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Sun J, Shi M, Mei R, Zhao Y, Huang Y, Song Z, Hua F, Zhang M, Liu J. LincR-PPP2R5C regulates the PP2A signaling pathway in the macrophage-myofibroblast transition in a mouse model of epidural fibrosis. Mol Immunol 2025; 177:85-95. [PMID: 39729722 DOI: 10.1016/j.molimm.2024.12.006] [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: 09/15/2024] [Revised: 11/18/2024] [Accepted: 12/23/2024] [Indexed: 12/29/2024]
Abstract
Low back pain after spine surgery is a major complication due to excessive epidural fibrosis, which compresses the lumbar nerve. Macrophage-myofibroblast transition (MMT) promoted epidural fibrosis in a mouse laminectomy model. Previously, we demonstrated that LincR-PPP2R5C regulated CD4 + T-cell differentiation. Here, we aimed to explore the roles and mechanisms of LincR-PPP2R5C in macrophages in epidural fibrosis. In M2 macrophages, the level of LincR-PPP2R5C was significantly decreased. Upon overexpression, LincR-PPP2R5C induced M1-macrophage polarization and reduced MMT. In contrast, LincR-PPP2R5C deficiency promoted M2-macrophage polarization and increased MMT. Mechanistically, LincR-PPP2R5C modulated the expression of α-SMA in macrophages via the PP2A signaling pathway. In vivo, LincR-PPP2R5C deficiency aggravated epidural fibrosis by enhancing MMT in a mouse model of laminectomy, and this effect was abolished in mice with macrophage depletion. Our study shed light on the effects of LincR-PPP2R5C on macrophage differentiation and MMT in epidural fibrosis.
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Affiliation(s)
- Jinpeng Sun
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mohan Shi
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Mei
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Youpeng Zhao
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yue Huang
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zeyuan Song
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Feng Hua
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Mingshun Zhang
- NHC Key Laboratory of Antibody Technique, Jiangsu Province Engineering Research Center of Antibody Drug, Department of Immunology, Nanjing Medical University, Nanjing, China.
| | - Jun Liu
- Department of Orthopedics, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China.
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2
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Elimam H, Alhamshry NAA, Hatawsh A, Elfar N, Moussa R, Radwan AF, Abd-Elmawla MA, Elkashlan AM, Zaki MB, Abdel-Reheim MA, Mohammed OA, Doghish AS. Natural products and long noncoding RNA signatures in gallbladder cancer: a review focuses on pathogenesis, diagnosis, and drug resistance. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:9549-9571. [PMID: 39028332 DOI: 10.1007/s00210-024-03279-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024]
Abstract
Gallbladder cancer (GBC) is an aggressive and lethal malignancy with a poor prognosis. Long noncoding RNAs (lncRNAs) and natural products have emerged as key orchestrators of cancer pathogenesis through widespread dysregulation across GBC transcriptomes. Functional studies have revealed that lncRNAs interact with oncoproteins and tumor suppressors to control proliferation, invasion, metastasis, angiogenesis, stemness, and drug resistance. Curcumin, baicalein, oleanolic acid, shikonin, oxymatrine, arctigenin, liensinine, fangchinoline, and dioscin are a few examples of natural compounds that have demonstrated promising anticancer activities against GBC through the regulation of important signaling pathways. The lncRNAs, i.e., SNHG6, Linc00261, GALM, OIP5-AS1, FOXD2-AS1, MINCR, DGCR5, MEG3, GATA6-AS, TUG1, and DILC, are key players in regulating the aforementioned processes. For example, the lncRNAs FOXD2-AS1, DILC, and HOTAIR activate oncogenes such as DNMT1, Wnt/β-catenin, BMI1, and c-Myc, whereas MEG3 and GATA6-AS suppress the tumor proteins NF-κB, EZH2, and miR-421. Clinically, specific lncRNAs can serve as diagnostic or prognostic biomarkers based on overexpression correlating with advanced TNM stage, metastasis, chemoresistance, and poor survival. Therapeutically, targeting aberrant lncRNAs with siRNA or antisense oligos disrupts their oncogenic signaling and inhibits GBC progression. Overall, dysfunctional lncRNA regulatory circuits offer multiple avenues for precision medicine approaches to improve early GBC detection and overcome this deadly cancer. They have the potential to serve as novel biomarkers as they are detectable in bodily fluids and tissues. These findings enhance gallbladder treatments, mitigating resistance to chemo- and radiotherapy.
