sadique Hussain
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Nusrat K Shaikh
- Department of Quality Assurance, Smt. N. M. Padalia Pharmacy College, Ahmedabad, India
| | - Ayesha Sultana
- Department of Pharmaceutics, Yenepoya Pharmacy College & Research Centre, Yenepoya University, Mangalore, India
| | - Ajay Singh Bisht
- Shri Guru Ram Rai University School of Pharmaceutical Sciences, Dehradun, India
| | - Mohit Agrawal
- Department of Pharmacology, School of Medical & Allied Sciences, K. R. Mangalam University, Gurugram, India
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Heydari R, Karimi P, Meyfour A. Long non-coding RNAs as pathophysiological regulators, therapeutic targets and novel extracellular vesicle biomarkers for the diagnosis of inflammatory bowel disease. Biomed Pharmacother 2024; 176:116868. [PMID: 38850647 DOI: 10.1016/j.biopha.2024.116868] [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: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disease of the gastrointestinal (GI) system that includes two groups, Crohn's disease (CD) and ulcerative colitis (UC). To cope with these two classes of IBD, the investigation of pathogenic mechanisms and the discovery of new diagnostic and therapeutic approaches are crucial. Long non-coding RNAs (lncRNAs) which are non-coding RNAs with a length of longer than 200 nucleotides have indicated significant association with the pathology of IBD and strong potential to be used as accurate biomarkers in diagnosing and predicting responses to the IBD treatment. In the current review, we aim to investigate the role of lncRNAs in the pathology and development of IBD. We first describe recent advances in research on dysregulated lncRNAs in the pathogenesis of IBD from the perspective of epithelial barrier function, intestinal immunity, mitochondrial function, and intestinal autophagy. Then, we highlight the possible translational role of lncRNAs as therapeutic targets, diagnostic biomarkers, and predictors of therapeutic response in colon tissues and plasma samples. Finally, we discuss the potential of extracellular vesicles and their lncRNA cargo in the pathophysiology, diagnosis, and treatment of IBD.
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Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Padideh Karimi
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Han Y, Pu Q, Fan T, Wei T, Xu Y, Zhao L, Liu S. Long non-coding RNAs as promising targets for controlling disease vector mosquitoes. INSECT SCIENCE 2024. [PMID: 38783627 DOI: 10.1111/1744-7917.13383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 04/10/2024] [Accepted: 04/16/2024] [Indexed: 05/25/2024]
Abstract
Hematophagous female mosquitoes are important vectors of numerous devastating human diseases, posing a major public health threat. Effective prevention and control of mosquito-borne diseases rely considerably on progress in understanding the molecular mechanisms of various life activities, and accordingly, the molecules that regulate the various life activities of mosquitoes are potential targets for implementing future vector control strategies. Many long non-coding RNAs (lncRNAs) have been identified in mosquitoes and significant progress has been made in determining their functions. Here, we present a comprehensive overview of the research advances on mosquito lncRNAs, including their molecular identification, function, and interaction with other non-coding RNAs, as well as their synergistic regulatory roles in mosquito life activities. We also highlight the potential roles of competitive endogenous RNAs in mosquito growth and development, as well as in insecticide resistance and virus-host interactions. Insights into the biological functions and mechanisms of lncRNAs in mosquito life activities, viral replication, pathogenesis, and transmission will contribute to the development of novel drugs and safe vaccines.
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Affiliation(s)
- Yujiao Han
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Qian Pu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Ting Fan
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Tianqi Wei
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Yankun Xu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Lu Zhao
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
| | - Shiping Liu
- State Key Laboratory of Resource Insects, Southwest University, Chongqing, 400716, China
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Sharma S, Houfani AA, Foster LJ. Pivotal functions and impact of long con-coding RNAs on cellular processes and genome integrity. J Biomed Sci 2024; 31:52. [PMID: 38745221 PMCID: PMC11092263 DOI: 10.1186/s12929-024-01038-1] [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: 10/24/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Recent advances in uncovering the mysteries of the human genome suggest that long non-coding RNAs (lncRNAs) are important regulatory components. Although lncRNAs are known to affect gene transcription, their mechanisms and biological implications are still unclear. Experimental research has shown that lncRNA synthesis, subcellular localization, and interactions with macromolecules like DNA, other RNAs, or proteins can all have an impact on gene expression in various biological processes. In this review, we highlight and discuss the major mechanisms through which lncRNAs function as master regulators of the human genome. Specifically, the objective of our review is to examine how lncRNAs regulate different processes like cell division, cell cycle, and immune responses, and unravel their roles in maintaining genomic architecture and integrity.
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Affiliation(s)
- Siddhant Sharma
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Aicha Asma Houfani
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada.
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Xie KY, Chen SZ, Wang Y, Zeng ML, Liu XY, Liang Y, Wei J. Establishment and validation of a prognostic immune-related lncRNA risk model for acute myeloid leukemia. Transl Cancer Res 2023; 12:3693-3702. [PMID: 38192996 PMCID: PMC10774049 DOI: 10.21037/tcr-23-429] [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: 03/14/2023] [Accepted: 09/01/2023] [Indexed: 01/10/2024]
Abstract
Background Acute myeloid leukemia (AML) is a cancer arising in the bone marrow and is the most common type of adult leukemia. AML has a poor prognosis, and currently, its prognosis evaluation does not include immune status assessment. This study established an immune-related long non-coding RNA (lncRNA) prognostic risk model for AML based on immune lncRNAs screening. Methods To construct training and validation cohorts, The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) public databases were accessed to obtain gene expression profiles and clinical data. The correlation between lncRNAs and immunity genes was analyzed using the "limma" package, and the immune-related lncRNAs were obtained. Through least absolute shrinkage and selection operator regression, a prognostic model was established with immune-related lncRNAs. Using the median risk score, patients were divided into high- and low-risk groups. The Kaplan-Meier method was used for survival analysis, whereas the accuracy of the risk model was evaluated using time-dependent receiver operating characteristic curves, risk score distribution, survival status, and risk heat maps. We utilized univariate and multivariate Cox regression to examine the association between risk score and clinical variables and AML survival and prognosis. Results In the immune-related lncRNA prognostic risk model, the prognosis was better for low-risk than for high-risk patients, indicating risk score of this model as an independent indicator of prognosis. The area under the curve value for 1-, 3-, and 5-year survival of TCGA patients was 0.817, 0.859, and 0.909, respectively, whereas that of GEO patients (of dataset GPL96-GSE37642) was 0.603, 0.652, and 0.624, respectively. Gene set enrichment analysis revealed the enrichment of multiple pathways, such as antigen processing, B-cell receptor signaling pathway, natural killer cell-mediated cytotoxicity, and chemokines, in high-risk patients. Conclusions In this study, immune-related lncRNA prognostic risk models effectively predicted AML survival and provided potential treatment targets.
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Affiliation(s)
- Kun-Ying Xie
- Department of Hematology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Shu-Zhao Chen
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Yun Wang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Meng-Lan Zeng
- Department of Hematology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Xiao-Ying Liu
- Department of Hematology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Yang Liang
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jing Wei
- Department of Hematology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
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Bergonzini M, Loreni F, Lio A, Russo M, Saitto G, Cammardella A, Irace F, Tramontin C, Chello M, Lusini M, Nenna A, Ferrisi C, Ranocchi F, Musumeci F. Panoramic on Epigenetics in Coronary Artery Disease and the Approach of Personalized Medicine. Biomedicines 2023; 11:2864. [PMID: 37893238 PMCID: PMC10604795 DOI: 10.3390/biomedicines11102864] [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: 07/28/2023] [Revised: 10/02/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
Epigenetic modifications play a fundamental role in the progression of coronary artery disease (CAD). This panoramic review aims to provide an overview of the current understanding of the epigenetic mechanisms involved in CAD pathogenesis and highlights the potential implications for personalized medicine approaches. Epigenetics is the study of heritable changes that do not influence alterations in the DNA sequence of the genome. It has been shown that epigenetic processes, including DNA/histone methylation, acetylation, and phosphorylation, play an important role. Additionally, miRNAs, lncRNAs, and circRNAs are also involved in epigenetics, regulating gene expression patterns in response to various environmental factors and lifestyle choices. In the context of CAD, epigenetic alterations contribute to the dysregulation of genes involved in inflammation, oxidative stress, lipid metabolism, and vascular function. These epigenetic changes can occur during early developmental stages and persist throughout life, predisposing individuals to an increased risk of CAD. Furthermore, in recent years, the concept of personalized medicine has gained significant attention. Personalized medicine aims to tailor medical interventions based on an individual's unique genetic, epigenetic, environmental, and lifestyle factors. In the context of CAD, understanding the interplay between genetic variants and epigenetic modifications holds promise for the development of more precise diagnostic tools, risk stratification models, and targeted therapies. This review summarizes the current knowledge of epigenetic mechanisms in CAD and discusses the fundamental principles of personalized medicine.
