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Li S, Cui H, Lu H, Zheng S, Yuan C. Advances in noncoding RNA in children allergic rhinitis. Int Forum Allergy Rhinol 2024; 14:1350-1362. [PMID: 38946149 DOI: 10.1002/alr.23393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/02/2024] [Accepted: 06/08/2024] [Indexed: 07/02/2024]
Abstract
BACKGROUND A chronic condition that significantly reduces a child's quality of life is allergic rhinitis (AR). The environment and allergens that the body is regularly exposed to can cause inflammatory and immunological reactions, which can change the expression of certain genes Epigenetic changes are closely linked to the onset and severity of allergy disorders according to mounting amounts of data. Noncoding RNAs (ncRNAs) are a group of RNA molecules that cannot be converted into polypeptides. The three main categories of ncRNAs include microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). NcRNAs play a crucial role in controlling gene expression and contribute to the development of numerous human diseases. METHODS Articles are selected based on Pubmed's literature review and the author's personal knowledge. The largest and highest quality studies were included. The search selection is not standardized. RESULTS Recent findings indicate that various categories of ncRNAs play distinct yet interconnected roles and actively contribute to intricate gene regulatory networks. CONCLUSION This article demonstrates the significance and progress of ncRNAs in children's AR. The database covers three key areas: miRNAs, lncRNAs, and circRNAs. Additionally, potential avenues for future research to facilitate the practical application of ncRNAs as therapeutic targets and biomarkers will be explore.
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Affiliation(s)
- Shuman Li
- Chongqing Medical University, Chongqing, China
| | - Hongtao Cui
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Huina Lu
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Shan Zheng
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Chao Yuan
- Department of Pediatrics, Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
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2
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Shi L, Han X, Liu F, Long J, Jin Y, Chen S, Duan G, Yang H. Review on Long Non-Coding RNAs as Biomarkers and Potentially Therapeutic Targets for Bacterial Infections. Curr Issues Mol Biol 2024; 46:7558-7576. [PMID: 39057090 PMCID: PMC11276060 DOI: 10.3390/cimb46070449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/13/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The confrontation between humans and bacteria is ongoing, with strategies for combating bacterial infections continually evolving. With the advancement of RNA sequencing technology, non-coding RNAs (ncRNAs) associated with bacterial infections have garnered significant attention. Recently, long ncRNAs (lncRNAs) have been identified as regulators of sterile inflammatory responses and cellular defense against live bacterial pathogens. They are involved in regulating host antimicrobial immunity in both the nucleus and cytoplasm. Increasing evidence indicates that lncRNAs are critical for the intricate interactions between host and pathogen during bacterial infections. This paper emphatically elaborates on the potential applications of lncRNAs in clinical hallmarks, cellular damage, immunity, virulence, and drug resistance in bacterial infections in greater detail. Additionally, we discuss the challenges and limitations of studying lncRNAs in the context of bacterial infections and highlight clear directions for this promising field.
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Affiliation(s)
| | | | | | | | | | | | | | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China; (L.S.); (X.H.); (F.L.); (J.L.); (Y.J.); (S.C.); (G.D.)
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3
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Rai A, Bhagchandani T, Tandon R. Transcriptional landscape of long non-coding RNAs (lncRNAs) and its implication in viral diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195023. [PMID: 38513793 DOI: 10.1016/j.bbagrm.2024.195023] [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: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/23/2024]
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts of size >200 bp that do not translate into proteins. Emerging data revealed that viral infection results in systemic changes in the host at transcriptional level. These include alterations in the lncRNA expression levels and triggering of antiviral immune response involving several effector molecules and diverse signalling pathways. Thus, lncRNAs have emerged as an essential mediatory element at distinct phases of the virus infection cycle. The complete eradication of the viral disease requires more precise and novel approach, thus manipulation of the lncRNAs could be one of them. This review shed light upon the existing knowledge of lncRNAs wherein the implication of differentially expressed lncRNAs in blood-borne, air-borne, and vector-borne viral diseases and its promising therapeutic applications under clinical settings has been discussed. It further enhances our understanding of the complex interplay at host-pathogen interface with respect to lncRNA expression and function.
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Affiliation(s)
- Ankita Rai
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Tannu Bhagchandani
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, India.
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4
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Olajide JS, Qu Z, Yang S, Yang B, Xu X, Wang J, Cai J. Eimeria falciformis extracellular vesicles differentially express host cell lncRNAs. J Eukaryot Microbiol 2024; 71:e13009. [PMID: 38073253 DOI: 10.1111/jeu.13009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 03/10/2024]
Abstract
Long noncoding RNAs (lncRNAs) are regulatory transcripts during protozoan infections in the host intestinal epithelial cells (IECs). Apicomplexan Eimeria falciformis sporozoite extracellular vesicles (EVs) contain virulence factors that modulate host IECs pro-inflammatory genes and immune responses. In this study, E. falciformis sporozoites were made to interact with inactivated host cells, and the parasite EVs were separated from total secretome by ultracentrifugation and purified on density gradient medium. Dose-dependent bio-activity of E. falciformis EVs was investigated by RNA sequencing, functional annotation and quantitative PCR. It was found that E. falciformis EVs induced mRNA, circRNA, and lncRNA expressions in mouse IECs. Of 38, 217 lncRNAs assembled, 157 and 152 were upwardly and downwardly expressed respectively. Differentially expressed lncRNAs were associated with cytokines, pyroptosis, and immune signaling pathways including FoxO, NF-κB, MAPK, and TGF-β. In essence, E. falciformis EVs altered host cell RNA expressions during the interaction with host IECs. Also, differentially expressed lncRNAs are potential diagnostic transcripts during Eimeria infections.
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Affiliation(s)
- Joshua S Olajide
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Centre for Distance Learning, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Zigang Qu
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shunli Yang
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- College of Animal Science and Technology, Hebei Normal University of Science and Technology, Qinhuangdao, China
| | - Bin Yang
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiao Xu
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jing Wang
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Jianping Cai
- State Key Laboratory of Animal Disease Control and Prevention, Key Laboratory of Veterinary Parasitology of Gansu, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
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5
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Kadian LK, Verma D, Lohani N, Yadav R, Ranga S, Gulshan G, Pal S, Kumari K, Chauhan SS. Long non-coding RNAs in cancer: multifaceted roles and potential targets for immunotherapy. Mol Cell Biochem 2024:10.1007/s11010-024-04933-1. [PMID: 38413478 DOI: 10.1007/s11010-024-04933-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
Cancer remains a major global health concern with high mortality rates mainly due to late diagnosis and poor prognosis. Long non-coding RNAs (lncRNAs) are emerging as key regulators of gene expression in human cancer, functioning through various mechanisms including as competing endogenous RNAs (ceRNAs) and indirectly regulating miRNA expression. LncRNAs have been found to have both oncogenic and tumor-suppressive roles in cancer, with the former promoting cancer cell proliferation, migration, invasion, and poor prognosis. Recent research has shown that lncRNAs are expressed in various immune cells and are involved in cancer cell immune escape and the modulation of the tumor microenvironment, thus highlighting their potential as targets for cancer immunotherapy. Targeting lncRNAs in cancer or immune cells could enhance the anti-tumor immune response and improve cancer immunotherapy outcomes. However, further research is required to fully understand the functional roles of lncRNAs in cancer and the immune system and their potential as targets for cancer immunotherapy. This review offers a comprehensive examination of the multifaceted roles of lncRNAs in human cancers, with a focus on their potential as targets for cancer immunotherapy. By exploring the intricate mechanisms underlying lncRNA-mediated regulation of cancer cell proliferation, invasion, and immune evasion, we provide insights into the diverse therapeutic applications of these molecules.
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Affiliation(s)
- Lokesh K Kadian
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
- Dept of Dermatology, Indiana University School of Medicine, Indianapolis, 46202, USA
| | - Deepika Verma
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Neelam Lohani
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Ritu Yadav
- Dept of Genetics, MD University, Rohtak, 124001, India
| | - Shalu Ranga
- Dept of Genetics, MD University, Rohtak, 124001, India
| | - Gulshan Gulshan
- Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, India
| | - Sanghapriya Pal
- Dept of Biochemistry, Maulana Azad Medical College and Associated Hospital, New Delhi, 110002, India
| | - Kiran Kumari
- Dept of Forensic Science, Lovely Professional University, Jalandhar, Punjab, 144411, India
| | - Shyam S Chauhan
- Dept of Biochemistry, All India Institute of Medical Sciences, New Delhi, 110029, India.
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Martinez-Castillo M, M. Elsayed A, López-Berestein G, Amero P, Rodríguez-Aguayo C. An Overview of the Immune Modulatory Properties of Long Non-Coding RNAs and Their Potential Use as Therapeutic Targets in Cancer. Noncoding RNA 2023; 9:70. [PMID: 37987366 PMCID: PMC10660772 DOI: 10.3390/ncrna9060070] [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: 06/27/2023] [Revised: 10/25/2023] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play pivotal roles in regulating immune responses, immune cell differentiation, activation, and inflammatory processes. In cancer, they are gaining prominence as potential therapeutic targets due to their ability to regulate immune checkpoint molecules and immune-related factors, suggesting avenues for bolstering anti-tumor immune responses. Here, we explore the mechanistic insights into lncRNA-mediated immune modulation, highlighting their impact on immunity. Additionally, we discuss their potential to enhance cancer immunotherapy, augmenting the effectiveness of immune checkpoint inhibitors and adoptive T cell therapies. LncRNAs as therapeutic targets hold the promise of revolutionizing cancer treatments, inspiring further research in this field with substantial clinical implications.
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Affiliation(s)
- Moises Martinez-Castillo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Liver, Pancreas and Motility Laboratory, Unit of Research in Experimental Medicine, School of Medicine, Universidad Nacional Autónoma de México (UNAM), Mexico City 06726, Mexico
| | - Abdelrahman M. Elsayed
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Al-Azhar University, Cairo 11754, Egypt;
- Havener Eye Institute, Department of Ophthalmology and Visual Science, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Gabriel López-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
| | - Cristian Rodríguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (M.M.-C.); (G.L.-B.); (P.A.)
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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7
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Li M, Li W, Zhao M, Li Z, Wang GL, Liu W, Liang C. Transcriptome analysis reveals a lncRNA-miRNA-mRNA regulatory network in OsRpp30-mediated disease resistance in rice. BMC Genomics 2023; 24:643. [PMID: 37884868 PMCID: PMC10604448 DOI: 10.1186/s12864-023-09748-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) play critical roles in various biological processes in plants. Extensive studies utilizing high-throughput RNA sequencing have revealed that many lncRNAs are involved in plant disease resistance. Oryza sativa RNase P protein 30 (OsRpp30) has been identified as a positive regulator of rice immunity against fungal and bacterial pathogens. Nevertheless, the specific functions of lncRNAs in relation to OsRpp30-mediated disease resistance in rice remain elusive. RESULTS We conducted a comprehensive analysis of lncRNAs, miRNAs, and mRNAs expression patterns in wild type (WT), OsRpp30 overexpression (OsRpp30-OE), and OsRpp30 knockout (OsRpp30-KO) rice plants. In total, we identified 91 differentially expressed lncRNAs (DElncRNAs), 1671 differentially expressed mRNAs (DEmRNAs), and 41 differentially expressed miRNAs (DEmiRNAs) across the different rice lines. To gain further insights, we investigated the interaction between DElncRNAs and DEmRNAs, leading to the discovery of 10 trans- and 27 cis-targeting pairs specific to the OsRpp30-OE and OsRpp30-KO samples. In addition, we constructed a competing endogenous RNA (ceRNA) network comprising differentially expressed lncRNAs, miRNAs, and mRNAs to elucidate their intricate interplay in rice disease resistance. The ceRNA network analysis uncovered a set of gene targets regulated by lncRNAs and miRNAs, which were found to be involved in pathogen recognition, hormone pathways, transcription factor activation, and other biological processes related to plant immunity. CONCLUSIONS Our study provides a comprehensive expression profiling of lncRNAs, miRNAs, and mRNAs in a collection of defense mutants in rice. To decipher the putative functional significance of lncRNAs, we constructed trans- and cis-targeting networks involving differentially expressed lncRNAs and mRNAs, as well as a ceRNA network incorporating differentially expressed lncRNAs, miRNAs, and mRNAs. Together, the findings from this study provide compelling evidence supporting the pivotal roles of lncRNAs in OsRpp30-mediated disease resistance in rice.
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Affiliation(s)
- Minghua Li
- Department of Biology, Miami University, Oxford, OH, 45056, USA
| | - Wei Li
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA
| | - Meixia Zhao
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32611, USA
| | - Zhiqiang Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Guo-Liang Wang
- Department of Plant Pathology, Ohio State University, Columbus, OH, 43210, USA.
| | - Wende Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Chun Liang
- Department of Biology, Miami University, Oxford, OH, 45056, USA.
