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Zhao J, Gui Y, Wu W, Li X, Wang L, Wang H, Luo Y, Zhou G, Yuan C. The function of long non-coding RNA IFNG-AS1 in autoimmune diseases. Hum Cell 2024:10.1007/s13577-024-01103-9. [PMID: 39004663 DOI: 10.1007/s13577-024-01103-9] [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: 04/20/2024] [Accepted: 07/08/2024] [Indexed: 07/16/2024]
Abstract
The prevalence of autoimmune diseases ranks as the third most common disease category globally, following cancer and heart disease. Numerous studies indicate that long non-coding RNA (lncRNA) plays a pivotal role in regulating human growth, development, and the pathogenesis of various diseases. It is more than 200 nucleotides in length and is mostly involve in the regulation of gene expression. Furthermore, lncRNAs are crucial in the development and activation of immune cells, with an expanding body of research exploring their association with autoimmune disorders in humans. LncRNA Ifng antisense RNA 1 (IFNG-AS1), a key regulatory factor in the immune system, also named NeST or TMEVPG1, is proximally located to IFNG and participates in the regulation of it. The dysregulation of IFNG-AS1 is implicated in the pathogenesis of several autoimmune diseases. This study examines the role and mechanism of IFNG-AS1 in various autoimmune diseases and considers its potential as a therapeutic target.
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Affiliation(s)
- Jiale Zhao
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Yibei Gui
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China
| | - Wei Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Xueqing Li
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Lijun Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China
| | - Hailin Wang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Yiyang Luo
- College of Medicine and Health Science, China Three Gorges University, Yichang, 443002, China
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China
| | - Gang Zhou
- College of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China.
- Yichang Hospital of Traditional Chinese Medicine, Yichang, 443002, China.
| | - Chengfu Yuan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, 443002, China.
- Third-Grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang, 443002, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, China.
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2
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Kandel A, Li L, Wang Y, Tuo W, Xiao Z. Differentiation and Regulation of Bovine Th2 Cells In Vitro. Cells 2024; 13:738. [PMID: 38727273 PMCID: PMC11083891 DOI: 10.3390/cells13090738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Bovine Th2 cells have usually been characterized by IL4 mRNA expression, but it is unclear whether their IL4 protein expression corresponds to transcription. We found that grass-fed healthy beef cattle, which had been regularly exposed to parasites on the grass, had a low frequency of IL4+ Th2 cells during flow cytometry, similar to animals grown in feedlots. To assess the distribution of IL4+ CD4+ T cells across tissues, samples from the blood, spleen, abomasal (draining), and inguinal lymph nodes were examined, which revealed limited IL4 protein detection in the CD4+ T cells across the examined tissues. To determine if bovine CD4+ T cells may develop into Th2 cells, naïve cells were stimulated with anti-bovine CD3 under a Th2 differentiation kit in vitro. The cells produced primarily IFNγ proteins, with only a small fraction (<10%) co-expressing IL4 proteins. Quantitative PCR confirmed elevated IFNγ transcription but no significant change in IL4 transcription. Surprisingly, GATA3, the master regulator of IL4, was highest in naïve CD4+ T cells but was considerably reduced following differentiation. To determine if the differentiated cells were true Th2 cells, an unbiased proteomic assay was carried out. The assay identified 4212 proteins, 422 of which were differently expressed compared to those in naïve cells. Based on these differential proteins, Th2-related upstream components were predicted, including CD3, CD28, IL4, and IL33, demonstrating typical Th2 differentiation. To boost IL4 expression, T cell receptor (TCR) stimulation strength was reduced by lowering anti-CD3 concentrations. Consequently, weak TCR stimulation essentially abolished Th2 expansion and survival. In addition, extra recombinant bovine IL4 (rbIL4) was added during Th2 differentiation, but, despite enhanced expansion, the IL4 level remained unaltered. These findings suggest that, while bovine CD4+ T cells can respond to Th2 differentiation stimuli, the bovine IL4 pathway is not regulated in the same way as in mice and humans. Furthermore, Ostertagia ostertagi (OO) extract, a gastrointestinal nematode in cattle, inhibited signaling via CD3, CD28, IL4, and TLRs/MYD88, indicating that external pathogens can influence bovine Th2 differentiation. In conclusion, though bovine CD4+ T cells can respond to IL4-driven differentiation, IL4 expression is not a defining feature of differentiated bovine Th2 cells.
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Affiliation(s)
- Anmol Kandel
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.K.); (L.L.)
| | - Lei Li
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.K.); (L.L.)
| | - Yan Wang
- Mass Spectrometry Facility, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, USA;
| | - Zhengguo Xiao
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.K.); (L.L.)
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3
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Ghahramani Almanghadim H, Karimi B, Poursalehi N, Sanavandi M, Atefi Pourfardin S, Ghaedi K. The biological role of lncRNAs in the acute lymphocytic leukemia: An updated review. Gene 2024; 898:148074. [PMID: 38104953 DOI: 10.1016/j.gene.2023.148074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
The cause of leukemia, a common malignancy of the hematological system, is unknown. The structure of long non-coding RNAs (lncRNAs) is similar to mRNA but no ability to encode proteins. Numerous malignancies, including different forms of leukemia, are linked to Lnc-RNAs. It is verified that the carcinogenesis and growth of a variety of human malignancies are significantly influenced by aberrant lncRNA expression. The body of evidence linking various types of lncRNAs to the etiology of leukemia has dramatically increased during the past ten years. Some lncRNAs are therefore anticipated to function as novel therapeutic targets, diagnostic biomarkers, and clinical outcome predictions. Additionally, these lncRNAs may provide new therapeutic options and insight into the pathophysiology of diseases, particularly leukemia. Thus, this review outlines the present comprehension of leukemia-associated lncRNAs.
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Affiliation(s)
| | - Bahareh Karimi
- Department of Cellular and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Negareh Poursalehi
- Department of Medical Biotechnology, School of Medicine Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | | | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Hezar Jerib Ave., Azadi Sq., 81746-73441 Isfahan, Iran.
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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5
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Baghdadi H, Heidari R, Zavvar M, Ahmadi N, Shakouri Khomartash M, Vahidi M, Mohammadimehr M, Bashash D, Ghorbani M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Noncoding RNA 2023; 9:44. [PMID: 37624036 PMCID: PMC10458434 DOI: 10.3390/ncrna9040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/09/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.
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Affiliation(s)
- Hamed Baghdadi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran;
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mahdi Zavvar
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran 443614177, Iran;
| | - Nazanin Ahmadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | | | - Mahmoud Vahidi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mojgan Mohammadimehr
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | - Mahdi Ghorbani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
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6
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Ivanov KI, Samuilova OV, Zamyatnin AA. The emerging roles of long noncoding RNAs in lymphatic vascular development and disease. Cell Mol Life Sci 2023; 80:197. [PMID: 37407839 PMCID: PMC10322780 DOI: 10.1007/s00018-023-04842-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 06/06/2023] [Accepted: 06/19/2023] [Indexed: 07/07/2023]
Abstract
Recent advances in RNA sequencing technologies helped uncover what was once uncharted territory in the human genome-the complex and versatile world of long noncoding RNAs (lncRNAs). Previously thought of as merely transcriptional "noise", lncRNAs have now emerged as essential regulators of gene expression networks controlling development, homeostasis and disease progression. The regulatory functions of lncRNAs are broad and diverse, and the underlying molecular mechanisms are highly variable, acting at the transcriptional, post-transcriptional, translational, and post-translational levels. In recent years, evidence has accumulated to support the important role of lncRNAs in the development and functioning of the lymphatic vasculature and associated pathological processes such as tumor-induced lymphangiogenesis and cancer metastasis. In this review, we summarize the current knowledge on the role of lncRNAs in regulating the key genes and pathways involved in lymphatic vascular development and disease. Furthermore, we discuss the potential of lncRNAs as novel therapeutic targets and outline possible strategies for the development of lncRNA-based therapeutics to treat diseases of the lymphatic system.
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Affiliation(s)
- Konstantin I Ivanov
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation.
- Department of Microbiology, University of Helsinki, Helsinki, Finland.
| | - Olga V Samuilova
- Department of Biochemistry, Sechenov First Moscow State Medical University, Moscow, Russian Federation
- HSE University, Moscow, Russian Federation
| | - Andrey A Zamyatnin
- Research Center for Translational Medicine, Sirius University of Science and Technology, Sochi, Russian Federation
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, UK
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7
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Cui K, Chen Z, Cao Y, Liu S, Ren G, Hu G, Fang D, Wei D, Liu C, Zhu J, Wu C, Zhao K. Restraint of IFN-γ expression through a distal silencer CNS-28 for tissue homeostasis. Immunity 2023; 56:944-958.e6. [PMID: 37040761 PMCID: PMC10175192 DOI: 10.1016/j.immuni.2023.03.006] [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: 06/05/2022] [Revised: 01/13/2023] [Accepted: 03/13/2023] [Indexed: 04/13/2023]
Abstract
Interferon-γ (IFN-γ) is a key cytokine in response to viral or intracellular bacterial infection in mammals. While a number of enhancers are described to promote IFN-γ responses, to the best of our knowledge, no silencers for the Ifng gene have been identified. By examining H3K4me1 histone modification in naive CD4+ T cells within Ifng locus, we identified a silencer (CNS-28) that restrains Ifng expression. Mechanistically, CNS-28 maintains Ifng silence by diminishing enhancer-promoter interactions within Ifng locus in a GATA3-dependent but T-bet-independent manner. Functionally, CNS-28 restrains Ifng transcription in NK cells, CD4+ cells, and CD8+ T cells during both innate and adaptive immune responses. Moreover, CNS-28 deficiency resulted in repressed type 2 responses due to elevated IFN-γ expression, shifting Th1 and Th2 paradigm. Thus, CNS-28 activity ensures immune cell quiescence by cooperating with other regulatory cis elements within the Ifng gene locus to minimize autoimmunity.