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Affiliation(s)
- Marcello Bergonzini
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Francesco Loreni
- Cardiac Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Antonio Lio
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Marco Russo
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Guglielmo Saitto
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Antonio Cammardella
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Francesco Irace
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Corrado Tramontin
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Massimo Chello
- Cardiac Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Mario Lusini
- Cardiac Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Antonio Nenna
- Cardiac Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Chiara Ferrisi
- Cardiac Surgery, Università Campus Bio-Medico di Roma, 00128 Rome, Italy
| | - Federico Ranocchi
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
| | - Francesco Musumeci
- Department of Cardiac Surgery and Heart Transplantation, San Camillo Forlanini Hospital, 00152 Rome, Italy
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Chen P, Cai M, Feng YJ, Li C, Dong ZQ, Xiao WF, Tang L, Zhu Y, Tian T, Deng BY, Pan MH, Lu C. Apoptosis-related long non-coding RNA LINC5438 of Bombyx mori promotes the proliferation of BmNPV. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2023; 191:105380. [PMID: 36963947 DOI: 10.1016/j.pestbp.2023.105380] [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: 12/25/2022] [Revised: 02/12/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Apoptosis, as an important part of the immune response, is one of the core events in the host-virus interaction. Studies have shown that long non-coding RNAs (lncRNAs) play important roles in the process of cell apoptosis and pathophysiology. To investigate the apoptosis-related lncRNAs involved in Bombyx mori nucleopolyhedrovirus (BmNPV) infecting silkworms, transcriptome sequencing was conducted based on silkworm cells infected with BmNPV before and after B. mori inhibitor of apoptosis (Bmiap) gene knockout. A total of 23 differentially expressed lncRNAs were identified as being associated with the mitochondrial apoptosis pathway. Moreover, we demonstrated that B. mori LINC5438 has the function of inhibiting apoptosis in silkworm cells. Overexpression of LINC5438 promoted the proliferation of BmNPV, while interference with LINC5438 inhibited its proliferation, indicating that LINC5438 plays an important role in BmNPV infection. Our results also showed that LINC5438 can regulate the expression of Bmiap, BmDronc, BmICE, and its predicted target gene BmAIF, suggesting that LINC5438 may function through the mitochondrial pathway. These findings provide important insights into the mechanisms of virus-host interaction and the applications of baculoviruses as biological insecticides.
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Affiliation(s)
- Peng Chen
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Min Cai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Yu-Jie Feng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Cong Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Zhan-Qi Dong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Wen-Fu Xiao
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China; Sericultural Research Institute Sichuan Academy of Agricultural Sciences, Nanchong 637000, China
| | - Liang Tang
- Sericulture Technology Promotion Station of Guangxi, Nanning 530007, China
| | - Yan Zhu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Ting Tian
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Bo-Yuan Deng
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China
| | - Min-Hui Pan
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
| | - Cheng Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Southwest University, Beibei 400715, China.
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Long Noncoding RNA: A Novel Insight into the Pathogenesis of Acute Lung Injury. J Clin Med 2023; 12:jcm12020604. [PMID: 36675533 PMCID: PMC9861694 DOI: 10.3390/jcm12020604] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/15/2023] Open
Abstract
Acute lung injury (ALI) and its severe form, acute respiratory distress syndrome (ARDS), represent an acute stage of lung inflammation where the alveolar epithelium loses its functionality. ALI has a devastating impact on the population as it not only has a high rate of incidence, but also has high rates of morbidity and mortality. Due to the involvement of multiple factors, the pathogenesis of ALI is complex and is not fully understood yet. Long noncoding RNAs (lncRNAs) are a group of non-protein-coding transcripts longer than 200 nucleotides. Growing evidence has shown that lncRNAs have a decisive role in the pathogenesis of ALI. LncRNAs can either promote or hinder the development of ALI in various cell types in the lungs. Mechanistically, current studies have found that lncRNAs play crucial roles in the pathogenesis of ALI via the regulation of small RNAs (e.g., microRNAs) or downstream proteins. Undoubtedly, lncRNAs not only have the potential to reveal the underlying mechanisms of ALI pathogenesis but also serve as diagnostic and therapeutic targets for the therapy of ALI.
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Karthikeyan R, Gayathri P, Ramasamy S, Suvekbala V, Jagannadham MV, Rajendhran J. Transcriptome responses of intestinal epithelial cells induced by membrane vesicles of Listeria monocytogenes. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100185. [PMID: 36942003 PMCID: PMC10023947 DOI: 10.1016/j.crmicr.2023.100185] [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: 03/08/2023] Open
Abstract
Membrane vesicles (MVs) serve as an essential virulence factor in several pathogenic bacteria. The release of MVs by Listeria monocytogenes is only recently recognized; still, the enigmatic role of MVs in pathogenesis is yet to be established. We report the transcriptome response of Caco-2 cells upon exposure to MVs and the L. monocytogenes that leads to observe the up-regulation of autophagy-related genes in the early phase of exposure to MVs. Transcription of inflammatory cytokines is to the peak at the fourth hour of exposure. An array of differentially expressed genes was associated with actin cytoskeleton rearrangement, autophagy, cell cycle arrest, and induction of oxidative stress. At a later time point, transcriptional programs are generated upon interaction with MVs to evade innate immune signals, by modulating the expression of anti-inflammatory genes. KEGG pathway analysis is palpably confirming that MVs appear principally responsible for the induction of immune signaling pathways. Besides, MVs induced the expression of cell cycle regulatory genes, likely responsible for the ability to prolong host cell survival, thus protecting the replicative niche for L. monocytogenes. Notably, we identified several non-coding RNAs (ncRNAs), possibly involved in the regulation of early manipulation of the host gene expression, essential for the persistence of L. monocytogenes.
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Affiliation(s)
- Raman Karthikeyan
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
| | - Pratapa Gayathri
- CSIR - Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad 500007, India
| | - Subbiah Ramasamy
- Department of Biochemistry, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
| | - Vemparthan Suvekbala
- EDII-Anna Business Incubation Research Foundation, University College of Engineering, BIT Campus, Anna University, Tiruchirappalli 620024, India
| | - Medicharla V. Jagannadham
- CSIR - Centre for Cellular and Molecular Biology, Tarnaka, Hyderabad 500007, India
- Corresponding authors.
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, 625021, Tamil Nadu, India
- Corresponding authors.
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Chen G, Liu SC, Fan XY, Jin YL, Li X, Du YT. Plasmodium manipulates the expression of host long non-coding RNA during red blood cell intracellular infection. Parasit Vectors 2022; 15:182. [PMID: 35643541 PMCID: PMC9148527 DOI: 10.1186/s13071-022-05298-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 04/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parasites interact with their host through "direct" and/or "indirect" mechanisms. Plasmodium, for example, either mediates direct physical interactions with host factors or triggers the immune system of the host indirectly, leading to changes in infectious outcomes. Long non-coding RNAs (lncRNAs) participate in regulating biological processes, especially host-pathogen interactions. However, research on the role of host lncRNAs during Plasmodium infection is limited. METHODS A RNA sequencing method (RNA-seq) was used to confirm the differential expression profiles of lncRNAs in Plasmodium yeolii 17XL (P.y17XL)-infected BALB/c mice. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to elucidate the potential functions of Plasmodium-induced genes. Subsequently, the effect of specific lncRNAs on the modulation of immune-related signaling pathways in malaria was determined by fluorescence-activated cell sorting, western blot and enzyme-linked immunosorbent assay. RESULTS The data showed that in P.y17XL-infected BALB/c mice, Plasmodium upregulated the expression of 132 lncRNAs and downregulated the expression of 159 lncRNAs. Differentially expressed lncRNAs clearly associated with malaria infection were annotated, including four novel dominant lncRNAs: ENMSUSG00000111521.1, XLOC_038009, XLOC_058629 and XLOC_065676. GO and KEGG pathway analyses demonstrated that these four differentially expressed lncRNAs were associated with co-localized/co-expressed protein-coding genes that were totally enriched in malaria and with the transforming growth factor beta (TGF-β) signaling pathway. Using the models of P.y17XL-infected BALB/c mice, data certified that the level of TGF-β production and activation of TGF-β/Smad2/3 signaling pathway were obviously changed in malaria infection. CONCLUSIONS These differentially expressed immune-related genes were deemed to have a role in the process of Plasmodium infection in the host via dendritic/T regulatory cells and the TGF-β/Smad2/3 signaling pathway. The results of the present study confirmed that Plasmodium infection-induced lncRNA expression is a novel mechanism used by Plasmodium parasites to modify host immune signaling. These results further enhance current understanding of the interaction between Plasmodium and host cells.
