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Jaroenlak P, McCarty KL, Xia B, Lam C, Zwack EE, Yanai I, Bhabha G, Ekiert DC. scRNA-seq reveals transcriptional dynamics of Encephalitozoon intestinalis parasites in human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596468. [PMID: 38853846 PMCID: PMC11160751 DOI: 10.1101/2024.05.30.596468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Microsporidia are single-celled intracellular parasites that cause opportunistic diseases in humans. Encephalitozoon intestinalis is a prevalent human-infecting species that invades the small intestine. Dissemination to other organ systems is also observed, and is potentially facilitated by macrophages. The macrophage response to infection and the developmental trajectory of the parasite are not well studied. Here we use single cell RNA sequencing to investigate transcriptional changes in both the host and parasite during infection. While a small population of infected macrophages mount a response, most remain transcriptionally unchanged, suggesting that the majority of parasites may avoid host detection. The parasite transcriptome reveals large transcriptional changes throughout the life cycle, providing a blueprint for parasite development. The stealthy microsporidian lifestyle likely allows these parasites to harness macrophages for replication and dissemination. Together, our data provide insights into the host response in primary human macrophages and the E. intestinalis developmental program.
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Affiliation(s)
- Pattana Jaroenlak
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kacie L. McCarty
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York 10016, USA
| | - Bo Xia
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cherry Lam
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
| | - Erin E. Zwack
- Department of Microbiology, New York University Grossman School of Medicine, New York 10016, USA
| | - Itai Yanai
- Institute for Computational Medicine, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gira Bhabha
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Damian C. Ekiert
- Department of Cell Biology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Microbiology, New York University Grossman School of Medicine, New York 10016, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
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Hong H, Wang Y, Menard M, Buckley J, Zhou L, Volpicelli-Daley L, Standaert D, Qin H, Benveniste E. Suppression of the JAK/STAT Pathway Inhibits Neuroinflammation in the Line 61-PFF Mouse Model of Parkinson's Disease. RESEARCH SQUARE 2024:rs.3.rs-4307273. [PMID: 38766241 PMCID: PMC11100885 DOI: 10.21203/rs.3.rs-4307273/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Parkinson's disease (PD) is characterized by neuroinflammation, progressive loss of dopaminergic neurons, and accumulation of a-synuclein (a-Syn) into insoluble aggregates called Lewy pathology. The Line 61 a-Syn mouse is an established preclinical model of PD; Thy-1 is used to promote human a-Syn expression, and features of sporadic PD develop at 9-18 months of age. To accelerate the PD phenotypes, we injected sonicated human a-Syn preformed fibrils (PFFs) into the striatum, which produced phospho-Syn (p-a-Syn) inclusions in the substantia nigra pars compacta and significantly increased MHC Class II-positive immune cells. Additionally, there was enhanced infiltration and activation of innate and adaptive immune cells in the midbrain. We then used this new model, Line 61-PFF, to investigate the effect of inhibiting the JAK/STAT signaling pathway, which is critical for regulation of innate and adaptive immune responses. After administration of the JAK1/2 inhibitor AZD1480, immunofluorescence staining showed a significant decrease in p-a-Syn inclusions and MHC Class II expression. Flow cytometry showed reduced infiltration of CD4+ T-cells, CD8+ T-cells, CD19+ B-cells, dendritic cells, macrophages, and endogenous microglia into the midbrain. Importantly, single-cell RNA-Sequencing analysis of CD45+ cells from the midbrain identified 9 microglia clusters, 5 monocyte/macrophage (MM) clusters, and 5 T-cell (T) clusters, in which potentially pathogenic MM4 and T3 clusters were associated with neuroinflammatory responses in Line 61-PFF mice. AZD1480 treatment reduced cell numbers and cluster-specific expression of the antigen-presentation genes H2-Eb1, H2-Aa, H2-Ab1, and Cd74 in the MM4 cluster and proinflammatory genes such as Tnf, Il1b, C1qa, and C1qc in the T3 cluster. Together, these results indicate that inhibiting the JAK/STAT pathway suppresses the activation and infiltration of innate and adaptive cells, reducing neuroinflammation in the Line 61-PFF mouse model.
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Valverde A, Naqvi RA, Naqvi AR. Macrophage-enriched novel functional long noncoding RNAs LRRC75A-AS1 and GAPLINC regulate polarization and innate immune responses. Inflamm Res 2024; 73:771-792. [PMID: 38592458 DOI: 10.1007/s00011-024-01865-w] [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: 01/11/2024] [Revised: 01/29/2024] [Accepted: 02/21/2024] [Indexed: 04/10/2024] Open
Abstract
INTRODUCTION Macrophages (Mφs) are functionally dynamic immune cells that bridge innate and adaptive immune responses; however, the underlying epigenetic mechanisms that control Mφ plasticity and innate immune functions are not well elucidated. OBJECTIVE To identify novel functions of macrophage-enriched lncRNAs in regulating polarization and innate immune responses. METHODS Total RNA isolated from differentiating monocyte-derived M1 and M2 Mφs was profiled for lncRNAs expression using RNAseq. Impact of LRRC75A-AS1, GAPLINC and AL139099.5 knockdown was examined on macrophage differentiation, polarization markers, phagocytosis, and antigen processing by flow cytometry and florescence microscopy. Cytokine profiles were examined by multiplex bead array and cytoskeletal signaling pathway genes were quantified by PCR-based array. Gingival biopsies were collected from periodontally healthy and diseased subjects to examine lncRNAs, M1/M2 marker expression. RESULTS Transcriptome profiling of M1 and M2 Mφs identified thousands of differentially expressed known and novel lncRNAs. We characterized three Mφ-enriched lncRNAs LRRC75A-AS1, GAPLINC and AL139099.5 in polarization and innate immunity. Knockdown of LRRC75A-AS1 and GAPLINC downregulated the Mφ differentiation markers and skewed Mφ polarization by decreasing M1 markers without a significant impact on M2 markers. LRRC75A-AS1 and GAPLINC knockdown also attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion in Mφs, supporting their functional role in potentiating innate immune functions. Mechanistically, LRRC75A-AS1 and GAPLINC knockdown impaired Mφ migration by downregulating the expression of multiple cytoskeletal signaling pathways suggesting their critical role in regulating Mφ migration. Finally, we showed that LRRC75A-AS1 and GAPLINC were upregulated in periodontitis and their expression correlates with higher M1 markers suggesting their role in macrophage polarization in vivo. CONCLUSION Our results show that polarized Mφs acquire a unique lncRNA repertoire and identified many previously unknown lncRNA sequences. LRRC75A-AS1 and GAPLINC, which are induced in periodontitis, regulate Mφ polarization and innate immune functions supporting their critical role in inflammation.
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Affiliation(s)
- Araceli Valverde
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA.
| | - Raza Ali Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA
| | - Afsar R Naqvi
- Department of Periodontics, College of Dentistry, University of Illinois Chicago, Chicago, IL, 60612, USA.
- Department of Microbiology and Immunology, College of Medicine, University of Illinois Chicago, Chicago, IL, 60612, USA.
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Tang W, Wu S, Tang Y, Ma J, Ao Y, Liu L, Wei K. Microarray analysis identifies lncFirre as a potential regulator of obesity-related acute lung injury. Life Sci 2024; 340:122459. [PMID: 38307237 DOI: 10.1016/j.lfs.2024.122459] [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: 11/08/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/04/2024]
Abstract
AIMS The inflammatory response in acute lung injury/acute respiratory distress syndrome (ALI/ARDS) is heightened in obesity. The aim of this study was to investigate whether lncRNAs are involved in the effects of obesity on acute lung injury and to find possible effector lncRNAs. MAIN METHODS Microarray analysis was used to assess the transcriptional profiles of lncRNAs and mRNAs in lung tissues from normal (CON), high-fat diet induced obese (DIO), and obese ALI mice (DIO-ALI). GO and KEGG analyses were employed to explore the biological functions of differentially expressed genes. A lncRNA-mRNA co-expression network was constructed to identify specific lncRNA. Lung tissues and peripheral blood samples from patients with obesity and healthy lean donors were utilized to confirm the expression characteristics of lncFirre through qRT-PCR. lncFirre was knocked down in MH-S macrophages to explore its function. ELISA and Griess reagent kit were used to detect PGE2 and NO. Flow cytometry was used to detect macrophages polarization. KEY FINDINGS There were 475 lncRNAs and 404 mRNAs differentially expressed between DIO and CON, while 1348 lncRNAs and 1349 mRNAs between DIO-ALI and DIO. Obesity increased lncFirre expression in both mice and patients, and PA elevated lncFirre in MH-S. PA exacerbated the inflammation and proinflammatory polarization of MH-S induced by LPS. LncFirre knockdown inhibited the secretion of PGE2 and NO, M1 differentiation while promoted the M2 differentiation in PA and LPS co-challenged MH-S. SIGNIFICANCE Interfering with lncFirre effectively inhibit inflammation in MH-S, lncFirre can serve as a promising target for treating obesity-related ALI.
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Affiliation(s)
- Wenjing Tang
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Siqi Wu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yin Tang
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Jingyue Ma
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Yichan Ao
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China
| | - Ling Liu
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
| | - Ke Wei
- Department of Anesthesiology, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, China.
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Nemeth K, Bayraktar R, Ferracin M, Calin GA. Non-coding RNAs in disease: from mechanisms to therapeutics. Nat Rev Genet 2024; 25:211-232. [PMID: 37968332 DOI: 10.1038/s41576-023-00662-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2023] [Indexed: 11/17/2023]
Abstract
Non-coding RNAs (ncRNAs) are a heterogeneous group of transcripts that, by definition, are not translated into proteins. Since their discovery, ncRNAs have emerged as important regulators of multiple biological functions across a range of cell types and tissues, and their dysregulation has been implicated in disease. Notably, much research has focused on the link between microRNAs (miRNAs) and human cancers, although other ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as relevant contributors to human disease. In this Review, we summarize our current understanding of the roles of miRNAs, lncRNAs and circRNAs in cancer and other major human diseases, notably cardiovascular, neurological and infectious diseases. Further, we discuss the potential use of ncRNAs as biomarkers of disease and as therapeutic targets.
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Affiliation(s)
- Kinga Nemeth
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, Bologna, Italy.
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy.
| | - George A Calin
- Translational Molecular Pathology Department, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The RNA Interference and Non-coding RNA Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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6
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Shin JJ, Park J, Shin HS, Arab I, Suk K, Lee WH. Roles of lncRNAs in NF-κB-Mediated Macrophage Inflammation and Their Implications in the Pathogenesis of Human Diseases. Int J Mol Sci 2024; 25:2670. [PMID: 38473915 DOI: 10.3390/ijms25052670] [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: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Over the past century, molecular biology's focus has transitioned from proteins to DNA, and now to RNA. Once considered merely a genetic information carrier, RNA is now recognized as both a vital element in early cellular life and a regulator in complex organisms. Long noncoding RNAs (lncRNAs), which are over 200 bases long but do not code for proteins, play roles in gene expression regulation and signal transduction by inducing epigenetic changes or interacting with various proteins and RNAs. These interactions exhibit a range of functions in various cell types, including macrophages. Notably, some macrophage lncRNAs influence the activation of NF-κB, a crucial transcription factor governing immune and inflammatory responses. Macrophage NF-κB is instrumental in the progression of various pathological conditions including sepsis, atherosclerosis, cancer, autoimmune disorders, and hypersensitivity. It orchestrates gene expression related to immune responses, inflammation, cell survival, and proliferation. Consequently, its malfunction is a key contributor to the onset and development of these diseases. This review aims to summarize the function of lncRNAs in regulating NF-κB activity in macrophage activation and inflammation, with a particular emphasis on their relevance to human diseases and their potential as therapeutic targets. The insights gained from studies on macrophage lncRNAs, as discussed in this review, could provide valuable knowledge for the development of treatments for various pathological conditions involving macrophages.
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Affiliation(s)
- Jae-Joon Shin
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeongkwang Park
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyeung-Seob Shin
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Imene Arab
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science and Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Won-Ha Lee
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
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Raghubeer S. The influence of epigenetics and inflammation on cardiometabolic risks. Semin Cell Dev Biol 2024; 154:175-184. [PMID: 36804178 DOI: 10.1016/j.semcdb.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Cardiometabolic diseases include metabolic syndrome, obesity, type 2 diabetes mellitus, and hypertension. Epigenetic modifications participate in cardiometabolic diseases through several pathways, including inflammation, vascular dysfunction, and insulin resistance. Epigenetic modifications, which encompass alterations to gene expression without mutating the DNA sequence, have gained much attention in recent years, since they have been correlated with cardiometabolic diseases and may be targeted for therapeutic interventions. Epigenetic modifications are greatly influenced by environmental factors, such as diet, physical activity, cigarette smoking, and pollution. Some modifications are heritable, indicating that the biological expression of epigenetic alterations may be observed across generations. Moreover, many patients with cardiometabolic diseases present with chronic inflammation, which can be influenced by environmental and genetic factors. The inflammatory environment worsens the prognosis of cardiometabolic diseases and further induces epigenetic modifications, predisposing patients to the development of other metabolism-associated diseases and complications. A deeper understanding of inflammatory processes and epigenetic modifications in cardiometabolic diseases is necessary to improve our diagnostic capabilities, personalized medicine approaches, and the development of targeted therapeutic interventions. Further understanding may also assist in predicting disease outcomes, especially in children and young adults. This review describes epigenetic modifications and inflammatory processes underlying cardiometabolic diseases, and further discusses advances in the research field with a focus on specific points for interventional therapy.
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Affiliation(s)
- Shanel Raghubeer
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health & Wellness Sciences, Cape Peninsula University of Technology, South Africa.