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Affiliation(s)
- Kairong Cui
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Gang Ren
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Gangqing Hu
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA
| | - Difeng Fang
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danping Wei
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chengyu Liu
- Transgenic Core Facility, DIR, NHLBI, NIH, Bethesda, MD, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, NIH, Bethesda, MD, USA.
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, NHLBI, NIH, Bethesda, MD, USA.
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8
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Premadasa LS, Lee E, McDew-White M, Alvarez X, Jayakumar S, Ling B, Okeoma CM, Byrareddy SN, Kulkarni S, Mohan M. Cannabinoid enhancement of lncRNA MMP25-AS1/MMP25 interaction reduces neutrophil infiltration and intestinal epithelial injury in HIV/SIV infection. JCI Insight 2023; 8:e167903. [PMID: 37036007 PMCID: PMC10132162 DOI: 10.1172/jci.insight.167903] [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: 12/09/2022] [Accepted: 02/16/2023] [Indexed: 04/11/2023] Open
Abstract
Intestinal epithelial barrier dysfunction, a hallmark of HIV/SIV infection, persists despite viral suppression by combination antiretroviral therapy (cART). Emerging evidence suggests a critical role for long noncoding RNAs (lncRNAs) in maintaining epithelial homeostasis. We simultaneously profiled lncRNA/mRNA expression exclusively in colonic epithelium (CE) of SIV-infected rhesus macaques (RMs) administered vehicle (VEH) or Δ-9-tetrahydrocannabinol (THC). Relative to controls, fewer lncRNAs were up- or downregulated in CE of THC/SIV compared with VEH/SIV RMs. Importantly, reciprocal expression of the natural antisense lncRNA MMP25-AS1 (up 2.3-fold) and its associated protein-coding gene MMP25 (attracts neutrophils by inactivating alpha-1 anti-trypsin/SERPINA1) (down 2.2-fold) was detected in CE of THC/SIV RMs. Computational analysis verified 2 perfectly matched complementary regions and an energetically stable (normalized binding free energy = -0.2626) MMP25-AS1/MMP25 duplex structure. MMP25-AS1 overexpression blocked IFN-γ-induced MMP25 mRNA and protein expression in vitro. Elevated MMP25 protein expression in CE of VEH/SIV but not THC/SIV RMs was associated with increased infiltration by myeloperoxidase/CD11b++ neutrophils (transendothelial migration) and epithelial CD47 (transepithelial migration) expression. Interestingly, THC administered in combination with cART increased MMP25-AS1 and reduced MMP25 mRNA/protein expression in jejunal epithelium of SIV-infected RMs. Our findings demonstrate that MMP25-AS1 is a potentially unique epigenetic regulator of MMP25 and that low-dose THC can reduce neutrophil infiltration and intestinal epithelial injury potentially by downregulating MMP25 expression through modulation of MMP25-AS1.
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Affiliation(s)
- Lakmini S. Premadasa
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Eunhee Lee
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Marina McDew-White
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Xavier Alvarez
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Sahana Jayakumar
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Binhua Ling
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Chioma M. Okeoma
- Department of Pathology, Microbiology and Immunology, New York Medical College, Valhalla, New York, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Smita Kulkarni
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Mahesh Mohan
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
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9
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Kulkarni V, Jayakumar S, Mohan M, Kulkarni S. Aid or Antagonize: Nuclear Long Noncoding RNAs Regulate Host Responses and Outcomes of Viral Infections. Cells 2023; 12:987. [PMID: 37048060 PMCID: PMC10093752 DOI: 10.3390/cells12070987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 03/12/2023] [Accepted: 03/15/2023] [Indexed: 04/14/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are transcripts measuring >200 bp in length and devoid of protein-coding potential. LncRNAs exceed the number of protein-coding mRNAs and regulate cellular, developmental, and immune pathways through diverse molecular mechanisms. In recent years, lncRNAs have emerged as epigenetic regulators with prominent roles in health and disease. Many lncRNAs, either host or virus-encoded, have been implicated in critical cellular defense processes, such as cytokine and antiviral gene expression, the regulation of cell signaling pathways, and the activation of transcription factors. In addition, cellular and viral lncRNAs regulate virus gene expression. Viral infections and associated immune responses alter the expression of host lncRNAs regulating immune responses, host metabolism, and viral replication. The influence of lncRNAs on the pathogenesis and outcomes of viral infections is being widely explored because virus-induced lncRNAs can serve as diagnostic and therapeutic targets. Future studies should focus on thoroughly characterizing lncRNA expressions in virus-infected primary cells, investigating their role in disease prognosis, and developing biologically relevant animal or organoid models to determine their suitability for specific therapeutic targeting. Many cellular and viral lncRNAs localize in the nucleus and epigenetically modulate viral transcription, latency, and host responses to infection. In this review, we provide an overview of the role of nuclear lncRNAs in the pathogenesis and outcomes of viral infections, such as the Influenza A virus, Sendai Virus, Respiratory Syncytial Virus, Hepatitis C virus, Human Immunodeficiency Virus, and Herpes Simplex Virus. We also address significant advances and barriers in characterizing lncRNA function and explore the potential of lncRNAs as therapeutic targets.
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Affiliation(s)
- Viraj Kulkarni
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Sahana Jayakumar
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Mahesh Mohan
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
| | - Smita Kulkarni
- Host-Pathogen Interaction Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (S.J.); (M.M.)
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10
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Tan JH, Ahmad Azahari AHS, Ali A, Ismail NAS. Scoping Review on Epigenetic Mechanisms in Primary Immune Thrombocytopenia. Genes (Basel) 2023; 14:555. [PMID: 36980827 PMCID: PMC10048672 DOI: 10.3390/genes14030555] [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: 12/24/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Immune Thrombocytopenia (ITP) is an autoimmune blood disorder that involves multiple pathways responsible for the homeostasis of the immune system. Numerous pieces of literature have proposed the potential of immune-related genes as diagnostic and prognostic biomarkers, which mostly implicate the role of B cells and T cells in the pathogenesis of ITP. However, a more in-depth understanding is required of how these immune-related genes are regulated. Thus, this scoping review aims to collate evidence and further elucidate each possible epigenetics mechanism in the regulation of immunological pathways pertinent to the pathogenesis of ITP. This encompasses DNA methylation, histone modification, and non-coding RNA. A total of 41 studies were scrutinized to further clarify how each of the epigenetics mechanisms is related to the pathogenesis of ITP. Identifying epigenetics mechanisms will provide a new paradigm that may assist in the diagnosis and treatment of immune thrombocytopenia.
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Affiliation(s)
- Jian Hong Tan
- Department of Paediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Ahmad Hazim Syakir Ahmad Azahari
- Department of Paediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Adli Ali
- Department of Paediatric, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
- Research Centre, Hospital Tunku Ampuan Besar Tuanku Aishah Rohani, UKM Specialist Children’s Hospital, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
| | - Noor Akmal Shareela Ismail
- Research Centre, Hospital Tunku Ampuan Besar Tuanku Aishah Rohani, UKM Specialist Children’s Hospital, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
- Department of Biochemistry, Faculty of Medicine, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Cheras, Kuala Lumpur 56000, Malaysia
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11
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Innate Immunity in Cardiovascular Diseases-Identification of Novel Molecular Players and Targets. J Clin Med 2023; 12:jcm12010335. [PMID: 36615135 PMCID: PMC9821340 DOI: 10.3390/jcm12010335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/20/2022] [Accepted: 12/25/2022] [Indexed: 01/03/2023] Open
Abstract
During the past few years, unexpected developments have driven studies in the field of clinical immunology. One driver of immense impact was the outbreak of a pandemic caused by the novel virus SARS-CoV-2. Excellent recent reviews address diverse aspects of immunological re-search into cardiovascular diseases. Here, we specifically focus on selected studies taking advantage of advanced state-of-the-art molecular genetic methods ranging from genome-wide epi/transcriptome mapping and variant scanning to optogenetics and chemogenetics. First, we discuss the emerging clinical relevance of advanced diagnostics for cardiovascular diseases, including those associated with COVID-19-with a focus on the role of inflammation in cardiomyopathies and arrhythmias. Second, we consider newly identified immunological interactions at organ and system levels which affect cardiovascular pathogenesis. Thus, studies into immune influences arising from the intestinal system are moving towards therapeutic exploitation. Further, powerful new research tools have enabled novel insight into brain-immune system interactions at unprecedented resolution. This latter line of investigation emphasizes the strength of influence of emotional stress-acting through defined brain regions-upon viral and cardiovascular disorders. Several challenges need to be overcome before the full impact of these far-reaching new findings will hit the clinical arena.
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12
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Liu C, Zhang Y, Ma Z, Yi H. Long Noncoding RNAs as Orchestrators of CD4+ T-Cell Fate. Front Cell Dev Biol 2022; 10:831215. [PMID: 35794862 PMCID: PMC9251064 DOI: 10.3389/fcell.2022.831215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 05/13/2022] [Indexed: 11/13/2022] Open
Abstract
CD4+ T cells differentiate towards different subpopulations through the regulation of lineage-specific cytokines and transcription factors, which flexibly respond to various immune challenges. However, considerable work has demonstrated that the CD4+ T-cell differentiation mechanism is complex and not limited to transcription factors and cytokines. Long noncoding RNAs (lncRNAs) are RNA molecules with lengths exceeding 200 base pairs that regulate various biological processes and genes. LncRNAs have been found to conciliate the plasticity of CD4+ T-cell differentiation. Then, we focused on lncRNAs involved in CD4+ T-cell differentiation and enlisted some molecular thought into the plasticity and functional heterogeneity of CD4+ T cells. Furthermore, elucidating how lncRNAs modulate CD4+ T-cell differentiation in disparate immune diseases may provide a basis for the pathological mechanism of immune-mediated diseases.