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Affiliation(s)
- Guang Chen
- Department of Basic Medical Sciences, Taizhou University, No. 1139 Shifu Road, Jiaojiang District, Taizhou, 318000, China
| | - Shuang-Chun Liu
- Municipal Hospital Affiliated to Medical School of Taizhou University, No. 381, Zhongshan East Road, Jiaojiang District, Taizhou, 318000, China
| | - Xiao-Yan Fan
- Department of Basic Medical Sciences, Taizhou University, No. 1139 Shifu Road, Jiaojiang District, Taizhou, 318000, China
| | - Yue-Lei Jin
- Department of Basic Medical Sciences, Taizhou University, No. 1139 Shifu Road, Jiaojiang District, Taizhou, 318000, China
| | - Xin Li
- Department of Basic Medical Sciences, Taizhou University, No. 1139 Shifu Road, Jiaojiang District, Taizhou, 318000, China
| | - Yun-Ting Du
- Department of Laboratory Medicine, Cancer Hospital of China Medical University-Liaoning Cancer Hospital & Institute, No. 44 Xiaoheyan Road, Dadong District, Shenyang, 110042, China.
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13
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Pandey PR, Young KH, Kumar D, Jain N. RNA-mediated immunotherapy regulating tumor immune microenvironment: next wave of cancer therapeutics. Mol Cancer 2022; 21:58. [PMID: 35189921 PMCID: PMC8860277 DOI: 10.1186/s12943-022-01528-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/31/2022] [Indexed: 12/16/2022] Open
Abstract
AbstractAccumulating research suggests that the tumor immune microenvironment (TIME) plays an essential role in regulation of tumor growth and metastasis. The cellular and molecular nature of the TIME influences cancer progression and metastasis by altering the ratio of immune- suppressive versus cytotoxic responses in the vicinity of the tumor. Targeting or activating the TIME components show a promising therapeutic avenue to combat cancer. The success of immunotherapy is both astounding and unsatisfactory in the clinic. Advancements in RNA-based technology have improved understanding of the complexity and diversity of the TIME and its effects on therapy. TIME-related RNA or RNA regulators could be promising targets for anticancer immunotherapy. In this review, we discuss the available RNA-based cancer immunotherapies targeting the TIME. More importantly, we summarize the potential of various RNA-based therapeutics clinically available for cancer treatment. RNA-dependent targeting of the TIME, as monotherapy or combined with other evolving therapeutics, might be beneficial for cancer patients’ treatment in the near future.
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14
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Han S, Zhang XL, Jiang X, Li X, Ding J, Zuo LJ, Duan SS, Chen R, Sun BB, Hu XY, Gao YN, Zhang XL. Long Non-Coding RNA and mRNA Expression Analysis in Liver of Mice With Clonorchis sinensis Infection. Front Cell Infect Microbiol 2022; 11:754224. [PMID: 35127549 PMCID: PMC8807509 DOI: 10.3389/fcimb.2021.754224] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/07/2021] [Indexed: 12/13/2022] Open
Abstract
Clonorchiasis is recognized as an important zoonotic parasitic disease worldwide. However, the roles of host long non-coding RNAs (lncRNAs) and messenger RNAs (mRNAs) in the response to Clonorchis sinensis (C. sinensis) infection remain unknown. Here we compared the expression of lncRNAs and mRNAs in the liver tissue of mice infected with C. sinensis, in order to further understand the molecular mechanisms of clonorchiasis. A total of 388 lncRNAs and 1,172 mRNAs were found to be differentially expressed with absolute value of fold change (FC) ≥ 2.0 and p < 0.05 by microarray. Compared with controls, Gm6135 and 4930581F22Rik were the most over- and under-expressed lncRNAs; flavin-containing monooxygenase 3 (Fmo3) and deleted in malignant brain tumors 1 (Dmbt1) were the most over- and under-expressed mRNAs. Moreover, functional annotation showed that the significantly different mRNAs were related with “FOXO signaling pathway”, “Wnt signaling pathway”, and “AMPK signaling pathway”. Remarkably, lncRNA Gm8801 were significantly correlated with mRNA glycerol-3-phosphate acyltransferase mitochondrial (Gpam), insulin receptor substrate 2 (Irs2), and tumor necrosis factor receptor superfamily member 19 (Tnfrsf19) in ceRNA networks. These results showed that the expression profiles of lncRNAs and mRNAs in the liver changed after C. sinensis infection. Our results provided valuable insights into the lncRNAs and mRNAs involved in clonorchiasis pathogenesis, which may be useful for future control strategies.
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Affiliation(s)
- Su Han
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Xue-Li Zhang
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Xu Jiang
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Xiang Li
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Jian Ding
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Li-Jiao Zuo
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Shan-Shan Duan
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Rui Chen
- Department of Orthopaedic Surgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bei-Bei Sun
- Clinical Laboratory, Zhuhai Maternal and Child Health Hospital, Zhuhai, China
| | - Xin-Yi Hu
- Department of Stomatology, Laixi People’s Hospital, Qingdao, China
| | - Yan-Nan Gao
- Department of Parasitology, Harbin Medical University, Harbin, China
| | - Xiao-Li Zhang
- Department of Parasitology, Harbin Medical University, Harbin, China
- *Correspondence: Xiao-Li Zhang,
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15
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Chen Y, Li H, Lai L, Huang Y, Shen J. Discovery of new long noncoding RNAs associated with ulcerative colitis with a novel general microarray expression data. Life Sci 2021; 287:120090. [PMID: 34715141 DOI: 10.1016/j.lfs.2021.120090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/13/2021] [Accepted: 10/21/2021] [Indexed: 01/01/2023]
Abstract
UC is a chronic, nonspecific disease and characterized by a chronic relapsing intestinal inflammation, which puts a person at a higher risk of developing bowel cancer, while the causes of UC are unknown. Recently, with the development of microarray technology, more and more studies are focusing on the potential roles of long noncoding RNAs (lncRNAs) in the pathogenesis of diseases. The purpose of this study is to devise a method, based on cDNA microarray probe genomics data, to computationally determine the potential function of evolutionary conserved lncRNAs in ulcerative colitis (UC). We analysed a total of 12,593 microarray probes present in the Ensembl, OMIM, UniGene, and Gene Ontology databases. We found that lncRNA n385775 was significantly higher (P < 0.001) in patients with active UC, while n336281 (P = 0.017), n341081 (P = 0.041), and n387236 (P = 0.006) were significantly lower. Then, we validated our findings by measuring the expression of lncRNAs in colon tissue samples from patients affected by UC. Moreover, we validated the expression pattern of the lncRNAs in two cell lines, Caco2/bbe and T84, treated with TNF-α. In Caco2/bbe cells, lncRNA n385775 was significantly upregulated after TNF-α treatment (P = 0.002). This study reports a novel method to re- annotate the transcriptome expression profile from existing cDNA microarray data as a potential approach to investigate the function of lncRNAs in UC.
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Affiliation(s)
- Yueying Chen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China
| | - HanyangLi Li
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China
| | - Lijie Lai
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China
| | - Yong Huang
- INMD Pulmonary, University of Virginia, 81 Hospital Dr CHARLOTTESVILLE, VA 22903, USA.
| | - Jun Shen
- Division of Gastroenterology and Hepatology, Key Laboratory of Gastroenterology and Hepatology, Ministry of Health, Inflammatory Bowel Disease Research Center, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Institute of Digestive Disease, 160# Pu Jian Ave, Shanghai 200127, China.
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16
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Huang SF, Peng XF, Jiang L, Hu CY, Ye WC. LncRNAs as Therapeutic Targets and Potential Biomarkers for Lipid-Related Diseases. Front Pharmacol 2021; 12:729745. [PMID: 34421622 PMCID: PMC8371450 DOI: 10.3389/fphar.2021.729745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 07/26/2021] [Indexed: 12/30/2022] Open
Abstract
Lipid metabolism is an essential biological process involved in nutrient adjustment, hormone regulation, and lipid homeostasis. An irregular lifestyle and long-term nutrient overload can cause lipid-related diseases, including atherosclerosis, myocardial infarction (MI), obesity, and fatty liver diseases. Thus, novel tools for efficient diagnosis and treatment of dysfunctional lipid metabolism are urgently required. Furthermore, it is known that lncRNAs based regulation like sponging microRNAs (miRNAs) or serving as a reservoir for microRNAs play an essential role in the progression of lipid-related diseases. Accordingly, a better understanding of the regulatory roles of lncRNAs in lipid-related diseases would provide the basis for identifying potential biomarkers and therapeutic targets for lipid-related diseases. This review highlighted the latest advances on the potential biomarkers of lncRNAs in lipid-related diseases and summarised current knowledge on dysregulated lncRNAs and their potential molecular mechanisms. We have also provided novel insights into the underlying mechanisms of lncRNAs which might serve as potential biomarkers and therapeutic targets for lipid-related diseases. The information presented here may be useful for designing future studies and advancing investigations of lncRNAs as biomarkers for diagnosis, prognosis, and therapy of lipid-related diseases.