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Wang Y, Zhang C, Liu T, Yu Z, Wang K, Ying J, Wang Y, Zhu T, Li J, Hu XL, Zhou Y, Lu G. Malat1 regulates PMN-MDSC expansion and immunosuppression through p-STAT3 ubiquitination in sepsis. Int J Biol Sci 2024; 20:1529-1546. [PMID: 38385073 PMCID: PMC10878150 DOI: 10.7150/ijbs.92267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/29/2024] [Indexed: 02/23/2024] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) expand during sepsis and contribute to the development of persistent inflammation-immunosuppression-catabolism syndrome. However, the underlying mechanism remains unclear. Exploring the mechanisms of MDSCs generation may provide therapeutic targets for improving immune status in sepsis. Here, a sepsis mouse model is established by cecal ligation and perforation. Bone marrow cells at different sepsis time points are harvested to detect the proportion of MDSCs and search for differentially expressed genes by RNA-sequence. In lethal models of sepsis, polymorphonuclear-MDSCs (PMN-MDSCs) decrease in early but increase and become activated in late sepsis, which is contrary to the expression of metastasis-associated lung adenocarcinoma transcript 1 (Malat1). In vivo, Malat1 inhibitor significantly increases the mortality in mice with late sepsis. And in vitro, Malat1 down-regulation increases the proportion of PMN-MDSCs and enhanced its immunosuppressive ability. Mechanistically, Malat1 limits the differentiation of PMN-MDSCs by accelerating the degradation of phosphorylated STAT3. Furthermore, Stattic, an inhibitor of STAT3 phosphorylation, improves the survival of septic mice by inhibiting PMN-MDSCs. Overall, the study identifies a novel insight into the mechanism of sepsis-induced MDSCs and provides more evidence for targeting MDSCs in the treatment of sepsis.
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Affiliation(s)
- Yaodong Wang
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Caiyan Zhang
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Tingyan Liu
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Zhenhao Yu
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Kexin Wang
- Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jiayun Ying
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Yao Wang
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Ting Zhu
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
| | - Jingjing Li
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Xiuchuan Lucas Hu
- Lungs for Living Research Centre, UCL Respiratory, University College London, London, UK
| | - Yufeng Zhou
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
- Institute of Pediatrics, Children's Hospital of Fudan University, National Children's Medical Center, and the Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- National Health Commission (NHC) Key Laboratory of Neonatal Diseases, Fudan University, Shanghai, China
- Fujian Key Laboratory of Neonatal Diseases, Fujian, China
| | - Guoping Lu
- Department of Critical Care Medicine, Children's Hospital of Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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Jasim SA, Aziz DZ, Mustafa YF, Margiana R, Al-Alwany AA, Hjazi A, Alawadi A, Yumashev A, Alsalamy A, Fenjan MN. Role of genetically engineered mesenchymal stem cell exosomes and LncRNAs in respiratory diseases treatment. Pathol Res Pract 2024; 254:155135. [PMID: 38295461 DOI: 10.1016/j.prp.2024.155135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 02/02/2024]
Abstract
The term acute respiratory disease encompasses a wide range of acute lung diseases, which in recent years have been ranked among the top three deadly diseases in the world. Since conventional treatment methods, including the use of anti-inflammatory drugs, have had no significant effect on the treatment process of these diseases, the attention of the medical community has been drawn to alternative methods. Mesenchymal stem cells (MSC) are multipotential stem/progenitor cells that have extensive immunomodulatory and anti-inflammatory properties and also play a critical role in the microenvironment of injured tissue. MSC secretomes (containing large extracellular vesicles, microvesicles, and exosomes) are a newly introduced option for cell-free therapies that can circumvent the hurdles of cell-based therapies while maintaining the therapeutic role of MSC themselves. The therapeutic capabilities of MSCs have been showed in many acute respiratory diseases, including chronic respiratory disease (CRD), novel coronavirus 2019 (COVID -19), and pneumonia. MSCs offer novel therapeutic approaches for chronic and acute lung diseases due to their anti-inflammatory and immunomodulatory properties. In this review, we summarize the current evidence on the efficacy and safety of MSC-derived products in preclinical models of lung diseases and highlight the biologically active compounds present in the MSC secretome and their mechanisms involved in anti-inflammatory activity and tissue regeneration.
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Affiliation(s)
| | - Dhifaf Zeki Aziz
- College of Science, Department of pathological Analyses, University of Kufa, Al-Najaf, Iraq.
| | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, Iraq.
| | - Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.
| | | | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Saudi Arabia.
| | - Ahmed Alawadi
- College of technical engineering, the Islamic University, Najaf, Iraq; College of technical engineering, the Islamic University of Al Diwaniyah, Al Diwaniyah, Iraq; College of technical engineering, the Islamic University of Babylon, Babylon, Iraq
| | - Alexey Yumashev
- Department of Prosthetic Dentistry, Sechenov First Moscow State Medical University, Russia.
| | - Ali Alsalamy
- College of technical engineering, Imam Ja'afar Al-Sadiq University, Al-Muthanna 66002, Iraq.
| | - Mohammed N Fenjan
- College of Health and Medical Technology, Al-Ayen University, Thi-Qar, Iraq.
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10
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Shaker O, El Amir M, Elfatah YA, Elwi HM. Expression patterns of lncRNA MALAT-1 in SARS-COV-2 infection and its potential effect on disease severity via miR-200c-3p and SIRT1. Biochem Biophys Rep 2023; 36:101562. [PMID: 37965063 PMCID: PMC10641570 DOI: 10.1016/j.bbrep.2023.101562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 11/16/2023] Open
Abstract
Downregulating Angiotensin Converting Enzyme2 (ACE2) expression may be a shared mechanism for RNA viruses. Aim Evaluate the expressions of ACE2 effectors: the long non-coding RNA 'MALAT-1', the micro-RNA 'miR-200c-3p' and the histone deacetylase 'SIRT1' in SARS-COV-2 patients and correlate to disease severity. Sera samples from 98 SARS-COV-2 patients and 30 healthy control participants were collected. qRT-PCR was used for MALAT-1 and miR-200c-3p expression. SIRT1 was measured using ELISA. Results In sera of COVID-19 patients, gene expression of miR-200c-3p is increased while MALAT-1 is decreased. SIRT1 protein level is decreased (P value < 0.001). Findings are accentuated with increased disease severity. Serum MALAT-1, miR-200c-3p and SIRT1 could be used as diagnostic markers at cut off values of 0.04 (95.9 % sensitivity), 5.59 (94.9 % sensitivity, 99 % specificity), and 7.4 (98 % sensitivity) respectively. A novel MALAT-1-miR-200c-3p-SIRT1 pathway may be involved in the regulation of SARS-COV-2 severity.
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Affiliation(s)
- Olfat Shaker
- Medical Biochemistry and Molecular Biology, Kasr Alainy Faculty of Medicine, Cairo University, Kasralainy st, Cairo, 11562, Egypt
| | - Monica El Amir
- Medical Biochemistry and Molecular Biology, Kasr Alainy Faculty of Medicine, Cairo University, Kasralainy st, Cairo, 11562, Egypt
| | - Yasmine Abd Elfatah
- Internal Medicine, Kasr Alainy Faculty of Medicine, Cairo University, Kasralainy st, Cairo, 11562, Egypt
| | - Heba M. Elwi
- Medical Biochemistry and Molecular Biology, Kasr Alainy Faculty of Medicine, Cairo University, Kasralainy st, Cairo, 11562, Egypt
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Li D, Wang J, Zeng J, Li S, Sun D, Qiu L, Huang Z, Wang K, Fu G, Gou D, Zhang Y. Identification and Validation of Genes Exhibiting Dynamic Alterations in Response to Bleomycin-Induced Pulmonary Fibrosis. Mol Biotechnol 2023:10.1007/s12033-023-00943-4. [PMID: 37924392 DOI: 10.1007/s12033-023-00943-4] [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: 08/04/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) carries a high mortality rate and has a poor prognosis. The pathogenesis of pulmonary fibrosis (PF) is highly related to dysregulation of multiple RNAs. This study aims to identify and validate dysregulated RNAs that exhibited dynamic alterations in response to bleomycin (BLM)-induced PF. The results will provide therapeutic targets for patients suffering from IPF. Whole transcriptomic profiles of BLM-induced PF were obtained through high-throughput RNA sequencing. miRNA profiling was downloaded from GSE45789 database in the Gene Expression Omnibus (GEO). We identified the differentially expressed RNAs (DERNAs) that exhibited dynamic alterations in response to BLM-induced PF. Subsequently, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis were conducted to discovery regulatory processes of PF. Weighted gene co-expression network analysis (WGCNA), protein-protein interaction (PPI) analysis, and co-expression analysis were performed to identify key genes and pathogenic pattern during the progression of PF. MiRanda, miRcode, and TargetScan were utilized to predict target relationships in the potential competing endogenous RNA (ceRNA) network. The results were verified by qRT-PCR analysis. In the context of BLM-induced PF, this study identified a total of 167 differentially expressed messenger RNAs (DEmRNAs), 115 differentially expressed long non-coding RNAs (DElncRNAs), 45 differentially expressed circular RNAs (DEcircRNAs), and 87 differentially expressed microRNAs (DEmiRNAs). These RNA molecules showed dynamic alterations in response to BLM-induced PF. These DEmRNAs exhibited a predominant association with the biological processes pertaining to the organization of extracellular matrix. A regulatory network was built in PF, encompassing 31 DEmRNAs, 18 DE lncRNAs, 13 DEcircRNAs, and 13 DEmiRNAs. Several DERNA molecules were subjected to validate using additional BLM-induced PF model. The outcomes of this validation process shown a strong correlation with the results obtained from RNA sequencing analysis. The GSE213001 dataset was utilized to validate the expression levels and diagnostic efficacy of four specific hub mRNAs (CCDC80, CLU, COL5A1, and COL6A3) in individuals diagnosed with PF. In this study, we identified and validated several RNA molecules that exhibited dynamic alternations in response to BLM-induced PF. These dysregulated RNAs participated in the pathogenesis of PF and can be used as therapeutic targets for early-stage IPF. Although more work must be done to confirm the results, our study may provide directions for future studies.
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Affiliation(s)
- Dengyuan Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, 650500, China
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650022, China
| | - Jun Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Jie Zeng
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650022, China
| | - Shujin Li
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Danxiong Sun
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650022, China
| | - Lin Qiu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Zhenming Huang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650022, China
| | - Ku Wang
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Gaohui Fu
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China
| | - Deming Gou
- Shenzhen Key Laboratory of Microbial Genetic Engineering, Vascular Disease Research Center, College of Life Sciences and Oceanography, Guangdong Provincial Key Laboratory of Regional Immunity and Disease, Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen, 518060, China.
| | - Yunhui Zhang
- Department of Pulmonary and Critical Care Medicine, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650022, China.
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12
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Ahmad I, Naqvi RA, Valverde A, Naqvi AR. LncRNA MALAT1/microRNA-30b axis regulates macrophage polarization and function. Front Immunol 2023; 14:1214810. [PMID: 37860007 PMCID: PMC10582718 DOI: 10.3389/fimmu.2023.1214810] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 09/21/2023] [Indexed: 10/21/2023] Open
Abstract
Macrophages (Mφ) are long-lived myeloid cells that can polarize towards the proinflammatory M1 or proresolving M2 phenotype to control diverse biological processes such as inflammation, tissue damage, and regeneration. Noncoding RNA are a class of nonprotein-coding transcriptome with numerous interdependent biological roles; however, their functional interaction in the regulation of Mφ polarization and immune responses remain unclear. Here, we show antagonistic relationship between lncRNA (MALAT1) and microRNA (miR-30b) in shaping macrophage polarization and immune functions. MALAT1 expression displays a time-dependent induction during Mφ differentiation and, upon challenge with TLR4 agonist (E. coli LPS). MALAT1 knockdown promoted the expression of M2Mφ markers without affecting M1Mφ markers, suggesting that MALAT1 favors the M1 phenotype by suppressing M2 differentiation. Compared to the control, MALAT1 knockdown resulted in reduced antigen uptake and processing, bacterial phagocytosis, and bactericidal activity, strongly supporting its critical role in regulating innate immune functions in Mφ. Consistent with this, MALAT1 knockdown showed impaired cytokine secretion upon challenge with LPS. Importantly, MALAT1 exhibit an antagonistic expression pattern with all five members of the miR-30 family during M2 Mφ differentiation. Dual-luciferase assays validated a novel sequence on MALAT1 that interacts with miR-30b, a microRNA that promotes the M2 phenotype. Phagocytosis and antigen processing assays unequivocally demonstrated that MALAT1 and miR-30b are functionally antagonistic. Concurrent MALAT1 knockdown and miR-30b overexpression exhibited the most significant attenuation in both assays. In human subjects with periodontal disease and murine model of ligature-induced periodontitis, we observed higher levels of MALAT1, M1Mφ markers and downregulation of miR-30b expression in gingival tissues suggesting a pro-inflammatory function of MALAT1 in vivo. Overall, we unraveled the role of MALAT1 in Mφ polarization and delineated the underlying mechanism of its regulation by involving MALAT-1-driven miR-30b sequestration.
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Affiliation(s)
| | | | | | - Afsar R. Naqvi
- Mucosal Immunology Lab, College of Dentistry, University of Illinois at Chicago, Chicago, IL, United States
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13
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Chang F, Wang C, Zheng P, Liu Z, Wang H, Gong L, Dong H, Jing Y, Mi S, Xie Z, Ge P, Yang J, Zhong L. Malat1 promotes macrophage-associated inflammation by increasing PPAR-γ methylation through binding to EZH2 in acute myocardial infarction. Int Immunopharmacol 2023; 123:110695. [PMID: 37591118 DOI: 10.1016/j.intimp.2023.110695] [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: 05/09/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 08/19/2023]
Abstract
The inflammatory microenvironment of macrophage plays an important role in acute myocardial infarction (AMI), but the regulatory mechanism is unknown. Here, we aimed to investigate the role of Malat1 on inflammation microenvironment of macrophage in AMI. Our study found that Malat1 expression was increased in AMI, which mainly expressed in macrophages. Malat1 inhibition improved collagen deposition and inflammation in infarcted heart. In vitro, Malat1 inhibition evidently reduced macrophage-associated inflammation. The results from ribonucleic acid pull-down (RNA pull-down) and RNA Immunoprecipitation (RIP) assay demonstrated that Malat1 directly binds to EZH2. Malat1 and EZH2 complex could increase histone H3K27me3 expression and further inhibit the production of PPAR-γ. In vivo, inhibition of Malat1 also leaded to the down-regulation of both EZH2 and H3K27me3, as well as up-regulation of PPAR-γ in infarcted heart. Therefore, these findings demonstrate a novel mechanism of Malat1 on inflammation microenvironment of macrophage in AMI, which provide a new target for its treatment.