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Carvalho LB, Dos Santos Sanna PL, Dos Santos Afonso CC, Bondan EF, da Silva Feltran G, Ferreira MR, Birbrair A, Andia DC, Latini A, Foganholi da Silva RA. MicroRNA biogenesis machinery activation and lncRNA and REST overexpression as neuroprotective responses to fight inflammation in the hippocampus. J Neuroimmunol 2023; 382:578149. [PMID: 37481910 DOI: 10.1016/j.jneuroim.2023.578149] [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: 01/24/2023] [Revised: 06/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Brain Long non-coding RNA (lncRNA) and microRNAs (miRs) play essential roles in the regulation of several important biological processes, including neuronal activity, cognitive processes, neurogenesis, angiogenesis, and neuroinflammation. In this context, the transcriptional repressor, RE1 silencing transcription factor (Rest), acts regulating the expression of neuronal genes as well as of lncRNAs and multiple miRNAs in the central nervous system. Nevertheless, its role in neuroinflammation was less explored. Here, we demonstrate, using an in vivo model of neuroinflammation induced by i.p. injection of LPS (0.33 mg/kg), that neuroinflammation increases gene expression of pro-inflammatory cytokines concomitant with the native and truncated forms of Rest and of non-coding RNAs. Additionally, the increased expression of enzymes Drosha ribonuclease III) (Drosha), Exportin 5 (Xpo5) and Endoribonuclease dicer (Dicer), associated with high expression of neuroprotective miRs 22 and 132 are indicative that the activation of biogenesis of miRs in the hippocampal region is a Central Nervous System (CNS) protective mechanism for the deleterious effects of neuroinflammation. Our results indicate that positive regulation of Rest gene expression in the hippocampal region by neuroinflammation correlates directly with the expression of miRs 22 and 132 and inversely with miR 335. In parallel, the confirmation of the possible alignment between the lncRNAs with miR 335 by bioinformatics corroborates with the sponge effect of Hottip and Hotair hybridizing and inhibiting the pro-inflammatory action of miR 335. This suggests the existence of a possible correlation between the activation of miR biogenesis machinery with increased expression of the transcription factor Rest, contributing to neuroprotection.
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Affiliation(s)
| | | | | | - Eduardo F Bondan
- CEEpiRG - Center for Epigenetic Study and Genic Regulation, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, SP, Brazil
| | - Geórgia da Silva Feltran
- Lab. of Bioassays and Cellular Dynamics, Department of Chemical and Biological Sciences, Institute of Biosciences, UNESP - São Paulo State University, Botucatu, SP, Brazil
| | - Marcel Rodrigues Ferreira
- Molecular Genetics and Bioinformatics Laboratory, Experimental Research Unity, Botucatu Medical School, São Paulo State University, USA
| | - Alexander Birbrair
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil; Department of Dermatology, University of Wisconsin-Madison, Madison, WI, USA; Department of Radiology, Columbia University Medical Center, New York, NY, USA
| | - Denise Carleto Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, São Paulo, Brazil
| | - Alexandra Latini
- Laboratory of Bioenergetics and Oxidative Stress, LABOX, Department of Biochemistry, Center for Biological Sciences, Federal University of Santa Catarina, Florianopolis, Brazil
| | - Rodrigo A Foganholi da Silva
- Dentistry, University of Taubaté, Taubaté, São Paulo, SP, Brazil; CEEpiRG - Center for Epigenetic Study and Genic Regulation, Program in Environmental and Experimental Pathology, Paulista University, São Paulo, SP, Brazil.
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9
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Hsieh YT, Chen YC, Chou YC, Kuo PY, Yen YT, Tsai HW, Wang CR. Long noncoding RNA SNHG16 regulates TLR4-mediated autophagy and NETosis formation in alveolar hemorrhage associated with systemic lupus erythematosus. J Biomed Sci 2023; 30:78. [PMID: 37700342 PMCID: PMC10496234 DOI: 10.1186/s12929-023-00969-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
BACKGROUND Dysregulated long noncoding RNA (lncRNA) expression with increased apoptosis has been demonstrated in systemic lupus erythematosus (SLE) patients with alveolar hemorrhage (AH). SNHG16, a lncRNA, can enhance pulmonary inflammation by sponging microRNAs, and upregulate toll-like receptor 4 (TLR4) expression via stabilizing its mRNAs. TRAF6, a TLR4 downstream signal transducer, can induce autophagy and NETosis formation. In this study, we investigated whether SNHG16 could regulate TLR4-mediated autophagy and NETosis formation in SLE-associated AH. METHODS Expression of SNHG16, TLR4 and TRAF6 and cell death processes were examined in lung tissues and peripheral blood (PB) leukocytes from AH patients associated with SLE and other autoimmune diseases, and in the lungs and spleen from a pristane-induced C57BL/6 mouse AH model. SNHG16-overexpressed or -silenced alveolar and myelocytic cells were stimulated with lipopolysaccharide (LPS), a TLR4 agonist, for analyzing autophagy and NETosis, respectively. Pristane-injected mice received the intra-pulmonary delivery of lentivirus (LV)-SNHG16 for overexpression and prophylactic/therapeutic infusion of short hairpin RNA (shRNA) targeting SNHG16 to evaluate the effects on AH. Renal SNHG16 expression was also examined in lupus nephritis (LN) patients and a pristane-induced BALB/c mouse LN model. RESULTS Up-regulated SNHG16, TLR4 and TRAF6 expression with increased autophagy and NETosis was demonstrated in the SLE-AH lungs. In such patients, up-regulated SNHG16, TLR4 and TRAF6 expression was found in PB mononuclear cells with increased autophagy and in PB neutrophils with increased NETosis. There were up-regulated TLR4 expression and increased LPS-induced autophagy and NETosis in SNHG16-overexpressed cells, while down-regulated TLR4 expression and decreased LPS-induced autophagy and NETosis in SNHG16-silenced cells. Pristane-injected lung tissues had up-regulated SNHG16, TLR4/TRAF6 levels and increased in situ autophagy and NETosis formation. Intra-pulmonary LV-SNHG16 delivery enhanced AH through up-regulating TLR4/TRAF6 expression with increased cell death processes, while intra-pulmonary prophylactic and early therapeutic sh-SNHG16 delivery suppressed AH by down-regulating TLR4/TRAF6 expression with reduced such processes. In addition, there was decreased renal SNHG16 expression in LN patients and mice. CONCLUSIONS Our results demonstrate that lncRNA SNHG16 regulates TLR4-mediated autophagy and NETosis formation in the human and mouse AH lungs, and provide a therapeutic potential of intra-pulmonary delivery of shRNA targeting SNHG16 in this SLE-related lethal manifestation.
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Affiliation(s)
- Yu-Tung Hsieh
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Cheng Chen
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chi Chou
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Pin-Yu Kuo
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ting Yen
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Wen Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chrong-Reen Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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10
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Bella F, Muscatello MRA, D’Ascola A, Campo S. Gene Expression Analysis of nc-RNAs in Bipolar and Panic Disorders: A Pilot Study. Genes (Basel) 2023; 14:1778. [PMID: 37761918 PMCID: PMC10530917 DOI: 10.3390/genes14091778] [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: 07/18/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Bipolar Disorder (BD) is a chronic, highly disabling mood disorder. Among the major comorbidities, Panic Disorder (PD) is often associated with BD. This could suggest a common genetic and pathophysiological background between these two conditions, as suggested by previous studies. Despite the widespread diffusion of these conditions, little is still known about the exact pathophysiological dynamics that underlies them. Non-coding RNAs have recently started to gain attention in psychiatry research, with several papers indicating the dysregulation of lncRNAs as a possible key factor in etiopathogenesis of several mental disorders. In the light of the above, the aim of this study is to evaluate the gene expression levels of MALAT1, PANDA, GAS5, HOTAIR lncRNAs and miR-221-5p microRNA, which are highly expressed in the CNS, in drug-naïve/drug-free bipolar and panic patients. METHODS the experimental plan envisaged the recruitment of sixteen patients with a first diagnosis of type one or type two BD and ten patients with PD. Patients with medical and/or psychiatric comorbidities were excluded. Peripheral venous blood was collected both from patients and healthy controls. Each of the patients recruited for the study was prescribed with therapy. Serum ncRNAs levels were remeasured after 5 months of therapy. RESULTS MALAT-1, GAS-5 and miR-221-5p are significantly up-regulated in BD after therapy, while PD group showed a down-regulation of all the ncRNAs investigated after therapy. CONCLUSIONS gene expression levels of the ncRNAs miR-221, MALAT1, GAS5, which are implicated in inhibitory modulation of the glucocorticoid receptor, are significantly over-expressed in bipolar patients following therapy, while all ncRNAs are significantly over-expressed in the PD T1 patients group compared with healthy controls. Data concerning PD represent, to our knowledge, a novelty.
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Affiliation(s)
- Fabrizio Bella
- Psychiatry Unit, Department of Clinical and Experimental Medicine, University of Catania, 95124 Catania, Italy
| | - Maria Rosaria Anna Muscatello
- Psychiatry Unit, Department of Biomedical Sciences and of Morphological and Functional Images, University of Messina, 98122 Messina, Italy;
| | - Angela D’Ascola
- Molecular Biology Laboratory, Department of Clinical and Experimental Medicine, University of Messina, 98122 Messina, Italy;
| | - Salvatore Campo
- Molecular Biology Laboratory, Department of Biomedical Sciences and of Morphological and Functional Images, University of Messina, 98122 Messina, Italy;
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11
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Santus L, Sopena-Rios M, García-Pérez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Melé M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun 2023; 14:3866. [PMID: 37391481 PMCID: PMC10313701 DOI: 10.1038/s41467-023-39627-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies.
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Affiliation(s)
- Luisa Santus
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Maria Sopena-Rios
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Raquel García-Pérez
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Katherine J Siddle
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shirlee Wohl
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA
| | - Ferran Reverter
- Department of Genetics, Microbiology and Statistics University of Barcelona, Barcelona, Spain
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, 80303, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA.
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain.
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12
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Chini A, Guha P, Malladi VS, Guo Z, Mandal SS. Novel long non-coding RNAs associated with inflammation and macrophage activation in human. Sci Rep 2023; 13:4036. [PMID: 36899011 PMCID: PMC10006430 DOI: 10.1038/s41598-023-30568-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/27/2023] [Indexed: 03/12/2023] Open
Abstract
Inflammation plays a central role in immune response and macrophage activation. Emerging studies demonstrate that along with proteins and genomic factors, noncoding RNA are potentially involved in regulation of immune response and inflammation. Our recent study demonstrated that lncRNA HOTAIR plays key roles in cytokine expression and inflammation in macrophages. The primary goal of this study is to discover novel lncRNAs that are crucial players in inflammation, macrophage activation, and immune response in humans. Towards this, we have stimulated THP1-derived macrophages (THP1-MΦ) with lipopolysaccharides (LPS) and performed the whole transcriptome RNA-seq analysis. Based on this analysis, we discovered that along with well-known marker for inflammation (such as cytokines), a series of long noncoding RNAs (lncRNAs) expression were highly induced upon LPS-stimulation of macrophages, suggesting their potential roles in inflammation and macrophage activation. We termed these family of lncRNAs as Long-noncoding Inflammation Associated RNA (LinfRNA). Dose and time dependent analysis demonstrated that many human LinfRNA (hLinfRNAs) expressions follow similar patterns as cytokine expressions. Inhibition of NF-κB suppressed the expression of most hLinfRNAs suggesting their potential regulation via NF-κB activation during inflammation and macrophage activation. Antisense-mediated knockdown of hLinfRNA1 suppressed the LPS-induced expression of cytokines and pro-inflammatory genes such as IL6, IL1β, and TNFα expression, suggesting potential functionality of the hLinfRNAs in cytokine regulation and inflammation. Overall, we discovered a series of novel hLinfRNAs that are potential regulators of inflammation and macrophage activation and may be linked to inflammatory and metabolic diseases.
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Affiliation(s)
- Avisankar Chini
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Prarthana Guha
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Venkat S Malladi
- Lyda Hill Department of Bioinformatics, Bioinformatics Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Zibiao Guo
- North Texas Genome Center, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Subhrangsu S Mandal
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA.