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Affiliation(s)
- Hanan Elimam
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Egypt.
| | - Nora A A Alhamshry
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Egypt
| | - Abdulrahman Hatawsh
- Biotechnology School, 26th of July Corridor, Sheikh Zayed City, Nile University, Giza, 12588, Egypt
| | - Nourhan Elfar
- School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, New Administrative Capital, Cairo, 11578, Egypt
- Egyptian Drug Authority (EDA), Ministry of Health and Population, Cairo, 11567, Egypt
| | - Rewan Moussa
- Faculty of Medicine, Helwan University, Cairo, 11795, Egypt
| | - Abdullah F Radwan
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Cairo, 11829, Egypt
| | - Mai A Abd-Elmawla
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Akram M Elkashlan
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Sadat City, 32897, Egypt
| | - Mustafa Ahmed Abdel-Reheim
- Department of Pharmaceutical Sciences, College of Pharmacy, Shaqra University, 11961, Shaqra, Saudi Arabia.
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Beni-Suef University, Beni Suef, 62521, Egypt.
| | - Osama A Mohammed
- Department of Pharmacology, College of Medicine, University of Bisha, 61922, Bisha, Saudi Arabia
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo, 11829, Egypt
- Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231, Cairo, Egypt
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Huang X, Chen J, Li H, Cai Y, Liu L, Dong Q, Li Y, Ren Y, Xiang W, He X. LncRNA SNHG12 suppresses adipocyte inflammation and insulin resistance by regulating the HDAC9/Nrf2 axis. FASEB J 2024; 38:e23794. [PMID: 38967258 DOI: 10.1096/fj.202400236rr] [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: 01/30/2024] [Revised: 06/12/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024]
Abstract
Obesity is often associated with low-grade inflammation. The incidence of obesity has increased annually worldwide, which seriously affects human health. A previous study indicated that long noncoding RNA SNHG12 was downregulated in obesity. Nevertheless, the role of SNHG12 in obesity remains to be elucidated. In this study, qRT-PCR, western blot, and ELISA were utilized to examine the gene and protein expression. Flow cytometry was employed to investigate the M2 macrophage markers. RNA pull-down assay and RIP were utilized to confirm the interactions of SNHG12, hnRNPA1, and HDAC9. Eventually, a high-fat diet-fed mouse model was established for in vivo studies. SNHG12 overexpression suppressed adipocyte inflammation and insulin resistance and promoted M2 polarization of macrophages that was caused by TNF-α treatment. SNHG12 interacted with hnRNPA1 to downregulate HDAC9 expression, which activated the Nrf2 signaling pathway. HDAC9 overexpression reversed the effect of SNHG12 overexpression on inflammatory response, insulin resistance, and M2 phenotype polarization. Overexpression of SNHG12 improved high-fat diet-fed mouse tissue inflammation. This study revealed the protective effect of SNHG12 against adipocyte inflammation and insulin resistance. This result further provides a new therapeutic target for preventing inflammation and insulin resistance in obesity.