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Affiliation(s)
- Fangyuan Chang
- School of Medicine, Shandong University, Jinan 250012, China
| | - Chunxiao Wang
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Ping Zheng
- Department of Clinical Laboratory, Shandong Cancer Hospital and Institute, Shandong Cancer Hospital Affiliated to Shandong First Medical University, Jinan 250117, China
| | - Zhen Liu
- School of Medicine, Shandong University, Jinan 250012, China
| | - Hua Wang
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Lei Gong
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Haibin Dong
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Yanyan Jing
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Shaohua Mi
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Zan Xie
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Peipei Ge
- Department of Cardiology, Yantai Yuhuangding Hospital, Yantai 264000, China
| | - Jun Yang
- Department of Cardiology, Yantai Yuhuangding Hospital, Shandong University, Jinan 250012, China.
| | - Lin Zhong
- Department of Cardiology, Yantai Yuhuangding Hospital, Shandong University, Jinan 250012, China.
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14
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Yu T, Sun S. Role and mechanism of ferroptosis in acute lung injury. Cell Cycle 2023; 22:2119-2129. [PMID: 37946318 PMCID: PMC10732650 DOI: 10.1080/15384101.2023.2278328] [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: 10/17/2022] [Accepted: 10/28/2023] [Indexed: 11/12/2023] Open
Abstract
Ferroptosis is a new non-apoptotic cell death caused by the accumulation of dysregulated metabolism of ferric iron, amino acids or lipid peroxidation. Increasing studies suggest that ferroptosis is involved in the acute lung injury (ALI). This article aims to review the role of ferroptosis in ALI. ALI is a common respiratory disease and presents a high mortality rate. Inhibiting cell ferroptosis of lung improves the ALI. In addition, several signaling pathways are related to ferroptosis in ALI, involving in iron homeostasis, lipid peroxidation, and amino acid metabolism. Moreover, there are various key factors to regulate the occurrence of ferroptosis in ALI, such as ACSL4, NRF2, and P53. The ACSL4 promotes the ferroptosis, while the NRF2 alleviates the ferroptosis in ALI. The main effect of P53 is to promote ferroptosis. Accordingly, ferroptosis is involved in ALI and may be an important therapeutic target for ALI.
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Affiliation(s)
- Tingting Yu
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Kunming Medical University, Kunming, China
- Pediatrics Class 1, Kunming Medical University, Kunming, China
| | - Shibo Sun
- Department of Pulmonary and Critical Care Medicine, First Affiliated Hospital, Kunming Medical University, Kunming, China
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15
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Wang Z, Wang Z. The role of macrophages polarization in sepsis-induced acute lung injury. Front Immunol 2023; 14:1209438. [PMID: 37691951 PMCID: PMC10483837 DOI: 10.3389/fimmu.2023.1209438] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
Sepsis presents as a severe infectious disease frequently documented in clinical settings. Characterized by its systemic inflammatory response syndrome, sepsis has the potential to trigger multi-organ dysfunction and can escalate to becoming life-threatening. A common fallout from sepsis is acute lung injury (ALI), which often progresses to acute respiratory distress syndrome (ARDS). Macrophages, due to their significant role in the immune system, are receiving increased attention in clinical studies. Macrophage polarization is a process that hinges on an intricate regulatory network influenced by a myriad of signaling molecules, transcription factors, epigenetic modifications, and metabolic reprogramming. In this review, our primary focus is on the classically activated macrophages (M1-like) and alternatively activated macrophages (M2-like) as the two paramount phenotypes instrumental in sepsis' host immune response. An imbalance between M1-like and M2-like macrophages can precipitate the onset and exacerbate the progression of sepsis. This review provides a comprehensive understanding of the interplay between macrophage polarization and sepsis-induced acute lung injury (SALI) and elaborates on the intervention strategy that centers around the crucial process of macrophage polarization.
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Affiliation(s)
| | - Zhong Wang
- Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, China
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16
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Shin HS, Shin JJ, Park J, Arab I, Suk K, Lee WH. Role of Macrophage lncRNAs in Mediating Inflammatory Processes in Atherosclerosis and Sepsis. Biomedicines 2023; 11:1905. [PMID: 37509544 PMCID: PMC10377468 DOI: 10.3390/biomedicines11071905] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/25/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are molecules >200 bases in length without protein-coding functions implicated in signal transduction and gene expression regulation via interaction with proteins or RNAs, exhibiting various functions. The expression of lncRNAs has been detected in many cell types, including macrophages, a type of immune cell involved in acute and chronic inflammation, removal of dead or damaged cells, and tissue repair. Increasing evidence indicates that lncRNAs play essential roles in macrophage functions and disease development. Additionally, many animal studies have reported that blockage or modulation of lncRNA functions alleviates disease severity or morbidity rate. The present review summarizes the current knowledge regarding lncRNAs expressed in macrophages, focusing on their molecular targets and the biological processes regulated by them during the development of inflammatory diseases such as atherosclerosis and sepsis. Possible application of this information to lncRNA-targeting therapy is also discussed. The studies regarding macrophage lncRNAs described in this review can help provide valuable information for developing treatments for various pathological conditions involving macrophages.
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Affiliation(s)
- Hyeung-Seob Shin
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jae-Joon Shin
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeongkwang Park
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Imene Arab
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyoungho Suk
- Department of Pharmacology, Brain Science & Engineering Institute, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu 41944, Republic of Korea
| | - Won-Ha Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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17
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Santus L, Sopena-Rios M, García-Pérez R, Lin AE, Adams GC, Barnes KG, Siddle KJ, Wohl S, Reverter F, Rinn JL, Bennett RS, Hensley LE, Sabeti PC, Melé M. Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques. Nat Commun 2023; 14:3866. [PMID: 37391481 PMCID: PMC10313701 DOI: 10.1038/s41467-023-39627-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 06/19/2023] [Indexed: 07/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a multi-tissue bulk RNAseq dataset from Ebola virus (EBOV) infected and not-infected rhesus macaques and identified 3979 novel lncRNAs. To profile lncRNA expression dynamics in immune circulating single-cells during EBOV infection, we design a metric, Upsilon, to estimate cell-type specificity. Our analysis reveals that lncRNAs are expressed in fewer cells than protein-coding genes, but they are not expressed at lower levels nor are they more cell-type specific when expressed in the same number of cells. In addition, we observe that lncRNAs exhibit similar changes in expression patterns to those of protein-coding genes during EBOV infection, and are often co-expressed with known immune regulators. A few lncRNAs change expression specifically upon EBOV entry in the cell. This study sheds light on the differential features of lncRNAs and protein-coding genes and paves the way for future single-cell lncRNA studies.
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Affiliation(s)
- Luisa Santus
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Maria Sopena-Rios
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Raquel García-Pérez
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain
| | - Aaron E Lin
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA
| | - Gordon C Adams
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kayla G Barnes
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, 02115, USA
- Liverpool School of Tropical Medicine, Liverpool, L3 5QA, UK
| | - Katherine J Siddle
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Shirlee Wohl
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- The Scripps Research Institute, Department of Immunology and Microbiology, La Jolla, CA, USA
| | - Ferran Reverter
- Department of Genetics, Microbiology and Statistics University of Barcelona, Barcelona, Spain
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, 80303, USA
| | - Richard S Bennett
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA
| | - Lisa E Hensley
- Integrated Research Facility, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Frederick, MD, 21702, USA.
| | - Pardis C Sabeti
- FAS Center for Systems Biology, Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Harvard Program in Virology, Harvard Medical School, Boston, MA, 02115, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
| | - Marta Melé
- Life Sciences Department, Barcelona Supercomputing Center, Barcelona, Catalonia, 08034, Spain.
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18
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Yuan Z, Huang Y, Sadikot RT. Long Noncoding RNA Metastasis-Associated Lung Adenocarcinoma Transcript 1 Promotes HIV-1 Replication through Modulating microRNAs in Macrophages. J Virol 2023; 97:e0005323. [PMID: 37255470 PMCID: PMC10308927 DOI: 10.1128/jvi.00053-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
Macrophages can serve as a reservoir for human immunodeficiency-1 (HIV-1) virus in host cells, constituting a barrier to eradication, even in patients who are receiving antiretroviral therapy. Although many noncoding RNAs have been characterized as regulators in HIV-1/AIDS-induced immune response and pathogenesis, only a few long noncoding RNAs (lncRNAs) have demonstrated a close association with HIV-1 replication, and the molecular mechanisms remain unknown. In this study, we investigated how lncRNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), related microRNAs, and key inflammatory genes alter HIV-1 replication in macrophages. Our data show that HIV-1 infection modulates the expression of miR-155 and miR-150-5p in a time-dependent manner, which is regulated by MALAT1. MALAT1 induced suppressor of cytokine signaling 1 (SOCS1) expression by sponging miR-150-5p in HIV-1-infected macrophages and stimulated inflammatory mediators triggering receptor expressed on myeloid cells/cold inducible RNA binding protein (TREM 1/CIRP) ligand/receptor. The RNA immunoprecipitation (RIP) assay validated the direct interaction within the MALAT1/miR-150-5p/SOCS1 axis. HIV-1 infection-mediated upregulation of MALAT1, SOCS1, and HIV-1 Gag was attenuated by SN50 (an NF-кB p50 inhibitor). MALAT1 antisense oligonucleotides (ASOs) suppressed HIV-1 p24 production and HIV-1 Gag gene expression and decreased expression of miR-155 and SOCS1, as well as the production of proinflammatory cytokines by HIV-1-infected macrophages. In conclusion, HIV-1 infection induces MALAT1, which attenuates miR-150-5p expression and increases SOCS1 expression, promoting HIV-1 replication and reactivation. These data provide new insights into how MALAT1 alters the macrophage microenvironment and subsequently promotes viral replication and suggest a potential role for targeting MALAT1 as a therapeutic approach to eliminate HIV-1 reservoirs. IMPORTANCE Viral reservoirs constitute an obstacle to curing HIV-1 diseases, despite antiretroviral therapy. Macrophages serve as viral reservoirs in HIV infection by promoting long-term replication and latency. Recent studies have shown that lncRNAs can modulate virus-host interactions, but the underlying mechanisms are not fully understood. In this study, we demonstrate how lncRNA MALAT1 contributes to HIV-1 replication through modulation of the miR-150/SOCS1 axis in human macrophages. Our findings have the potential to identify new therapies for eliminating HIV-1 reservoirs in immune cells.
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Affiliation(s)
- Zhihong Yuan
- VA Nebraska Western Iowa Health Care System, Omaha, Nebraska, USA
- Division of Pulmonary, Critical Care & Sleep, Department of Internal Medicine, University of 0Nebraska Medical Center, Omaha, Nebraska, USA
| | - Yunlong Huang
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Ruxana T. Sadikot
- VA Nebraska Western Iowa Health Care System, Omaha, Nebraska, USA
- Division of Pulmonary, Critical Care & Sleep, Department of Internal Medicine, University of 0Nebraska Medical Center, Omaha, Nebraska, USA
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19
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Pan J, Zhan C, Yuan T, Gu W, Wang W, Sun Y, Chen L. Long noncoding RNA signatures in intrauterine infection/inflammation-induced lung injury: an integrative bioinformatics study. BMC Pulm Med 2023; 23:194. [PMID: 37280583 DOI: 10.1186/s12890-023-02505-5] [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: 08/08/2022] [Accepted: 05/31/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND Intrauterine infection/inflammation can result in fetal and neonatal lung injury. However, the biological mechanisms of intrauterine infection/inflammation on fetal and neonatal lung injury and development are poorly known. To date, there are no reliable biomarkers for improving intrauterine infection/inflammation-induced lung injury. METHODS An animal model of intrauterine infection/inflammation-induced lung injury was established with pregnant Sprague-Dawley rats inoculated with Escherichia coli suspension. The intrauterine inflammatory status was assessed through the histological examination of the placenta and uterus. A serial of histological examinations of the fetal and neonatal rats lung tissues were performed. The fetal and neonatal rat lung tissues were harvested for next generation sequencing at embryonic day 17 and postnatal day 3, respectively. Differentially expressed mRNAs and lncRNAs were identified by conducting high-throughput sequencing technique. The target genes of identified differentially expressed lncRNAs were analyzed. Homology analyses for important differentially expressed lncRNAs were performed. RESULTS The histopathological results showed inflammatory infiltration, impaired alveolar vesicular structure, less alveolar numbers, and thickened alveolar septa in fetal and neonatal rat lung tissues. Transmission electron micrographs revealed inflammatory cellular swelling associated with diffuse alveolar damage and less surfactant-storing lamellar bodies in alveolar epithelial type II cells. As compared with the control group, there were 432 differentially expressed lncRNAs at embryonic day 17 and 125 differentially expressed lncRNAs at postnatal day 3 in the intrauterine infection group. The distribution, expression level, and function of these lncRNAs were shown in the rat genome. LncRNA TCONS_00009865, lncRNA TCONS_00030049, lncRNA TCONS_00081686, lncRNA TCONS_00091647, lncRNA TCONS_00175309, lncRNA TCONS_00255085, lncRNA TCONS_00277162, and lncRNA TCONS_00157962 may play an important role in intrauterine infection/inflammation-induced lung injury. Fifty homologous sequences in Homo sapiens were also identified. CONCLUSIONS This study provides genome-wide identification of novel lncRNAs which may serve as potential diagnostic biomarkers and therapeutic targets for intrauterine infection/inflammation-induced lung injury.