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13
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Zhu N, Zhang F, Zhou H, Ma W, Mao H, Wang M, Ke Z, Wang J, Qi L. Mechanisms of Immune-Related Long Non-Coding RNAs in Spleens of Mice Vaccinated with 23-Valent Pneumococcal Polysaccharide Vaccine (PPV23). Vaccines (Basel) 2023; 11:vaccines11030529. [PMID: 36992112 DOI: 10.3390/vaccines11030529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/05/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023] Open
Abstract
The 23-valent pneumococcal vaccine (PPV23) is a classical common vaccine used to prevent pneumococcal disease. In past decades, it was thought that vaccination with this vaccine induces humoral immunity, thereby reducing the disease associated with infection with 23 common serotypes of Streptococcus pneumoniae (Sp). However, for this polysaccharide vaccine, the mechanism of immune response at the transcriptional level has not been fully studied. To identify the lncRNAs (long noncoding RNAs) and mRNAs in spleens related to immunity after PPV23 vaccination in mice, high-throughput RNA sequencing of spleens between a PPV23 treatment group and a control group were performed and evaluated in this study. The RNA-seq results identified a total of 41,321 mRNAs and 34,375 lncRNAs, including 55 significantly differentially expressed (DE) mRNAs and 389 DE lncRNAs (p < 0.05) between the two groups. GO and KEGG annotation analysis indicated that the target genes of DE lncRNAs and DE mRNAs were related to T-cell costimulation, positive regulation of alpha–beta T-cell differentiation, the CD86 biosynthetic process, and the PI3K-Akt signaling pathway, indicating that the polysaccharide component antigens of PPV23 might activate a cellular immune response during the PPV23 immunization process. Moreover, we found that Trim35 (tripartite motif containing 35), a target gene of lncRNA MSTRG.9127, was involved in regulating immunity. Our study provides a catalog of lncRNAs and mRNAs associated with immune cells’ proliferation and differentiation, and they deserve further study to deepen the understanding of the biological processes in the regulation of PPV23 during humoral immunity and cellular immunity.
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Affiliation(s)
- Nan Zhu
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Fan Zhang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Huan Zhou
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Wei Ma
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
- Aimei Vacin BioPharm (Zhejiang) Co., Ltd., Ningbo 315000, China
| | - Haiguang Mao
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Mengting Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Zhijian Ke
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Jinbo Wang
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
| | - Lili Qi
- School of Biological and Chemical Engineering, NingboTech University, Qianhunan Road 1, Ningbo 315100, China
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14
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Rheumatoid arthritis and non-coding RNAs; how to trigger inflammation. Life Sci 2023; 315:121367. [PMID: 36639050 DOI: 10.1016/j.lfs.2023.121367] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/31/2022] [Accepted: 12/31/2022] [Indexed: 01/12/2023]
Abstract
Rheumatoid arthritis (RA) is a systemic and chronic inflammatory disease categorized by continuous synovitis in the joints and systemic inflammatory responses that can cause lifelong disability. The major cause of RA is the dysregulation of the immune response. The development of RA disease includes multiplex association of several interleukins and cells, which leads to synovial cell growth, cartilage and bone damage. The primary stage of RA disease is related to the modification of both the innate and adaptive immune systems, which leads to the formation of autoantibodies. This process results in many damaged molecules and epitope spreading. Both the innate (e.g., dendritic cells, macrophages, and neutrophils) and acquired immune cells (e.g., T and B lymphocytes) will increase and continue the chronic inflammatory condition in the next stages of the RA disease. In recent years, non-coding RNAs have been proved as significant controllers of biological functions, especially immune cell expansion and reactions. Non-coding RNAs were primarily containing microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA). Various studies confirmed non-coding RNAs as hopeful markers for diagnosing and curing RA. This review will describe and cover existing knowledge about RA pathogenesis, which might be favorable for discovering possible ncRNA markers for RA.
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15
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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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16
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Haridevamuthu B, Guru A, Velayutham M, Snega Priya P, Arshad A, Arockiaraj J. Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost. REVIEWS IN AQUACULTURE 2023; 15:163-178. [DOI: 10.1111/raq.12709] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/18/2022] [Indexed: 10/16/2023]
Abstract
AbstractThe global aquaculture boom, fuelled by a reduction in wild population and detection of novel viruses, has created a demanding market, hence, there is a pressing need to investigate the immune system of fish, further. As the most diverse community of vertebrates and a central contributor to the progressing global aquaculture market, teleost continues to draw vast scientific interest. Recent breakthroughs in multi‐omics technologies have provided a platform to understand the role of long non‐coding RNA (lncRNA) in the host immune system during infection. Emerging evidence shows that teleost lncRNA might have a regulatory role in immune responses, mostly through lncRNA–microRNA (miRNA) sponging. Teleost lncRNA shares a functionally active short sequence complement to target the miRNA which is conserved among the several fish species. Recent report suggests that rhabdovirus exploits a lncRNA in teleost and, to dodge the host immune mechanism and negatively regulate the immune system. This observation reveals the essentiality of lncRNA in pathogen‐driven immunity in teleost. Reports available on the function of teleost lncRNA are still in early stages and experimental verifications are a limiting factor. Unravelling the lncRNA‐mediated immune regulation in fishes could be used against the invading pathogens to strengthen the aquaculture production. This review elaborates on the experimentally identified and functionally characterized lncRNA and its regulatory role in the teleost immune response during infection and pathogen‐driven host immune evolution, which could eventually lead to achieving high standards in aquaculture productivity.
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Affiliation(s)
- B. Haridevamuthu
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Ajay Guru
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Manikandan Velayutham
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - P. Snega Priya
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I‐AQUAS) Universiti Putra Malaysia Port Dickson Malaysia
| | - Jesu Arockiaraj
- Department of Biotechnology, College of Science and Humanities SRM Institute of Science and Technology Chennai Tamil Nadu India
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17
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Wang M, Zhang Y, Chang W, Zhang L, Syrigos KN, Li P. Noncoding RNA-mediated regulation of pyroptotic cell death in cancer. Front Oncol 2022; 12:1015587. [PMID: 36387211 PMCID: PMC9659888 DOI: 10.3389/fonc.2022.1015587] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/18/2022] [Indexed: 07/30/2023] Open
Abstract
Pyroptosis is a newly discovered form of programmed cell death, which is manifested by DNA fragmentation, cell swelling, cell membrane rupture and leakage of cell contents. Previous studies have demonstrated that pyroptosis is tightly associated with the initiation and development of various cancers, whereas the molecular mechanisms underlying pyroptosis remain obscure. Noncoding RNAs (ncRNAs) are a type of heterogeneous transcripts that are broadly expressed in mammalian cells. Owing to their potency of regulating gene expression, ncRNAs play essential roles in physiological and pathological processes. NcRNAs are increasingly acknowledged as important regulators of the pyroptosis process. Importantly, the crosstalk between ncRNAs and pyroptosis affects various hallmarks of cancer, including cell growth, survival, metastasis and therapeutic resistance. The study of the involvement of pyroptosis-associated ncRNAs in cancer pathobiology has become a hot area in recent years, while there are limited reviews on this topic. Herein, we provide an overview of the complicated roles of ncRNAs, mainly including microRNAs (miRNAs), long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs), in modulating pyroptosis, with a focus on the underlying mechanisms of the ncRNA-pyroptosis axis in cancer pathogenesis. Finally, we discuss the potential applications and challenges of exploiting pyroptosis-regulating ncRNAs as molecular biomarkers and therapeutic targets in cancer.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Wenguang Chang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lei Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Konstantinos N. Syrigos
- Third Department of Internal Medicine and Laboratory, National & Kapodistrian University of Athens, Athens, Greece
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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Macovei LA, Burlui A, Bratoiu I, Rezus C, Cardoneanu A, Richter P, Szalontay A, Rezus E. Adult-Onset Still's Disease-A Complex Disease, a Challenging Treatment. Int J Mol Sci 2022; 23:12810. [PMID: 36361602 PMCID: PMC9655522 DOI: 10.3390/ijms232112810] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 12/02/2022] Open
Abstract
Adult-onset Still's disease (AOSD) is a systemic inflammatory disorder with an unknown cause characterized by high-spiking fever, lymphadenopathy, hepatosplenomegaly, hyperferritinemia, and leukocytosis. The clinical course can be divided into three significant patterns, each with a different prognosis: Self-limited or monophasic, intermittent or polycyclic systemic, and chronic articular. Two criteria sets have been validated. The Yamaguchi criteria are the most generally used, although the Fautrel criteria offer the benefit of adding ferritin and glycosylated ferritin values. AOSD's pathogenesis is not yet completely understood. Chemokines and pro-inflammatory cytokines, including interferon (IFN)-γ, tumor necrosis factor α (TNFα), interleukin (IL)-1, IL-6, IL-8, and IL-18, play a crucial role in the progression of illness, resulting in the development of innovative targeted therapeutics. There are no treatment guidelines for AOSD due to its rarity, absence of controlled research, and lack of a standard definition for remission and therapy objectives. Non-steroidal anti-inflammatory drugs (NSAIDs), corticosteroids (CS), and conventional synthetic disease-modifying antirheumatic drugs (csDMARDs) are used in AOSD treatment. Biological therapy, including IL-1, IL-6, IL-18, and IL-17 inhibitors, as well as TNFα or Janus-kinases (JAKs) inhibitors, is administered to patients who do not react to CS and csDMARDs or achieve an inadequate response.
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Affiliation(s)
- Luana Andreea Macovei
- Department of Rheumatology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
- Clinical Rehabilitation Hospital, 700661 Iasi, Romania
| | - Alexandra Burlui
- Department of Rheumatology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
- Clinical Rehabilitation Hospital, 700661 Iasi, Romania
| | - Ioana Bratoiu
- Department of Rheumatology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
- Clinical Rehabilitation Hospital, 700661 Iasi, Romania
| | - Ciprian Rezus
- Department of Internal Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- III Internal Medicine Clinic, “St. Spiridon” County Emergency Clinical Hospital, 700111 Iasi, Romania
| | - Anca Cardoneanu
- Department of Rheumatology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
- Clinical Rehabilitation Hospital, 700661 Iasi, Romania
| | - Patricia Richter
- Department of Rheumatology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
- Clinical Rehabilitation Hospital, 700661 Iasi, Romania
| | - Andreea Szalontay
- Department of Psychiatry, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania
- Institute of Psychiatry “Socola”, 700282 Iasi, Romania
| | - Elena Rezus
- Department of Rheumatology, “Grigore T. Popa” University of Medicine and Pharmacy, 16 Universitatii Street, 700115 Iasi, Romania
- Clinical Rehabilitation Hospital, 700661 Iasi, Romania
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19
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Lei Z, Feng G, Wang Z, Ning Z. Noncoding RNAs and Virus and Treatment in Allergic Rhinitis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:1979447. [PMID: 36285160 PMCID: PMC9588333 DOI: 10.1155/2022/1979447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/31/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023]
Abstract
Allergic rhinitis (AR) is a type I hypersensitivity reaction disease caused by inhaled allergens and immunoglobulin E (IgE)-mediated. Noncoding RNA (ncRNA) is an important regulator involved in gene expression and can be detected in the cytoplasm or extracellular fluid, which mainly includes microRNAs (miRNA, length 22-24 nucleotides), long noncoding RNAs (lncRNA, length >200 nucleotides), and circRNAs. LncRNA and miRNA both participate in the regulation of immune function. Some respiratory viral infections can aggravate allergic rhinitis, such as a respiratory syncytial virus (RSV) and human metapneumovirus (hMPV). However, the interaction between viral infection and allergy is complex and the mechanism is still unclear. In this review, we summarized the interactions of noncoding RNAs and viruses in the occurrence and development of AR, along with the treatments focusing on the noncoding RNAs in the past five years.
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Affiliation(s)
- Zhu Lei
- Otolaryngology Department, Xianning First People's Hospital, Xianning 437100, Hubei, China
| | - Guangrui Feng
- Cardiovascular Medicine Department, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437100, Hubei, China
| | - Zhiguo Wang
- Dermatology Department, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning 437100, Hubei, China
| | - Zhifeng Ning
- Human Anatomy Department, Basic Medicine College, Hubei University of Science and Technology, Xianning 437100, Hubei, China
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20
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The Role of Noncoding RNA in Airway Allergic Diseases through Regulation of T Cell Subsets. Mediators Inflamm 2022; 2022:6125698. [PMID: 36248190 PMCID: PMC9553461 DOI: 10.1155/2022/6125698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/31/2022] [Accepted: 09/23/2022] [Indexed: 11/18/2022] Open
Abstract
Allergic rhinitis and asthma are common airway allergic diseases, the incidence of which has increased annually in recent years. The human body is frequently exposed to allergens and environmental irritants that trigger immune and inflammatory responses, resulting in altered gene expression. Mounting evidence suggested that epigenetic alterations were strongly associated with the progression and severity of allergic diseases. Noncoding RNAs (ncRNAs) are a class of transcribed RNA molecules that cannot be translated into polypeptides and consist of three major categories, microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs). Previous studies showed that ncRNAs were involved in the physiopathological mechanisms of airway allergic diseases and contributed to their occurrence and development. This article reviews the current state of understanding of the role of noncoding RNAs in airway allergic diseases, highlights the limitations of recent studies, and outlines the prospects for further research to facilitate the clinical translation of noncoding RNAs as therapeutic targets and biomarkers.