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Affiliation(s)
- Shi-Feng Huang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Xiao-Fei Peng
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Lianggui Jiang
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
| | - Ching Yuan Hu
- Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Wen-Chu Ye
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, China
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17
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Bhat B, Ganai NA, Singh A, Mir R, Ahmad SM, Majeed Zargar S, Malik F. Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation. Front Genet 2021; 12:695178. [PMID: 34354739 PMCID: PMC8329486 DOI: 10.3389/fgene.2021.695178] [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: 04/14/2021] [Accepted: 06/22/2021] [Indexed: 11/13/2022] Open
Abstract
Pashmina goats produce the world's finest and the most costly animal fiber (Pashmina) with an average fineness of 11-13 microns and have more evolved mechanisms than any known goat breed around the globe. Despite the repute of Pashmina goat for producing the finest and most sought-after animal fiber, meager information is available in the public domain about Pashmina genomics and transcriptomics. Here we present a 2.94 GB genome sequence from a male Changthangi white Pashmina goat. We generated 294.8 GB (>100X coverage) of the whole-genome sequence using the Illumina HiSeq 2500 sequencer. All cleaned reads were mapped to the goat reference genome (2,922,813,246 bp) which covers 97.84% of the genome. The Unaligned reads were used for de novo assembly resulting in a total of 882 MB non-reference contigs. De novo assembly analysis presented in this study provides important insight into the adaptation of Pashmina goats to cold stress and helps enhance our understanding of this complex phenomenon. A comparison of the Pashmina goat genome with a wild goat genome revealed a total of 2,823 high impact single nucleotide variations and small insertions and deletions, which may be associated with the evolution of Pashmina goats. The Pashmina goat genome sequence provided in this study may improve our understanding of complex traits found in Pashmina goats, such as annual fiber cycling, defense mechanism against hypoxic, survival secret in extremely cold conditions, and adaptation to a sparse diet. In addition, the genes identified from de novo assembly could be utilized in differentiating Pashmina fiber from other fibers to avoid falsification at marketing practices.
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Affiliation(s)
- Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Nazir A Ganai
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Ashutosh Singh
- Department of Life Science, Shiv Nadar University, Greater Noida, India
| | - Rakeeb Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Sajad Majeed Zargar
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences Technology of Kashmir, Srinagar, India
| | - Firdose Malik
- Division of Temperate Sericulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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18
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Pi YN, Qi WC, Xia BR, Lou G, Jin WL. Long Non-Coding RNAs in the Tumor Immune Microenvironment: Biological Properties and Therapeutic Potential. Front Immunol 2021; 12:697083. [PMID: 34295338 PMCID: PMC8290853 DOI: 10.3389/fimmu.2021.697083] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022] Open
Abstract
Cancer immunotherapy (CIT) is considered a revolutionary advance in the fight against cancer. The complexity of the immune microenvironment determines the success or failure of CIT. Long non-coding RNA (lncRNA) is an extremely versatile molecule that can interact with RNA, DNA, or proteins to promote or inhibit the expression of protein-coding genes. LncRNAs are expressed in many different types of immune cells and regulate both innate and adaptive immunity. Recent studies have shown that the discovery of lncRNAs provides a novel perspective for studying the regulation of the tumor immune microenvironment (TIME). Tumor cells and the associated microenvironment can change to escape recognition and elimination by the immune system. LncRNA induces the formation of an immunosuppressive microenvironment through related pathways, thereby controlling the escape of tumors from immune surveillance and promoting the development of metastasis and drug resistance. Using lncRNA as a therapeutic target provides a strategy for studying and improving the efficacy of immunotherapy.
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Affiliation(s)
- Ya-Nan Pi
- Department of Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wen-Cai Qi
- Department of Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Bai-Rong Xia
- Department of Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ge Lou
- Department of Gynecology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wei-Lin Jin
- Institute of Cancer Neuroscience, Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, The First Clinical Medical College of Lanzhou University, Lanzhou, China
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19
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Xu X, Zhong Z, Shao Y, Yi Y. Prognostic Value of MEG3 and Its Correlation With Immune Infiltrates in Gliomas. Front Genet 2021; 12:679097. [PMID: 34220951 PMCID: PMC8242350 DOI: 10.3389/fgene.2021.679097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 12/24/2022] Open
Abstract
Accumulating evidence has revealed that dysregulated lncRNA expression contributes to the onset and progression of cancer. However, the mechanistic role of lncRNA in glioma progression and tumor immunology remains largely unknown. This study aimed to evaluate the significance of maternally expressed gene 3 (MEG3) in the prognosis of and its immune-related roles in gliomas. The expression levels of MEG3 were analyzed using Oncomine and TIMER database. As an important imprinted gene, the copy number variation (CNV) of MEG3 in both glioblastoma multiforme (GBM) and low-grade glioma (LGG) were analyzed using GSCALite database, whereas its prognostic significance was assessed using PrognoScan and GEPIA databases. The relationship between MEG3 and tumor-infiltrated immune cells was analyzed using TIMER. Results showed that MEG3 expression was lower in most of the human cancer tissues than in the normal tissues. We also found that heterozygous deletion of MEG3 occurred more frequent than heterozygous amplification in gliomas, and mRNA expression of MEG3 was significantly positively correlated with its CNV in both the GBM and LGG group. Survival analysis showed that the CNV level of MEG3 had significant correlation with overall survival (OS) and progression-free survival (PFS) compared with wild type in LGG. Lower MEG3 expression was related with poor prognosis. Further analysis showed that in GBM, MEG3 expression level was significantly positively correlated with that of infiltrating CD8+ T cells and significantly negatively correlated with that of infiltrating dendritic cells. In LGG, MEG3 expression level was significantly negatively correlated with levels of infiltrating B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. Univariate Cox survival analysis demonstrated that only the level of infiltrating dendritic cells significantly affected the survival time of patients with GBM, while all six types of immune cells had a significant effect on the survival time of patients with LGG. Furthermore, MEG3 expression showed strong correlations with multiple immune markers in gliomas, especially in LGG. The current findings suggest that MEG3 expression might serve as a possible prognostic marker and potential immunotherapeutic target for gliomas.
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Affiliation(s)
- Xiaoping Xu
- Department of Neurosurgery, The Second People's Hospital of Yibin, Yibin, China
| | - Zhenglan Zhong
- Department of Health Examination, The Second People's Hospital of Yibin, Yibin, China
| | - Yongxiang Shao
- Department of Neurosurgery, The Second People's Hospital of Yibin, Yibin, China
| | - Yong Yi
- Department of Neurosurgery, The Second People's Hospital of Yibin, Yibin, China
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20
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Chang L, Li J, Ding J, Lian Y, Huangfu C, Wang K. Roles of long noncoding RNAs on tumor immune escape by regulating immune cells differentiation and function. Am J Cancer Res 2021; 11:2369-2385. [PMID: 34249405 PMCID: PMC8263655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/20/2021] [Indexed: 06/13/2023] Open
Abstract
A long noncoding RNA (lncRNA) transcript is generally more than 200 nucleotides in length and rarely codes for any protein. Currently, many lncRNAs have been identified among mammalian genomes, and their known functions are associated with various physiological activities or pathological processes. Some lncRNAs are dysregulated in a variety of malignant tumors, while increasing evidence indicates that abnormal expression can contribute to the regulation of immune cells in tumors and to shaping the immune response. More specifically, lncRNAs participate in regulating the differentiation of immune cells, also known as myeloid and lymphoid cells, as well as recruiting various immunosuppressive factors to influence the tumor microenvironment, thereby promoting tumor cell immune escape. However, we still know very little about the specific mechanism of lncRNAs in immune escape of cancer. Nonetheless, although unprecedented achievements have allowed the development of a new generation of anti-tumor immune therapies to be applied in clinical trials, the drug resistance caused by immune escape has become a major clinical challenge. The focus of this review is to describe the relationship among lncRNAs, immune cells, and tumor immune escape, in order to identify novel diagnostic and therapeutic targets in human cancers.