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Affiliation(s)
- Jiarong Pan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Canyang Zhan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Tianming Yuan
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China.
| | - Weizhong Gu
- Zhejiang Key Laboratory for Diagnosis and Therapy of Neonatal Diseases, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Weiyan Wang
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Yi Sun
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
| | - Lihua Chen
- Department of Neonatology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, Zhejiang, China
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20
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Valverde AM, Naqvi RA, Naqvi AR. Global Profiling of Differentiating Macrophages Identifies Novel Functional Long Non-coding RNAs Regulating Polarization and Innate Immune Responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.09.536159. [PMID: 37066353 PMCID: PMC10104173 DOI: 10.1101/2023.04.09.536159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Macrophages (Mφ) are functionally dynamic immune cells that bridge innate and adaptive immune responses. However, the underlying epigenetic mechanisms that control the macrophage plasticity and innate immune functions are not well-elucidated. Here we performed transcriptome profiling of differentiating M1Mφ and M2Mφ and identified thousands of previously known and novel lncRNAs. We characterized three Mφ-enriched lncRNAs (LRRC75A-As1, GAPLINC and AL139099.5) with novel functions in Mφ differentiation, polarization and innate immunity. Knockdown of LRRC75A-As1, and GAPLINC downregulated Mφ differentiation markers CDw93 and CD68, and skewed macrophage polarization by decreasing M1 markers but had no significant impact on M2 markers. LRRC75A-As1, and GAPLINC RNAi in Mφ attenuated bacterial phagocytosis, antigen processing and inflammatory cytokine secretion supporting their functional role in potentiating innate immune functions. Mechanistically, lncRNA knockdown perturbed the expression of multiple cytoskeleton signaling thereby impairing Mφ migration suggesting their critical role in regulating macrophage polarity and motility. Together, our results show that Mφ acquire a unique repertoire of lncRNAs to shape differentiation, polarization and innate immune functions.
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Sabikunnahar B, Caldwell S, Varnum S, Hogan T, Cooper A, Lahue KG, Bivona JJ, Cousens PM, Symeonides M, Ballif BA, Poynter ME, Krementsov DN. Long Noncoding RNA U90926 Is Induced in Activated Macrophages, Is Protective in Endotoxic Shock, and Encodes a Novel Secreted Protein. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:807-819. [PMID: 36705532 PMCID: PMC9998366 DOI: 10.4049/jimmunol.2200215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 01/03/2023] [Indexed: 01/28/2023]
Abstract
Thousands of long noncoding RNAs are encoded in mammalian genomes, yet most remain uncharacterized. In this study, we functionally characterized a mouse long noncoding RNA named U90926. Analysis of U90926 RNA levels revealed minimal expression across multiple tissues at steady state. However, the expression of this gene was highly induced in macrophages and dendritic cells by TLR activation, in a p38 MAPK- and MyD88-dependent manner. To study the function of U90926, we generated U90926-deficient (U9-KO) mice. Surprisingly, we found minimal effects of U90926 deficiency in cultured macrophages. Given the lack of macrophage-intrinsic effect, we investigated the subcellular localization of U90926 transcript and its protein-coding potential. We found that U90926 RNA localizes to the cytosol, associates with ribosomes, and contains an open reading frame that encodes a novel glycosylated protein (termed U9-ORF), which is secreted from the cell. An in vivo model of endotoxic shock revealed that, in comparison with wild type mice, U9-KO mice exhibited increased sickness responses and mortality. Mechanistically, serum levels of IL-6 were elevated in U9-KO mice, and IL-6 neutralization improved endotoxemia outcomes in U9-KO mice. Taken together, these results suggest that U90926 expression is protective during endotoxic shock, potentially mediated by the paracrine and/or endocrine actions of the novel U9-ORF protein secreted by activated myeloid cells.
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Affiliation(s)
- Bristy Sabikunnahar
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
- Cellular, Molecular, and Biomedical Sciences Doctoral Program, University of Vermont, Burlington, VT
| | - Sydney Caldwell
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Stella Varnum
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Tyler Hogan
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Alexei Cooper
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Karolyn G Lahue
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
| | - Joseph J Bivona
- Cellular, Molecular, and Biomedical Sciences Doctoral Program, University of Vermont, Burlington, VT
- Department of Medicine, University of Vermont, Burlington, VT
| | | | - Menelaos Symeonides
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT
| | - Bryan A Ballif
- Department of Biology, University of Vermont, Burlington, VT
| | | | - Dimitry N Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT
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Li Y, Xiao W, Lin X. Long noncoding RNA MALAT1 inhibition attenuates sepsis-induced acute lung injury through modulating the miR-129-5p/PAX6/ZEB2 axis. Microbiol Immunol 2023; 67:142-153. [PMID: 36537561 DOI: 10.1111/1348-0421.13045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/05/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
This research aimed to investigate the role of the long noncoding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1)/microRNA-129-5p (miR-129-5p)/paired box gene 6 (PAX6) axis in sepsis-induced acute lung injury (ALI). MLE-12 cells and C57BL/6 mice were induced by LPS to establish lung injury in in vitro and in vivo models. Cell viability and apoptosis were measured by cell counting kit-8 assay and TUNEL (terminal deoxynucleotidyl transferase dUTP nick end labeling) staining, respectively. Levels of inflammatory cytokines in cell supernatants and bronchoalveolar lavage fluid (BALF) were detected by ELISA. Lung injury was evaluated by lung wet weight-to-dry weight ratio and hematoxylin-eosin staining. MALAT1, PAX6, and zinc finger E-box-binding homeobox 2 (ZEB2) expression was elevated and miR-129-5p expression was reduced in the serum of patients with sepsis-induced ALI, LPS-induced MLE-12 cells, and lung tissues of ALI mice. MALAT1 interference delayed the LPS-induced cell proliferation decrease, apoptosis increase, and inflammatory factor increase. miR-129-5p inhibition could reverse the delaying effect of MALAT1 interference on LPS-induced lung cell injury. PAX6 overexpression (oe) reversed the inhibitory effect of miR-129-5p oe on LPS-induced lung cell injury. Downregulating MALAT1 reduced pulmonary edema, inflammatory cytokine levels, lung injury, and apoptosis in ALI mice. Moreover, miR-129-5p suppression or PAX6 oe reversed the delaying effect of MALAT1 interference on sepsis-induced ALI. MALAT1 aggravates sepsis-induced ALI via the miR-129-5p/PAX6/ZEB2 axis.
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Affiliation(s)
- Ying Li
- Department of Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Wenbiao Xiao
- Department of Critical Care Medicine, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
| | - Xiao Lin
- Department of Critical Care Medicine, The First Affiliated Hospital, Fujian Medical University, Fujian, Fuzhou, China
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Ahmad I, Naqvi RA, Valverde A, Naqvi AR. LncRNA MALAT1/microRNA-30b axis regulate macrophage polarization and function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526668. [PMID: 36778373 PMCID: PMC9915644 DOI: 10.1101/2023.02.01.526668] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Introduction Macrophages (Mφ) can polarize towards the proinflammatory M1 or proresolving M2 phenotype to control diverse biological processes such as inflammation, and tissue regeneration. Noncoding RNAs play critical roles in numerous biological pathways; however, their functional interaction in the regulation of Mφ polarization and immune responses remain unclear. Objectives To examine relationship between lncRNA (MALAT1) and microRNA (miR-30b) in shaping macrophage polarization and immune functions. Methods Expression of MALAT1 and miR-30b was examined in differentiating M1/M2 Mφ, human and murine inflamed gingival biopsies by RT-qPCR. MALAT1 and miR-30b direct interaction was examined by dual luciferase assays. Impact of MALAT1 knockdown and miR-30b overexpression was examined on macrophage polarization markers, bacterial phagocytosis, antigen uptake/processing and cytokine profiles. Results MALAT1 expression displays a time-dependent induction during Mφ differentiation and, upon challenge with TLR4 agonist ( E. coli LPS). Knockdown of MALAT1 enhanced the expression of M2Mφ markers without affecting the M1Mφ markers, suggesting that MALAT1 favors the M1 phenotype by suppressing M2 polarization. MALAT1 knockdown Mφ exhibit reduced antigen uptake and processing, bacterial phagocytosis, and bactericidal activity, strongly supporting its critical role in regulating innate immune functions. Consistent with this, MALAT1 knockdown showed impaired cytokine secretion upon challenge with LPS. Importantly, MALAT1 exhibit an antagonistic expression pattern with all five members of the miR-30 family during M2Mφ differentiation. Dual-luciferase assays validated a novel sequence on MALAT1 that interacts with miR-30b, a microRNA that promotes the M2 phenotype. Phagocytosis and antigen processing assays unequivocally demonstrated that MALAT1 and miR-30b are functionally antagonistic. In human subjects with periodontal disease and murine model of ligature-induced periodontitis, we observed higher levels of MALAT1, and downregulation of miR-30b that correlates with higher M1Mφ markers expression in gingival tissues suggesting a pro-inflammatory function of MALAT1. Conclusion MALAT1/miR-30b antagonistic interaction shapes Mφ polarization in vitro and in inflamed gingival biopsies.
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Nuclear SPHK2/S1P induces oxidative stress and NLRP3 inflammasome activation via promoting p53 acetylation in lipopolysaccharide-induced acute lung injury. Cell Death Dis 2023; 9:12. [PMID: 36653338 PMCID: PMC9847446 DOI: 10.1038/s41420-023-01320-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 01/03/2023] [Accepted: 01/10/2023] [Indexed: 01/19/2023]
Abstract
A bulk of evidence identified that macrophages, including resident alveolar macrophages and recruited macrophages from the blood, played an important role in the pathogenesis of acute respiratory distress syndrome (ARDS). However, the molecular mechanisms of macrophages-induced acute lung injury (ALI) by facilitating oxidative stress and inflammatory responses remain unclear. Herein, we noticed that the levels of mitochondrial reactive oxygen species (mtROS), SPHK2 and activated NLRP3 inflammasome were higher in peripheral blood mononuclear cells (PBMCs) of ARDS patients than that in healthy volunteers. Similar observations were recapitulated in LPS-treated RAW264.7 and THP-1 cells. After exposure to LPS, the SPHK2 enzymatic activity, NLRP3 inflammasome activation and mtROS were significantly upregulated in macrophages. Moreover, knockdown SPHK2 via shRNA or inhibition SPHK2 could prominently decrease LPS-induced M1 macrophage polarization, oxidative stress and NLRP3 inflammasome activation. Further study indicated that upregulated SPHK2 could increase nuclear sphingosine-1-phosphate (S1P) levels and then restrict the enzyme activity of HDACs to facilitate p53 acetylation. Acetylation of p53 reinforced its binding to the specific region of the NLRP3 promoter and drove expression of NLRP3. In the in vivo experiments, it was also observed that treating with Opaganib (ABC294640), a specific SPHK2 inhibitor, could observably alleviate LPS-induced ALI, evidencing by lowered infiltration of inflammatory cells, increased M2 macrophages polarization and reduced oxidative damage in lung tissues. Besides, SPHK2 inhibition can also decrease the accumulation of acetylated p53 protein and the activation of NLRP3 inflammasome. Taken together, our results demonstrated for the first time that nuclear S1P can regulate the acetylation levels of non-histone protein through affecting HDACs enzyme activities, linking them to oxidative stress and inflammation in response to environmental signals. These data provide a theoretical basis that SPHK2 may be an effective therapeutic target of ARDS.
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Qiao X, Ding Y, Wu D, Zhang A, Yin Y, Wang Q, Wang W, Kang J. The roles of long noncoding RNA-mediated macrophage polarization in respiratory diseases. Front Immunol 2023; 13:1110774. [PMID: 36685535 PMCID: PMC9849253 DOI: 10.3389/fimmu.2022.1110774] [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: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Macrophages play an essential role in maintaining the normal function of the innate and adaptive immune responses during host defence. Macrophages acquire diverse functional phenotypes in response to various microenvironmental stimuli, and are mainly classified into classically activated macrophages (M1) and alternatively activated macrophages (M2). Macrophage polarization participates in the inflammatory, fibrotic, and oncogenic processes of diverse respiratory diseases by changing phenotype and function. In recent decades, with the advent of broad-range profiling methods such as microarrays and next-generation sequencing, the discovery of RNA transcripts that do not encode proteins termed "noncoding RNAs (ncRNAs)" has become more easily accessible. As one major member of the regulatory ncRNA family, long noncoding RNAs (lncRNAs, transcripts >200 nucleotides) participate in multiple pathophysiological processes, including cell proliferation, differentiation, and apoptosis, and vary with different stimulants and cell types. Emerging evidence suggests that lncRNAs account for the regulation of macrophage polarization and subsequent effects on respiratory diseases. In this review, we summarize the current published literature from the PubMed database concerning lncRNAs relevant to macrophage polarization and the underlying molecular mechanisms during the occurrence and development of respiratory diseases. These differentially expressed lncRNAs are expected to be biomarkers and targets for the therapeutic regulation of macrophage polarization during disease development.