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21
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Lei B, Song H, Xu F, Wei Q, Wang F, Tan G, Ma H. When does hepatitis B virus meet long-stranded noncoding RNAs? Front Microbiol 2022; 13:962186. [PMID: 36118202 PMCID: PMC9479684 DOI: 10.3389/fmicb.2022.962186] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/22/2022] [Indexed: 01/16/2023] Open
Abstract
Hepatitis B virus (HBV) infection in humans and its associated diseases are long-standing problems. HBV can produce a large number of non-self-molecules during its life cycle, which acts as targets for innate immune recognition and initiation. Among these, interferon and its large number of downstream interferon-stimulated gene molecules are important early antiviral factors. However, the development of an effective antiviral immune response is not simple and depends not only on the delicate regulation of the immune response but also on the various mechanisms of virus-related immune escape and immune tolerance. Therefore, despite there being a relatively well-established consensus on the major pathways of the antiviral response and their component molecules, the complete clearance of HBV remains a challenge in both basic and clinical research. Long-noncoding RNAs (lncRNAs) are generally >200 bp in length and perform different functions in the RNA strand encoding the protein. As an important part of the IFN-inducible genes, interferon-stimulated lncRNAs are involved in the regulation of several HBV infection-related pathways. This review traces the basic elements of such pathways and characterizes the various recent targets of lncRNAs, which not only complement the regulatory mechanisms of pathways related to chronic HBV infection, fibrosis, and cancer promotion but also present with new potential therapeutic targets for controlling HBV infection and the malignant transformation of hepatocytes.
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Affiliation(s)
- Bingxin Lei
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Department of Immunology, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, Jilin, China
- Department of Anesthesiology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Hongxiao Song
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Department of Immunology, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Fengchao Xu
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Department of Immunology, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qi Wei
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Department of Immunology, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, Jilin, China
- Department of Anesthesiology, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Fei Wang
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Department of Immunology, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Guangyun Tan
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Department of Immunology, Center for Pathogen Biology and Infectious Diseases, The First Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Guangyun Tan,
| | - Haichun Ma
- Department of Anesthesiology, The First Hospital of Jilin University, Changchun, Jilin, China
- Haichun Ma,
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22
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Thá EL, Gagosian VSC, Canavez ADPM, Schuck DC, Brohem CA, Gradia DF, de Freitas RA, Prado KB, Cestari MM, Lorencini M, Leme DM. In vitro evaluation of the inhalation toxicity of the cosmetic ingredient aluminum chlorohydrate. J Appl Toxicol 2022; 42:2016-2029. [PMID: 35883269 DOI: 10.1002/jat.4371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 07/14/2022] [Accepted: 07/22/2022] [Indexed: 11/08/2022]
Abstract
Aluminum chlorohydrate (ACH) is a major aerosol component frequently used as the active ingredient in antiperspirants, and in vivo studies have raised a concern about its inhalation toxicity. Still, few studies have addressed its effects on the human respiratory tract. Therefore, we developed a study on ACH inhalation toxicity using an in vitro human alveolar cell model (A549 cells) with molecular and cellular markers of oxidative stress, immunotoxicity, and epigenetic changes. The chemical characterization of ACH suspensions indicated particle instability and aggregation; however, side-scatter analysis demonstrated significant particle uptake in cells exposed to ACH. Exposure of A549 cells to non-cytotoxic concentrations of ACH (0.25, 0.5, and 1 mg/ml) showed that ACH induced reactive oxygen species. Moreover, ACH upregulated TNF, IL6, IL8, and IL1A genes, but not the lncRNAs NEAT1 and MALAT1. Finally, no alterations on the global DNA methylation pattern (5-methylcytosine and 5-hydroxymethylcytosine) or the phosphorylation of histone H2AX (γ-H2AX) were observed. Our data suggest that ACH may induce oxidative stress and inflammation on alveolar cells, and A549 cells may be useful to identify cellular and molecular events that may be associated with adverse effects on the lungs. Still, further research is needed to ensure the inhalation safety of ACH.
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Affiliation(s)
- Emanoela Lundgren Thá
- Graduate Program in Genetics, Department of Genetics-Federal University of Paraná (UFPR), Curitiba, Brazil
| | | | | | | | - Carla Abdo Brohem
- Product Safety Management-Q&PP, Grupo Boticário, São José dos Pinhais, Brazil
| | | | | | - Karin Braun Prado
- Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
| | | | - Márcio Lorencini
- Product Safety Management-Q&PP, Grupo Boticário, São José dos Pinhais, Brazil
| | - Daniela Morais Leme
- Department of Genetics, Federal University of Paraná (UFPR), Curitiba, Brazil
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23
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen PR. Photocatalytic Chemical Crosslinking for Profiling RNA–Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022; 61:e202202008. [DOI: 10.1002/anie.202202008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Huixin Luo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines Institute of Materia Medica Chinese Academy of Medical Sciences and Peking UnionMedical College Beijing 100050 China
| | - Wei Tang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Hongyu Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Xiangmei Zeng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - William Shu Ching Ngai
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Rui Gao
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Heyun Li
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Ran Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Huangtao Zheng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Jianting Guo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Fangfei Qin
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Gang Wang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Kexin Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Xinyuan Fan
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
- Chinese Institute for Brain Research (CIBR) Beijing 102206 China
| | - Peng R. Chen
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
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24
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen P. Photocatalytic Chemical Crosslinking for Profiling RNA‐Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Huixin Luo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Wei Tang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Hongyu Liu
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Xiangmei Zeng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | | | - Rui Gao
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Heyun Li
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Ran Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Huangtao Zheng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Jianting Guo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Fangfei Qin
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Gang Wang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Kexin Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Xinyuan Fan
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Zou
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Chen
- Peking University tional Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering 100871 Beijing CHINA
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25
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Jia L, Wang J, Luoreng Z, Wang X, Wei D, Yang J, Hu Q, Ma Y. Progress in Expression Pattern and Molecular Regulation Mechanism of LncRNA in Bovine Mastitis. Animals (Basel) 2022; 12:ani12091059. [PMID: 35565486 PMCID: PMC9105470 DOI: 10.3390/ani12091059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Bovine mastitis is an inflammatory disease of the mammary glands that causes serious harm to cow health and huge economic losses. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate a variety of diseases of humans and animals, especially the immune response and inflammatory disease process. This paper reviews the role of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of lncRNA expression and the molecular regulatory mechanism in bovine mastitis, and looks forward to the research and application prospect of lncRNA in bovine mastitis, intending to provide a reference for scientific researchers to systematically understand this research field. Abstract Bovine mastitis is an inflammatory disease caused by pathogenic microbial infection, trauma, or other factors. Its morbidity is high, and it is difficult to cure, causing great harm to the health of cows and the safety of dairy products. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are a class of endogenous non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate the immune response of humans and animals on three levels (transcription, epigenetic modification, and post-transcription), and are widely involved in the pathological process of inflammatory diseases. Over the past few years, extensive findings revealed basic roles of lncRNAs in inflammation, especially bovine mastitis. This paper reviews the expression pattern and mechanism of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of the lncRNA expression pattern and molecular regulatory mechanism in bovine mastitis, analyzes the molecular regulatory network of differentially expressed lncRNAs, and looks forward to the research and application prospect of lncRNA in bovine mastitis, laying a foundation for molecular breeding and the biological therapy of bovine mastitis.
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Affiliation(s)
- Li Jia
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jinpeng Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jian Yang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Qichao Hu
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
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26
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Płaczkiewicz J, Adamczyk-Popławska M, Kozłowska E, Kwiatek A. Both Neisseria gonorrhoeae and Neisseria sicca Induce Cytokine Secretion by Infected Human Cells, but Only Neisseria gonorrhoeae Upregulates the Expression of Long Non-Coding RNAs. Pathogens 2022; 11:pathogens11040394. [PMID: 35456069 PMCID: PMC9031631 DOI: 10.3390/pathogens11040394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 12/04/2022] Open
Abstract
Bacteria of the Neisseria genus are Gram-negative diplococci including both pathogenic and commensal species. We focused on pathogenic Neisseria gonorrhoeae and commensal Neisseria sicca. We have demonstrated that not only N. gonorrhoeae, but also N. sicca induce the secretion of pro-inflammatory cytokines IL-6, TNF-α, and chemokines CXCL8 and CCL20 by infected epithelial cells. However, N. sicca triggers a lesser effect than does N. gonorrhoeae. Furthermore, N. gonorrhoeae and N. sicca invoke distinct effects on the expression of genes (JUNB, FOSB, NFKB1, NFKBIA) encoding protein components of AP-1 and NF-κB transcription factors. We have also shown that the infection of epithelial cells by N. gonorrhoeae leads to significant overexpression of the long non-coding RNAs (lncRNAs), including MALAT1, ERICD, and RP11-510N19.5. This effect was not identified for N. sicca. In conclusion, data on the expression of lncRNAs and cytokine secretion in response to Neisseria spp. exposure indicate new directions for research on Neisseria-host interactions and can provide further insights into virulence of not only pathogenic, but also commensal Neisseria spp.
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Affiliation(s)
- Jagoda Płaczkiewicz
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (J.P.); (M.A.-P.)
- International Centre for Translational Eye Research, Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Monika Adamczyk-Popławska
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (J.P.); (M.A.-P.)
| | - Ewa Kozłowska
- Department of Immunology, Institute of Functional Biology and Ecology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland;
| | - Agnieszka Kwiatek
- Department of Molecular Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, 02-096 Warsaw, Poland; (J.P.); (M.A.-P.)
- Correspondence:
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27
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García-Pérez I, Molsosa-Solanas A, Perelló-Amorós M, Sarropoulou E, Blasco J, Gutiérrez J, Garcia de la serrana D. The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream ( Sparus aurata) Fast Skeletal Muscle. Cells 2022; 11:428. [PMID: 35159240 PMCID: PMC8834446 DOI: 10.3390/cells11030428] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/22/2022] [Indexed: 02/05/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are an emerging group of ncRNAs that can modulate gene expression at the transcriptional or translational levels. In the present work, previously published transcriptomic data were used to identify lncRNAs expressed in gilthead sea bream skeletal muscle, and their transcription levels were studied under different physiological conditions. Two hundred and ninety lncRNAs were identified and, based on transcriptomic differences between juveniles and adults, a total of seven lncRNAs showed potential to be important for muscle development. Our data suggest that the downregulation of most of the studied lncRNAs might be linked to increased myoblast proliferation, while their upregulation might be necessary for differentiation. However, with these data, as it is not possible to propose a formal mechanism to explain their effect, bioinformatic analysis suggests two possible mechanisms. First, the lncRNAs may act as sponges of myoblast proliferation inducers microRNAs (miRNAs) such as miR-206, miR-208, and miR-133 (binding energy MEF < -25.0 kcal). Secondly, lncRNA20194 had a strong predicted interaction towards the myod1 mRNA (ndG = -0.17) that, based on the positive correlation between the two genes, might promote its function. Our study represents the first characterization of lncRNAs in gilthead sea bream fast skeletal muscle and provides evidence regarding their involvement in muscle development.
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Affiliation(s)
- Isabel García-Pérez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Anna Molsosa-Solanas
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Miquel Perelló-Amorós
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, 71003 Crete, Greece;
| | - Josefina Blasco
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Joaquim Gutiérrez
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
| | - Daniel Garcia de la serrana
- Department of Cell Biology, Physiology and Immunology, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain; (I.G.-P.); (A.M.-S.); (M.P.-A.); (J.B.); (J.G.)