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Affiliation(s)
- Lisha Chang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical UniversityNanjing, Jiangsu, People’s Republic of China
| | - Juan Li
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical UniversityNanjing, Jiangsu, People’s Republic of China
| | - Jie Ding
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical UniversityNanjing, Jiangsu, People’s Republic of China
| | - Yifan Lian
- Department of Gastroenterology, Zhongshan Hospital, Xiamen UniversityXiamen, Fujian, People’s Republic of China
| | - Chaonan Huangfu
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical UniversityNanjing, Jiangsu, People’s Republic of China
| | - Keming Wang
- Department of Oncology, Second Affiliated Hospital, Nanjing Medical UniversityNanjing, Jiangsu, People’s Republic of China
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21
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Ganguly B. A parsimonious approach for recognizing SARS-CoV-2 and host interactions. J Med Virol 2021; 93:4576-4584. [PMID: 33506962 PMCID: PMC8014500 DOI: 10.1002/jmv.26824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/04/2021] [Accepted: 01/22/2021] [Indexed: 11/23/2022]
Abstract
Effective countermeasures against the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) demand a better understanding of the pathogen‐host interactions. However, such information about the targets, responses, and effects in the host due to the virus is limited, especially so in the case of newly emerged pathogens. The peptide domains that form the interfaces of host and pathogen interacting proteins being evolutionarily conserved, it may be hypothesized that such interactions can be inferred from the similarities in the nucleotide sequences between the host and the pathogen. This communication reports the results of a study based on a parsimonious approach for the identification of the host‐virus interactions, where sequence complementarity between the human and SARS‐Cov‐2 genomes was used to predict several interactions between the host and SARS‐CoV‐2 at different levels of biological organization. In particular, the findings are suggestive of a direct effect of SARS‐CoV‐2 on cardiac health. The existing literature on host responses to SARS‐CoV‐2 and other viruses attest to many of these predicted interactions, supporting the utility of the proposed approach for the identification of host interactions with other novel pathogens.
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Affiliation(s)
- Bhaskar Ganguly
- Department of Clinical Research, Research and Development Division, Ayurvet Limited, Baddi, Himachal Pradesh, India
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22
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Hu J, Li W, Huang B, Zhao Q, Fan X. The Profiles of Long Non-coding RNA and mRNA Transcriptome Reveals the Genes and Pathway Potentially Involved in Pasteurella multocida Infection of New Zealand Rabbits. Front Vet Sci 2021; 8:591273. [PMID: 34026883 PMCID: PMC8131872 DOI: 10.3389/fvets.2021.591273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 03/19/2021] [Indexed: 12/22/2022] Open
Abstract
Infection with Pasteurella multocida (P. multocida) causes severe epidemic diseases in rabbits and is responsible for the pronounced economic losses in the livestock industry. Long non-coding RNAs (lncRNAs) have been proven to exert vital functions in regulating the host immune responses to bacterial attacks. However, little is known about how lncRNAs participate in the rabbit's immune response against P. multocida infection in the lungs. LncRNA and mRNA expression profiles were analyzed by transcriptomics and bioinformatics during P. multocida infection. A total of 336 lncRNAs and 7,014 mRNAs were differentially regulated at 1 day and 3 days post infection (dpi). Nearly 80% of the differentially expressed lncRNAs exhibited an increased expression at 3 dpi suggesting that the P. multocida genes are responsible for regulation. Moreover, GO and KEGG enriched analysis indicated that the immune-related pathways including pattern recognition receptors (PRRs), cytokines, and chemokines were significantly enriched at 3 dpi. These results indicate that the dysregulated immune-related genes may play crucial roles in defending against P. multocida attacks. Overall, these results advance our cognition of the role of lncRNAs and mRNAs in modulating the rabbit's innate immune response against P. multocida attacks, which will offer a valuable clue for further studies into exploring P. multocida-related diseases in human.
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Affiliation(s)
- Jiaqing Hu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Wenqiang Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
| | - Bing Huang
- Shandong Provincial Key Laboratory of Poultry Disease Diagnose and Immune, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Qiaoya Zhao
- Shandong Provincial Key Laboratory of Poultry Disease Diagnose and Immune, Institute of Poultry, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xinzhong Fan
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Taian, China
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23
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Donkel SJ, Portilla Fernández E, Ahmad S, Rivadeneira F, van Rooij FJA, Ikram MA, Leebeek FWG, de Maat MPM, Ghanbari M. Common and Rare Variants Genetic Association Analysis of Circulating Neutrophil Extracellular Traps. Front Immunol 2021; 12:615527. [PMID: 33717105 PMCID: PMC7944992 DOI: 10.3389/fimmu.2021.615527] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/04/2021] [Indexed: 12/27/2022] Open
Abstract
Introduction Neutrophils contribute to host defense through different mechanisms, including the formation of neutrophil extracellular traps (NETs). The genetic background and underlying mechanisms contributing to NET formation remain unclear. Materials and Methods We performed a genome-wide association study (GWAS) and exome-sequencing analysis to identify common and rare genetic variants associated with plasma myeloperoxidase (MPO)-DNA complex levels, a biomarker for NETs, in the population-based Rotterdam Study cohort. GWAS was performed using haplotype reference consortium(HRC)-imputed genotypes of common variants in 3,514 individuals from the first and 2,076 individuals from the second cohort of the Rotterdam Study. We additionally performed exome-sequencing analysis in 960 individuals to investigate rare variants in candidate genes. Results The GWAS yielded suggestive associations (p-value < 5.0 × 10-6) of SNPs annotated to four genes. In the exome-sequencing analysis, a variant in TMPRSS13 gene was significantly associated with MPO-DNA complex levels (p-value < 3.06×10-8). Moreover, gene-based analysis showed ten genes (OR10H1, RP11-461L13.5, RP11-24B19.4, RP11-461L13.3, KHDRBS1, ZNF200, RP11-395I6.1, RP11-696P8.2, RGPD1, AC007036.5) to be associated with MPO-DNA complex levels (p-value between 4.48 × 10-9 and 1.05 × 10-6). Pathway analysis of the identified genes showed their involvement in cellular development, molecular transport, RNA trafficking, cell-to-cell signaling and interaction, cellular growth and proliferation. Cancer was the top disease linked to the NET-associated genes. Conclusion In this first GWAS and exome-sequencing analysis of NETs levels, we found several genes that were associated with NETs. The precise mechanism of how these genes may contribute to neutrophil function or the formation of NETs remains unclear and should be further investigated in experimental studies.
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Affiliation(s)
- Samantha J Donkel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | | | - Shahzad Ahmad
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands.,Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, Netherlands
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands.,Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Frank W G Leebeek
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Moniek P M de Maat
- Department of Hematology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, Netherlands
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24
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LncRNAs and Immunity: Coding the Immune System with Noncoding Oligonucleotides. Int J Mol Sci 2021; 22:ijms22041741. [PMID: 33572313 PMCID: PMC7916124 DOI: 10.3390/ijms22041741] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/03/2021] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) represent key regulators of gene transcription during the inflammatory response. Recent findings showed lncRNAs to be dysregulated in human diseases, such as inflammatory bowel disease, diabetes, allergies, asthma, and cancer. These noncoding RNAs are crucial for immune mechanism, as they are involved in differentiation, cell migration and in the production of inflammatory mediators through regulating protein–protein interactions or their ability to assemble with RNA and DNA. The last interaction can occur in cis or trans and is responsible for all the possible lncRNAs biological effects. Our proposal is to provide an overview on lncRNAs roles and functions related to immunity and immune mediated diseases, since these elucidations could be beneficial to untangle the complex bond between them.