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Affiliation(s)
- Chang Liu
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, China
| | - Yanli Zhang
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, China
| | - Zhanchuan Ma
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, China
| | - Huanfa Yi
- Central Laboratory, The First Hospital of Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation, Ministry of Education, Changchun, China
- *Correspondence: Huanfa Yi,
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13
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Peltier DC, Roberts A, Reddy P. LNCing RNA to immunity. Trends Immunol 2022; 43:478-495. [DOI: 10.1016/j.it.2022.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/31/2022] [Accepted: 04/04/2022] [Indexed: 12/29/2022]
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14
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Wang Y, Xu H, Chen N, Yang J, Zhou H. LncRNA: A Potential Target for Host-Directed Therapy of Candida Infection. Pharmaceutics 2022; 14:pharmaceutics14030621. [PMID: 35335994 PMCID: PMC8954347 DOI: 10.3390/pharmaceutics14030621] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/25/2022] [Accepted: 03/09/2022] [Indexed: 02/01/2023] Open
Abstract
Despite various drugs work against Candida, candidiasis represents clinical management challenges worldwide due to the rising incidence and recurrence rate, as well as epidemics, of new drug-resistant pathogens. Recent insights into interactions between Candida and hosts contribute to exploring novel therapeutic strategies, termed host-directed therapies (HDTs). HDTs are viable adjuncts with good efficacy for the existing standard antifungal regimens. However, HDTs induce other response unintendedly, thus requiring molecular targets with highly specificity. Long noncoding RNAs (lncRNAs) with highly specific expression patterns could affect biological processes, including the immune response. Herein, this review will summarize recent advances of HDTs based on the Candida–host interaction. Especially, the findings and application strategies of lncRNAs related to the host response are emphasized. We propose it is feasible to target lncRNAs to modulate the host defense during Candida infection, which provides a new perspective in identifying options of HDTs for candidiasis.
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15
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She C, Yang Y, Zang B, Yao Y, Liu Q, Leung PSC, Liu B. Effect of LncRNA XIST on Immune Cells of Primary Biliary Cholangitis. Front Immunol 2022; 13:816433. [PMID: 35309298 PMCID: PMC8931309 DOI: 10.3389/fimmu.2022.816433] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/15/2022] [Indexed: 01/23/2023] Open
Abstract
Objective Primary biliary cholangitis (PBC) is an autoimmune disease with significant gender difference. X chromosome inactivation (XCI) plays important roles in susceptibility to diseases between genders. This work focuses on the differences of LncRNA XIST in several defined immune cells populations as well as its effects on naive CD4+ T cells proliferation and differentiation in patients with PBC. Methods NKs, B cells, CD4+ T, and CD8+ T cells were separated by MicroBeads from peripheral blood mononuclear cells (PBMCs) of PBC patients and healthy control (HC). The expression levels of LncRNA XIST in these immune cells were quantified by qRT-PCR and their subcellular localized analyzed by FISH. Lentivirus were used to interfere the expression of LncRNA XIST, and CCK8 was used to detect the proliferation of naive CD4+ T cells in PBC patients. Finally, naive CD4+ T cells were co-cultured with the bile duct epithelial cells (BECs), and the effects of LncRNA XIST on the typing of naive CD4+ T cells and related cytokines were determined by qRT-PCR and ELISA. Results The expression levels of LncRNA XIST in NKs and CD4+ T cells in PBC patients were significantly higher than those in HC, and were primarily located at the nucleus. LncRNA XIST could promote the proliferation of naive CD4+ T cells. When naive CD4+ T cells were co-cultured with BECs, the expressions of IFN-γ, IL-17, T-bet and RORγt in naive CD4+ T cells were decreased. Conclusion LncRNA XIST was associated with lymphocyte abnormalities in patients with PBC. The high expression of LncRNA XIST could stimulate proliferation and differentiation of naive CD4+ T cells, which might account for the high occurrence of PBC in female.
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Affiliation(s)
- Chunhui She
- Department of Rheumatology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yifei Yang
- Department of Rheumatology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Bo Zang
- Department of Rheumatology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuan Yao
- Department of Rheumatology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qixuan Liu
- Epidemiology and Biostatistics, Maternal and Child Health, School of Public Health (SPH) Department, Boston University, Boston, MA, United States
| | - Patrick S. C. Leung
- Division of Rheumatology, Allergy and Clinical Immunology, University of California at Davis, Davis, CA, United States
| | - Bin Liu
- Department of Rheumatology, Affiliated Hospital of Qingdao University, Qingdao, China
- *Correspondence: Bin Liu,
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16
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Liu Y, Hao H, Hou T. Concanavalin A-induced autoimmune hepatitis model in mice: Mechanisms and future outlook. Open Life Sci 2022; 17:91-101. [PMID: 35291566 PMCID: PMC8886606 DOI: 10.1515/biol-2022-0013] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/29/2021] [Accepted: 01/03/2022] [Indexed: 12/11/2022] Open
Abstract
Abstract
The concanavalin A (Con A)-induced liver injury mouse model is a typical animal model focusing on T cell-dependent hepatic damage in the field of autoimmune hepatitis (AIH). However, the underlying mechanism of hepatic dysfunction due to cell activation or signaling pathways triggered by Con A has not been fully clarified. Therefore, the controversy on this model remains in the academic community. In this article, we first summarized the merit and demerit of this contentious model from the perspectives of cell dysfunction, microcirculation disturbance, involved signaling pathways, as well as the properties of Con A. Then, we summed up the scientific implications of the model in elucidating the pathogenesis of AIH, and the shortcomings of this model were also summarized to elucidate the pathogenesis and application prospect of this classical liver injury mouse model in the study of AIH.
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Affiliation(s)
- Yang Liu
- College of Basic Medical Sciences, Shanxi University of Chinese Medicine , Jinzhong , 030619 , PR China
- Basic Laboratory of Integrated Traditional Chinese and Western Medicine, Shanxi University of Chinese Medicine , Jinzhong , 030619 , PR China
| | - Huiqin Hao
- College of Basic Medical Sciences, Shanxi University of Chinese Medicine , Jinzhong , 030619 , PR China
- Basic Laboratory of Integrated Traditional Chinese and Western Medicine, Shanxi University of Chinese Medicine , Jinzhong , 030619 , PR China
| | - Tiezheng Hou
- College of Basic Medical Sciences, Shanxi University of Chinese Medicine , Jinzhong , 030619 , PR China
- Basic Laboratory of Integrated Traditional Chinese and Western Medicine, Shanxi University of Chinese Medicine , Jinzhong , 030619 , PR China
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17
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Morrison TA, Hudson WH, Chisolm DA, Kanno Y, Shih HY, Ahmed R, Henao-Mejia J, Hafner M, O'Shea JJ. Evolving Views of Long Noncoding RNAs and Epigenomic Control of Lymphocyte State and Memory. Cold Spring Harb Perspect Biol 2022; 14:a037952. [PMID: 34001528 PMCID: PMC8725624 DOI: 10.1101/cshperspect.a037952] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Not simply an attribute of the adaptive immune system, immunological memory can be viewed on multiple levels. Accordingly, the molecular basis of memory comprises multiple mechanisms. The advent of new sequencing technologies has greatly enhanced the understanding of gene regulation and lymphocyte specification, and improved measurement of chromatin states affords new insights into the epigenomic and transcriptomic programs that underlie memory. Beyond canonical genes, the involvement of long noncoding RNAs (lncRNAs) is becoming increasingly apparent, and it appears that there are more than two to three times as many lncRNAs as protein-coding genes. lncRNAs can directly interact with DNA, RNA, and proteins, and a single lncRNA can contain multiple modular domains and thus interact with different classes of molecules. Yet, most lncRNAs have not been tested for function, and even fewer knockout mice have been generated. It is therefore timely to consider new potential mechanisms that may contribute to immune memory.
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Affiliation(s)
- Tasha A Morrison
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - William H Hudson
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Danielle A Chisolm
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Jorge Henao-Mejia
- Institute for Immunology, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA
| | - Markus Hafner
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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18
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Functional Implications of Intergenic GWAS SNPs in Immune-Related LncRNAs. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1363:147-160. [DOI: 10.1007/978-3-030-92034-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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19
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Potential Roles of Exosomal lncRNAs in the Intestinal Mucosal Immune Barrier. J Immunol Res 2021; 2021:7183136. [PMID: 34485536 PMCID: PMC8413039 DOI: 10.1155/2021/7183136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 08/15/2021] [Accepted: 08/17/2021] [Indexed: 12/31/2022] Open
Abstract
The intestinal mucosal immune barrier protects the host from the invasion of foreign pathogenic microorganisms. Immune cells and cytokines in the intestinal mucosa maintain local and systemic homeostasis by participating in natural and adaptive immunity. Deficiency of the intestinal mucosal immune barrier is associated with a variety of intestinal illnesses. Exosomes are phospholipid bilayer nanovesicles that allow cell-cell communication by secreting physiologically active substances including proteins, lipids, transcription factors, mRNAs, micro-RNAs (miRNAs), and long noncoding RNAs (lncRNAs). Exosomal lncRNAs are involved in immune cell differentiation and the modulation of the immune response. This review briefly introduces the potential role of exosomal lncRNAs in the intestinal mucosal immune barrier and discusses their relevance to intestinal illnesses.