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28
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Lin HH, Horie M, Tomonaga K. A comprehensive profiling of innate immune responses in Eptesicus bat cells. Microbiol Immunol 2021; 66:97-112. [PMID: 34842304 DOI: 10.1111/1348-0421.12952] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/11/2021] [Accepted: 11/11/2021] [Indexed: 11/29/2022]
Abstract
Bats (the order Chiroptera), including those of the genus Eptesicus, have been reported to serve as reservoirs of several zoonotic viruses. Notably, bats have been reported to lack obvious symptoms of infection with such viruses and are thought to have unique immune system responses. However, the responses of their innate immune system, the first line of immunity, remain largely unclear. Here, we comprehensively analyzed the expression profiles in two Eptesicus bat cell lines to investigate their innate immune responses. The gene expression profiles after polyinosinic-polycytidylic acid (poly (I:C)) induction were similar between the two bat cell lines, but uniquely upregulated differentially expressed genes were also identified. We also revealed that the upregulated genes of Eptesicus bat cells were distinct from those of human epithelial cells in response to induction. Moreover, the basal expression levels of several immune-related genes were higher in bat cells than in human cells. We also identified unannotated novel transcripts that were upregulated after induction and novel microRNAs expressed in bat cells, some of which were upregulated by poly (I:C) treatment. This is the first report to illustrate the innate immune response in Eptesicus bat cells; therefore, this study provides basic and novel insights into bat innate immunity. Our data represent a valuable resource for future studies into bat immunity and the biology of Eptesicus bats. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Hsien-Hen Lin
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT), Kyoto University, Kyoto, Japan.,Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Masayuki Horie
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT), Kyoto University, Kyoto, Japan.,Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan.,Laboratory of Veterinary Microbiology, Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences (InFRONT), Kyoto University, Kyoto, Japan.,Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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29
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Liang H, Li F, Li H, Wang R, Du M. Overexpression of lncRNA HULC Attenuates Myocardial Ischemia/reperfusion Injury in Rat Models and Apoptosis of Hypoxia/reoxygenation Cardiomyocytes via Targeting miR-377-5p through NLRP3/Caspase‑1/IL‑1β Signaling Pathway Inhibition. Immunol Invest 2021; 50:925-938. [PMID: 32674625 DOI: 10.1080/08820139.2020.1791178] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVE Acute myocardial infarction (AMI) is characterized by myocardial tissue necrosis and activation of inflammatory response. This study aims to elucidate the potential mechanism underlying the protective effects of long non-coding RNA (lncRNA) highly up-regulated in liver cancer (HULC) against myocardial ischemia/reperfusion (I/R) injury in rat models and apoptosis of cardiomyocytes. METHODS We firstly established rat models of myocardial I/R injury and rat cardiomyocyte (H9c2 cells) models of hypoxia/reoxygenation (H/R) injury. Sprague-Dawley (SD) neonatal rats were randomized into four groups: sham, I/R, I/R+ microRNA (miR) -377-5p mimic, and I/R+ miR-377-5p antagomir, respectively. Then, histopathological examination was applied. Apoptosis was evaluated by transferase-mediated dUTP nick end labeling (TUNEL) staining. Cell vitality was measured using MTT assay. The concentrations of creatine kinase MB (CK-MB), cardiac troponin I (cTnI), interleukin (IL) -6 (IL-6), and tumor necrosis factor-α (TNF-α) were detected by enzyme-linked immunosorbent assay (ELISA). The expression of Cleaved-Caspase-3, Caspase-3, NOD-like receptor P3 (NLRP3), Caspase-1, and IL-1β was analyzed by immunohistochemical (IHC) or Western blot analysis. RESULTS We found that HULC was downregulated and miR-377-5p was upregulated in IR-injured myocardial tissue and the H/R-induced H9c2 cell. Overexpression of miR-377-5p increased myocardial dysfunction and apoptosis and activated formation and secretion of IL-6 and TNF-α. The preprocessing of miR-377-5p silencing emerged opposite results. Strikingly, dual luciferase reporter assay showed that HULC was a sponge of miR-377-5p. Subsequently, mechanism experiments revealed that NLRP3/Caspase‑1/IL‑1β was a target axis of miR-377-5p. In vitro, the protective effect of HULC overexpression on H9c2 cell viability and inflammation was offset by miR-377-5p silencing. Finally, rescue assay suggested that HULC-miR-377-5p -NLRP3/Caspase‑1/IL‑1β axis regulated the apoptosis and inflammation of H/R-induced H9c2 cells. CONCLUSIONS Overall, these results indicate that the protective effect of HULC against myocardial I/R injury and H/R cardiomyocyte apoptosis partially relies on the inhibition of NLRP3/Caspase‑1/IL‑1β signaling pathway.
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Affiliation(s)
- Huiqing Liang
- Department of Cardiology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Fangjiang Li
- Department of Cardiology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Huixian Li
- Department of Cardiology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Rui Wang
- Department of Cardiology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
| | - Meiling Du
- Department of Cardiology, The First Affiliated Hospital of Hebei North University, Zhangjiakou, China
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30
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Zhang L, Zheng X, Li J, Wang G, Hu Z, Chen Y, Wang X, Gu M, Gao R, Hu S, Liu X, Jiao X, Peng D, Hu J, Liu X. Long noncoding RNA#45 exerts broad inhibitory effect on influenza a virus replication via its stem ring arms. Virulence 2021; 12:2443-2460. [PMID: 34517783 PMCID: PMC8451462 DOI: 10.1080/21505594.2021.1975494] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
A growing body of evidence suggests the pivotal role of long non-coding RNA (lncRNA) in influenza virus infection. Based on next-generation sequencing, we previously demonstrated that Lnc45 was distinctively stimulated by H5N1 influenza virus in mice. In this study, we systematically investigated the specific role of Lnc45 during influenza A virus (IAV) infection. Through qRT-PCR, we first demonstrated that Lnc45 is highly up-regulated by different subtypes of IAV strains, including H5N1, H7N9, and H1N1 viruses. Using RNA-FISH and qRT-PCR, we then found that Lnc45 can translocate from nuclear to cytoplasm during H5N1 virus infection. In addition, forced Lnc45 expression dramatically impeded viral replication of H1N1, H5N1, and H7N9 virus, while abolish of Lnc45 expression by RNA interference favored replication of these viruses, highlighting the potential broad antiviral activity of Lnc45 to IAV. Correspondingly, overexpression of Lnc45 inhibited viral polymerase activity and suppressed IAV-induced cell apoptosis. Moreover, Lnc45 significantly restrained nuclear aggregation of viral NP and PA proteins during H5N1 virus infection. Further functional study revealed that the stem ring arms of Lnc45 mainly mediated the antiviral effect. Therefore, we here demonstrated that Lnc45 functions as a broad-spectrum antiviral factor to inhibit influenza virus replication probably through inhibiting polymerase activity and NP and PA nuclear accumulation via its stem ring arms. Our study not only advances our understanding of the complexity of the IAV pathogenesis but also lays the foundation for developing novel anti-IAV therapeutics targeting the host lncRNA.
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Affiliation(s)
- Lei Zhang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xinxin Zheng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Jun Li
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Guoqing Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Zenglei Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Yu Chen
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Min Gu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Ruyi Gao
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Daxin Peng
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Jiao Hu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, School of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou, China.,Key Laboratory of Prevention and Control of Biological Hazard Factors (Animal Origin) for Agri-food Safety and Quality, Ministry of Agriculture of China (26116120), Yangzhou University, Yangzhou, China
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31
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Krappinger JC, Bonstingl L, Pansy K, Sallinger K, Wreglesworth NI, Grinninger L, Deutsch A, El-Heliebi A, Kroneis T, Mcfarlane RJ, Sensen CW, Feichtinger J. Non-coding Natural Antisense Transcripts: Analysis and Application. J Biotechnol 2021; 340:75-101. [PMID: 34371054 DOI: 10.1016/j.jbiotec.2021.08.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 06/30/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
Non-coding natural antisense transcripts (ncNATs) are regulatory RNA sequences that are transcribed in the opposite direction to protein-coding or non-coding transcripts. These transcripts are implicated in a broad variety of biological and pathological processes, including tumorigenesis and oncogenic progression. With this complex field still in its infancy, annotations, expression profiling and functional characterisations of ncNATs are far less comprehensive than those for protein-coding genes, pointing out substantial gaps in the analysis and characterisation of these regulatory transcripts. In this review, we discuss ncNATs from an analysis perspective, in particular regarding the use of high-throughput sequencing strategies, such as RNA-sequencing, and summarize the unique challenges of investigating the antisense transcriptome. Finally, we elaborate on their potential as biomarkers and future targets for treatment, focusing on cancer.
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Affiliation(s)
- Julian C Krappinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria
| | - Lilli Bonstingl
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Katrin Pansy
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria
| | - Katja Sallinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Nick I Wreglesworth
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Lukas Grinninger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Austrian Biotech University of Applied Sciences, Konrad Lorenz-Straße 10, 3430 Tulln an der Donau, Austria
| | - Alexander Deutsch
- Division of Haematology, Medical University of Graz, Stiftingtalstrasse 24, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
| | - Amin El-Heliebi
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Thomas Kroneis
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Center for Biomarker Research in Medicine, Stiftingtalstraße 5, 8010 Graz, Austria
| | - Ramsay J Mcfarlane
- North West Cancer Research Institute, School of Medical Sciences, Bangor University, LL57 2UW Bangor, United Kingdom
| | - Christoph W Sensen
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria; Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14/V, 8010 Graz, Austria; HCEMM Kft., Római blvd. 21, 6723 Szeged, Hungary
| | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center for Cell Signalling, Metabolism and Aging, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; Christian Doppler Laboratory for innovative Pichia pastoris host and vector systems, Division of Cell Biology, Histology and Embryology, Medical University of Graz, Neue Stiftingtalstraße 6/II, 8010 Graz, Austria; BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria.
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32
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Xie G, Zhu Y, Lin Z, Sun Y, Gu G, Wang W, Chen H. HOPMCLDA: predicting lncRNA-disease associations based on high-order proximity and matrix completion. Mol Omics 2021; 17:760-768. [PMID: 34251001 DOI: 10.1039/d1mo00138h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In recent years, emerging evidence has shown that long noncoding RNAs (lncRNAs) have important roles in the biological processes of complex diseases. However, experiments to determine the associations between diseases and lncRNAs are time consuming and costly. Therefore, there is a need to develop effective computational methods for exploring potential lncRNA-disease associations. In this study, we present a computational prediction method based on high-order proximity and matrix completion to predict lncRNA-disease associations (HOPMCLDA). HOPMCLDA integrates explicit similarity and high-order proximity information on lncRNAs and diseases and constructs a heterogeneous disease-lncRNA network to utilize similarity information. Finally, nuclear norm regularization is carried out on the heterogeneous network for the recovery of a lncRNA-disease association matrix. By implementing leave-one-out cross validation (LOOCV) and five-fold cross validation (5-fold CV), we compare HOPMCLDA with five other methods. HOPMCLDA outperforms the other methods, with area under the receiver operating characteristic curve values of 0.8755 and 0.8353 ± 0.0045 using LOOCV and 5-fold CV, respectively. Furthermore, case studies of three human diseases (gastric cancer, osteosarcoma, and hepatocellular carcinoma) confirm the reliable predictive performance of HOPMCLDA.
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Affiliation(s)
- Guobo Xie
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Yinting Zhu
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Zhiyi Lin
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Yuping Sun
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Guosheng Gu
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Weiming Wang
- School of Computers, Guangdong University of Technology, Guangzhou, China.
| | - Hui Chen
- School of Computers, Guangdong University of Technology, Guangzhou, China.
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33
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Huang M, Dong J, Guo H, Xiao M, Wang D. Identification of long noncoding RNAs reveals the effects of dinotefuran on the brain in Apis mellifera (Hymenopptera: Apidae). BMC Genomics 2021; 22:502. [PMID: 34217210 PMCID: PMC8254963 DOI: 10.1186/s12864-021-07811-y] [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: 03/10/2021] [Accepted: 06/14/2021] [Indexed: 12/19/2022] Open
Abstract
Background Dinotefuran (CAS No. 165252–70-0), a neonicotinoid insecticide, has been used to protect various crops against invertebrate pests and has been associated with numerous negative sublethal effects on honey bees. Long noncoding RNAs (lncRNAs) play important roles in mediating various biological and pathological processes, involving transcriptional and gene regulation. The effects of dinotefuran on lncRNA expression and lncRNA function in the honey bee brain are still obscure. Results Through RNA sequencing, a comprehensive analysis of lncRNAs and mRNAs was performed following exposure to 0.01 mg/L dinotefuran for 1, 5, and 10 d. In total, 312 lncRNAs and 1341 mRNAs, 347 lncRNAs and 1458 mRNAs, and 345 lncRNAs and 1155 mRNAs were found to be differentially expressed (DE) on days 1, 5 and 10, respectively. Gene set enrichment analysis (GSEA) indicated that the dinotefuran-treated group showed enrichment in carbohydrate and protein metabolism and immune-inflammatory responses such as glycine, serine and threonine metabolism, pentose and glucuronate interconversion, and Hippo and transforming growth factor-β (TGF-β) signaling pathways. Moreover, the DE lncRNA TCONS_00086519 was shown by fluorescence in situ hybridization (FISH) to be distributed mainly in the cytoplasm, suggesting that it may serve as a competing endogenous RNA and a regulatory factor in the immune response to dinotefuran. Conclusion This study characterized the expression profile of lncRNAs upon exposure to neonicotinoid insecticides in young adult honey bees and provided a framework for further study of the role of lncRNAs in honey bee growth and the immune response. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07811-y.