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Zablowsky N, Farack L, Rofall S, Kramer J, Meyer H, Nguyen D, Ulrich AKC, Bader B, Steigemann P. High Throughput FISH Screening Identifies Small Molecules That Modulate Oncogenic lncRNA MALAT1 via GSK3B and hnRNPs. Noncoding RNA 2023; 9:ncrna9010002. [PMID: 36649031 PMCID: PMC9844399 DOI: 10.3390/ncrna9010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Traditionally, small molecule-based drug discovery has mainly focused on proteins as the drug target. Opening RNA as an additional target space for small molecules offers the possibility to therapeutically modulate disease-driving non-coding RNA targets as well as mRNA of otherwise undruggable protein targets. MALAT1 is a highly conserved long-noncoding RNA whose overexpression correlates with poor overall patient survival in some cancers. We report here a fluorescence in-situ hybridization-based high-content imaging screen to identify small molecules that modulate the oncogenic lncRNA MALAT1 in a cellular setting. From a library of FDA approved drugs and known bioactive molecules, we identified two compounds, including Niclosamide, an FDA-approved drug, that lead to a rapid decrease of MALAT1 nuclear levels with good potency. Mode-of-action studies suggest a novel cellular regulatory pathway that impacts MALAT1 lncRNA nuclear levels by GSK3B activation and the involvement of the RNA modulating family of heterogenous nuclear ribonucleoproteins (hnRNPs). This study is the basis for the identification of novel targets that lead to a reduction of the oncogenic lncRNA MALAT1 in a cancer setting.
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Kumar D, Sahoo SS, Chauss D, Kazemian M, Afzali B. Non-coding RNAs in immunoregulation and autoimmunity: Technological advances and critical limitations. J Autoimmun 2023; 134:102982. [PMID: 36592512 PMCID: PMC9908861 DOI: 10.1016/j.jaut.2022.102982] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 01/02/2023]
Abstract
Immune cell function is critically dependent on precise control over transcriptional output from the genome. In this respect, integration of environmental signals that regulate gene expression, specifically by transcription factors, enhancer DNA elements, genome topography and non-coding RNAs (ncRNAs), are key components. The first three have been extensively investigated. Even though non-coding RNAs represent the vast majority of cellular RNA species, this class of RNA remains historically understudied. This is partly because of a lag in technological and bioinformatic innovations specifically capable of identifying and accurately measuring their expression. Nevertheless, recent progress in this domain has enabled a profusion of publications identifying novel sub-types of ncRNAs and studies directly addressing the function of ncRNAs in human health and disease. Many ncRNAs, including circular and enhancer RNAs, have now been demonstrated to play key functions in the regulation of immune cells and to show associations with immune-mediated diseases. Some ncRNAs may function as biomarkers of disease, aiding in diagnostics and in estimating response to treatment, while others may play a direct role in the pathogenesis of disease. Importantly, some are relatively stable and are amenable to therapeutic targeting, for example through gene therapy. Here, we provide an overview of ncRNAs and review technological advances that enable their study and hold substantial promise for the future. We provide context-specific examples by examining the associations of ncRNAs with four prototypical human autoimmune diseases, specifically rheumatoid arthritis, psoriasis, inflammatory bowel disease and multiple sclerosis. We anticipate that the utility and mechanistic roles of these ncRNAs in autoimmunity will be further elucidated in the near future.
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Affiliation(s)
- Dhaneshwar Kumar
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Subhransu Sekhar Sahoo
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Daniel Chauss
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA
| | - Majid Kazemian
- Departments of Biochemistry and Computer Science, Purdue University, West Lafayette, IN, USA
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, MD, USA.
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Wu W, Wang S, Zhang L, Mao B, Wang B, Wang X, Zhao D, Zhao P, Mou Y, Yan P. Mechanistic studies of MALAT1 in respiratory diseases. Front Mol Biosci 2022; 9:1031861. [PMID: 36419933 PMCID: PMC9676952 DOI: 10.3389/fmolb.2022.1031861] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/24/2022] [Indexed: 10/11/2023] Open
Abstract
Background: The incidence of respiratory diseases and the respiratory disease mortality rate have increased in recent years. Recent studies have shown that long non-coding RNA (lncRNA) MALAT1 is involved in various respiratory diseases. In vascular endothelial and cancer cells, MALAT1 expression triggers various changes such as proinflammatory cytokine expression, cancer cell proliferation and metastasis, and increased endothelial cell permeability. Methods: In this review, we performed a relative concentration index (RCI) analysis of the lncRNA database to assess differences in MALAT1 expression in different cell lines and at different locations in the same cell, and summarize the molecular mechanisms of MALAT1 in the pathophysiology of respiratory diseases and its potential therapeutic application in these conditions. Results: MALAT1 plays an important regulatory role in lncRNA with a wide range of effects in respiratory diseases. The available evidence shows that MALAT1 plays an important role in the regulation of multiple respiratory diseases. Conclusion: MALAT1 is an important regulatory biomarker for respiratory disease. Targeting the regulation MALAT1 could have important applications for the future treatment of respiratory diseases.
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Affiliation(s)
- Wenzheng Wu
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Shihao Wang
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Lu Zhang
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Beibei Mao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Bin Wang
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaoxu Wang
- The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Dongsheng Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Pan Zhao
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yunying Mou
- College of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Peizheng Yan
- College of Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, China
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Zhang J, Wang H, Chen H, Li H, Xu P, Liu B, Zhang Q, Lv C, Song X. ATF3 -activated accelerating effect of LINC00941/lncIAPF on fibroblast-to-myofibroblast differentiation by blocking autophagy depending on ELAVL1/HuR in pulmonary fibrosis. Autophagy 2022; 18:2636-2655. [PMID: 35427207 PMCID: PMC9629064 DOI: 10.1080/15548627.2022.2046448] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is characterized by lung scarring and has no effective treatment. Fibroblast-to-myofibroblast differentiation and myofibroblast proliferation and migration are major clinical manifestations of this disease; hence, blocking these processes is a practical treatment strategy. Here, highly upregulated LINC00941/lncIAPF was found to accelerate pulmonary fibrosis by promoting fibroblast-to-myofibroblast differentiation and myofibroblast proliferation and migration. Assay for transposase-accessible chromatin using sequencing and chromatin immunoprecipitation experiments elucidated that histone 3 lysine 27 acetylation (H3K27ac) activated the chromosome region opening in the LINC00941 promoter. As a consequence, the transcription factor ATF3 (activating transcription factor 3) bound to this region, and LINC00941 transcription was enhanced. RNA affinity isolation, RNA immunoprecipitation (RIP), RNase-RIP, half-life analysis, and ubiquitination experiments unveiled that LINC00941 formed a RNA-protein complex with ELAVL1/HuR (ELAV like RNA binding protein 1) to exert its pro-fibrotic function. Dual-fluorescence mRFP-GFP-MAP1LC3/LC3 (microtubule associated protein 1 light chain 3) adenovirus monitoring technology, human autophagy RT2 profiler PCR array, and autophagic flux revealed that the LINC00941-ELAVL1 axis inhibited autophagosome fusion with a lysosome. ELAVL1 RIP-seq, RIP-PCR, mRNA stability, and rescue experiments showed that the LINC00941-ELAVL1 complex inhibited autophagy by controlling the stability of the target genes EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit), STAT1 (signal transducer and activators of transcription 1) and FOXK1 (forkhead box K1). Finally, the therapeutic effect of LINC00941 was confirmed in a mouse model and patients with IPF. This work provides a therapeutic target and a new effective therapeutic strategy related to autophagy for IPF.Abbreviations: ACTA2/a-SMA: actin alpha 2, smooth muscle; ATF3: activating transcription factor 3; ATG: autophagy related; Baf-A1: bafilomycin A1; BLM: bleomycin; CDKN: cyclin dependent kinase inhibitor; CLN3: CLN3 lysosomal/endosomal transmembrane protein, battenin; COL1A: collagen type I alpha; COL3A: collagen type III alpha; CXCR4: C-X-C motif chemokine receptor 4; DRAM2: DNA damage regulated autophagy modulator 2; ELAVL1/HuR: ELAV like RNA binding protein 1; EZH2: enhancer of zeste 2 polycomb repressive complex 2 subunit; FADD: Fas associated via death domain; FAP/FAPα: fibroblast activation protein alpha; FOXK1: forkhead box K1; FVC: forced vital capacity; GABARAP: GABA type A receptor-associated protein; GABARAPL2: GABA type A receptor associated protein like 2; IGF1: insulin like growth factor 1; IPF: idiopathic pulmonary fibrosis; LAMP: lysosomal associated membrane protein; lncRNA: long noncoding RNA; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NPC1: NPC intracellular cholesterol transporter 1; RGS: regulator of G protein signaling; RPLP0: ribosomal protein lateral stalk subunit P0; ROC: receiver operating characteristic; S100A4: S100 calcium binding protein A4; SQSTM1/p62: sequestosome 1; STAT1: signal transducers and activators of transcription 1; TGFB1/TGF-β1: transforming growth factor beta 1; TNF: tumor necrosis factor; UIP: usual interstitial pneumonia; ULK1: unc-51 like autophagy activating kinase 1; VIM: vimentin.
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Affiliation(s)
- Jinjin Zhang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China,Medical Research Center, Binzhou Medical University, Yantai, Shandong, China
| | - Haixia Wang
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China,Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Hongbin Chen
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Hongbo Li
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Pan Xu
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Bo Liu
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Qian Zhang
- Department of Pathology, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China
| | - Changjun Lv
- Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China,Changjun Lv Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University
| | - Xiaodong Song
- Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai, Shandong, China,Department of Respiratory and Critical Care Medicine, Binzhou Medical University Hospital, Binzhou Medical University, Binzhou, Province, China,CONTACT Xiaodong Song Department of Cellular and Genetic Medicine, School of Pharmaceutical Sciences, Binzhou Medical University, Yantai264003, Shandong, China
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Lai X, Zhong J, Zhang A, Zhang B, Zhu T, Liao R. Focus on long non-coding RNA MALAT1: Insights into acute and chronic lung diseases. Front Genet 2022; 13:1003964. [PMID: 36186445 PMCID: PMC9523402 DOI: 10.3389/fgene.2022.1003964] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/06/2022] [Indexed: 12/12/2022] Open
Abstract
Acute lung injury (ALI) is a pulmonary illness with a high burden of morbidity and mortality around the world. Chronic lung diseases also represent life-threatening situations. Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a type of long non-coding RNA (lncRNA) and is highly abundant in lung tissues. MALAT1 can function as a competitive endogenous RNA (ceRNA) to impair the microRNA (miRNA) inhibition on targeted messenger RNAs (mRNAs). In this review, we summarized that MALAT1 mainly participates in pulmonary cell biology and lung inflammation. Therefore, MALAT1 can positively or negatively regulate ALI and chronic lung diseases (e.g., chronic obstructive pulmonary disease (COPD), bronchopulmonary dysplasia (BPD), pulmonary fibrosis, asthma, and pulmonary hypertension (PH)). Besides, we also found a MALAT1-miRNA-mRNA ceRNA regulatory network in acute and chronic lung diseases. Through this review, we hope to cast light on the regulatory mechanisms of MALAT1 in ALI and chronic lung disease and provide a promising approach for lung disease treatment.
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Affiliation(s)
- Xingning Lai
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdou, Sichuan, China
- Research Unit for Perioperative Stress Assessment and Clinical Decision, Chinese Academy of Medical Sciences (2018RU012), West China Hospital, Sichuan University, Chengdou, Sichuan, China
| | - Jie Zhong
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdou, Sichuan, China
- Research Unit for Perioperative Stress Assessment and Clinical Decision, Chinese Academy of Medical Sciences (2018RU012), West China Hospital, Sichuan University, Chengdou, Sichuan, China
| | - Aihua Zhang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdou, Sichuan, China
- Research Unit for Perioperative Stress Assessment and Clinical Decision, Chinese Academy of Medical Sciences (2018RU012), West China Hospital, Sichuan University, Chengdou, Sichuan, China
| | - Boyi Zhang
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdou, Sichuan, China
- Research Unit for Perioperative Stress Assessment and Clinical Decision, Chinese Academy of Medical Sciences (2018RU012), West China Hospital, Sichuan University, Chengdou, Sichuan, China
| | - Tao Zhu
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdou, Sichuan, China
- Research Unit for Perioperative Stress Assessment and Clinical Decision, Chinese Academy of Medical Sciences (2018RU012), West China Hospital, Sichuan University, Chengdou, Sichuan, China
- *Correspondence: Tao Zhu, ; Ren Liao,
| | - Ren Liao
- Department of Anesthesiology, West China Hospital, Sichuan University, Chengdou, Sichuan, China
- Research Unit for Perioperative Stress Assessment and Clinical Decision, Chinese Academy of Medical Sciences (2018RU012), West China Hospital, Sichuan University, Chengdou, Sichuan, China
- *Correspondence: Tao Zhu, ; Ren Liao,
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31
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Non-coding RNA in idiopathic interstitial pneumonia and Covid-19 pulmonary fibrosis. Mol Biol Rep 2022; 49:11535-11546. [PMID: 36097114 PMCID: PMC9467421 DOI: 10.1007/s11033-022-07820-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/20/2022] [Accepted: 07/24/2022] [Indexed: 12/02/2022]
Abstract
Pulmonary fibrosis is the key feature of majority of idiopathic interstitial pneumonias (IIPs) as well as many patients with post-COVID-19. The pathogenesis of pulmonary fibrosis is a complex molecular process that involves myriad of cells, proteins, genes, and regulatory elements. The non-coding RNA mainly miRNA, circRNA, and lncRNA are among the key regulators of many protein coding genes and pathways that are involved in pulmonary fibrosis. Identification and molecular mechanisms, by which these non-coding RNA molecules work, are crucial to understand the molecular basis of the disease. Additionally, elucidation of molecular mechanism could also help in deciphering a potential diagnostic/prognostic marker as well as therapeutic targets for IIPs and post-COVID-19 pulmonary fibrosis. In this review, we have provided the latest findings and discussed the role of these regulatory elements in the pathogenesis of pulmonary fibrosis associated with Idiopathic Interstitial Pneumonia and Covid-19.