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Zhang Y, Dong X, Wang Y, Wang L, Han G, Jin L, Fan Y, Xu G, Yuan D, Zheng J, Guo X, Gao P. Overexpression of LncRNA BM466146 Predicts Better Prognosis of Breast Cancer. Front Oncol 2021; 10:628757. [PMID: 33585256 PMCID: PMC7878538 DOI: 10.3389/fonc.2020.628757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/10/2020] [Indexed: 12/19/2022] Open
Abstract
This study analyzes the expression and clinical significance of long non-coding RNA (lncRNA) BM466146 in breast cancer, and explores the role of BM466146 in immune regulation. The expression of BM466146 in 89 cases of breast cancer and their corresponding non-cancerous breast tissues was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Kaplan-Meier survival analysis was applied to evaluate patient survival. EDU and CCK-8 experiments on breast cancer cells were performed to verify the function of BM466146 in vitro. The target genes of BM466146 were screened by informatics analysis to predict associated miRNAs and their corresponding mRNAs, immune genes associated with lncRNAs and chemokines associated with CD8. Immunohistochemistry was used to detect the expression of CD8, Ki-67, and CXCL-13 in the 89 breast cancer tissues. It was found that the expression of lncRNA BM466146 in breast cancer tissues was significantly lower than that in normal breast tissues (P < 0.001). In breast cancer, tissues that overexpressed BM466146 exhibited a lower Ki-67 index compared with that of low BM466146 expression (P = 0.048). Kaplan-Meier survival analysis showed that breast cancer patients with overexpression of BM466146 had longer overall survival. EDU and CCK8 experiments showed that overexpression of BM466146 inhibited the proliferation of breast cancer cells. The hsa-miR-224-3p is associated with BM466146, and its target gene might be CXCL-13. The positive CD8 cells in the BM466146 overexpression group was higher than that in the low BM466146 expression group (P=0.027), and the positive CD8 cells in the CXCL-13 positive group was higher (P=0.023) than that of the negative group. Our results indicate that the lncRNA BM466146 has the function of tumor suppressor gene. Overexpression of BM466146 is associated with better prognosis. BM466146 could regulate CXCL-13 by adsorbing hsa-miR-224-3p and inducing CD8+ T cells to accumulate in the tumor area which regulate immune response. Therefore, BM466146 could be a prognostic biomarker and a molecular immune target of breast cancer.
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Affiliation(s)
- Yunxiang Zhang
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China.,Pathology Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Xiaotong Dong
- Pathology Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Yang Wang
- Breast Surgery Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Liquan Wang
- Breast Surgery Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Guiyan Han
- Pathology Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Lvcheng Jin
- Pathology Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Yanping Fan
- Pathology Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Guodong Xu
- Pathology Department, First Affiliated Hospital of Weifang Medical University, (Weifang People's Hospital), Weifang, China
| | - Dawei Yuan
- Precision Medicine Department, Geneis Beijing Co., Ltd., Beijing, China
| | - Jie Zheng
- Department of Diagnostic Pathology, Weifang Medical University, Weifang, China
| | - Xiangyu Guo
- Department of Pathology, Qilu Hospital, Shandong University, Jinan, China
| | - Peng Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, China
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26
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Sumi MP, Mahajan B, Sattar RSA, Nimisha, Apurva, Kumar A, Sharma AK, Ahmad E, Ali A, Saluja SS. Elucidation of Epigenetic Landscape in Coronary Artery Disease: A Review on Basic Concept to Personalized Medicine. Epigenet Insights 2021; 14:2516865720988567. [PMID: 33598635 PMCID: PMC7863167 DOI: 10.1177/2516865720988567] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/26/2020] [Indexed: 12/11/2022] Open
Abstract
Despite extensive clinical research and management protocols applied in the field of coronary artery diseases (CAD), it still holds the number 1 position in mortality worldwide. This indicates that we need to work on precision medicine to discover the diagnostic, therapeutic, and prognostic targets to improve the outcome of CAD. In precision medicine, epigenetic changes play a vital role in disease onset and progression. Epigenetics is the study of heritable changes that do not affect the alterations of DNA sequence in the genome. It comprises various covalent modifications that occur in DNA or histone proteins affecting the spatial arrangement of the DNA and histones. These multiple modifications include DNA/histone methylation, acetylation, phosphorylation, and SUMOylation. Besides these covalent modifications, non-coding RNAs-viz. miRNA, lncRNA, and circRNA are also involved in epigenetics. Smoking, alcohol, diet, environmental pollutants, obesity, and lifestyle are some of the prime factors affecting epigenetic alterations. Novel molecular techniques such as next-generation sequencing, chromatin immunoprecipitation, and mass spectrometry have been developed to identify important cross points in the epigenetic web in relation to various diseases. The studies regarding exploration of epigenetics, have led researchers to identify multiple diagnostic markers and therapeutic targets that are being used in different disease diagnosis and management. Here in this review, we will discuss various ground-breaking contributions of past and recent studies in the epigenetic field in concert with coronary artery diseases. Future prospects of epigenetics and its implication in CAD personalized medicine will also be discussed in brief.
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Affiliation(s)
- Mamta P Sumi
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
| | - Bhawna Mahajan
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
- Department of Biochemistry, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
| | - Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
| | - Abhay Kumar Sharma
- Department of Biochemistry, All India Institute of Medical Science, Patna, Bihar, India
| | - Ejaz Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
| | - Asgar Ali
- Department of Biochemistry, All India Institute of Medical Science, Patna, Bihar, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant Institute of Post Graduate Medical Education and Research (GIPMER), University of Delhi, New Delhi, India
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Xu Y, Yu J, Ma C, Gong Z, Wu X, Deng G. Impact of knockdown LincRNA-Cox2 on apoptosis of macrophage infected with Bacillus Calmette-Guérin. Mol Immunol 2020; 130:85-95. [PMID: 33250268 DOI: 10.1016/j.molimm.2020.11.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 09/23/2020] [Accepted: 11/09/2020] [Indexed: 02/06/2023]
Abstract
Mycobacterium tuberculosis (Mtb)-induced apoptosis of alveolar macrophages plays an important role in the pathogenesis of tuberculosis. Previous studies indicated that massive LncRNAs could deteriorate MTB invasion or latent infection by regulating macrophage's apoptosis. However, whether LincRNA-Cox2 is involved in apoptosis of macrophage infected with Mtb is unclear. In this study, we found Bacillus Calmette-Guerin(BCG)infection induced cell apoptosis with a increasing LincRNA-Cox2 expression in RAW264.7 cells. Furthermore, the activation of TLR signal pathway elevated the expression of lincRNA-Cox2. In this regard, we used small interfering RNA to explore the role of LincRNA-Cox2 on regulating apoptosis of RAW264.7 cells infected with BCG. The results showed that si-LincRNA-Cox2 was capable of increased the expression of apoptosis-associated proteins and accumulation of ROS in BCG-infected RAW264.7 cells. Mechanically, si-LincRNA-Cox2 facilitated BCG-induced macrophage apoptosis by activating the intrinsic apoptotic pathway as well as increased the genes expression of PERK/eIF2α/CHOP. These results provide novel insights into host-pathogen interactions and highlight the potential role of LincRNA-Cox2 in regulating apoptosis induced by BCG-infection.
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Affiliation(s)
- Yanan Xu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, NingXia University, NingXia, Yinchuan, 750021, China; School of Life Science, NingXia University, NingXia, Yinchuan, 750021, China
| | - Jialin Yu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, NingXia University, NingXia, Yinchuan, 750021, China; School of Life Science, NingXia University, NingXia, Yinchuan, 750021, China
| | - Chenjie Ma
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, NingXia University, NingXia, Yinchuan, 750021, China; School of Life Science, NingXia University, NingXia, Yinchuan, 750021, China
| | - Zhaoqian Gong
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, NingXia University, NingXia, Yinchuan, 750021, China; School of Life Science, NingXia University, NingXia, Yinchuan, 750021, China
| | - Xiaoling Wu
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, NingXia University, NingXia, Yinchuan, 750021, China; School of Life Science, NingXia University, NingXia, Yinchuan, 750021, China.
| | - Guangcun Deng
- Key Lab of Ministry of Education for Protection and Utilization of Special Biological Resources in Western China, NingXia University, NingXia, Yinchuan, 750021, China; School of Life Science, NingXia University, NingXia, Yinchuan, 750021, China.
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Wang W, Xin J, Chen W, Jing L, Zhang P. Icariin alleviates hypoxia-induced damage in MC3T3-E1 cells by downregulating TALNEC2. Biotechnol Appl Biochem 2019; 67:1000-1010. [PMID: 31845407 DOI: 10.1002/bab.1874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 12/11/2019] [Indexed: 12/27/2022]
Abstract
Osteonecrosis is a harmful musculoskeletal disease. We aim to detect the effects of icariin (ICA) in MC3T3-E1 cell. MC3T3-E1 cell was pretreated with ICA and was subjected to hypoxia stimuli. The tumor-associated long noncoding RNA expressed on chromosome 2 (TALNEC2) overexpression or silencing vectors (pTALNEC2 or si-TALNEC2) was utilized for MC3T3-E1 cell transfection. Viability and apoptosis rate were individually tested by cell counting kit-8 and Annexin V-fluorescein isothiocyanate/propidium iodide kit untied with flow cytometry. The alkaline phosphatase activity (ALP) activity was tested through ALP assay. The quantitative reverse transcription PCR or Western blot was performed for elements detection at the RNA or protein level. Hypoxia treatment induced viability inhibition and CyclinD1 reduction, but elevation of p53 and p16. It also promoted apoptosis by increasing apoptotic cells, Bax, and cleaved-poly ADP-ribose polymerase but decreasing Bcl-2. Also, hypoxia stimuli restrained ALP activity, and osteopontin, osteocalcin, and Runt-related transcription factor 2 expression. Those effects caused by hypoxia stimuli were all reversed by ICA. TALNEC2 was downregulated by ICA, whose impacts were subsequently abolished by pTALNEC2. Silencing TALNEC2 displayed similar effects with ICA. But the apoptosis was not affected by si-TALNEC2. ICA blocked ste20-related proline/alanine-rich kinase/c-Jun N-terminal kinase (SPAK/JNK) but triggered phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin (PI3K/AKT/mTOR) pathway in MC3T3-E1 cell by suppressing TALNEC2. ICA relieved hypoxia-stimulated damage by restraining TALNEC2 through blocking SPAK/JNK and triggering PI3K/AKT/mTOR in the MC3T3-E1 cell.