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Affiliation(s)
- Minjie Huang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jie Dong
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Haikun Guo
- Institute of Quality and Standard for Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Minghui Xiao
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.,State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Deqian Wang
- Institute of Animal Husbandry and Veterinary Science, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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34
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May JM, Bylicky M, Chopra S, Coleman CN, Aryankalayil MJ. Long and short non-coding RNA and radiation response: a review. Transl Res 2021; 233:162-179. [PMID: 33582242 PMCID: PMC8475769 DOI: 10.1016/j.trsl.2021.02.005] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 12/12/2022]
Abstract
Once thought of as arising from "junk DNA," noncoding RNAs (ncRNAs) have emerged as key molecules in cellular processes and response to stress. From diseases such as cancer, coronary artery disease, and diabetes to the effects of ionizing radiation (IR), ncRNAs play important roles in disease progression and as biomarkers of damage. Noncoding RNAs regulate cellular processes by competitively binding DNA, mRNA, proteins, and other ncRNAs. Through these interactions, specific ncRNAs can modulate the radiosensitivity of cells and serve as diagnostic and prognostic biomarkers of radiation damage, whether from incidental exposure in radiotherapy or in accidental exposure scenarios. Analysis of RNA expression after radiation exposure has shown alterations not only in mRNAs, but also in ncRNAs (primarily miRNA, circRNA, and lncRNA), implying an important role in cellular stress response. Due to their abundance and stability in serum and other biofluids, ncRNAs also have great potential as minimally invasive biomarkers with advantages over current biodosimetry methods. Several studies have examined changes in ncRNA expression profiles in response to IR and other forms of oxidative stress. Furthermore, some studies have reported modulation of radiosensitivity by altering expression levels of these ncRNAs. This review discusses the roles of ncRNAs in the radiation response and evaluates prior research on ncRNAs as biomarkers of radiation damage. Future directions and applications of ncRNAs in radiation research are introduced, including the potential for a clinical ncRNA assay for assessing radiation damage and for the therapeutic use of RNA interference (RNAi).
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Affiliation(s)
- Jared M May
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Michelle Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland; Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Molykutty J Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland.
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35
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Bella F, Campo S. Long non-coding RNAs and their involvement in bipolar disorders. Gene 2021; 796-797:145803. [PMID: 34175394 DOI: 10.1016/j.gene.2021.145803] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/22/2021] [Indexed: 01/22/2023]
Abstract
Non-coding RNAs (nc-RNAs) can be defined as RNA molecules that are not translated into proteins. Although the functional meaning of many nc-RNAs remains still to be verified, several of these molecules have a clear biological importance, which goes from translation of mRNAs to DNA replication. Indeed, regulatory nc-RNAs can be classified into two groups: short non-coding RNAs (sncRNAs) and long-non coding RNAs (lncRNAs). In the last years, lncRNAs have gained increasing importance in the study of gene regulation, helping authors understand the molecular mechanisms underlying cellular physiology and pathology. LncRNAs are greater than 200 bp and accumulate in nucleus, cytoplasm and exosomes with high tissue specificity, acting in cis or in trans in order to exert enhancer or silencer modulation on gene expression. Such regulatory features, which are widespread in human cells and tissues, can be disrupted in several morbid states. Recent evidences may suggest a disruption of lncRNAs in bipolar disorders, a cluster of severe, chronic and disabling psychiatric diseases, which are characterized by major depressive states cyclically alternating with manic episodes. Here, the authors reviewed genes, classification, biogenesis, structures, functions and databases regarding lncRNAs, and also focused on bipolar disorders, in which some lncRNAs, especially those involved in inflammation and neuronal development, has reported to be dysregulated.
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Affiliation(s)
- Fabrizio Bella
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy
| | - Salvatore Campo
- Department of Biomedical and Dental Sciences and Morphofunctional Images, University of Messina, via Consolare Valeria, 1, Messina 98125 Italy.
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36
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Kundu M, Basu J. The Role of microRNAs and Long Non-Coding RNAs in the Regulation of the Immune Response to Mycobacterium tuberculosis Infection. Front Immunol 2021; 12:687962. [PMID: 34248974 PMCID: PMC8264550 DOI: 10.3389/fimmu.2021.687962] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022] Open
Abstract
Non-coding RNAs have emerged as critical regulators of the immune response to infection. MicroRNAs (miRNAs) are small non-coding RNAs which regulate host defense mechanisms against viruses, bacteria and fungi. They are involved in the delicate interplay between Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), and its host, which dictates the course of infection. Differential expression of miRNAs upon infection with M. tuberculosis, regulates host signaling pathways linked to inflammation, autophagy, apoptosis and polarization of macrophages. Experimental evidence suggests that virulent M. tuberculosis often utilize host miRNAs to promote pathogenicity by restricting host-mediated antibacterial signaling pathways. At the same time, host- induced miRNAs augment antibacterial processes such as autophagy, to limit bacterial proliferation. Targeting miRNAs is an emerging option for host-directed therapies. Recent studies have explored the role of long non-coding RNA (lncRNAs) in the regulation of the host response to mycobacterial infection. Among other functions, lncRNAs interact with chromatin remodelers to regulate gene expression and also function as miRNA sponges. In this review we attempt to summarize recent literature on how miRNAs and lncRNAs are differentially expressed during the course of M. tuberculosis infection, and how they influence the outcome of infection. We also discuss the potential use of non-coding RNAs as biomarkers of active and latent tuberculosis. Comprehensive understanding of the role of these non-coding RNAs is the first step towards developing RNA-based therapeutics and diagnostic tools for the treatment of TB.
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Affiliation(s)
| | - Joyoti Basu
- Department of Chemistry, Bose Institute, Kolkata, India
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37
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Mushimiyimana I, Tomas Bosch V, Niskanen H, Downes NL, Moreau PR, Hartigan K, Ylä-Herttuala S, Laham-Karam N, Kaikkonen MU. Genomic Landscapes of Noncoding RNAs Regulating VEGFA and VEGFC Expression in Endothelial Cells. Mol Cell Biol 2021; 41:e0059420. [PMID: 33875575 PMCID: PMC8224232 DOI: 10.1128/mcb.00594-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/29/2020] [Accepted: 04/03/2021] [Indexed: 12/26/2022] Open
Abstract
Vascular endothelial growth factors (VEGFs) are best known as key regulators of angiogenesis and lymphangiogenesis. Although VEGFs have been promising therapeutic targets for various cardiovascular diseases, their regulatory landscape in endothelial cells remains elusive. Several studies have highlighted the involvement of noncoding RNAs (ncRNAs) in the modulation of VEGF expression. In this study, we investigated the role of two classes of ncRNAs, long ncRNAs (lncRNAs) and enhancer RNAs (eRNAs), in the transcriptional regulation of VEGFA and VEGFC. By integrating genome-wide global run-on sequencing (GRO-Seq) and chromosome conformation capture (Hi-C) data, we identified putative lncRNAs and eRNAs associated with VEGFA and VEGFC genes in endothelial cells. A subset of the identified putative enhancers demonstrated regulatory activity in a reporter assay. Importantly, we demonstrate that deletion of enhancers and lncRNAs by CRISPR/Cas9 promoted significant changes in VEGFA and VEGFC expression. Transcriptome sequencing (RNA-Seq) data from lncRNA deletions showed downstream factors implicated in VEGFA- and VEGFC-linked pathways, such as angiogenesis and lymphangiogenesis, suggesting functional roles for these lncRNAs. Our study uncovers novel lncRNAs and eRNAs regulating VEGFA and VEGFC that can be targeted to modulate the expression of these important molecules in endothelial cells.
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Affiliation(s)
- Isidore Mushimiyimana
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Vanesa Tomas Bosch
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Henri Niskanen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Nicholas L. Downes
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Pierre R. Moreau
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | | | - Seppo Ylä-Herttuala
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
- Heart Center and Gene Therapy Unit, Kuopio University Hospital, Kuopio, Finland
| | - Nihay Laham-Karam
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Minna U. Kaikkonen
- A. I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
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38
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Di Fiore R, Suleiman S, Felix A, O’Toole SA, O’Leary JJ, Ward MP, Beirne J, Sabol M, Ozretić P, Yordanov A, Vasileva-Slaveva M, Kostov S, Nikolova M, Said-Huntingford I, Ayers D, Ellul B, Pentimalli F, Giordano A, Calleja-Agius J. An Overview of the Role of Long Non-Coding RNAs in Human Choriocarcinoma. Int J Mol Sci 2021; 22:ijms22126506. [PMID: 34204445 PMCID: PMC8235025 DOI: 10.3390/ijms22126506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 02/08/2023] Open
Abstract
Choriocarcinoma (CC), a subtype of trophoblastic disease, is a rare and highly aggressive neoplasm. There are two main CC subtypes: gestational and non-gestational, (so called when it develops as a component of a germ cell tumor or is related to a somatic mutation of a poorly differentiated carcinoma), each with very diverse biological activity. A therapeutic approach is highly effective in patients with early-stage CC. The advanced stage of the disease also has a good prognosis with around 95% of patients cured following chemotherapy. However, advancements in diagnosis and treatment are always needed to improve outcomes for patients with CC. Long non-coding (lnc) RNAs are non-coding transcripts that are longer than 200 nucleotides. LncRNAs can act as oncogenes or tumor suppressor genes. Deregulation of their expression has a key role in tumor development, angiogenesis, differentiation, migration, apoptosis, and proliferation. Furthermore, detection of cancer-associated lncRNAs in body fluids, such as blood, saliva, and urine of cancer patients, is emerging as a novel method for cancer diagnosis. Although there is evidence for the potential role of lncRNAs in a number of cancers of the female genital tract, their role in CC is poorly understood. This review summarizes the current knowledge of lncRNAs in gestational CC and how this may be applied to future therapeutic strategies in the treatment of this rare cancer.
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Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Correspondence: (R.D.F.); (J.C.-A.); Tel.: +356-2340-3871 (R.D.F.); +356-2340-1892 (J.C.-A.)
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
| | - Ana Felix
- Department of Pathology, Campo dos Mártires da Pátria, Instituto Portugues de Oncologia de Lisboa, NOVA Medical School, UNL, 130, 1169-056 Lisboa, Portugal;
| | - Sharon A. O’Toole
- Departments of Obstetrics and Gynaecology and Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, 8 Dublin, Ireland;
| | - John J. O’Leary
- Department of Histopathology, Trinity College Dublin, Trinity St James’s Cancer Institute, 8 Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - Mark P. Ward
- Department of Histopathology, Trinity College Dublin, Trinity St James’s Cancer Institute, 8 Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - James Beirne
- Department of Gynaecological Oncology, Trinity St James Cancer Institute, St James Hospital, 8 Dublin, Ireland;
| | - Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.S.); (P.O.)
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.S.); (P.O.)
| | - Angel Yordanov
- Department of Gynecologic Oncology, Medical University Pleven, 5800 Pleven, Bulgaria;
| | | | - Stoyan Kostov
- Department of Gynecology, Medical University Varna “Prof. Dr. Paraskev Stoyanov”, 9002 Varna, Bulgaria;
| | - Margarita Nikolova
- Saint Marina University Hospital—Pleven, Medical University Pleven, 5800 Pleven, Bulgaria;
| | - Ian Said-Huntingford
- Department of Histopathology, Mater Dei Hospital, Birkirkara Bypass, MSD 2090 Msida, Malta;
| | - Duncan Ayers
- Centre for Molecular Medicine & Biobanking, University of Malta, MSD 2080 Msida, Malta; (D.A.); (B.E.)
- Faculty of Biology, Medicine and Human Sciences, The University of Manchester, Manchester M1 7DN, UK
| | - Bridget Ellul
- Centre for Molecular Medicine & Biobanking, University of Malta, MSD 2080 Msida, Malta; (D.A.); (B.E.)
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Napoli, Italy;
| | - Antonio Giordano
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Correspondence: (R.D.F.); (J.C.-A.); Tel.: +356-2340-3871 (R.D.F.); +356-2340-1892 (J.C.-A.)
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Chen W, Liu S, Wang F. Potential impact and mechanism of Long Non-coding RNAs on cancer and associated T cells. J Cancer 2021; 12:4873-4882. [PMID: 34234857 PMCID: PMC8247393 DOI: 10.7150/jca.58859] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/30/2021] [Indexed: 01/01/2023] Open
Abstract
The discovery of many aberrant expressions of long non-coding RNAs (lncRNAs) in various cancers has focused attention on the effects of lncRNA on cancer cells themselves, including cell proliferation, growth inhibition, cell migration, cell immortality, vascular regeneration and cell viability. But with the increasing role of immunotherapy in cancer therapy, a large number of studies have revealed that the regulatory role of lncRNAs in immunity such as differentiation of immune cells can also influence the development and progression of cancer. In particular, recent publications have suggested that lncRNAs play critical roles in T-lymphocyte activation, proliferation, differentiation, function, apoptosis and metabolism. To elucidate the actual functions of lncRNAs at the molecular level of cancer pathogenesis, we summarize some of the current lncRNA regulatory mechanisms associated with T cell to discuss their effects in cancer in the hope of providing potential cancer therapeutic targets or cancer biomarkers. However, we all know that the differentiation and function of T cells is an extremely complex process that involves the expression and regulation of multiple lncRNAs. As a result, more regulatory mechanisms of lncRNAs need to be further studied.