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32
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Devadoss D, Acharya A, Manevski M, Houserova D, Cioffi MD, Pandey K, Nair M, Chapagain P, Mirsaeidi M, Borchert GM, Byrareddy SN, Chand HS. Immunomodulatory LncRNA on antisense strand of ICAM-1 augments SARS-CoV-2 infection-associated airway mucoinflammatory phenotype. iScience 2022; 25:104685. [PMID: 35789750 PMCID: PMC9242679 DOI: 10.1016/j.isci.2022.104685] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/25/2022] [Accepted: 06/23/2022] [Indexed: 01/20/2023] Open
Abstract
Noncoding RNAs are important regulators of mucoinflammatory response, but little is known about the contribution of airway long noncoding RNAs (lncRNAs) in COVID-19. RNA-seq analysis showed a more than 4-fold increased expression of IL-6, ICAM-1, CXCL-8, and SCGB1A1 inflammatory factors; MUC5AC and MUC5B mucins; and SPDEF, FOXA3, and FOXJ1 transcription factors in COVID-19 patient nasal samples compared with uninfected controls. A lncRNA on antisense strand to ICAM-1 or LASI was induced 2-fold in COVID-19 patients, and its expression was directly correlated with viral loads. A SARS-CoV-2-infected 3D-airway model largely recapitulated these clinical findings. RNA microscopy and molecular modeling indicated a possible interaction between viral RNA and LASI lncRNA. Notably, blocking LASI lncRNA reduced the SARS-CoV-2 replication and suppressed MUC5AC mucin levels and associated inflammation, and select LASI-dependent miRNAs (e.g., let-7b-5p and miR-200a-5p) were implicated. Thus, LASI lncRNA represents an essential facilitator of SARS-CoV-2 infection and associated airway mucoinflammatory response.
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Affiliation(s)
- Dinesh Devadoss
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Marko Manevski
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Dominika Houserova
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Michael D. Cioffi
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Madhavan Nair
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Mehdi Mirsaeidi
- Miller School of Medicine, Division of Pulmonary, Critical Care, and Sleep Medicine, University of Miami, Miami, FL 33136, USA
| | - Glen M. Borchert
- Department of Pharmacology, University of South Alabama, Mobile, AL 36688, USA
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hitendra S. Chand
- Department of Immunology and Nano-Medicine, Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
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33
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Zhong Y, Ashley CL, Steain M, Ataide SF. Assessing the suitability of long non-coding RNAs as therapeutic targets and biomarkers in SARS-CoV-2 infection. Front Mol Biosci 2022; 9:975322. [PMID: 36052163 PMCID: PMC9424846 DOI: 10.3389/fmolb.2022.975322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are RNA transcripts that are over 200 nucleotides and rarely encode proteins or peptides. They regulate gene expression and protein activities and are heavily involved in many cellular processes such as cytokine secretion in respond to viral infection. In severe COVID-19 cases, hyperactivation of the immune system may cause an abnormally sharp increase in pro-inflammatory cytokines, known as cytokine release syndrome (CRS), which leads to severe tissue damage or even organ failure, raising COVID-19 mortality rate. In this review, we assessed the correlation between lncRNAs expression and cytokine release syndrome by comparing lncRNA profiles between COVID-19 patients and health controls, as well as between severe and non-severe cases. We also discussed the role of lncRNAs in CRS contributors and showed that the lncRNA profiles display consistency with patients’ clinic symptoms, thus suggesting the potential of lncRNAs as drug targets or biomarkers in COVID-19 treatment.
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Affiliation(s)
- Yichen Zhong
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Caroline L. Ashley
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Megan Steain
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Sandro Fernandes Ataide
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
- *Correspondence: Sandro Fernandes Ataide,
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Cui H, Xie N, Banerjee S, Dey T, Liu RM, Antony VB, Sanders YY, Adams TS, Gomez JL, Thannickal VJ, Kaminski N, Liu G. CD38 Mediates Lung Fibrosis by Promoting Alveolar Epithelial Cell Aging. Am J Respir Crit Care Med 2022; 206:459-475. [PMID: 35687485 DOI: 10.1164/rccm.202109-2151oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 06/06/2022] [Indexed: 01/10/2023] Open
Abstract
Rationale: A prevailing paradigm recognizes idiopathic pulmonary fibrosis (IPF) originating from various alveolar epithelial cell (AEC) injuries, and there is a growing appreciation of AEC aging as a key driver of the pathogenesis. Despite this progress, it is incompletely understood what main factor(s) contribute to the worsened alveolar epithelial aging in lung fibrosis. It remains a challenge how to dampen AEC aging and thereby mitigate the disease progression. Objectives: To determine the role of AEC CD38 (cluster of differentiation 38) in promoting cellular aging and lung fibrosis. Methods: We used single-cell RNA sequencing, real-time PCR, flow cytometry, and Western blotting. Measurements and Main Results: We discovered a pivotal role of CD38, a cardinal nicotinamide adenine dinucleotide (NAD) hydrolase, in AEC aging and its promotion of lung fibrosis. We found increased CD38 expression in IPF lungs that inversely correlated with the lung functions of patients. CD38 was primarily located in the AECs of human lung parenchyma and was markedly induced in IPF AECs. Similarly, CD38 expression was elevated in the AECs of fibrotic lungs of young mice and further augmented in those of old mice, which was in accordance with a worsened AEC aging phenotype and an aggravated lung fibrosis in the old animals. Mechanistically, we found that CD38 elevation downregulated intracellular NAD, which likely led to the aging promoting impairment of the NAD-dependent cellular and molecular activities. Furthermore, we demonstrated that genetic and pharmacological inactivation of CD38 improved these NAD dependent events and ameliorated bleomycin-induced lung fibrosis. Conclusions: Our study suggests targeting alveolar CD38 as a novel and effective therapeutic strategy to treat this pathology.
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Affiliation(s)
- Huachun Cui
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Na Xie
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Sami Banerjee
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tapan Dey
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rui-Ming Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Veena B Antony
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yan Y Sanders
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Taylor S Adams
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Jose L Gomez
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Victor J Thannickal
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana
| | - Naftali Kaminski
- Pulmonary, Critical Care and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut; and
| | - Gang Liu
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
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35
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Hu L, Liu S, Peng Y, Ge R, Su R, Senevirathne C, Harada BT, Dai Q, Wei J, Zhang L, Hao Z, Luo L, Wang H, Wang Y, Luo M, Chen M, Chen J, He C. m 6A RNA modifications are measured at single-base resolution across the mammalian transcriptome. Nat Biotechnol 2022; 40:1210-1219. [PMID: 35288668 PMCID: PMC9378555 DOI: 10.1038/s41587-022-01243-z] [Citation(s) in RCA: 119] [Impact Index Per Article: 59.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 01/28/2022] [Indexed: 01/28/2023]
Abstract
Functional studies of the RNA N6-methyladenosine (m6A) modification have been limited by an inability to map individual m6A-modified sites in whole transcriptomes. To enable such studies, here, we introduce m6A-selective allyl chemical labeling and sequencing (m6A-SAC-seq), a method for quantitative, whole-transcriptome mapping of m6A at single-nucleotide resolution. The method requires only ~30 ng of poly(A) or rRNA-depleted RNA. We mapped m6A modification stoichiometries in RNA from cell lines and during in vitro monocytopoiesis from human hematopoietic stem and progenitor cells (HSPCs). We identified numerous cell-state-specific m6A sites whose methylation status was highly dynamic during cell differentiation. We observed changes of m6A stoichiometry as well as expression levels of transcripts encoding or regulated by key transcriptional factors (TFs) critical for HSPC differentiation. m6A-SAC-seq is a quantitative method to dissect the dynamics and functional roles of m6A sites in diverse biological processes using limited input RNA.
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Affiliation(s)
- Lulu Hu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
- Fudan University Institutes of Biomedical Sciences, Shanghai Cancer Center, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Shanghai Medical College of Fudan University, Shanghai, China.
| | - Shun Liu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Yong Peng
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ruiqi Ge
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - Chamara Senevirathne
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bryan T Harada
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Qing Dai
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Jiangbo Wei
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Lisheng Zhang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Ziyang Hao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Liangzhi Luo
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Huanyu Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Yuru Wang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Minkui Luo
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Program of Pharmacology, Weill Cornell Medical College of Cornell University, New York, NY, USA
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, USA.
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA, USA.
| | - Chuan He
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
- Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA.
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36
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen PR. Photocatalytic Chemical Crosslinking for Profiling RNA–Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022; 61:e202202008. [DOI: 10.1002/anie.202202008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Huixin Luo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines Institute of Materia Medica Chinese Academy of Medical Sciences and Peking UnionMedical College Beijing 100050 China
| | - Wei Tang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Hongyu Liu
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Xiangmei Zeng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - William Shu Ching Ngai
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Rui Gao
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Heyun Li
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Ran Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Huangtao Zheng
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Jianting Guo
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Fangfei Qin
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Gang Wang
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Kexin Li
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
| | - Xinyuan Fan
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
| | - Peng Zou
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
- PKU-IDG/McGovern Institute for Brain Research Beijing 100871 China
- Chinese Institute for Brain Research (CIBR) Beijing 102206 China
| | - Peng R. Chen
- College of Chemistry and Molecular Engineering Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education Peking University Beijing 100871 China
- Peking-Tsinghua Center for Life Sciences Beijing 100871 China
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37
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Chen S, Xia J, Zhang Y, Zhan Q. IL35 attenuated LPS-induced acute lung injury by regulating macrophage polarization. Mol Biol Rep 2022; 49:5811-5820. [PMID: 35748972 PMCID: PMC9244303 DOI: 10.1007/s11033-022-07293-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 01/27/2022] [Accepted: 02/23/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Interleukin 35 (IL35) has been reported to play a role in acute lung injury (ALI); however, the current results regarding the relationship between IL35 and ALI are inconsistent. Therefore, we aimed to further determine the function of IL35 in ALI in mice and the potential mechanism in this paper. MATERIALS AND METHODS Hematoxylin-eosin (HE) staining and Masson staining were used to evaluate lung injury in mice. Immunohistochemical staining was used to evaluate the expression of IL35 p35, TLR4 and MD2 and the Bax/Bcl2 and p-P65/P65 ratios. The expression levels of IL35 EBi3, CD68, CD206 and MPO were assessed by immunofluorescence staining. RT-PCR was used to examine the expression levels of IL1β and IL6. Terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining was performed to detect apoptotic cells. RESULTS Overexpression of IL35 alleviated LPS-induced ALI in mice. IL35 overexpression decreased the expression of CD68 and increased the expression of CD206 in mice with ALI. Furthermore, upregulation of IL35 expression obviously reduced the expression of MPO, IL1β and IL6 in the lung tissues of mice with ALI. Mechanistically, IL35 suppressed the TLR4/NFκB-P65 pathway, leading to the promotion of the M1 to M2 macrophage transition and alleviation of inflammation in mice with ALI. CONCLUSIONS IL35 relieved LPS-induced inflammation and ALI in mice by regulating M1/M2 macrophage polarization and inhibiting the activation of the TLR4/NFκB-P65 pathway.
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Affiliation(s)
- Shengsong Chen
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, No 9, Dongdan Santao, Dongcheng District, 100730, Beijing, P. R. China
- National Center for Respiratory Medicine, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- National Clinical Research Center for Respiratory Diseases, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
| | - Jingen Xia
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- National Center for Respiratory Medicine, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- National Clinical Research Center for Respiratory Diseases, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
- WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China
| | - Yi Zhang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- National Center for Respiratory Medicine, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- National Clinical Research Center for Respiratory Diseases, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
| | - Qingyuan Zhan
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, China-Japan Friendship Hospital, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, No 9, Dongdan Santao, Dongcheng District, 100730, Beijing, P. R. China.
- National Center for Respiratory Medicine, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- National Clinical Research Center for Respiratory Diseases, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
- WHO Collaborating Centre for Tobacco Cessation and Respiratory Diseases Prevention, No 2, East Yinghua Road, Chaoyang District, 100029, Beijing, P. R. China.
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38
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Shen QY, Wang D, Xu HY, Wei CS, Xiao XY, Liu J, Shen YJ, Fang L, Feng LJ, Shen YX. Mesencephalic astrocyte-derived neurotrophic factor attenuates acute lung injury via inhibiting macrophages' activation. Biomed Pharmacother 2022; 150:112943. [PMID: 35405395 DOI: 10.1016/j.biopha.2022.112943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022] Open
Abstract
Acute lung injury (ALI) is an urgent respiratory disease without effective treatment. Mesencephalic astrocyte-derived neurotrophic factor (MANF)has been demonstrated to play a suppressive role in some inflammatory conditions. However, the effect of MANF on ALI has not yet been reported. In this study, we collected bronchoalveolar lavage fluid (BALF) from the patients with or without pulmonary inflammation, and used lipopolysaccharide (LPS) to induce mice ALI model. Mono-macrophage-specific MANF knockout (MKO) mice were constructed and recombinant human MANF protein was used to ALI mice. We found that the endogenous MANF protein in both human BALF and mice lung tissues was increased in inflammatory conditions. MANF level in the macrophages of inflammatory lung was higher than that in normal controls in both human and mice. MANF deficiency in macrophages induced lung inflammation and aggravated LPS-induced lung injury. MANF lowered LPS-induced lung injury, inhibited macrophage polarization to M1 functional type. Meanwhile, MANF inhibited-LPS induced activation of NF-κB signal pathway by down regulating phosphorylated p65in lung tissue and macrophages. These results indicate that MANF acts as a suppressor in ALI via negatively regulating NF-κB activation and macrophages polarization, which may be a novel potential target and shed light on ALI therapy.