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Affiliation(s)
- Weiguo Wang
- Department of Orthopaedics, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Jian Xin
- Department of Orthopaedics, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Wenming Chen
- Department of Orthopaedics, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Lizhong Jing
- Department of Orthopaedics, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
| | - Peng Zhang
- Department of Orthopaedics, The Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, People's Republic of China
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Wu J, Peng X, Qiao M, Zhao H, Li M, Liu G, Mei S. Genome-wide analysis of long noncoding RNA and mRNA profiles in PRRSV-infected porcine alveolar macrophages. Genomics 2019; 112:1879-1888. [PMID: 31682919 DOI: 10.1016/j.ygeno.2019.10.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/07/2019] [Accepted: 10/09/2019] [Indexed: 12/19/2022]
Abstract
Porcine reproductive and respiratory syndrome (PRRS), which is caused by PRRS virus (PRRSV), is one of the most globally devastating swine diseases. It is essential to develop new strategy to control PRRS via an understanding of mechanisms that PRRSV utilizes to interfere with the host's innate immunity. In this study, we deeply sequenced and analyzed long noncoding RNA (lncRNA) and mRNA expression profiles of the porcine alveolar macrophages (PAMs) after PRRSV infection. 126 lncRNAs and 753 mRNAs were differentially expressed between PRRSV-infected and control PAMs. The co-expressed genes of down-regulated lncRNAs were significantly enriched within NF-kappa B and toll-like receptor signaling pathways. Co-expression network analysis indicated that part of the dysregulated lncRNAs associated with the interferon-induced genes. These dysregulated lncRNAs may play an important role in the host's innate immune responses to PRRSV infection. However, further research is required to characterize the function of these lncRNAs.
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Affiliation(s)
- Junjing Wu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan 430064, China
| | - Xianwen Peng
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan 430064, China
| | - Mu Qiao
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan 430064, China
| | - Haizhong Zhao
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan 430064, China
| | - Mingbo Li
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan 430064, China
| | - Guisheng Liu
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan 430064, China
| | - Shuqi Mei
- Hubei Key Laboratory of Animal Embryo and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Provincial Academy of Agricultural Sciences, Wuhan 430064, China.
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Rochet E, Appukuttan B, Ma Y, Ashander LM, Smith JR. Expression of Long Non-Coding RNAs by Human Retinal Müller Glial Cells Infected with Clonal and Exotic Virulent Toxoplasma gondii. Noncoding RNA 2019; 5:ncrna5040048. [PMID: 31547203 PMCID: PMC6958423 DOI: 10.3390/ncrna5040048] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 12/14/2022] Open
Abstract
Retinal infection with Toxoplasma gondii-ocular toxoplasmosis-is a common cause of vision impairment worldwide. Pathology combines parasite-induced retinal cell death and reactive intraocular inflammation. Müller glial cells, which represent the supporting cell population of the retina, are relatively susceptible to infection with T. gondii. We investigated expression of long non-coding RNAs (lncRNAs) with immunologic regulatory activity in Müller cells infected with virulent T. gondii strains-GT1 (haplogroup 1, type I) and GPHT (haplogroup 6). We first confirmed expression of 33 lncRNA in primary cell isolates. MIO-M1 human retinal Müller cell monolayers were infected with T. gondii tachyzoites (multiplicity of infection = 5) and harvested at 4, 12, 24, and 36 h post-infection, with infection being tracked by the expression of parasite surface antigen 1 (SAG1). Significant fold-changes were observed for 31 lncRNAs at one or more time intervals. Similar changes between strains were measured for BANCR, CYTOR, FOXD3-AS1, GAS5, GSTT1-AS1, LINC-ROR, LUCAT1, MALAT1, MIR22HG, MIR143HG, PVT1, RMRP, SNHG15, and SOCS2-AS1. Changes differing between strains were measured for APTR, FIRRE, HOTAIR, HOXD-AS1, KCNQ1OT1, LINC00968, LINC01105, lnc-SGK1, MEG3, MHRT, MIAT, MIR17HG, MIR155HG, NEAT1, NeST, NRON, and PACER. Our findings suggest roles for lncRNAs in regulating retinal Müller cell immune responses to T. gondii, and encourage future studies on lncRNA as biomarkers and/or drug targets in ocular toxoplasmosis.
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Affiliation(s)
- Elise Rochet
- Flinders University College of Medicine & Public Health, Adelaide, SA 5042, Australia.
| | - Binoy Appukuttan
- Flinders University College of Medicine & Public Health, Adelaide, SA 5042, Australia.
| | - Yuefang Ma
- Flinders University College of Medicine & Public Health, Adelaide, SA 5042, Australia.
| | - Liam M Ashander
- Flinders University College of Medicine & Public Health, Adelaide, SA 5042, Australia.
| | - Justine R Smith
- Flinders University College of Medicine & Public Health, Adelaide, SA 5042, Australia.
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Wang Y, Song X, Li Z, Liu B. Long non-coding RNAs in coronary atherosclerosis. Life Sci 2018; 211:189-197. [PMID: 30195033 DOI: 10.1016/j.lfs.2018.08.072] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 12/26/2022]
Abstract
Coronary atherosclerosis (CAS), a leading cause of cardiovascular disease, is a major cause of death worldwide. CAS is a chronic disease in the aorta that can be caused by dyslipidemia, abnormal glucose metabolism, endothelial cell dysfunction, vascular smooth muscle cell (VSMC) or fibrous connective tissue hyperplasia, immune inflammatory reactions, and many other factors. The pathogenesis of CAS is not fully understood, as it is a complex lesion complicated by multiple factors. Damage-response theories have put forward endothelial cell (EC) injury as the initiating factor for CAS; the addition of lipid metabolism disorders may enhance monocyte adhesion, increase the proliferation and migration of fibroblasts and VSMCs, and accelerate the development of CAS. Furthermore, inflammatory and immune responses can create a vicious cycle of endothelial injury, which also plays key roles in the formation of CAS. Therefore, in order to elucidate the mechanisms controlling CAS, it is important to study the etiology of vascular cell dysfunction, abnormal energy and metabolism disorders, and immune and inflammatory reactions. Non-coding RNAs play regulatory roles in the pathogenesis of CAS, especially long non-coding RNAs (lncRNAs); lncRNAs have recently become a major focus for cardiovascular disease mechanisms, as they play numerous roles in the progression of CAS. Therefore, in this review, we discuss the role of lncRNAs in the pathogenesis of coronary CAS, and their role in the prevention and treatment of coronary CAS.
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Affiliation(s)
- Yiran Wang
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Xianjing Song
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Zhibo Li
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China
| | - Bin Liu
- Department of Cardiology, The Second Hospital of Jilin University, Changchun, Jilin 130021, China.