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Affiliation(s)
- Wenxiu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
| | - Shuna Liu
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
| | - Fang Wang
- Department of Laboratory Medicine, the First Affiliated Hospital of Nanjing Medical University, Nanjing, China, 210029.,National Key Clinical Department of Laboratory Medicine, Nanjing, China, 210029
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Soltanmoradi S, Tavakolpour V, Moghadasi AN, Kouhkan F. Expression analysis of NF-κB-associated long noncoding RNAs in peripheral blood mononuclear cells from relapsing-remitting multiple sclerosis patients. J Neuroimmunol 2021; 356:577602. [PMID: 33979709 DOI: 10.1016/j.jneuroim.2021.577602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/05/2021] [Accepted: 05/02/2021] [Indexed: 12/19/2022]
Abstract
Long noncoding RNAs (lncRNAs) as potential disease biomarkers might be related to severe course of multiple sclerosis (MS). We evaluated expression levels of NF-κB-associated lncRNAs including HOTAIR, THRIL, H19, NKILA, and ANRIL; as well as expression of IL-6, TNF-α and MMP9, in peripheral blood mononuclear cells (PBMCs) from 60 relapse-remitting MS (RRMS) patients. At relapse phase of RRMS, up-regulation of ANRIL and H19 was positively correlated with the overexpression of IL-6; high levels of THRIL and HOTAIR was positively correlated with increased levels of TNF-α and MMP9, respectively; however, the NKILA expression was negatively correlated with the expression of TNF-α.
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Affiliation(s)
| | - Vahid Tavakolpour
- Stem Cell Technology Research Center, Tehran, Iran; Department of Stem Cells and Regenerative Medicine, Faculty of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Abdorreza Naser Moghadasi
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
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Servaas NH, Mariotti B, van der Kroef M, Wichers CGK, Pandit A, Bazzoni F, Radstake TRDJ, Rossato M. Characterization of Long Non-Coding RNAs in Systemic Sclerosis Monocytes: A Potential Role for PSMB8-AS1 in Altered Cytokine Secretion. Int J Mol Sci 2021; 22:4365. [PMID: 33922041 PMCID: PMC8122435 DOI: 10.3390/ijms22094365] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/14/2022] Open
Abstract
Systemic sclerosis (SSc) is a chronic autoimmune disease mainly affecting the connective tissue. In SSc patients, monocytes are increased in circulation, infiltrate affected tissues, and show a pro-inflammatory activation status, including the so-called interferon (IFN) signature. We previously demonstrated that the dysregulation of the IFN response in SSc monocytes is sustained by altered epigenetic factors as well as by upregulation of the long non-coding RNA (lncRNA) NRIR. Considering the enormously diverse molecular functions of lncRNAs in immune regulation, the present study investigated the genome-wide profile of lncRNAs in SSc monocytes, with the aim to further unravel their possible role in monocyte dysregulation and disease pathogenesis. Transcriptomic data from two independent cohorts of SSc patients identified 886 lncRNAs with an altered expression in SSc monocytes. Differentially expressed lncRNAs were correlated with neighboring protein coding genes implicated in the regulation of IFN responses and apoptotic signaling in SSc monocytes. In parallel, gene co-expression network analysis identified the lncRNA PSMB8-AS1 as a top-ranking hub gene in co-expression modules implicated in cell activation and response to viral and external stimuli. Functional characterization of PSMB8-AS1 in monocytes demonstrated that this lncRNA is involved in the secretion of IL-6 and TNFα, two pivotal pro-inflammatory cytokines altered in the circulation of SSc patients and associated with fibrosis and disease severity. Collectively, our data showed that lncRNAs are linked to monocyte dysregulation in SSc, and highlight their potential contribution to disease pathogenesis.
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Affiliation(s)
- Nila H. Servaas
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (N.H.S.); (M.v.d.K.); (C.G.K.W.); (A.P.); (T.R.D.J.R.)
- University Medical Center Utrecht, Department of Rheumatology and Clinical Immunology, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Barbara Mariotti
- Division of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy; (B.M.); (F.B.)
| | - Maarten van der Kroef
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (N.H.S.); (M.v.d.K.); (C.G.K.W.); (A.P.); (T.R.D.J.R.)
- University Medical Center Utrecht, Department of Rheumatology and Clinical Immunology, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Catharina G. K. Wichers
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (N.H.S.); (M.v.d.K.); (C.G.K.W.); (A.P.); (T.R.D.J.R.)
- University Medical Center Utrecht, Department of Rheumatology and Clinical Immunology, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Aridaman Pandit
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (N.H.S.); (M.v.d.K.); (C.G.K.W.); (A.P.); (T.R.D.J.R.)
- University Medical Center Utrecht, Department of Rheumatology and Clinical Immunology, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Flavia Bazzoni
- Division of General Pathology, Department of Medicine, University of Verona, 37134 Verona, Italy; (B.M.); (F.B.)
| | - Timothy R. D. J. Radstake
- Center for Translational Immunology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands; (N.H.S.); (M.v.d.K.); (C.G.K.W.); (A.P.); (T.R.D.J.R.)
- University Medical Center Utrecht, Department of Rheumatology and Clinical Immunology, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Marzia Rossato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
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Chen X, Guo DY, Yin TL, Yang J. Non-Coding RNAs Regulate Placental Trophoblast Function and Participate in Recurrent Abortion. Front Pharmacol 2021; 12:646521. [PMID: 33967782 PMCID: PMC8100504 DOI: 10.3389/fphar.2021.646521] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/15/2021] [Indexed: 12/12/2022] Open
Abstract
Recurrent spontaneous abortion (RSA) is a serious pregnancy complication with an increasing clinical incidence. The various causes of recurrent abortion are complicated. Developments in genetics, immunology, and cell biology have identified important roles of non-coding RNAs (ncRNAs) in the occurrence and progress of recurrent abortion. NcRNAs can affect the growth, migration, and invasion of placental trophoblasts by regulating cell processes such as the cell cycle, apoptosis, and epithelial-mesenchymal transformation. Therefore, their abnormal expression might lead to the occurrence and development of RSA. NcRNAs include small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), ribosomal RNA (rRNA), transfer, RNA (tRNA), circular RNA (cRNA), and Piwi-interacting RNA (piRNA). In this review, we discuss recent research that focused on the function and mechanism of microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNA (circRNA) in regulating placental trophoblasts. The use of ncRNAs as potential diagnostic and predictive biomarkers in RSA is also discussed to provide future research insights.
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Affiliation(s)
- Xin Chen
- Reproductive Medical Center, Renmin Hospital of Wuhan University and Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Duan-Ying Guo
- Department of Gynecology, Longgang District People's Hospital of Shenzhen, Shenzhen, China
| | - Tai-Lang Yin
- Reproductive Medical Center, Renmin Hospital of Wuhan University and Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
| | - Jing Yang
- Reproductive Medical Center, Renmin Hospital of Wuhan University and Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan, China
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Ping J, Huang S, Wu J, Bao P, Su T, Gu K, Cai H, Guo X, Lipworth L, Blot WJ, Zheng W, Cai Q, Shu XO. Association between lincRNA expression and overall survival for patients with triple-negative breast cancer. Breast Cancer Res Treat 2021; 186:769-777. [PMID: 33247368 PMCID: PMC8088339 DOI: 10.1007/s10549-020-06021-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 11/13/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE Long intergenic non-coding RNAs (lincRNAs) are increasingly recognized as important regulators for pathogenesis and/or prognosis of breast cancer, including triple-negative breast cancer (TNBC) subtype. However, few previous studies used RNA-sequencing (RNA-Seq) technology, and none included an independent replication. METHODS To systematically evaluate the association between expression of lincRNAs and TNBC survival, we examined lincRNA expression profiles in TNBC tissues using RNA-Seq data for 200 TNBC patients from the Shanghai Breast Cancer Survival Study (SBCSS) and Southern Community Cohort Study (SCCS). RESULTS Twenty-five lincRNAs were found to be associated with overall survival (P < 0.05 and no significant heterogeneity across studies at Q statistic P > 0.1), and 61 lincRNAs were associated with disease-free survival (DFS). Among these, two lincRNAs (LINC01270 and LINC00449) were significantly associated with both worse overall survival and DFS and were expressed at significantly higher levels in tumor tissues compared with adjacent normal breast tissues (log2[Fold Change] > 0.5 and FDR < 0.05). We further evaluated the potential functions of LINC01270 and LINC00449 using in vitro functional experiments and found that siRNA-mediated knockdown of LINC01270 and LINC00449 expression significantly decreased cell viability, colony formation and cell migration ability in TNBC cells (P < 0.05). CONCLUSIONS Evidence from observational studies and in vitro experiments indicates that LINC00449 and LINC01270 may be prognostic biomarkers for TNBC.
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Affiliation(s)
- Jie Ping
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Shuya Huang
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
- Department of Breast Surgery, The Second Hospital of Shandong University, Jinan, 250033, Shandong, People's Republic of China
| | - Jie Wu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Pingping Bao
- Department of Chronic Non-Communicable Disease Surveillance, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Timothy Su
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Kai Gu
- Department of Chronic Non-Communicable Disease Surveillance, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People's Republic of China
| | - Hui Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Xingyi Guo
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Loren Lipworth
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - William J Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Qiuyin Cai
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA
| | - Xiao-Ou Shu
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Suite 800, Nashville, TN, 37203, USA.
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Guo W, Wang Y, Yang M, Wang Z, Wang Y, Chaurasia S, Wu Z, Zhang M, Yadav GS, Rathod S, Concha-Benavente F, Fernandez C, Li S, Xie W, Ferris RL, Kammula US, Lu B, Yang D. LincRNA-immunity landscape analysis identifies EPIC1 as a regulator of tumor immune evasion and immunotherapy resistance. SCIENCE ADVANCES 2021; 7:eabb3555. [PMID: 33568470 PMCID: PMC7875530 DOI: 10.1126/sciadv.abb3555] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 12/23/2020] [Indexed: 05/11/2023]
Abstract
Through an integrative analysis of the lincRNA expression and tumor immune response in 9,626 tumor samples across 32 cancer types, we developed a lincRNA-based immune response (LIMER) score that can predict the immune cells infiltration and patient prognosis in multiple cancer types. Our analysis also identified tumor-specific lincRNAs, including EPIC1, that potentially regulate tumor immune response in multiple cancer types. Immunocompetent mouse models and in vitro co-culture assays demonstrated that EPIC1 induces tumor immune evasion and resistance to immunotherapy by suppressing tumor cell antigen presentation. Mechanistically, lincRNA EPIC1 interacts with the histone methyltransferase EZH2, leading to the epigenetic silencing of IFNGR1, TAP1/2, ERAP1/2, and MHC-I genes. Genetic and pharmacological inhibition of EZH2 abolish EPIC1's immune-related oncogenic effect and its suppression of interferon-γ signaling. The EPIC1-EZH2 axis emerges as a potential mechanism for tumor immune evasion that can serve as therapeutic targets for immunotherapy.
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Affiliation(s)
- Weiwei Guo
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yue Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Min Yang
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zehua Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Yifei Wang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Smriti Chaurasia
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Zhiyuan Wu
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Min Zhang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ghanshyam Singh Yadav
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Sanjay Rathod
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Fernando Concha-Benavente
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Christian Fernandez
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Song Li
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wen Xie
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Robert L Ferris
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Udai S Kammula
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Division of Surgical Oncology, Department of Surgery, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15213, USA
| | - Binfeng Lu
- Department of Immunology, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Da Yang
- Center for Pharmacogenetics, Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- UPMC Hillman Cancer Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Ahmad P, Bensaoud C, Mekki I, Rehman MU, Kotsyfakis M. Long Non-Coding RNAs and Their Potential Roles in the Vector-Host-Pathogen Triad. Life (Basel) 2021; 11:life11010056. [PMID: 33466803 PMCID: PMC7830631 DOI: 10.3390/life11010056] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/09/2021] [Accepted: 01/12/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding (lnc)RNAs have emerged as critical regulators of gene expression and are involved in almost every cellular process. They can bind to other molecules including DNA, proteins, or even other RNA types such messenger RNA or small RNAs. LncRNAs are typically expressed at much lower levels than mRNA, and their expression is often restricted to tissue- or time-specific developmental stages. They are also involved in several inter-species interactions, including vector–host–pathogen interactions, where they can be either vector/host-derived or encoded by pathogens. In these interactions, they function via multiple mechanisms including regulating pathogen growth and replication or via cell-autonomous antimicrobial defense mechanisms. Recent advances suggest that characterizing lncRNAs and their targets in different species may hold the key to understanding the role of this class of non-coding RNA in interspecies crosstalk. In this review, we present a general overview of recent studies related to lncRNA-related regulation of gene expression as well as their possible involvement in regulating vector–host–pathogen interactions.