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20
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Varier KM, Dhandapani H, Liu W, Song J, Wang C, Hu A, Ben-David Y, Shen X, Li Y, Gajendran B. An immunotherapeutic approach to decipher the role of long non-coding RNAs in cancer progression, resistance and epigenetic regulation of immune cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:242. [PMID: 34303380 PMCID: PMC8305593 DOI: 10.1186/s13046-021-01997-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023]
Abstract
Immunotherapeutic treatments are gaining attention due to their effective anti-tumor response. Particularly, the revolution of immune checkpoint inhibitors (ICIs) produces promising outcomes for various cancer types. However, the usage of immunotherapy is limited due to its low response rate, suggesting that tumor cells escape the immune surveillance. Rapid advances in transcriptomic profiling have led to recognize immune-related long non-coding RNAs (LncRNAs), as regulators of immune cell-specific gene expression that mediates immune stimulatory as well as suppression of immune response, indicating LncRNAs as targets to improve the efficacy of immunotherapy against tumours. Moreover, the immune-related LncRNAs acting as epigenetic modifiers are also under deep investigation. Thus, herein, is a summarised knowledge of LncRNAs and their regulation in the adaptive and innate immune system, considering their importance in autophagy and predicting putative immunotherapeutic responses.
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Affiliation(s)
- Krishnapriya M Varier
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Hemavathi Dhandapani
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India.,Department of Biosciences & Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Wuling Liu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Jialei Song
- Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, Guizhou Province, People's Republic of China
| | - Chunlin Wang
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Anling Hu
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China.,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China
| | - Yaacov Ben-David
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Xiangchun Shen
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
| | - Yanmei Li
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China.
| | - Babu Gajendran
- State Key Laboratory for Functions and Applications of Medicinal Plants, Guizhou Medical University, Guiyang, 550014, Guizhou Province, People's Republic of China. .,The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academic of Sciences, Guiyang, 550014, Guizhou Province, People's Republic of China. .,School of Pharmaceutical Sciences, Guizhou Medical University, Guiyang, 550025, Guizhou Province, People's Republic of China.
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21
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Bayyurt B, Bakir M, Engin A, Oksuz C, Arslan S. Investigation of NEAT1, IFNG-AS1, and NRIR expression in Crimean-Congo hemorrhagic fever. J Med Virol 2021; 93:3300-3304. [PMID: 33064349 DOI: 10.1002/jmv.26606] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 09/22/2020] [Accepted: 10/13/2020] [Indexed: 12/23/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF), whose causative agent is CCHF orthonairovirus (CCHFV), demonstrates different symptoms in patients. Long noncoding RNAs (lncRNAs) take part in various pathological processes of viral diseases. They are prominent regulators of antiviral immune responses. To our knowledge, this study is the first study to investigate nuclear paraspeckle assembly transcript 1 (NEAT1), interferon (IFN) gamma antisense RNA 1 (IFNG-AS1), and negative regulator of IFN response (NRIR) expression in CCHF in the literature. We selected these lncRNAs because they are related to IFN signal or IFN-stimulated genes. We investigated NEAT1, IFNG-AS1, and NRIR gene expression in patients with CCHF. Total RNA was extracted from blood samples of 100 volunteers and NEAT1, IFNG-AS1, and NRIR expression were measured using a quantitative real-time polymerase chain reaction. NRIR expression was statistically significant in cases versus controls (p < .001), fatals versus controls (p < .001), and fatals versus nonfatals (p = .01). Furthermore, NRIR was found statistically significant at some clinical parameters including alanine aminotransferase (p = .03), international normalized ratio (p = .03), prothrombin time (p = .02), and active partial thromboplastin time (p = .01) in CCHF cases. NEAT1 and IFNG-AS1 expression were downregulated in the case and fatal groups which were compared with controls. Our results demonstrate that NRIR may be important in CCHF pathogenesis and the target of CCHF treatment.
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Affiliation(s)
- Burcu Bayyurt
- Department of Medical Biology, Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkey
| | - Mehmet Bakir
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkey
| | - Aynur Engin
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkey
| | - Caner Oksuz
- Department of Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkey
| | - Serdal Arslan
- Department of Medical Biology, Faculty of Medicine, Sivas Cumhuriyet University, Sivas, Turkey
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22
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Zeni PF, Mraz M. LncRNAs in adaptive immunity: role in physiological and pathological conditions. RNA Biol 2021; 18:619-632. [PMID: 33094664 PMCID: PMC8078528 DOI: 10.1080/15476286.2020.1838783] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/19/2022] Open
Abstract
The adaptive immune system is responsible for generating immunological response and immunological memory. Regulation of adaptive immunity including B cell and T cell biology was mainly understood from the protein and microRNA perspective. However, long non-coding RNAs (lncRNAs) are an emerging class of non-coding RNAs (ncRNAs) that influence key factors in lymphocyte biology such as NOTCH, PAX5, MYC and EZH2. LncRNAs were described to modulate lymphocyte activation by regulating pathways such as NFAT, NFκB, MYC, interferon and TCR/BCR signalling (NRON, NKILA, BCALM, GAS5, PVT1), and cell effector functions (IFNG-AS1, TH2-LCR). Here we review lncRNA involvement in adaptive immunity and the implications for autoimmune diseases (multiple sclerosis, inflammatory bowel disease, rheumatoid arthritis) and T/B cell leukaemias and lymphomas (CLL, MCL, DLBCL, T-ALL). It is becoming clear that lncRNAs are important in adaptive immune response and provide new insights into its orchestration.
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Affiliation(s)
- Pedro Faria Zeni
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Marek Mraz
- Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
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23
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Fernando N, Sciumè G, O'Shea JJ, Shih HY. Multi-Dimensional Gene Regulation in Innate and Adaptive Lymphocytes: A View From Regulomes. Front Immunol 2021; 12:655590. [PMID: 33841440 PMCID: PMC8034253 DOI: 10.3389/fimmu.2021.655590] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/09/2021] [Indexed: 12/24/2022] Open
Abstract
The precise control of cytokine production by innate lymphoid cells (ILCs) and their T cell adaptive system counterparts is critical to mounting a proper host defense immune response without inducing collateral damage and autoimmunity. Unlike T cells that differentiate into functionally divergent subsets upon antigen recognition, ILCs are developmentally programmed to rapidly respond to environmental signals in a polarized manner, without the need of T cell receptor (TCR) signaling. The specification of cytokine production relies on dynamic regulation of cis-regulatory elements that involve multi-dimensional epigenetic mechanisms, including DNA methylation, transcription factor binding, histone modification and DNA-DNA interactions that form chromatin loops. How these different layers of gene regulation coordinate with each other to fine tune cytokine production, and whether ILCs and their T cell analogs utilize the same regulatory strategy, remain largely unknown. Herein, we review the molecular mechanisms that underlie cell identity and functionality of helper T cells and ILCs, focusing on networks of transcription factors and cis-regulatory elements. We discuss how higher-order chromatin architecture orchestrates these components to construct lineage- and state-specific regulomes that support ordered immunoregulation.
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Affiliation(s)
- Nilisha Fernando
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Giuseppe Sciumè
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci-Bolognetti, Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Han-Yu Shih
- Neuro-Immune Regulome Unit, National Eye Institute, National Institutes of Health, Bethesda, MD, United States.,National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, United States
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Plasek LM, Valadkhan S. lncRNAs in T lymphocytes: RNA regulation at the heart of the immune response. Am J Physiol Cell Physiol 2021; 320:C415-C427. [PMID: 33296288 PMCID: PMC8294623 DOI: 10.1152/ajpcell.00069.2020] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Genome-wide analyses in the last decade have uncovered the presence of a large number of long non-protein-coding transcripts that show highly tissue- and state-specific expression patterns. High-throughput sequencing analyses in diverse subsets of immune cells have revealed a complex and dynamic expression pattern for these long noncoding RNAs (lncRNAs) that correlate with the functional states of immune cells. Although the vast majority of lncRNAs expressed in immune cells remain unstudied, functional studies performed on a small subset have indicated that their state-specific expressions pattern frequently has a regulatory impact on the function of immune cells. In vivo and in vitro studies have pointed to the involvement of lncRNAs in a wide variety of cellular processes, including both the innate and adaptive immune response through mechanisms ranging from epigenetic and transcriptional regulation to sequestration of functional molecules in subcellular compartments. This review will focus mainly on the role of lncRNAs in CD4+ and CD8+ T cells, which play pivotal roles in adaptive immunity. Recent studies have pointed to key physiological functions for lncRNAs during several developmental and functional stages of the life cycle of lymphocytes. Although lncRNAs play important physiological roles in lymphocytic response to antigenic stimulation, differentiation into effector cells, and secretion of cytokines, their dysregulated expression can promote or sustain pathological states such as autoimmunity, chronic inflammation, cancer, and viremia. This, together with their highly cell type-specific expression patterns, makes lncRNAs ideal therapeutic targets and underscores the need for additional studies into the role of these understudied transcripts in adaptive immune response.
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25
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LncRNAs Landscape in the patients of primary gout by microarray analysis. PLoS One 2021; 16:e0232918. [PMID: 33600466 PMCID: PMC7891695 DOI: 10.1371/journal.pone.0232918] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 01/30/2021] [Indexed: 02/05/2023] Open
Abstract
To determine the expression profile and clinical significance of long non-coding RNAs (lncRNAs) in peripheral blood mononuclear cells (PBMCs) of patients with primary gout and healthy control subjects. Human lncRNA microarrays were used to identify the differentially expressed lncRNAs and mRNAs in primary gout patients (n = 6) and healthy control subjects (n = 6). Bioinformatics analyses were performed to predict the roles of differently expressed lncRNAs and mRNAs. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect the expression levels of 8 lnRNAs in 64 primary gout patients and 32 healthy control subjects. Spearman’s correlation was used to analyze the correlation between these eight lncRNAs and the laboratory values of gout patients. A receiver operating characteristic (ROC) curve was constructed to evaluate the diagnostic value of the lncRNAs identified in gout. The microarray analysis identified 1479 differentially expressed lncRNAs (879 more highly expressed and 600 more lowly expressed), 862 differentially expressed mRNAs (390 more highly expressed and 472 more lowly expressed) in primary gout (fold change > 2, P < 0.05), respectively. The bioinformatic analysis indicated that the differentially expressed lncRNAs regulated the abnormally expressed mRNAs, which were involved in the pathogenesis of gout through several different pathways. The expression levels of TCONS_00004393 and ENST00000566457 were significantly increased in the acute gout flare group than those in the intercritical gout group or healthy subjects (P<0.01). Moreover, inflammation indicators were positive correlated with TCONS_00004393 and ENST00000566457 expression levels. The areas under the ROC curve of ENST00000566457 and NR-026756 were 0.868 and 0.948, respectively. Our results provide novel insight into the mechanisms of primary gout, and reveal that TCONS_00004393 and ENST00000566457 might be as candidate targets for the treatment of gout flare; ENST00000566457 and NR-026756 could effectively discriminate between the gout and the healthy control groups.