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Affiliation(s)
- Xiaoyan Huang
- Department of Genetics, Metabolism and Endocrinology, Hainan Women and Children's Medical Center, Haikou, China
| | - Jixiong Chen
- Department of Medical Care Center, Hainan Provincial People's Hospital, Haikou, China
| | - Haidan Li
- Department of Genetics, Metabolism and Endocrinology, Hainan Women and Children's Medical Center, Haikou, China
| | - Yuhua Cai
- Department of Genetics, Metabolism and Endocrinology, Hainan Women and Children's Medical Center, Haikou, China
| | - Li Liu
- Department of Genetics, Metabolism and Endocrinology, Hainan Women and Children's Medical Center, Haikou, China
| | - Qi Dong
- Department of Genetics, Metabolism and Endocrinology, Hainan Women and Children's Medical Center, Haikou, China
| | - Yan Li
- Department of Genetics, Metabolism and Endocrinology, Hainan Women and Children's Medical Center, Haikou, China
| | - Yi Ren
- Department of Pediatrics, Haikou Hospital of the Maternal and Child Health, Haikou, China
| | - Wei Xiang
- Hainan Women and Children's Medical Center, Haikou, China
| | - Xiaojie He
- Laboratory of Pediatric Nephrology, Institute of Pediatrics, The Second Xiangya Hospital, Central South University, Changsha, China
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Jiang M, Dai J, Jiang C, Pan Y, Ren M, Xing M. Long noncoding RNA MEG8 induces an imbalance of Th17/Treg cells through the miR-107/STAT3 axis in Henoch-Schonlein purpura rats. Aging (Albany NY) 2023; 15:13854-13864. [PMID: 38054824 PMCID: PMC10756103 DOI: 10.18632/aging.205266] [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: 02/03/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
T-helper (Th) 17/ T-regulatory (Treg) cell dysregulation underlies the pathogenesis of Henoch-Schonlein purpura (HSP). This research focused on the implication/s of the long noncoding RNA (lncRNAs) maternally expressed gene 8 (MEG8) in Th17 and Treg cell differentiation in HSP rats. MEG8, miR-107, signal transducer and activator of transcription-3 (STAT3), receptor-related orphan receptor γt (RORγt), and the transcription factor forkhead box P3 (Foxp3) expression levels were detected using real-time quantitative polymerase chain reaction and Western blot analyses. Flow cytometry was employed for measuring Th17 and Treg cells within the CD4+ T cell population. The interaction between miR-107 and MEG8 or STAT3 was examined. A low proportion of MEG8 and Treg cells together with Th17 cells were denoted within HSP rats. Moreover, MEG8 overexpression altered the Th17/Treg imbalance in peripheral blood CD4+ T-cell population, and the miR-107 mimic and STAT3 silencing reversed this effect. Thus, MEG8 served as a sponge for miR-107, lowering binding activity to STAT3 and thus overexpressing the molecule. Taken together, MEG8 induces an imbalance of Th17/Treg cells through the miR-107/STAT3 axis in HSP rats.
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Affiliation(s)
- Mingyu Jiang
- Department of Pediatrics, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Jicheng Dai
- Department of Pediatrics, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Chunming Jiang
- Department of Neonatology, Zhuhai Women and Children’s Hospital, Zhuhai 519060, P.R. China
| | - Yanbo Pan
- Department of Neurosurgery, Tieling Central Hospital, Tieling 112000, P.R. China
| | - Mingyong Ren
- Department of Pediatrics, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
| | - Mengnan Xing
- Department of Pediatrics, The First Affiliated Hospital of Harbin Medical University, Harbin 150001, P.R. China
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Tanwar VS, Reddy MA, Das S, Samara VA, Abdollahi M, Dey S, Malek V, Ganguly R, Stapleton K, Lanting L, Pirrotte P, Natarajan R. Palmitic Acid-Induced Long Noncoding RNA PARAIL Regulates Inflammation via Interaction With RNA-Binding Protein ELAVL1 in Monocytes and Macrophages. Arterioscler Thromb Vasc Biol 2023; 43:1157-1175. [PMID: 37128912 PMCID: PMC10287039 DOI: 10.1161/atvbaha.122.318536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 04/14/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Obesity and diabetes are associated with elevated free fatty acids like palmitic acid (PA), which promote chronic inflammation and impaired inflammation resolution associated with cardiometabolic disorders. Long noncoding RNAs (lncRNAs) are implicated in inflammatory processes; however, their roles in PA-regulated inflammation and resolution are unclear. METHODS We performed RNA-sequencing analysis to identify PA-regulated coding genes and novel lncRNAs in CD14+ monocytes from healthy volunteers. We investigated the regulation and function of an uncharacterized PA-induced lncRNA PARAIL (PA-regulated anti-inflammatory lncRNA). We examined its role in inflammation resolution by employing knockdown and overexpression strategies in human and mouse macrophages. We also used RNA pulldown coupled with mass spectrometry to identify PARAIL interacting nuclear proteins and their mechanistic involvement in PARAIL functions in human macrophages. RESULTS Treatment of human CD14+ monocytes with PA-induced several lncRNAs and genes associated with inflammatory phenotype. PA strongly induced lncRNA PARAIL expressed near RIPK2. PARAIL was also induced by cytokines and infectious agents in human monocytes/macrophages and was