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Affiliation(s)
- Parwez Ahmad
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice (Budweis), Czech Republic; (P.A.); (C.B.); (I.M.)
| | - Chaima Bensaoud
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice (Budweis), Czech Republic; (P.A.); (C.B.); (I.M.)
| | - Imen Mekki
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice (Budweis), Czech Republic; (P.A.); (C.B.); (I.M.)
- Faculty of Science, University of South Bohemia, 37005 Ceske Budejovice, Czech Republic
| | - Mujeeb Ur Rehman
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu 611130, China;
| | - Michail Kotsyfakis
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 Ceske Budejovice (Budweis), Czech Republic; (P.A.); (C.B.); (I.M.)
- Correspondence:
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LncRNA HOTAIR regulates glucose transporter Glut1 expression and glucose uptake in macrophages during inflammation. Sci Rep 2021; 11:232. [PMID: 33420270 PMCID: PMC7794310 DOI: 10.1038/s41598-020-80291-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/17/2020] [Indexed: 12/11/2022] Open
Abstract
Inflammation plays central roles in the immune response. Inflammatory response normally requires higher energy and therefore is associated with glucose metabolism. Our recent study demonstrates that lncRNA HOTAIR plays key roles in NF-kB activation, cytokine expression, and inflammation. Here, we investigated if HOTAIR plays any role in the regulation of glucose metabolism in immune cells during inflammation. Our results demonstrate that LPS-induced inflammation induces the expression of glucose transporter isoform 1 (Glut1) which controls the glucose uptake in macrophages. LPS-induced Glut1 expression is regulated via NF-kB activation. Importantly, siRNA-mediated knockdown of HOTAIR suppressed the LPS-induced expression of Glut1 suggesting key roles of HOTAIR in LPS-induced Glut1 expression in macrophage. HOTAIR induces NF-kB activation, which in turn increases Glut1 expression in response to LPS. We also found that HOTAIR regulates glucose uptake in macrophages during LPS-induced inflammation and its knockdown decreases LPS-induced increased glucose uptake. HOTAIR also regulates other upstream regulators of glucose metabolism such as PTEN and HIF1α, suggesting its multimodal functions in glucose metabolism. Overall, our study demonstrated that lncRNA HOTAIR plays key roles in LPS-induced Glut1 expression and glucose uptake by activating NF-kB and hence HOTAIR regulates metabolic programming in immune cells potentially to meet the energy needs during the immune response.
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Mathy NW, Burleigh O, Kochvar A, Whiteford ER, Behrens M, Marta P, Tian C, Gong AY, Drescher KM, Steyger PS, Chen XM, Shibata A. A novel long intergenic non-coding RNA, Nostrill, regulates iNOS gene transcription and neurotoxicity in microglia. J Neuroinflammation 2021; 18:16. [PMID: 33407594 PMCID: PMC7789650 DOI: 10.1186/s12974-020-02051-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 12/09/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Microglia are resident immunocompetent and phagocytic cells in the CNS. Pro-inflammatory microglia, stimulated by microbial signals such as bacterial lipopolysaccharide (LPS), viral RNAs, or inflammatory cytokines, are neurotoxic and associated with pathogenesis of several neurodegenerative diseases. Long non-coding RNAs (lncRNA) are emerging as important tissue-specific regulatory molecules directing cell differentiation and functional states and may help direct proinflammatory responses of microglia. Characterization of lncRNAs upregulated in proinflammatory microglia, such as NR_126553 or 2500002B13Rik, now termed Nostrill (iNOS Transcriptional Regulatory Intergenic LncRNA Locus) increases our understanding of molecular mechanisms in CNS innate immunity. METHODS Microglial gene expression array analyses and qRT-PCR were used to identify a novel long intergenic non-coding RNA, Nostrill, upregulated in LPS-stimulated microglial cell lines, LPS-stimulated primary microglia, and LPS-injected mouse cortical tissue. Silencing and overexpression studies, RNA immunoprecipitation, chromatin immunoprecipitation, chromatin isolation by RNA purification assays, and qRT-PCR were used to study the function of this long non-coding RNA in microglia. In vitro assays were used to examine the effects of silencing the novel long non-coding RNA in LPS-stimulated microglia on neurotoxicity. RESULTS We report here characterization of intergenic lncRNA, NR_126553, or 2500002B13Rik now termed Nostrill (iNOS Transcriptional Regulatory Intergenic LncRNA Locus). Nostrill is induced by LPS stimulation in BV2 cells, primary murine microglia, and in cortical tissue of LPS-injected mice. Induction of Nostrill is NF-κB dependent and silencing of Nostrill decreased inducible nitric oxide synthase (iNOS) expression and nitric oxide (NO) production in BV2 and primary microglial cells. Overexpression of Nostrill increased iNOS expression and NO production. RNA immunoprecipitation assays demonstrated that Nostrill is physically associated with NF-κB subunit p65 following LPS stimulation. Silencing of Nostrill significantly reduced NF-κB p65 and RNA polymerase II recruitment to the iNOS promoter and decreased H3K4me3 activating histone modifications at iNOS gene loci. In vitro studies demonstrated that silencing of Nostrill in microglia reduced LPS-stimulated microglial neurotoxicity. CONCLUSIONS Our data indicate a new regulatory role of the NF-κB-induced Nostrill and suggest that Nostrill acts as a co-activator of transcription of iNOS resulting in the production of nitric oxide by microglia through modulation of epigenetic chromatin remodeling. Nostrill may be a target for reducing the neurotoxicity associated with iNOS-mediated inflammatory processes in microglia during neurodegeneration.
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Affiliation(s)
- Nicholas W Mathy
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Olivia Burleigh
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0100, USA
| | - Andrew Kochvar
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0100, USA
| | - Erin R Whiteford
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Matthew Behrens
- University of Nebraska College of Medicine, 987020 Nebraska Medical Center, Omaha, NE, 68198-7020, USA
| | - Patrick Marta
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Cong Tian
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Ai-Yu Gong
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Kristen M Drescher
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Peter S Steyger
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Xian-Ming Chen
- School of Medicine, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0010, USA
| | - Annemarie Shibata
- Biology Department, Creighton University, 2500 California Plaza, Omaha, NE, 68178-0100, USA.
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Up-Regulated Expression of Pro-Apoptotic Long Noncoding RNA lincRNA-p21 with Enhanced Cell Apoptosis in Lupus Nephritis. Int J Mol Sci 2020; 22:ijms22010301. [PMID: 33396699 PMCID: PMC7795010 DOI: 10.3390/ijms22010301] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 02/07/2023] Open
Abstract
Accelerated cell apoptosis with dysregulated long noncoding RNAs is the crucial pathogenesis in lupus nephritis (LN). Pro-apoptotic lincRNA-p21 was studied in LN patients, cell lines with lentivirus-mediated overexpression and CRISPR interference (CRISPRi)-conducted repression, and a mouse model. Clinical samples were from patients and age/sex-matched controls. Expression of lincRNA-p21 and endogenous RNA target miR-181a, were examined in mononuclear and urine cells. Guide RNA sequences targeting lincRNA-p21 were cloned into CRISPRi with dCas9/ Krüppel-associated box (KRAB) domain. LincRNA-p21-silened transfectants were investigated for apoptosis and miR-181a expression. LincRNA-p21-overexpressed cells were evaluated for apoptosis and p53-related down-stream molecules. Balb/C mice were injected with pristane to induce LN and examined for apoptosis and lincRNA-p21. Higher lincRNA-p21 levels were found in LN mononuclear and urine cells, positively correlated with activity. There were lower miR-181a levels in LN mononuclear cells, negatively correlated with activity. Doxorubicin-induced apoptotic cells had up-regulated lincRNA-p21 levels. CRISPRi with dCas9/KARA domain showed efficient repression ability on transcription initiation/elongation. CRISPRi-conducted lincRNA-p21-silenced transfectants displayed reduced apoptosis with up-regulated miR-181a levels, whereas lentivirus-mediated lincRNA-p21-overexpressed cells revealed enhanced apoptosis with up-regulated downstream PUMA/Bax expression. LN mice had glomerular apoptosis with progressive increased lincRNA-p21 levels. Our results demonstrate up-regulated lincRNA-p21 expression in LN, implicating a potential diagnostic marker and therapeutic target.
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Swanson LC, Trujillo EA, Thiede GH, Katzenberger RJ, Shishkova E, Coon JJ, Ganetzky B, Wassarman DA. Survival Following Traumatic Brain Injury in Drosophila Is Increased by Heterozygosity for a Mutation of the NF-κB Innate Immune Response Transcription Factor Relish. Genetics 2020; 216:1117-1136. [PMID: 33109529 PMCID: PMC7768241 DOI: 10.1534/genetics.120.303776] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/26/2020] [Indexed: 12/16/2022] Open
Abstract
Traumatic brain injury (TBI) pathologies are caused by primary and secondary injuries. Primary injuries result from physical damage to the brain, and secondary injuries arise from cellular responses to primary injuries. A characteristic cellular response is sustained activation of inflammatory pathways commonly mediated by nuclear factor-κB (NF-κB) transcription factors. Using a Drosophila melanogaster TBI model, we previously found that the main proximal transcriptional response to primary injuries is triggered by activation of Toll and Imd innate immune response pathways that engage NF-κB factors Dif and Relish (Rel), respectively. Here, we found by mass spectrometry that Rel protein level increased in fly heads at 4-8 hr after TBI. To investigate the necessity of Rel for secondary injuries, we generated a null allele, Reldel , by CRISPR/Cas9 editing. When heterozygous but not homozygous, the Reldel mutation reduced mortality at 24 hr after TBI and increased the lifespan of injured flies. Additionally, the effect of heterozygosity for Reldel on mortality was modulated by genetic background and diet. To identify genes that facilitate effects of Reldel on TBI outcomes, we compared genome-wide mRNA expression profiles of uninjured and injured +/+, +/Reldel , and Reldel /Reldel flies at 4 hr following TBI. Only a few genes changed expression more than twofold in +/Reldel flies relative to +/+ and Reldel /Reldel flies, and they were not canonical innate immune response genes. Therefore, Rel is necessary for TBI-induced secondary injuries but in complex ways involving Rel gene dose, genetic background, diet, and possibly small changes in expression of innate immune response genes.
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Affiliation(s)
- Laura C Swanson
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Edna A Trujillo
- Department of Chemistry, College of Letters & Science, University of Wisconsin-Madison, Madison, Wisconsin 53706
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Gene H Thiede
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Rebeccah J Katzenberger
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Joshua J Coon
- Department of Chemistry, College of Letters & Science, University of Wisconsin-Madison, Madison, Wisconsin 53706
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Morgridge Institute for Research, Madison, Wisconsin 53706
| | - Barry Ganetzky
- Department of Genetics, College of Agricultural and Life Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - David A Wassarman
- Department of Medical Genetics, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53706
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50
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Piipponen M, Li D, Landén NX. The Immune Functions of Keratinocytes in Skin Wound Healing. Int J Mol Sci 2020; 21:E8790. [PMID: 33233704 PMCID: PMC7699912 DOI: 10.3390/ijms21228790] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/16/2020] [Accepted: 11/17/2020] [Indexed: 02/07/2023] Open
Abstract
As the most dominant cell type in the skin, keratinocytes play critical roles in wound repair not only as structural cells but also exerting important immune functions. This review focuses on the communications between keratinocytes and immune cells in wound healing, which are mediated by various cytokines, chemokines, and extracellular vesicles. Keratinocytes can also directly interact with T cells via antigen presentation. Moreover, keratinocytes produce antimicrobial peptides that can directly kill the invading pathogens and contribute to wound repair in many aspects. We also reviewed the epigenetic mechanisms known to regulate keratinocyte immune functions, including histone modifications, non-protein-coding RNAs (e.g., microRNAs, and long noncoding RNAs), and chromatin dynamics. Lastly, we summarized the current evidence on the dysregulated immune functions of keratinocytes in chronic nonhealing wounds. Based on their crucial immune functions in skin wound healing, we propose that keratinocytes significantly contribute to the pathogenesis of chronic wound inflammation. We hope this review will trigger an interest in investigating the immune roles of keratinocytes in chronic wound pathology, which may open up new avenues for developing innovative wound treatments.
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Affiliation(s)
| | | | - Ning Xu Landén
- Center for Molecular Medicine, Ming Wai Lau Centre for Reparative Medicine, Department of Medicine Solna, Dermatology and Venereology Division, Karolinska Institute, 17176 Stockholm, Sweden; (M.P.); (D.L.)
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