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26
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Wen Y, Chen H, Luo F, Zhou H, Li Z. Roles of long noncoding RNAs in bacterial infection. Life Sci 2020; 263:118579. [DOI: 10.1016/j.lfs.2020.118579] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/28/2020] [Accepted: 10/03/2020] [Indexed: 02/09/2023]
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27
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Wu M, Fu P, Qu L, Liu J, Lin A. Long Noncoding RNAs, New Critical Regulators in Cancer Immunity. Front Oncol 2020; 10:550987. [PMID: 33194608 PMCID: PMC7662117 DOI: 10.3389/fonc.2020.550987] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/09/2020] [Indexed: 12/11/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play crucial roles in various aspects of cellular functions. Recent studies have revealed that lncRNAs are critical players in the immune system by modulating immune cell differentiation and functions, particularly in cancer immunity. Here we systematically summarize how lncRNAs are involved in different processes of the cancer immunity cycle, including immune cell differentiation, proliferation, trafficking, and infiltration. Moreover, the limitations of the current understanding of lncRNA’s functions in cancer immunity are described, such as the complexity of the cancer immunity system, the inclusive functions of lncRNAs in this system, and the associated immune response. In sum, the comprehensive investigation of the roles of lncRNAs in cancer immunity aids in cancer diagnosis and therapies.
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Affiliation(s)
- Minjie Wu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Peifen Fu
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lei Qu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jian Liu
- Reproductive and Developmental Biology Laboratory, National Institute of Environmental Health Sciences, Durham, NC, United States
| | - Aifu Lin
- Breast Center of the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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28
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Radens CM, Blake D, Jewell P, Barash Y, Lynch KW. Meta-analysis of transcriptomic variation in T-cell populations reveals both variable and consistent signatures of gene expression and splicing. RNA (NEW YORK, N.Y.) 2020; 26:1320-1333. [PMID: 32554554 PMCID: PMC7491319 DOI: 10.1261/rna.075929.120] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/12/2020] [Indexed: 06/11/2023]
Abstract
Human CD4+ T cells are often subdivided into distinct subtypes, including Th1, Th2, Th17, and Treg cells, that are thought to carry out distinct functions in the body. Typically, these T-cell subpopulations are defined by the expression of distinct gene repertoires; however, there is variability between studies regarding the methods used for isolation and the markers used to define each T-cell subtype. Therefore, how reliably studies can be compared to one another remains an open question. Moreover, previous analysis of gene expression in CD4+ T-cell subsets has largely focused on gene expression rather than alternative splicing. Here we take a meta-analysis approach, comparing eleven independent RNA-seq studies of human Th1, Th2, Th17, and/or Treg cells to determine the consistency in gene expression and splicing within each subtype across studies. We find that known master-regulators are consistently enriched in the appropriate subtype; however, cytokines and other genes often used as markers are more variable. Importantly, we also identify previously unknown transcriptomic markers that appear to consistently differentiate between subsets, including a few Treg-specific splicing patterns. Together this work highlights the heterogeneity in gene expression between samples designated as the same subtype, but also suggests additional markers that can be used to define functional groupings.
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Affiliation(s)
- Caleb M Radens
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Davia Blake
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Paul Jewell
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Computer Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Yoseph Barash
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Computer Science, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Kristen W Lynch
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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29
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Extracellular vesicle long non-coding RNAs and circular RNAs: Biology, functions and applications in cancer. Cancer Lett 2020; 489:111-120. [DOI: 10.1016/j.canlet.2020.06.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/22/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022]
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30
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Liu Y, Chen H, Hao J, Li Z, Hou T, Hao H. Microarray-based transcriptional profiling of a mouse model of autoimmune hepatitis. FEBS Open Bio 2020; 10:2040-2054. [PMID: 32808463 PMCID: PMC7530384 DOI: 10.1002/2211-5463.12953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/03/2020] [Accepted: 08/13/2020] [Indexed: 12/23/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules longer than 200 nucleotides that do not typically code for a protein. lncRNAs have regulatory roles in many physiological processes, and their dysregulation can contribute to cancer, cardiovascular and neurodegenerative diseases, as well as the onset of autoimmune diseases, including systemic lupus erythematosus and rheumatoid arthritis. However, lncRNA expression changes in autoimmune hepatitis (AIH), a form of inflammation induced by immunological tolerance disorders, are poorly understood. Here, for the first time to our knowledge, we used microarrays to profile 1161 differentially expressed lncRNAs (DELs; 608 up- and 553 down-regulated) and 11 512 differentially expressed mRNAs (DEMs; 5189 up- and 6323 down- regulated) in a concanavalin A-induced AIH mouse model. We used quantitative real-time PCR to confirm the expression of eight DELs and DEMs, and analyzed the coexpression relationship between them. Potential biological functions of screened DELs and DEMs were predicted with Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. DEL-DEM interaction networks were also constructed. Our study revealed the roles of DELs and DEMs in the pathogenesis of AIH. We also provided potential candidate biomarkers that may have potential for future development into possible diagnostics or as a treatment for this disorder.
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Affiliation(s)
- Yang Liu
- College of Basic Medical SciencesShanxi University of Chinese MedicineJinzhongChina
- Basic Laboratory of Integrated Traditional Chinese and Western MedicineShanxi University of Chinese MedicineJinzhongChina
| | - Hao Chen
- College of Basic Medical SciencesShanxi University of Chinese MedicineJinzhongChina
- Basic Laboratory of Integrated Traditional Chinese and Western MedicineShanxi University of Chinese MedicineJinzhongChina
| | - Jian‐heng Hao
- College of Basic Medical SciencesShanxi University of Chinese MedicineJinzhongChina
- Basic Laboratory of Integrated Traditional Chinese and Western MedicineShanxi University of Chinese MedicineJinzhongChina
| | - Zhen‐cheng Li
- College of Basic Medical SciencesShanxi University of Chinese MedicineJinzhongChina
- Basic Laboratory of Integrated Traditional Chinese and Western MedicineShanxi University of Chinese MedicineJinzhongChina
| | - Tiezheng Hou
- College of Basic Medical SciencesShanxi University of Chinese MedicineJinzhongChina
- Basic Laboratory of Integrated Traditional Chinese and Western MedicineShanxi University of Chinese MedicineJinzhongChina
| | - Hui‐qin Hao
- College of Basic Medical SciencesShanxi University of Chinese MedicineJinzhongChina
- Basic Laboratory of Integrated Traditional Chinese and Western MedicineShanxi University of Chinese MedicineJinzhongChina
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31
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Pappalardo JL, Zhang L, Pecsok MK, Perlman K, Zografou C, Raddassi K, Abulaban A, Krishnaswamy S, Antel J, van Dijk D, Hafler DA. Transcriptomic and clonal characterization of T cells in the human central nervous system. Sci Immunol 2020; 5:eabb8786. [PMID: 32948672 PMCID: PMC8567322 DOI: 10.1126/sciimmunol.abb8786] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/26/2020] [Indexed: 08/04/2023]
Abstract
T cells provide critical immune surveillance to the central nervous system (CNS), and the cerebrospinal fluid (CSF) is thought to be a main route for their entry. Further characterization of the state of T cells in the CSF in healthy individuals is important for understanding how T cells provide protective immune surveillance without damaging the delicate environment of the CNS and providing tissue-specific context for understanding immune dysfunction in neuroinflammatory disease. Here, we have profiled T cells in the CSF of healthy human donors and have identified signatures related to cytotoxic capacity and tissue adaptation that are further exemplified in clonally expanded CSF T cells. By comparing profiles of clonally expanded T cells obtained from the CSF of patients with multiple sclerosis (MS) and healthy donors, we report that clonally expanded T cells from the CSF of patients with MS have heightened expression of genes related to T cell activation and cytotoxicity.
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Affiliation(s)
- Jenna L Pappalardo
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Le Zhang
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Maggie K Pecsok
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Kelly Perlman
- Montreal Neurologic Institute, Montreal, Quebec, Canada
| | - Chrysoula Zografou
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Khadir Raddassi
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Ahmad Abulaban
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA
| | - Smita Krishnaswamy
- Departments of Genetics and Computer Science, Yale School of Medicine, New Haven, CT 06511, USA
| | - Jack Antel
- Montreal Neurologic Institute, Montreal, Quebec, Canada
| | - David van Dijk
- Departments of Internal Medicine (Cardiology), Cardiovascular Research Center, and Computer Science, New Haven, CT 06511, USA.
| | - David A Hafler
- Departments of Neurology and Immunobiology, Yale School of Medicine, New Haven, CT 06511, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
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32
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Saw PE, Xu X, Chen J, Song EW. Non-coding RNAs: the new central dogma of cancer biology. SCIENCE CHINA-LIFE SCIENCES 2020; 64:22-50. [PMID: 32930921 DOI: 10.1007/s11427-020-1700-9] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 07/27/2020] [Indexed: 02/07/2023]
Abstract
The central dogma of molecular biology states that the functions of RNA revolve around protein translation. Until the last decade, most researches were geared towards characterization of RNAs as intermediaries in protein translation, namely, messenger RNAs (mRNAs) as temporary copies of genetic information, ribosomal RNAs (rRNAs) as a main component of ribosome, or translators of codon sequence (tRNAs). The statistical reality, however, is that these processes account for less than 2% of the genome, and insufficiently explain the functionality of 98% of transcribed RNAs. Recent discoveries have unveiled thousands of unique non-coding RNAs (ncRNAs) and shifted the perception of them from being "junk" transcriptional products to "yet to be elucidated"-and potentially monumentally important-RNAs. Most ncRNAs are now known as key regulators in various networks in which they could lead to specific cellular responses and fates. In major cancers, ncRNAs have been identified as both oncogenic drivers and tumor suppressors, indicating a complex regulatory network among these ncRNAs. Herein, we provide a comprehensive review of the various ncRNAs and their functional roles in cancer, and the pre-clinical and clinical development of ncRNA-based therapeutics. A deeper understanding of ncRNAs could facilitate better design of personalized therapeutics.