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Affiliation(s)
- Qi-Ying Shen
- Department of Anesthesiology, the First Affiliated Hospital of Anhui Medical University, Hefei 230022, China; Department of Anesthesiology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei 230000, China; Key Laboratory of Anesthesiology and Perioperative Medicine of Anhui Higher Education Institutes, Anhui Medical University, Hefei 230022, China
| | - Dong Wang
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Han-Yang Xu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China; Biopharmaceutical Research Institute, Anhui Medical University, Hefei 230032,China
| | - Chuan-Sheng Wei
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China; Biopharmaceutical Research Institute, Anhui Medical University, Hefei 230032,China
| | - Xue-Ying Xiao
- Department of Anesthesiology, the Fourth Affiliated Hospital of Anhui Medical University, Hefei 230000, China
| | - Jun Liu
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China; Biopharmaceutical Research Institute, Anhui Medical University, Hefei 230032,China
| | - Yu-Jun Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China; Biopharmaceutical Research Institute, Anhui Medical University, Hefei 230032,China
| | - Lei Fang
- Department of Geriatric Respiratory and Critical Care, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Li-Jie Feng
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China; Biopharmaceutical Research Institute, Anhui Medical University, Hefei 230032,China
| | - Yu-Xian Shen
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China; Biopharmaceutical Research Institute, Anhui Medical University, Hefei 230032,China.
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Hu C, Li J, Tan Y, Liu Y, Bai C, Gao J, Zhao S, Yao M, Lu X, Qiu L, Xing L. Tanreqing Injection Attenuates Macrophage Activation and the Inflammatory Response via the lncRNA-SNHG1/HMGB1 Axis in Lipopolysaccharide-Induced Acute Lung Injury. Front Immunol 2022; 13:820718. [PMID: 35547731 PMCID: PMC9084914 DOI: 10.3389/fimmu.2022.820718] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/29/2022] [Indexed: 11/15/2022] Open
Abstract
The etiology of acute lung injury (ALI) is not clear, and the treatment of ALI presents a great challenge. This study aimed to investigate the pathogenesis and potential therapeutic targets of ALI and to define the target gene of Tanreqing (TRQ), which is a traditional Chinese medicine formula composed of five medicines, scutellaria baicalensis, bear bile powder, goat horn powder, honeysuckle and forsythia. Macrophage activation plays a critical role in many pathophysiological processes, such as inflammation. Although the regulation of macrophage activation has been extensively investigated, there is little knowledge of the role of long noncoding RNAs (lncRNAs) in this process. In this study, we found that lncRNA-SNHG1 expression is distinctly regulated in differently activated macrophages in that it is upregulated in LPS. LncRNA-SNHG1 knockdown attenuates LPS-induced M1 macrophage activation. The SNHG1 promoter was bound by NF-κB subunit p65, indicative of SNHG1 being a direct transcriptional target of LPS-induced NF-κB activation. SNHG1 acts as a proinflammatory driver that leads to the production of inflammatory cytokines and the activation of macrophages and cytokine storms by physically interacting with high-mobility group box 1 (HMGB1) in ALI. TRQ inhibited NF-κB signaling activation and binding of NF-κB to the SNHG1 promoter. In conclusion, this study defined TRQ target genes, which can be further elucidated as mechanism(s) of TRQ action, and provides insight into the molecular pathogenesis of ALI. The lncRNA-SNHG1/HMGB1 axis is an ideal therapeutic for ALI treatment.
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Affiliation(s)
- Chunling Hu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Junlu Li
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingshuai Tan
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yang Liu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chen Bai
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, China
| | - Jing Gao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shilong Zhao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengying Yao
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoxiao Lu
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lingxiao Qiu
- Department of Respiratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Lihua Xing
- Department of Respiratory Intensive Care Unit, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Zhu T, Brown AP, Cai LP, Quon G, Ji H. Single-Cell RNA-Seq Analysis Reveals Lung Epithelial Cell Type-Specific Responses to HDM and Regulation by Tet1. Genes (Basel) 2022; 13:genes13050880. [PMID: 35627266 PMCID: PMC9140484 DOI: 10.3390/genes13050880] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/06/2022] [Accepted: 05/11/2022] [Indexed: 11/16/2022] Open
Abstract
Tet1 protects against house dust mite (HDM)-induced lung inflammation in mice and alters the lung methylome and transcriptome. In order to explore the role of Tet1 in individual lung epithelial cell types in HDM-induced inflammation, we established a model of HDM-induced lung inflammation in Tet1 knockout and littermate wild-type mice, then studied EpCAM+ lung epithelial cells using single-cell RNA-seq analysis. We identified eight EpCAM+ lung epithelial cell types, among which AT2 cells were the most abundant. HDM challenge altered the relative abundance of epithelial cell types and resulted in cell type-specific transcriptomic changes. Bulk and cell type-specific analysis also showed that loss of Tet1 led to the altered expression of genes linked to augmented HDM-induced lung inflammation, including alarms, detoxification enzymes, oxidative stress response genes, and tissue repair genes. The transcriptomic regulation was accompanied by alterations in TF activities. Trajectory analysis supports that HDM may enhance the differentiation of AP and BAS cells into AT2 cells, independent of Tet1. Collectively, our data showed that lung epithelial cells had common and unique transcriptomic signatures of allergic lung inflammation. Tet1 deletion altered transcriptomic networks in various lung epithelial cells, which may promote allergen-induced lung inflammation.
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Affiliation(s)
- Tao Zhu
- California National Primate Research Center, University of California, Davis, CA 95616, USA; (T.Z.); (A.P.B.); (L.P.C.)
| | - Anthony P. Brown
- California National Primate Research Center, University of California, Davis, CA 95616, USA; (T.Z.); (A.P.B.); (L.P.C.)
| | - Lucy P. Cai
- California National Primate Research Center, University of California, Davis, CA 95616, USA; (T.Z.); (A.P.B.); (L.P.C.)
| | - Gerald Quon
- Department of Molecular and Cellular Biology, Genome Center, University of California, Davis, CA 95616, USA;
| | - Hong Ji
- California National Primate Research Center, University of California, Davis, CA 95616, USA; (T.Z.); (A.P.B.); (L.P.C.)
- Department of Anatomy, Physiology and Cell biology, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
- Correspondence: ; Tel.: +1-530-754-0679
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Abbasi-Kolli M, Sadri Nahand J, Kiani SJ, Khanaliha K, Khatami A, Taghizadieh M, Torkamani AR, Babakhaniyan K, Bokharaei-Salim F. The expression patterns of MALAT-1, NEAT-1, THRIL, and miR-155-5p in the acute to the post-acute phase of COVID-19 disease. Braz J Infect Dis 2022; 26:102354. [PMID: 35500644 PMCID: PMC9035361 DOI: 10.1016/j.bjid.2022.102354] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 04/07/2022] [Accepted: 04/11/2022] [Indexed: 12/11/2022] Open
Abstract
Introduction One of the hallmarks of COVID-19 is overwhelming inflammation, which plays a very important role in the pathogenesis of COVID-19. Thus, identification of inflammatory factors that interact with the SARS-CoV-2 can be very important to control and diagnose the severity of COVID-19. The aim of this study was to investigate the expression patterns of inflammation-related non-coding RNAs (ncRNAs) including MALAT-1, NEAT-1, THRIL, and miR-155-5p from the acute phase to the recovery phase of COVID-19. Methods Total RNA was extracted from Peripheral Blood Mononuclear Cell (PBMC) samples of 20 patients with acute COVID-19 infection and 20 healthy individuals and the expression levels of MALAT-1, NEAT-1, THRIL, and miR-155-5p were evaluated by real-time PCR assay. Besides, in order to monitor the expression pattern of selected ncRNAs from the acute phase to the recovery phase of COVID-19 disease, the levels of ncRNAs were re-measured 6‒7 weeks after the acute phase. Result The mean expression levels of MALAT-1, THRIL, and miR-155-5p were significantly increased in the acute phase of COVID-19 compared with a healthy control group. In addition, the expression levels of MALAT-1 and THRIL in the post-acute phase of COVID-19 were significantly lower than in the acute phase of COVID-19. According to the ROC curve analysis, these ncRNAs could be considered useful biomarkers for COVID-19 diagnosis and for discriminating between acute and post-acute phase of COVID-19. Discussion Inflammation-related ncRNAs (MALAT-1, THRIL, and miR-150-5p) can act as hopeful biomarkers for the monitoring and diagnosis of COVID-19 disease.
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Affiliation(s)
| | - Javid Sadri Nahand
- Tabriz University of Medical Sciences, Infectious and Tropical Diseases Research Center, Tabriz, Iran
| | - Seyed Jalal Kiani
- Iran University of Medical Sciences, School of Medicine, Department of Virology, Tehran, Iran
| | - Khadijeh Khanaliha
- University of Medical Sciences, Institute of Immunology and Infectious Diseases, Research Center of Pediatric Infectious Diseases, Tehran, Iran
| | - AliReza Khatami
- Iran University of Medical Sciences, School of Medicine, Department of Virology, Tehran, Iran
| | - Mohammad Taghizadieh
- Tabriz University of Medical Sciences, Center for Women's Health Research Zahra, School of Medicine, Department of Pathology, Tabriz, Iran
| | - Ali Rajabi Torkamani
- Tehran University of Medical Sciences, School of Medicine, Department of Clinical Biochemistry, Tehran, Iran
| | - Kimiya Babakhaniyan
- Iran University of Medical Sciences, School of Nursing and Midwifery, Department of Medical Surgical Nursing, Tehran, Iran
| | - Farah Bokharaei-Salim
- Iran University of Medical Sciences, School of Medicine, Department of Virology, Tehran, Iran.
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Luo H, Tang W, Liu H, Zeng X, Ngai WSC, Gao R, Li H, Li R, Zheng H, Guo J, Qin F, Wang G, Li K, Fan X, Zou P, Chen P. Photocatalytic Chemical Crosslinking for Profiling RNA‐Protein Interactions in Living Cells. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202202008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Huixin Luo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Wei Tang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Hongyu Liu
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Xiangmei Zeng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | | | - Rui Gao
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Heyun Li
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Ran Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Huangtao Zheng
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Jianting Guo
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Fangfei Qin
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Gang Wang
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Kexin Li
- PKU: Peking University Peking-Tsinghua Center for Life Sciences CHINA
| | - Xinyuan Fan
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Zou
- PKU: Peking University College of Chemistry and Molecular Engineering CHINA
| | - Peng Chen
- Peking University tional Laboratory for Molecular Sciences College of Chemistry and Molecular Engineering 100871 Beijing CHINA
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Dichev V, Mehterov N, Kazakova M, Karalilova R, Batalov A, Sarafian V. The lncRNAs/miR-30e/CHI3L1 Axis Is Dysregulated in Systemic Sclerosis. Biomedicines 2022; 10:496. [PMID: 35203705 PMCID: PMC8962397 DOI: 10.3390/biomedicines10020496] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/25/2022] Open
Abstract
Systemic sclerosis (SSc) is an autoimmune disease with completely undefined etiology and treatment difficulties. The expression of both protein coding and non-coding RNAs is dysregulated during disease development. We aimed to examine a possible regulatory axis implemented in the control of chitinase-3 like protein 1 (CHI3L1) or YKL-40, an inflammation-associated glycoprotein, shown to be elevated in SSc. A panel of seven miRNAs and three lncRNAs potentially involved in the control of CHI3L1 were selected on the basis of in silico analysis. TagMan assay was used to evaluate the expression levels of miRNAs and RT-qPCR for lncRNAs in white blood cells (WBCs) and plasma from SSc patients and healthy controls. Among the eight screened miRNAs, miR-30e-5p (p = 0.04) and miR-30a-5p (p = 0.01) were significantly downregulated in WBCs and plasma of SSc patients, respectively. On the contrary, the expression of the metastasis associated lung adenocarcinoma transcript 1 (MALAT1) (p = 0.044) and the Nuclear enriched abundant transcript 1 (NEAT1) (p = 0.008) in WBCs was upregulated compared to the controls. Increased levels of MALAT1 and NEAT1 could be associated with the downregulation of miR-30e-5p and miR-30a-5p expression in WBCs and plasma. We present novel data on the involvement of a possible regulatory axis lncRNAs/miR-30e/CHI3L1 in SSc and hypothesize that MALAT1 and NEAT1 could act as miR-30e-5p and miR-30a-5p decoys. This may be a reason for the increased serum levels of CHI3L1 in SSc patients.
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Affiliation(s)
- Valentin Dichev
- Department of Medical Biology, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria; (V.D.); (M.K.); (V.S.)
- Research Institute, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria
| | - Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria; (V.D.); (M.K.); (V.S.)
- Research Institute, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria; (V.D.); (M.K.); (V.S.)
- Research Institute, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria
| | - Rositsa Karalilova
- Department of Propedeutics of Internal Diseases, Medical University-Plovdiv, Vasil Aprilov Blvd. 15A, 4001 Plovdiv, Bulgaria; (R.K.); (A.B.)
- Clinic of Rheumatology, University Hospital “Kaspela”, 64 Sofia Str., 4001 Plovdiv, Bulgaria
| | - Anastas Batalov
- Department of Propedeutics of Internal Diseases, Medical University-Plovdiv, Vasil Aprilov Blvd. 15A, 4001 Plovdiv, Bulgaria; (R.K.); (A.B.)
- Clinic of Rheumatology, University Hospital “Kaspela”, 64 Sofia Str., 4001 Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria; (V.D.); (M.K.); (V.S.)