regulated by NF-κB (nuclear factor-kappa B). Time course studies showed PARAIL was induced during inflammation resolution phase in PA-treated macrophages. PARAIL knockdown with antisense oligonucleotides upregulated key inflammatory genes and vice versa with PARAIL overexpression. We found that PARAIL interacts with ELAVL1 (ELAV-like RNA-binding protein 1) protein via adenylate/uridylate-rich elements (AU-rich elements; AREs). ELAVL1 knockdown inhibited the anti-inflammatory functions of PARAIL. Moreover, PARAIL knockdown increased cytosolic localization of ELAVL1 and increased the stability of ARE-containing inflammatory genes. Mouse orthologous Parail was downregulated in macrophages from mice with diabetes and atherosclerosis. Parail overexpression attenuated proinflammatory genes in mouse macrophages. CONCLUSIONS Upregulation of PARAIL under acute inflammatory conditions contributes to proresolution mechanisms via PARAIL-ELAVL1 interactions. Conversely, PARAIL downregulation in cardiometabolic diseases enhances ELAVL1 function and impairs inflammation resolution to further augment inflammation. Thus, inflammation-resolving lncRNAs like PARAIL represent novel targets to combat inflammatory cardiometabolic diseases.
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Affiliation(s)
- Vinay Singh Tanwar
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Marpadga A. Reddy
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Sadhan Das
- Department of Biological Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab 140306, India
| | - Vishnu Amaram Samara
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Current affiliation: Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Maryam Abdollahi
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Suchismita Dey
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Vajir Malek
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Rituparna Ganguly
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Kenneth Stapleton
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Linda Lanting
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Patrick Pirrotte
- Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
- Cancer & Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
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6
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Cynn E, Li D, O’Reilly ME, Wang Y, Bashore AC, Jha A, Foulkes A, Zhang H, Winter H, Maegdefessel L, Yan H, Li M, Ross L, Xue C, Reilly MP. Human Macrophage Long Intergenic Noncoding RNA, SIMALR, Suppresses Inflammatory Macrophage Apoptosis via NTN1 (Netrin-1). Arterioscler Thromb Vasc Biol 2023; 43:286-299. [PMID: 36546321 PMCID: PMC10162399 DOI: 10.1161/atvbaha.122.318353] [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: 09/09/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) have emerged as novel regulators of macrophage biology and inflammatory cardiovascular diseases. However, studies focused on lncRNAs in human macrophage subtypes, particularly human lncRNAs that are not conserved in rodents, are limited. METHODS Through RNA-sequencing of human monocyte-derived macrophages, we identified suppressor of inflammatory macrophage apoptosis lncRNA (SIMALR). Lipopolysaccharide/IFNγ (interferon γ) stimulated human macrophages were treated with SIMALR antisense oligonucleotides and subjected to RNA-sequencing to investigate the function of SIMALR. Western blots, luciferase assay, and RNA immunoprecipitation were performed to validate function and potential mechanism of SIMALR. RNAscope was performed to identify SIMALR expression in human carotid atherosclerotic plaques. RESULTS RNA-sequencing of human monocyte-derived macrophages identified SIMALR, a human macrophage-specific long intergenic noncoding RNA that is highly induced in lipopolysaccharide/IFNγ-stimulated macrophages. SIMALR knockdown in lipopolysaccharide/IFNγ stimulated THP1 human macrophages induced apoptosis of inflammatory macrophages, as shown by increased protein expression of cleaved PARP (poly[ADP-ribose] polymerase), caspase 9, caspase 3, and Annexin V+. RNA-sequencing of control versus SIMALR knockdown in lipopolysaccharide/IFNγ-stimulated macrophages showed Netrin-1 (NTN1) to be significantly decreased upon SIMALR knockdown. We confirmed that NTN1 knockdown in lipopolysaccharide/IFNγ-stimulated macrophages induced apoptosis. The SIMALR knockdown-induced apoptotic phenotype was rescued by adding recombinant NTN1. NTN1 promoter-luciferase reporter activity was increased in HEK293T (human embryonic kidney 293) cells treated with lentiviral overexpression of SIMALR. NTN1 promoter activity is known to require HIF1α (hypoxia-inducible factor 1 subunit alpha), and our studies suggest that SIMALR may interact with HIF1α to regulate NTN1 transcription, thereby regulating macrophages apoptosis. SIMALR was found to be expressed in macrophages in human carotid atherosclerotic plaques of symptomatic patients. CONCLUSIONS SIMALR is a nonconserved, human macrophage lncRNA expressed in atherosclerosis that suppresses macrophage apoptosis. SIMALR partners with HIF1α (hypoxia-inducible factor 1 subunit alpha) to regulate NTN1, which is a known macrophage survival factor. This work illustrates the importance of interrogating the functions of human lncRNAs and exploring their translational and therapeutic potential in human atherosclerosis.