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Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Xiaoding Xu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Jianing Chen
- Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China
| | - Er-Wei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China. .,Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, 510120, China.
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33
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Dutta A, Roy A, Chatterjee S. Long noncoding RNAs in cancer immunity: a new avenue in drug discovery. Drug Discov Today 2020; 26:264-272. [PMID: 32827755 DOI: 10.1016/j.drudis.2020.07.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/23/2022]
Abstract
The central role of the nonprotein-coding portion of the genome, such as long noncoding (lnc)RNAs is emerging as a hidden player manipulating the immune system in cancer. lncRNAs, in association with their interacting partners, regulate the expression of various immune system genes, which are perturbed during cancer. The tissue-specific expression of lncRNAs and their importance in cellular proliferation, the tumor microenvironment (TME), epithelial-mesenchymal transition (EMT), and modulation of the cells of the innate and adaptive immune system have novel therapeutic implications in establishing lncRNAs as biomarkers and targets to overcome cancer-associated immunosuppression. In this review, we establish and strengthen the link between lncRNAs and cancer immunity.
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Affiliation(s)
- Anindya Dutta
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
| | - Ananya Roy
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India.
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34
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Recent advances of long noncoding RNAs involved in the development of multiple sclerosis. Chin J Nat Med 2020; 18:36-46. [PMID: 31955822 DOI: 10.1016/s1875-5364(20)30003-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Indexed: 12/12/2022]
Abstract
Given the rapid increase of patients with autoimmune diseases and the lack of satisfactory therapies, the discovery of novel and effective therapeutic targets have been in an urgent demand. Recent studies have revealed that long noncoding RNAs (lncRNAs) play crucial roles in the development of multiple sclerosis (MS), which provides a new opportunity of uncovering novel mechanism associated with the progression of MS. This review highlights the dysregulation of lncRNAs in the development of MS in patients and animal models. Additionally, the potential clinical relevance of lncRNAs severed as therapeutic targets and diagnostic markers are discussed.
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35
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Huang N, Fan Z, Ma L, Ma H, Huang H, Yu H, Zhou X. Long non‑coding RNA RP11‑340F14.6 promotes a shift in the Th17/Treg ratio by binding with P2X7R in juvenile idiopathic arthritis. Int J Mol Med 2020; 46:859-868. [PMID: 32467993 DOI: 10.3892/ijmm.2020.4618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/08/2020] [Indexed: 11/06/2022] Open
Affiliation(s)
- Na Huang
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Zhidan Fan
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Le Ma
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Huihui Ma
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Hui Huang
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Haiguo Yu
- Department of Rheumatology and Immunology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
| | - Xiaoyu Zhou
- Department of Neonatology, Children's Hospital of Nanjing Medical University, Nanjing, Jiangsu 210008, P.R. China
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36
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Investigation of Linc-MAF-4 expression as an effective marker in brucellosis. Mol Immunol 2020; 123:60-63. [PMID: 32417631 DOI: 10.1016/j.molimm.2020.04.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 04/14/2020] [Accepted: 04/20/2020] [Indexed: 11/24/2022]
Abstract
Brucellosis is a zoonotic disease that is one of the most common infectious diseases. Cellular immunity is the main immune response against brucella. Long non coding RNAs are a new subset of genes that could regulate cell function and may gene regulation. We aim to investigate whether the level of Linc-MAF-4 and cMAF have considerable differences in brucella infection. In this experiment 99 patients with brucellosis were divided into three groups of acute, undertreatment and relapse and 30 volunteers with negative serologic tests as control group. The expression levels were detected using quantitative polymerase chain reaction (qPCR). Statistical analysis was performed using SPSS software version 25.0. Results showed that the expression of Linc-MAF-4 was significantly increased in the acute group in comparison to control and relapse groups. Also, cMAF expression was significantly increased in the relapse group versus the control group. Our study showed these genes play important roles in the immune response include regulating naïve T cell differentiation to T helper cells in Brucella infection. We propose that Linc-MAF-4 could be a potential biomarker for the screening, diagnosis and treatment of brucellosis.
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37
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Taghizadeh E, Taheri F, Samadian MM, Soudyab M, Abi A, Gheibi Hayat SM. Role of long non-coding RNAs (LncRNAs) in multiple sclerosis: a brief review. Neurol Sci 2020; 41:2443-2451. [PMID: 32350675 DOI: 10.1007/s10072-020-04425-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 04/13/2020] [Indexed: 01/05/2023]
Abstract
Multiple sclerosis (MS) as chronic autoimmune inflammatory neurological disease of the central nervous system (CNS) occurs due to several environmental and genetic factors, whose pathogenesis is associated with genes with regulatory role in the immune system. Long non-coding RNAs (LncRNAs) are able to reportedly regulate responses of immune systems and expression of genes, and show the tissue specificity and complexity of biofunctions. Various studies have suggested that the aberrant LncRNA expression is an underlying factor involved in the incidence of MS and that the analysis of the expression profile of these molecules can be a specific biomarker of MS for preventing the course of the disease or responding to treatment. The purpose of this research was to review the recent studies for exploring the functions of LncRNAs in the processes leading to MS disease.
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Affiliation(s)
- Eskandar Taghizadeh
- Cellular and Molecular Research Center, Yasuj University of Medical Sciences, Yasuj, Iran
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Forough Taheri
- Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Mohammad Mahdi Samadian
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Soudyab
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abbas Abi
- Department of Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Gheibi Hayat
- Department of Medical Genetics, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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38
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Fragliasso V, Verma A, Manzotti G, Tameni A, Bareja R, Heavican TB, Iqbal J, Wang R, Fiore D, Mularoni V, Chan WC, Lhoumaud P, Skok J, Zanetti E, Merli F, Ciarrocchi A, Elemento O, Inghirami G. The novel lncRNA BlackMamba controls the neoplastic phenotype of ALK - anaplastic large cell lymphoma by regulating the DNA helicase HELLS. Leukemia 2020; 34:2964-2980. [PMID: 32123306 DOI: 10.1038/s41375-020-0754-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 01/09/2023]
Abstract
The molecular mechanisms leading to the transformation of anaplastic lymphoma kinase negative (ALK-) anaplastic large cell lymphoma (ALCL) have been only in part elucidated. To identify new culprits which promote and drive ALCL, we performed a total transcriptome sequencing and discovered 1208 previously unknown intergenic long noncoding RNAs (lncRNAs), including 18 lncRNAs preferentially expressed in ALCL. We selected an unknown lncRNA, BlackMamba, with an ALK- ALCL preferential expression, for molecular and functional studies. BlackMamba is a chromatin-associated lncRNA regulated by STAT3 via a canonical transcriptional signaling pathway. Knockdown experiments demonstrated that BlackMamba contributes to the pathogenesis of ALCL regulating cell growth and cell morphology. Mechanistically, BlackMamba interacts with the DNA helicase HELLS controlling its recruitment to the promoter regions of cell-architecture-related genes, fostering their expression. Collectively, these findings provide evidence of a previously unknown tumorigenic role of STAT3 via a lncRNA-DNA helicase axis and reveal an undiscovered role for lncRNA in the maintenance of the neoplastic phenotype of ALK-ALCL.
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Affiliation(s)
- Valentina Fragliasso
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Akanksha Verma
- Institute for Computational Biomedicine & Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.,Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, 10065, USA
| | - Gloria Manzotti
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Annalisa Tameni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy.,Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, 41125, Italy
| | - Rohan Bareja
- Institute for Computational Biomedicine & Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Tayla B Heavican
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68182, USA
| | - Javeed Iqbal
- Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, 68182, USA
| | - Rui Wang
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Danilo Fiore
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Valentina Mularoni
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Priscillia Lhoumaud
- Department of Pathology, New York University School of Medicine, Langone Medical Center, New York, NY, 10016, USA
| | - Jane Skok
- Department of Pathology, New York University School of Medicine, Langone Medical Center, New York, NY, 10016, USA
| | - Eleonora Zanetti
- Pathology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Francesco Merli
- Hematology Unit, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy
| | - Alessia Ciarrocchi
- Laboratory of Translational Research, Azienda USL-IRCCS di Reggio Emilia, Reggio Emilia, 42123, Italy.
| | - Oliver Elemento
- Institute for Computational Biomedicine & Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, 10065, USA.
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Long non-coding RNAs in immune regulation and their potential as therapeutic targets. Int Immunopharmacol 2020; 81:106279. [PMID: 32058929 DOI: 10.1016/j.intimp.2020.106279] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs (lncRNAs) are potent regulators of immune cell development and function. Their implication in multiple immune-mediated disorders highlights lncRNAs as exciting biomarkers and potential drug targets. Recent technological innovations in oligo-based therapeutics, development of RNA-targeting small molecules, and CRISPR-based approaches, position RNA as the next therapeutic frontier. Here, we review the latest advances made toward understanding the role of lncRNAs in human immunological disorders and further discuss RNA-targeting approaches that could be potentially exploited to manipulate lncRNA function as a clinical intervention.