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Liao K, Xu J, Yang W, You X, Zhong Q, Wang X. The research progress of LncRNA involved in the regulation of inflammatory diseases. Mol Immunol 2018; 101:182-188. [DOI: 10.1016/j.molimm.2018.05.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 05/23/2018] [Accepted: 05/31/2018] [Indexed: 02/07/2023]
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Pei X, Wang X, Li H. LncRNA SNHG1 regulates the differentiation of Treg cells and affects the immune escape of breast cancer via regulating miR-448/IDO. Int J Biol Macromol 2018; 118:24-30. [PMID: 29886172 DOI: 10.1016/j.ijbiomac.2018.06.033] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Revised: 06/06/2018] [Accepted: 06/07/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVE To investigate the mechanism of lncRNA SNHG1 in the immune escape of breast cancer (BC). METHODS SNHG1, miR-448 and IL-10 levels were evaluated by qRT-PCR. The protein levels of IDO and Foxp3 were measured by Western blot. SNHG1 and miR-448 interaction was tested by RIP assay and RNA pull-down assay. MiR-448 and IDO interaction was observed by luciferase reporter assay. RESULTS Compared with CD4+T cells, miR-448 expression in CD4+ TIL cells was decreased, while the expression of SNHG1, IDO, IL-10 and Foxp3 were increased. Moreover, SNHG1 directly contacted with miR-448, which could negatively regulate IDO. In cells treated with siRNA-SNHG and miR-448 inhibitor, interference SNHG1 up-regulated miR-448 expression and down-regulated IDO expression, while miR-448 inhibitor reversed this effect. In addition, miR-448 inhibitor reversed the inhibitory effect of siRNA-SNHG1 on Treg cell differentiation, and siRNA-SNHG1 could reduce tumor volume and down-regulated the expressions of SNHG1, IL-10, IDO and Foxp3. CONCLUSION Interference SNHG1 could inhibit the differentiation of Treg cells by promoting miR-448 expression and reducing IDO level, thereby impeding the immune escape of BC.
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Affiliation(s)
- Xinhong Pei
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Xinxing Wang
- Department of Breast Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China
| | - Huixiang Li
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, People's Republic of China.
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Xu B, Wang Y, Li X, Mao Y, Deng X. RNA‑sequencing analysis of aberrantly expressed long non‑coding RNAs and mRNAs in a mouse model of ventilator‑induced lung injury. Mol Med Rep 2018; 18:882-892. [PMID: 29845294 PMCID: PMC6059720 DOI: 10.3892/mmr.2018.9034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/22/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are closely associated with the regulation of various biological processes and are involved in the pathogenesis of numerous diseases. However, to the best of our knowledge, the role of lncRNAs in ventilator‑induced lung injury (VILI) has yet to be evaluated. In the present study, high‑throughput sequencing was applied to investigate differentially expressed lncRNAs and mRNAs (fold change >2; false discovery rate <0.05). Bioinformatics analysis was employed to predict the functions of differentially expressed lncRNAs. A total of 104 lncRNAs (74 upregulated and 30 downregulated) and 809 mRNAs (521 upregulated and 288 downregulated) were differentially expressed in lung tissues from the VILI group. Gene ontology analysis demonstrated that the differentially expressed lncRNAs and mRNAs were mainly associated with biological functions, including apoptosis, angiogenesis, neutrophil chemotaxis and skeletal muscle cell differentiation. The top four enriched pathways were the tumor necrosis factor (TNF) signaling pathway, P53 signaling pathway, neuroactive ligand‑receptor interaction and the forkhead box O signaling pathway. Several lncRNAs were predicted to serve a vital role in VILI. Subsequently, three lncRNAs [mitogen‑activated protein kinase kinase 3, opposite strand (Map2k3os), dynamin 3, opposite strand and abhydrolase domain containing 11, opposite strand] and three mRNAs (growth arrest and DNA damage‑inducible α, claudin 4 and thromboxane A2 receptor) were measured by reverse transcription‑quantitative polymerase chain reaction, in order to confirm the veracity of RNA‑sequencing analysis. In addition, Map2k3os small interfering RNA transfection inhibited the expression of stretch‑induced cytokines [TNF‑α, interleukin (IL)‑1β and IL‑6] in MLE12 cells. In conclusion, the results of the present study provided a profile of differentially expressed lncRNAs in VILI. Several important lncRNAs may be involved in the pathological process of VILI, which may be useful to guide further investigation into the pathogenesis for this disease.
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Affiliation(s)
- Bo Xu
- Department of Anesthesiology and Intensive Care, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yizhou Wang
- Department of Hepatic Surgery IV, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, P.R. China
| | - Xiujuan Li
- Department of Anesthesiology and Intensive Care, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
| | - Yanfei Mao
- Department of Anesthesiology and SICU, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai 200092, P.R. China
| | - Xiaoming Deng
- Department of Anesthesiology and Intensive Care, Changhai Hospital, Second Military Medical University, Shanghai 200433, P.R. China
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Lopez-Ezquerra A, Mitschke A, Bornberg-Bauer E, Joop G. Tribolium castaneum gene expression changes after Paranosema whitei infection. J Invertebr Pathol 2018; 153:92-98. [DOI: 10.1016/j.jip.2018.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/10/2018] [Accepted: 02/12/2018] [Indexed: 12/24/2022]
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SNHG1 promotes cell proliferation by acting as a sponge of miR-145 in colorectal cancer. Oncotarget 2017; 9:2128-2139. [PMID: 29416759 PMCID: PMC5788627 DOI: 10.18632/oncotarget.23255] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 12/05/2017] [Indexed: 02/07/2023] Open
Abstract
ncRNAs are important regulatory molecules and involve in many physiological cellular processes. Small nucleolar RNA host gene 1 (SNHG1) is a host to 8 snoRNAs and is located in 11q12.3 region of the chromosome. It has been reported to be involved in several cancers. However, the role of SNHG1 in the tumorigenesis of colorectal cancer is still unknown. In this study, SNHG1 was upregulated in colorectal cancers, and SNHG1 expression was correlated with advanced colorectal cancer stage and tumor recurrence. We found that SNHG1 promoted cell proliferation by acting as a sponge of miR-145, a well known tumor suppressor of colorectal cancer. Furthermore, the survival analysis indicated that colorectal cancer patients with higher expression of SNHG1 had a worse prognosis. These findings suggested that SNHG1 may act as a potential therapeutic target for the treatment of colorectal cancer.
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Screening and identification of lncRNAs as potential biomarkers for pulmonary tuberculosis. Sci Rep 2017; 7:16751. [PMID: 29196714 PMCID: PMC5711916 DOI: 10.1038/s41598-017-17146-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 11/22/2017] [Indexed: 11/21/2022] Open
Abstract
Pulmonary tuberculosis (TB) is among the diseases with the highest morbidity and mortality worldwide. Effective diagnostic methods for TB are lacking. In this study, we investigated long non-coding RNAs (lncRNAs) in plasma using microarray and the potential diagnostic value of lncRNAs for TB. We found a total of 163 up-regulated lncRNAs and 348 down-regulated lncRNAs. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) and coding-noncoding co-expression (CNC) analyses showed that functions of differentially expressed lncRNAs were mainly enriched in the regulation of alpha-beta T cell activation and the T cell receptor signalling pathway. Four differentially expressed lncRNAs, NR_038221 (fold change = 3.79, P < 0.01), NR_003142 (fold change = 1.69, P < 0.05), ENST00000570366 (fold change = 3.04, P < 0.05), and ENST00000422183 (fold change = 2.11, P < 0.001), were verified using RT-qPCR. Among those, NR_038221, NR_003142, and ENST00000570366 were found to be up-regulated, while ENST00000422183 was down-regulated. The value of the area under the curve (AUC) for the diagnostic model consisting of the four lncRNAs was 0.845 (sensitivity = 79.2%, specificity = 75%). We further predicted 85 mRNAs and 404 miRNAs that potentially interact with these lncRNAs. Our study revealed the potential value of lncRNAs as biomarkers for early diagnosis of TB and the underlying mechanisms of these abnormally expressed lncRNAs in the pathogenesis of TB.
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Elucidating the Role of Host Long Non-Coding RNA during Viral Infection: Challenges and Paths Forward. Vaccines (Basel) 2017; 5:vaccines5040037. [PMID: 29053596 PMCID: PMC5748604 DOI: 10.3390/vaccines5040037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 10/12/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022] Open
Abstract
Research over the past decade has clearly shown that long non-coding RNAs (lncRNAs) are functional. Many lncRNAs can be related to immunity and the host response to viral infection, but their specific functions remain largely elusive. The vast majority of lncRNAs are annotated with extremely limited knowledge and tend to be expressed at low levels, making ad hoc experimentation difficult. Changes to lncRNA expression during infection can be systematically profiled using deep sequencing; however, this often produces an intractable number of candidate lncRNAs, leaving no clear path forward. For these reasons, it is especially important to prioritize lncRNAs into high-confidence “hits” by utilizing multiple methodologies. Large scale perturbation studies may be used to screen lncRNAs involved in phenotypes of interest, such as resistance to viral infection. Single cell transcriptome sequencing quantifies cell-type specific lncRNAs that are less abundant in a mixture. When coupled with iterative experimental validations, new computational strategies for efficiently integrating orthogonal high-throughput data will likely be the driver for elucidating the functional role of lncRNAs during viral infection. This review highlights new high-throughput technologies and discusses the potential for integrative computational analysis to streamline the identification of infection-related lncRNAs and unveil novel targets for antiviral therapeutics.
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