- Research Institute, Medical University-Plovdiv, Blvd. 15A Vasil Aprilov, 4002 Plovdiv, Bulgaria
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Liu Y, Tang G, Li J. Long non-coding RNA NEAT1 participates in ventilator-induced lung injury by regulating miR-20b expression. Mol Med Rep 2022; 25:66. [PMID: 34981816 PMCID: PMC8767541 DOI: 10.3892/mmr.2022.12582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/11/2021] [Indexed: 11/06/2022] Open
Abstract
Long non‑coding (lnc)RNA nuclear enriched abundant transcript 1 (NEAT1) has been reported to serve an important role in cancer, but its effects on ventilator‑induced lung injury (VILI) remain unclear. The present study aimed to investigate the role of lncRNA NEAT1 in alveolar macrophages (AMs) on ventilator‑induced lung injury (VILI). Mouse and cell models were established to detect NEAT1 expression, pathological changes in lung tissues, apoptosis of AMs, expression of the M1 phenotype marker, CD86 and M2 phenotype marker, CD206, and the expression levels of interleukin (IL)‑1β, IL‑6, tumor necrosis factor (TNF)‑α and inducible nitric oxide synthase (iNOS). The associations between NEAT1, microRNA (miRNA/miR)‑20b and STAT3 were predicted using StarBase and TargetScan, and verified via the dual‑luciferase reporter and RIP assays. NEAT1 short hairpin RNA and miR‑20b inhibitor were co‑transfected into AMs to assess the effect of NEAT1 and miR‑20b in VILI. The results demonstrated that NEAT1 was highly expressed in lung tissues of VILI mice and cell stretch (CS) treated AMs. Furthermore, NEAT1 knockdown inhibited lung injury and cell apoptosis induced by VILI. Compared with VILI mice or CS‑treated AMs, NEAT1 knockdown accelerated the phenotypic transformation from M1 to M2, and decreased the expression levels of IL‑1β, IL‑6, TNF‑α and iNOS. Notably, miR‑20b was identified as the target of NEAT1, and STAT3 was the target of miR‑20b. NEAT1 knockdown decreased STAT3 protein expression, the effects of which were reversed following transfection with miR‑20b inhibitor. Furthermore, the protective effect of NEAT1 knockdown on VILI was reversed following transfection with miR‑20b inhibitor. Taken together, the results of the present study suggest that NEAT1 knockdown promotes phenotypic transformation of AMs from M1 to M2 and alleviates lung injury and apoptosis of VILI by regulating miR‑20b expression.
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Affiliation(s)
- Yi Liu
- Department of Anesthesiology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 211100, P.R. China
| | - Gang Tang
- Department of Anesthesiology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 211100, P.R. China
| | - Jinyu Li
- Department of Anesthesiology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu 211100, P.R. China
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45
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Xue Y, Ke J, Zhou X, Chen Q, Chen M, Huang T, Lin F, Chen F. Knockdown of LncRNA MALAT1 Alleviates Coxsackievirus B3-Induced Acute Viral Myocarditis in Mice via Inhibiting Th17 Cells Differentiation. Inflammation 2022; 45:1186-1198. [PMID: 35088199 DOI: 10.1007/s10753-021-01612-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/08/2021] [Accepted: 12/10/2021] [Indexed: 11/05/2022]
Abstract
Acute viral myocarditis (AVMC), most often caused by coxsackievirus B3 (CVB3) infection, is characterized by myocardial inflammation associated with high morbidity and mortality. A pathogenic role for T helper (Th) 17 cells in AVMC is well established. Long noncoding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been shown to play a key role in various inflammatory diseases. However, the expression of MALAT1 and its impact on Th17 cells differentiation in AVMC remain unclear. In the present study, we found that MALAT1 was highly expressed in mice with AVMC, and the expression was correlated positively with cardiac pathological scores, cardiac IL-17 mRNA expression, and the percentages of splenic Th17 cells. We further demonstrated that MALAT1 knockdown could significantly alleviate the severity of disease and inhibit the differentiation of Th17 cells, accompanying the reduced mRNA expression of RORγt and productions of Th17-related pro-inflammatory cytokines in vivo. Additionally, in vitro analysis showed that MALAT1 knockdown suppressed naïve CD4+ T cells differentiation towards Th17 cells. In conclusion, our results suggest that MALAT1 knockdown alleviates CVB3-induced AVMC in mice, which may be partially attributable to the decline in Th17 cells responses. MALAT1 may serve as a novel therapeutic option in AVMC.
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Affiliation(s)
- Yimin Xue
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China.,The Fourth Department of Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, 350001, Fujian, People's Republic of China
| | - Jun Ke
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China.,Department of Emergency, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, 350001, Fujian, People's Republic of China
| | - Xiaofen Zhou
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China.,The Fourth Department of Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China.,Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, 350001, Fujian, People's Republic of China
| | - Qian Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China.,The Fourth Department of Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China
| | - Mingguang Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China.,The Fourth Department of Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China
| | - Tingfeng Huang
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China.,The Fourth Department of Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China
| | - Fenghui Lin
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China.,The Fourth Department of Intensive Care Unit, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China
| | - Feng Chen
- Shengli Clinical Medical College of Fujian Medical University, Fuzhou, 350001, Fujian, People's Republic of China. .,Department of Emergency, Fujian Provincial Hospital, Fuzhou, 350001, Fujian, People's Republic of China. .,Fujian Provincial Key Laboratory of Emergency Medicine, Fuzhou, 350001, Fujian, People's Republic of China.
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Huang K, Wang C, Vagts C, Raguveer V, Finn PW, Perkins DL. Long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 are differentially expressed in severe COVID-19 patients: An integrated single-cell analysis. PLoS One 2022; 17:e0261242. [PMID: 35007307 PMCID: PMC8746747 DOI: 10.1371/journal.pone.0261242] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 11/25/2021] [Indexed: 01/08/2023] Open
Abstract
Hyperactive and damaging inflammation is a hallmark of severe rather than mild Coronavirus disease 2019 (COVID-19). To uncover key inflammatory differentiators between severe and mild COVID-19, we applied an unbiased single-cell transcriptomic analysis. We integrated two single-cell RNA-seq datasets with COVID-19 patient samples, one that sequenced bronchoalveolar lavage (BAL) cells and one that sequenced peripheral blood mononuclear cells (PBMCs). The combined cell population was then analyzed with a focus on genes associated with disease severity. The immunomodulatory long non-coding RNAs (lncRNAs) NEAT1 and MALAT1 were highly differentially expressed between mild and severe patients in multiple cell types. Within those same cell types, the concurrent detection of other severity-associated genes involved in cellular stress response and apoptosis regulation suggests that the pro-inflammatory functions of these lncRNAs may foster cell stress and damage. Thus, NEAT1 and MALAT1 are potential components of immune dysregulation in COVID-19 that may provide targets for severity related diagnostic measures or therapy.
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Affiliation(s)
- Kai Huang
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Catherine Wang
- College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Christen Vagts
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Vanitha Raguveer
- College of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Patricia W. Finn
- Division of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - David L. Perkins
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Division of Nephrology, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Surgery, University of Illinois at Chicago, Chicago, Illinois, United States of America
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Abstract
Regulatory RNAs like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) control vascular and immune cells' phenotype and thus play a crucial role in atherosclerosis. Moreover, the mutual interactions between miRNAs and lncRNAs link both types of regulatory RNAs in a functional network that affects lesion formation. In this review, we deduce novel concepts of atherosclerosis from the analysis of the current data on regulatory RNAs' role in endothelial cells (ECs) and macrophages. In contrast to arterial ECs, which adopt a stable phenotype by adaptation to high shear stress, macrophages are highly plastic and quickly change their activation status. At predilection sites of atherosclerosis, such as arterial bifurcations, ECs are exposed to disturbed laminar flow, which generates a dysadaptive stress response mediated by miRNAs. Whereas the highly abundant miR-126-5p promotes regenerative proliferation of dysadapted ECs, miR-103-3p stimulates inflammatory activation and impairs endothelial regeneration by aberrant proliferation and micronuclei formation. In macrophages, miRNAs are essential in regulating energy and lipid metabolism, which affects inflammatory activation and foam cell formation.Moreover, lipopolysaccharide-induced miR-155 and miR-146 shape inflammatory macrophage activation through their oppositional effects on NF-kB. Most lncRNAs are not conserved between species, except a small group of very long lncRNAs, such as MALAT1, which blocks numerous miRNAs by providing non-functional binding sites. In summary, regulatory RNAs' roles are highly context-dependent, and therapeutic approaches that target specific functional interactions of miRNAs appear promising against cardiovascular diseases.
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Affiliation(s)
- Andreas Schober
- Institute for Cardiovascular Prevention, University Hospital, Ludwig-Maximilians-University, Munich, Germany.
| | - Saffiyeh Saboor Maleki
- Institute for Cardiovascular Prevention, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Maliheh Nazari-Jahantigh
- Institute for Cardiovascular Prevention, University Hospital, Ludwig-Maximilians-University, Munich, Germany
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48
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Hsa_circ_0004287 inhibits macrophage-mediated inflammation in an N6-methyladenosine-dependent manner in atopic dermatitis and psoriasis. J Allergy Clin Immunol 2021; 149:2021-2033. [PMID: 34953789 DOI: 10.1016/j.jaci.2021.11.024] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 11/03/2021] [Accepted: 11/26/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Circular RNA (circRNA) was reported to involve in various diseases; however, its role in atopic dermatitis (AD) or psoriasis remains unclear.background Objective: We sought to determine the differential expression profiles of circRNAs in peripheral blood mononuclear cells (PBMCs) between healthy controls and AD patients, and explore the mechanisms underlying the effects of circRNAs on the pathogenesis of AD. METHODS The differential expression profiles of circRNAs were analyzed by circRNA microarray. In vitro function and mechanisms by which circRNAs regulate macrophage-mediated inflammation were detected by RT-qPCR, western blotting, RNA stability assay, immunoprecipitation, enzyme-linked immunosorbent assay (ELISA), and methylated RNA immunoprecipitation (MeRIP) assay. In vivo roles of circRNAs were determined in 2,4-dinitrochlorobenzene (DNCB)-induced dermatitis and imiquimod (IMQ)-induced psoriasis mouse model. RESULTS We identified a functional unknown circRNA hsa_circ_0004287 from 88750 circRNAs, which was upregulated in PBMCs of both AD and psoriasis patients, and mainly expressed by macrophages under inflammatory conditions. hsa_circ_0004287 inhibited M1 macrophage activation in vitro, and macrophage-specific overexpression of hsa_circ_0004287 alleviated skin inflammation in both AD- and psoriasis-like mice. Mechanistically, hsa_circ_0004287 reduced the stability of its host gene metastasis associated lung adenocarcinoma transcript 1 (MALAT1) by competitively binding to IGF2BP3 with MALAT1 in an N6-methyladenosine (m6A)-dependent manner. Lower levels of MALAT1 promoted the ubiquitination degradation of S100A8/S100A9, thereby impeding p38/MAPK phosphorylation and macrophage-mediated inflammation.results CONCLUSION: Hsa_circ_0004287 inhibits M1 macrophage activation in an m6A-dependent manner in AD and psoriasis, and may serve as a general therapeutic candidate for AD and psoriasis. CONCLUSION
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Zhao Q, Pang G, Yang L, Chen S, Xu R, Shao W. Long Noncoding RNAs Regulate the Inflammatory Responses of Macrophages. Cells 2021; 11:cells11010005. [PMID: 35011565 PMCID: PMC8750547 DOI: 10.3390/cells11010005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 12/18/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are defined as transcripts with more than 200 nucleotides that have little or no coding potential. In recent years, due to the development of next-generation sequencing (NGS), a large number of studies have revealed that lncRNAs function as key regulators to maintain immune balance and participate in diverse physiological and pathological processes in the human body. Notably, overwhelming evidence suggests that lncRNAs can regulate innate immune responses, the differentiation and development of immune cells, inflammatory autoimmune diseases, and many other immunological processes with distinct regulatory mechanisms. In this review, we summarized the emerging roles of lncRNAs in macrophage development and polarization. In addition, the potential value of lncRNAs as diagnostic biomarkers and novel therapeutic targets for the treatment of aberrant immune responses and inflammatory diseases are discussed.
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Rodrigues AC, Adamoski D, Genelhould G, Zhen F, Yamaguto GE, Araujo‐Souza PS, Nogueira MB, Raboni SM, Bonatto AC, Gradia DF, Carvalho de Oliveira J. NEAT1 and MALAT1 are highly expressed in saliva and nasopharyngeal swab samples of COVID-19 patients. Mol Oral Microbiol 2021; 36:291-294. [PMID: 34463043 PMCID: PMC8661855 DOI: 10.1111/omi.12351] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022]
Abstract
COVID-19, caused by the SARS-CoV-2 virus, has become a significant global public health problem, with a wide variety of clinical manifestations and disease progression outcomes. LncRNAs are key regulators of the immune response and have been associated with COVID-19 risk infection. Previous studies focused mainly on in-silico analysis of lncRNA expression in the lungs or peripheral blood cells. We evaluated the expression of lncRNAs NEAT1, MALAT1, and MIR3142 in saliva and nasopharyngeal swab from SARS-CoV-2 positive (n = 34) and negative patients (n = 46). A higher expression of the lncRNAs NEAT1 and MALAT1 (p < 0.05) were found in positive samples. NEAT1 had a higher expression mainly in saliva samples (p < 0.001), and MALAT1 was upregulated in nasopharyngeal samples (p < 0.05). Area under the ROC curve for NEAT1 in saliva was 0.8067. This study was the first to investigate the expression of lncRNAs in saliva and nasopharyngeal samples of COVID-19 patients, which gives new insights into the initial response to infection and infectivity and may provide new biomarkers for severity and targets for therapy.
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Affiliation(s)
- Ana Carolina Rodrigues
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Douglas Adamoski
- Brazilian Biosciences National Laboratory (LNBio)Brazilian Center for Research in Energy and Materials (CNPEM)Sao PauloBrazil
| | - Gustavo Genelhould
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Laboratório de VirologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Felipe Zhen
- Unidade de InfectologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Guilherme Eiji Yamaguto
- Unidade de InfectologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Patrícia Savio Araujo‐Souza
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Meri Bordignon Nogueira
- Laboratório de VirologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Sonia Mara Raboni
- Laboratório de VirologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
- Unidade de InfectologiaComplexo Hospital de ClínicasUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Ana Claudia Bonatto
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Daniela Fiori Gradia
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
| | - Jaqueline Carvalho de Oliveira
- Departamento de GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
- Programa de Pos‐graduação em GenéticaUniversidade Federal do ParanáCuritibaParanáBrazil
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