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Elevated Expression of the Long Noncoding RNA IFNG-AS1 in the Peripheral Blood from Patients with Rheumatoid Arthritis. J Immunol Res 2020; 2020:6401978. [PMID: 32377535 PMCID: PMC7193778 DOI: 10.1155/2020/6401978] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) have been increasingly recognized as key immune molecules that participate in the pathogenesis of autoimmune diseases. Previous studies have demonstrated that the lncRNA Ifng-AS1, a key scaffold that contributes to the transcription of IFN-γ, depends on T-bet for active transcription in Th1 cells. However, the effect of its human ortholog, IFNG-AS1, on the pathogenesis of rheumatoid arthritis (RA) remains unclear. In this study, we found that the transcript level of lncRNA IFNG-AS1 was increased in the peripheral blood of RA patients. IFNG, as a target gene of IFNG-AS1, was overexpressed and positively correlated with the transcript level of IFNG-AS1 in the RA patients. Our data also showed that the transcript level of T-bet was upregulated and positively correlated with IFNG-AS1 expression. T-bet regulated the transcription of IFNG-AS1 in human CD4+ T cells in vitro. Furthermore, strong positive correlations were observed between the increased transcript level of IFNG-AS1 and the serum level of rheumatoid factor, the erythrocyte sedimentation rate, and the C-reactive protein in RA patients, and patients positive for anticyclic citrullinated peptide antibodies had increased levels of IFNG-AS1. Finally, receiver operating characteristic (ROC) curve analysis suggested that IFNG-AS1 might be a potential biomarker of RA. Taken together, our findings indicated that IFNG-AS1, guided by T-bet, is augmented in the peripheral blood of RA patients and may play a critical role in the pathogenesis of RA by regulating the expression of IFNG.
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Ahmad I, Valverde A, Ahmad F, Naqvi AR. Long Noncoding RNA in Myeloid and Lymphoid Cell Differentiation, Polarization and Function. Cells 2020; 9:cells9020269. [PMID: 31979061 PMCID: PMC7072530 DOI: 10.3390/cells9020269] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Long noncoding RNA (lncRNA) are a class of endogenous, non-protein coding RNAs that are increasingly being associated with various cellular functions and diseases. Yet, despite their ubiquity and abundance, only a minute fraction of these molecules has an assigned function. LncRNAs show tissue-, cell-, and developmental stage-specific expression, and are differentially expressed under physiological or pathological conditions. The role of lncRNAs in the lineage commitment of immune cells and shaping immune responses is becoming evident. Myeloid cells and lymphoid cells are two major classes of immune systems that work in concert to initiate and amplify innate and adaptive immunity in vertebrates. In this review, we provide mechanistic roles of lncRNA through which these noncoding RNAs can directly participate in the differentiation, polarization, and activation of myeloid (monocyte, macrophage, and dendritic cells) and lymphoid cells (T cells, B cells, and NK cells). While our knowledge on the role of lncRNA in immune cell differentiation and function has improved in the past decade, further studies are required to unravel the biological role of lncRNAs and identify novel mechanisms of lncRNA functions in immune cells. Harnessing the regulatory potential of lncRNAs can provide novel diagnostic and therapeutic targets in treating immune cell related diseases.
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Rankin CR, Shao L, Elliott J, Rowe L, Patel A, Videlock E, Benhammou JN, Sauk JS, Ather N, Corson M, Alipour O, Gulati A, Pothoulakis C, Padua DM. The IBD-associated long noncoding RNA IFNG-AS1 regulates the balance between inflammatory and anti-inflammatory cytokine production after T-cell stimulation. Am J Physiol Gastrointest Liver Physiol 2020; 318:G34-G40. [PMID: 31545920 PMCID: PMC6985849 DOI: 10.1152/ajpgi.00232.2019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The inflammatory bowel diseases (IBD) are a complex set of chronic gastrointestinal inflammatory conditions arising from the interplay of genetic and environmental factors. This study focuses on noncoding RNA transcripts as potential mediators of IBD pathophysiology. One particular gene, interferon γ-antisense 1 (IFNG-AS1), has been consistently observed to be elevated in the intestinal mucosa of patients with actively inflamed IBD versus healthy controls. This study builds on these observations, demonstrating that the second splice variant is specifically altered, and this alteration even stratifies within inflamed patients. With the use of a CRISPR-based overexpression system, IFNG-AS1 was selectively overexpressed directly from its genomic loci in T cells. An unbiased mRNA array on these cells identified a large increase in many inflammatory cytokines and a decrease in anti-inflammatory cytokines after IFNG-AS1 overexpression. Media from T cells overexpressing IFNG-AS1 elicited an inflammatory signaling cascade in primary human peripheral blood mononuclear cells, suggesting the potential functional importance of IFNG-AS1 in IBD pathophysiology. The significance of these results is amplified by studies suggesting that a single-nucleotide polymorphism in IFNG-AS1, rs7134599, was associated with both subtypes of patients with IBD independently of race.NEW & NOTEWORTHY Long noncoding RNAs are an emerging field of inflammatory bowel disease (IBD) research. This study mechanistically analyzes the role of a commonly upregulated gene in IBD and shows IFNG-AS1 as a mediator of an inflammatory signaling cascade.
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Affiliation(s)
- Carl Robert Rankin
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Ling Shao
- 2Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Julie Elliott
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Lorraine Rowe
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Ami Patel
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Elizabeth Videlock
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California,3Division of Gastroenterology, Hepatology, and Parenteral Nutrition, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Jihane N. Benhammou
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California,3Division of Gastroenterology, Hepatology, and Parenteral Nutrition, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
| | - Jenny S. Sauk
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Nimah Ather
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Melissa Corson
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - Omeed Alipour
- 2Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Alakh Gulati
- 2Division of Gastrointestinal and Liver Diseases, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Charalabos Pothoulakis
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
| | - David Miguel Padua
- 1Vatche and Tamar Manoukian Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California,3Division of Gastroenterology, Hepatology, and Parenteral Nutrition, Veterans Affairs Greater Los Angeles Healthcare System, Los Angeles, California
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43
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Kumar P, Sen C, Peters K, Frizzell RA, Biswas R. Comparative analyses of long non-coding RNA profiles in vivo in cystic fibrosis lung airway and parenchyma tissues. Respir Res 2019; 20:284. [PMID: 31842871 PMCID: PMC6916039 DOI: 10.1186/s12931-019-1259-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 12/09/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Recent advances in the functional analyses of endogenous non-coding RNA (ncRNA) molecules, including long non-coding RNAs (LncRNAs), have provided a new perspective on the crucial roles of RNA in gene regulation. Consequently, LncRNA deregulation is a key factor in various diseases, including pulmonary disorders like Cystic Fibrosis (CF). CF is the most common life limiting recessive disease in the U.S., and is due to mutations in the CFTR gene. CF mutations, of which the most common is F508del-CFTR, prevents correct folding, trafficking and function of the mutant CFTR protein and is further manifested by the hyper-expression of pro-inflammatory cytokines and chemokines into the airway lumen leading to bronchiectasis and culminating in lung destruction. METHODS Here we report a distinct LncRNA signature and corresponding mRNAs that distinguishes CF lung (airway and parenchyma) tissues from matched non-CF controls (n = 4 each group), generated by microarray specific for LncRNAs which includes corresponding mRNA expressions. In silico analyses of the cellular processes that are impacted by these LncRNAs was performed using Gene Ontology (GO). A selected subset of LncRNAs were validated by quantitative real-time PCR. RESULTS We have identified 636 LncRNAs differentially expressed in CF airway epithelium and 1974 in CF lung parenchyma compared to matched non-CF controls (fold change ≥2, p < 0.05), majority of which (> 50%) are intergenic. Interestingly, 15 of these differentially expressed LncRNAs and 9 coding mRNAs are common to airway and parenchyma tissues. GO analyses indicates that signaling pathways and cell membrane functions are significantly affected by the alteration in LncRNA expressions in CF lung tissues. Seven of the differentially expressed LncRNAs, exhibit similar expression trends in CFBE41o- compared to control cells. CONCLUSION Understanding the mechanisms by which these LncRNAs regulate CF disease phenotype will help develop novel therapeutic targets for CF and related pulmonary diseases, such as COPD and Asthma.
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Affiliation(s)
- Parameet Kumar
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Room B4024, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
| | - Chaitali Sen
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Room B4024, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
| | - Kathryn Peters
- Departments of Pediatrics and Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Raymond A Frizzell
- Departments of Pediatrics and Cell Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Roopa Biswas
- Department of Anatomy, Physiology and Genetics, School of Medicine, Uniformed Services University of the Health Sciences, Room B4024, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA.
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44
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Vishnubalaji R, Shaath H, Elango R, Alajez NM. Noncoding RNAs as potential mediators of resistance to cancer immunotherapy. Semin Cancer Biol 2019; 65:65-79. [PMID: 31733291 DOI: 10.1016/j.semcancer.2019.11.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/31/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
Substantial evolution in cancer therapy has been witnessed lately, steering mainly towards immunotherapeutic approaches, replacing or in combination with classical therapies. Whereas the use of various immunotherapy approaches, such as adoptive T cell therapy, genetically-modified T cells, or immune checkpoint inhibitors, has been a triumph for cancer immunotherapy, the great challenge is the ability of the immune system to sustain long lasting anti-tumor response. Additionally, epigenetic changes in a suppressive tumor microenvironment can pertain to T cell exhaustion, limiting their functionality. Noncoding RNAs (ncRNAs) have emerged over the last years as key players in epigenetic regulation. Among those, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have been studied extensively for their potential role in regulating tumor immunity through direct regulation of genes involved in immune activation or suppression. In this review, we will provide an overview of contemporary approaches for cancer immunotherapy and will present the current state of knowledge implicating miRNAs and lncRNAs in regulating immune response against human cancer and their potential implications in resistance to cancer immunotherapy, with main emphasis on immune checkpoints regulation.
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Affiliation(s)
- Radhakrishnan Vishnubalaji
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Hibah Shaath
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar
| | - Ramesh Elango
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- Cancer Research Center, Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), Doha, Qatar.
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45
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Gupta SC, Awasthee N, Rai V, Chava S, Gunda V, Challagundla KB. Long non-coding RNAs and nuclear factor-κB crosstalk in cancer and other human diseases. Biochim Biophys Acta Rev Cancer 2019; 1873:188316. [PMID: 31639408 DOI: 10.1016/j.bbcan.2019.188316] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 12/29/2022]
Abstract
The regulation of the pleiotropic transcription factor, nuclear factor-κB (NF-κB) by miRNAs and proteins is extensively studied. More recently, the NF-κB signaling was also reported to be regulated by several long non-coding RNAs (lncRNAs) that constitute the major portion of the noncoding component of the human genome. The common NF-κB associated lncRNAs include NKILA, HOTAIR, MALAT1, ANRIL, Lethe, MIR31HG, and PACER. The lncRNA and NF-κB signaling crosstalk during cancer and other diseases such as cardiomyopathy, celiac disease, cerebral infarction, chronic kidney disease, diabetes mellitus, Kawasaki disease, pregnancy loss, and rheumatoid arthritis. Some NF-κB related lncRNAs can affect gene expression without modulating NF-κB signaling. Most of the lncRNAs with a potential to modulate NF-κB signaling are regulated by NF-κB itself suggesting a feedback regulation. The discovery of lncRNAs have provided a new type of regulation for the NF-κB signaling and thus could be explored for therapeutic interventions. The manner in which lncRNA and NF-κB crosstalk affects human pathophysiology is discussed in this review. The challenges associated with the therapeutic interventions of this crosstalk are also discussed.
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Affiliation(s)
- Subash C Gupta
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India.
| | - Nikee Awasthee
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Vipin Rai
- Department of Biochemistry, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India
| | - Srinivas Chava
- Department of Biochemistry & Molecular Biology, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Venugopal Gunda
- Pediatric Oncology Laboratory, Child Health Research Institute, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishore B Challagundla
- Department of Biochemistry & Molecular Biology, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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46
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Gheitasi R, Jourghasemi S, Pakzad I, Hosseinpour Sarmadi V, Samieipour Y, Sekawi Z, Azizi Jalilian F. A potential marker in brucellosis, long non coding RNA IFNG-AS1. Mol Biol Rep 2019; 46:6495-6500. [PMID: 31595441 DOI: 10.1007/s11033-019-05095-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/22/2019] [Indexed: 10/25/2022]
Abstract
Brucellosis is the most common bacterial zoonotic infection. This pathogen may survive and sustain in host. The aim of this study is to define relationship between long noncoding (lnc) RNA-IFNG-AS1 and interferon gamma (IFN-γ) in different groups of patients with brucellosis compared to control group. In this study, associations of lncRNA IFNG-AS1 expression with secretion of IFN-γ level in Sixty patients with brucellosis, which were divided into 3 groups (acute, chronic and relapse groups), as a case group were compared with 20 subjects with negative serological tests and brucellosis clinical manifestation as a control group. In this regard, RNA were extracted from isolated peripheral blood mononuclear cells (PBMCs). LncRNA IFNG-AS1, T-box transcription factor (T-bet) and IFN-γ expressions were detected using quantitative polymerase chain reaction (qPCR). Serum level IFN-γ was assessed using enzyme linked immunosorbent assay (ELISA). The results showed that expression level of LncRNA IFNG-AS1, T-bet and IFN-γ increased significantly in all patient groups in compared to healthy subjects (P < 0.0001, P < 0.01, P < 0.001). However, there was no significant difference in T-bet expression between chronic and healthy groups (P = 0.98). Additionally, further analysis revealed that the serum level of IFN-γ in acute and relapsed groups were higher than control group (P < 0.0001, P < 0.001). The effective role of IFNG-AS1 in many protective actions, including enhancing the expression of INF-γ in the immune response of brucellosis patients, revealed new potential marker, LncRNA IFNG-AS1 in screening, diagnosis or treatment of brucellosis.
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Affiliation(s)
- Reza Gheitasi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Sanaz Jourghasemi
- Department of Immunology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Iraj Pakzad
- Department Microbiology, Faculty of Medicine and Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | | | - Yazdan Samieipour
- Institute of Virology, Technical University of Munich, Munich, Germany
| | - Zamberi Sekawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, University Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Farid Azizi Jalilian
- Department of Medical Virology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
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Petermann F, Pękowska A, Johnson CA, Jankovic D, Shih HY, Jiang K, Hudson WH, Brooks SR, Sun HW, Villarino AV, Yao C, Singleton K, Akondy RS, Kanno Y, Sher A, Casellas R, Ahmed R, O'Shea JJ. The Magnitude of IFN-γ Responses Is Fine-Tuned by DNA Architecture and the Non-coding Transcript of Ifng-as1. Mol Cell 2019; 75:1229-1242.e5. [PMID: 31377117 PMCID: PMC6754279 DOI: 10.1016/j.molcel.2019.06.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/05/2019] [Accepted: 06/18/2019] [Indexed: 12/24/2022]
Abstract
Interferon gamma (IFN-γ), critical for host defense and tumor surveillance, requires tight control of its expression. Multiple cis-regulatory elements exist around Ifng along with a non-coding transcript, Ifng-as1 (also termed NeST). Here, we describe two genetic models generated to dissect the molecular functions of this locus and its RNA product. DNA deletion within the Ifng-as1 locus disrupted chromatin organization of the extended Ifng locus, impaired Ifng response, and compromised host defense. Insertion of a polyA signal ablated the Ifng-as1 full-length transcript and impaired host defense, while allowing proper chromatin structure. Transient knockdown of Ifng-as1 also reduced IFN-γ production. In humans, discordant expression of IFNG and IFNG-AS1 was evident in memory T cells, with high expression of this long non-coding RNA (lncRNA) and low expression of the cytokine. These results establish Ifng-as1 as an important regulator of Ifng expression, as a DNA element and transcribed RNA, involved in dynamic and cell state-specific responses to infection.
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Affiliation(s)
- Franziska Petermann
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | | | - Catrina A Johnson
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Dragana Jankovic
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Han-Yu Shih
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Kan Jiang
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - William H Hudson
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Hong-Wei Sun
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Alejandro V Villarino
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Chen Yao
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Kentner Singleton
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Rama S Akondy
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - Yuka Kanno
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA.
| | - Alan Sher
- Immunobiology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA; Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, USA
| | - John J O'Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA.
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48
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Chen J, Ao L, Yang J. Long non-coding RNAs in diseases related to inflammation and immunity. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:494. [PMID: 31700930 DOI: 10.21037/atm.2019.08.37] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been key regulators of gene expression in innate and adaptive immunity. Although lncRNAs have been reported to be associated with some diseases, its expression and function in diseases related to inflammation and immunity are still unknown. We reviewed how lncRNA regulated transcription and controlled the function and balance of the cells in the immune response. In addition, we discussed the impacts and challenges of lncRNAs on immunity in diseases.
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Affiliation(s)
- Jiao Chen
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan 430000, China.,Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan 430000, China
| | - Liangfei Ao
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan 430000, China.,Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan 430000, China
| | - Jing Yang
- Reproductive Medicine Center, Renmin Hospital of Wuhan University, Wuhan 430000, China.,Hubei Clinic Research Center for Assisted Reproductive Technology and Embryonic Development, Wuhan 430000, China
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49
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West KA, Lagos D. Long Non-Coding RNA Function in CD4 + T Cells: What We Know and What Next? Noncoding RNA 2019; 5:ncrna5030043. [PMID: 31336952 PMCID: PMC6789709 DOI: 10.3390/ncrna5030043] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/03/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023] Open
Abstract
The non-coding genome has previously been regarded as "junk" DNA; however, emerging evidence suggests that the non-coding genome accounts for some of the greater biological complexity observed in mammals. Research into long non-coding RNAs (lncRNAs) has gathered speed in recent years, and a growing body of evidence has implicated lncRNAs in a vast range of cellular functions including gene regulation, chromosome organisation and splicing. T helper cells offer an ideal platform for the study of lncRNAs given they function as part of a complex cellular network and undergo remarkable and finely regulated gene expression changes upon antigenic stimulation. Using various knock down and RNA interaction studies several lncRNAs have been shown to be crucial for T helper cell differentiation, activation and function. Given that RNA targeting therapeutics are rapidly gaining attention, further understanding the mechanistic role of lncRNAs in a T helper context is an exciting area of research, as it may unearth a wide range of new candidate targets for treatment of CD4+ mediated pathologies.
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Affiliation(s)
- Katie A West
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5DD, UK
- Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
- Hull York Medical School, University of York, Wentworth Way, York YO10 5DD, UK
| | - Dimitris Lagos
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5DD, UK.
- Hull York Medical School, University of York, Wentworth Way, York YO10 5DD, UK.
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Abstract
Rheumatic diseases are a group of chronic heterogeneous autoimmune disorders characterized by abnormal regulation of the innate and adaptive immune systems. Despite extensive efforts, the full spectrum of molecular factors that contribute to the pathogenesis of rheumatic diseases remains unclear. ncRNAs can govern gene expression at the transcriptional and post-transcriptional levels in multiple diseases. Recent studies have demonstrated an important role for ncRNAs, such as miRNAs and lncRNAs, in the development of immune cells and rheumatic diseases. Here, we focus on the epigenetic regulatory roles of ncRNAs in the pathogenesis of rheumatic diseases and as biomarkers of disease state.
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Affiliation(s)
- Weilin Chen
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Di Liu
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Quan-Zhen Li
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
| | - Honglin Zhu
- Department of Rheumatology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China
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