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Affiliation(s)
- Esther Cynn
- Department of Medicine, Cardiology Division, Columbia University Irving Medical Center, New York, NY
| | - Daniel Li
- Mission Bio, South San Francisco, CA
| | - Marcella E. O’Reilly
- Department of Medicine, Cardiology Division, Columbia University Irving Medical Center, New York, NY
| | - Ying Wang
- Laboratory of Metabolic Regulation and Genetics, The Rockefeller University, New York, NY
| | - Alexander C. Bashore
- Department of Medicine, Cardiology Division, Columbia University Irving Medical Center, New York, NY
| | - Anjali Jha
- Biostatistics Center, Massachusetts General Hospital, Boston, MA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA
| | - Andrea Foulkes
- Biostatistics Center, Massachusetts General Hospital, Boston, MA
- Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA
- Department of Medicine, Harvard Medical School, Boston, MA
| | - Hanrui Zhang
- Department of Medicine, Cardiology Division, Columbia University Irving Medical Center, New York, NY
| | - Hanna Winter
- Department of Vascular and Endovascular Surgery, Technical University Munich, Germany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Technical University Munich, Germany
- German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance
- Karolinksa Institute, Department of Medicine
| | - Hanying Yan
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, University of Pennsylvania School of Medicine, Philadelphia, PA
| | - Leila Ross
- Department of Medicine, Cardiology Division, Columbia University Irving Medical Center, New York, NY
| | - Chenyi Xue
- Department of Medicine, Cardiology Division, Columbia University Irving Medical Center, New York, NY
| | - Muredach P. Reilly
- Department of Medicine, Cardiology Division, Columbia University Irving Medical Center, New York, NY
- Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York, NY
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7
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Yao Q, Xie Y, Xu D, Qu Z, Wu J, Zhou Y, Wei Y, Xiong H, Zhang XL. Lnc-EST12, which is negatively regulated by mycobacterial EST12, suppresses antimycobacterial innate immunity through its interaction with FUBP3. Cell Mol Immunol 2022; 19:883-897. [PMID: 35637281 PMCID: PMC9149337 DOI: 10.1038/s41423-022-00878-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 05/02/2022] [Indexed: 02/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been implicated in the pathogenesis of intracellular pathogens. However, the role and mechanism of the important lncRNAs in Mycobacterium tuberculosis (M.tb) infection remain largely unexplored. Recently, we found that a secreted M.tb Rv1579c (an early secreted target with a molecular weight of 12 kDa, named EST12) protein activates NLRP3-gasdermin D (GSDMD)-mediated pyroptosis and plays a pivotal role in M.tb-induced immunity. In the present study, M.tb and the EST12 protein negatively regulated the expression of a key lncRNA (named lnc-EST12) in mouse macrophages by activating the JAK2-STAT5a signaling pathway. Lnc-EST12, with a size of 1583 bp, is mainly expressed in immune-related organs (liver, lung and spleen). Lnc-EST12 not only reduces the expression of the proinflammatory cytokines IL-1β, IL-6, and CCL5/8 but also suppresses the NLRP3 inflammasome and GSDMD pyroptosis-IL-1β immune pathway through its interaction with the transcription factor far upstream element-binding protein 3 (FUBP3). The KH3 and KH4 domains of FUBP3 are the critical sites for binding to lnc-EST12. Deficiency of mouse lnc-EST12 or FUBP3 in macrophages increased M.tb clearance and inflammation in mouse macrophages or mice. In conclusion, we report a new immunoregulatory mechanism in which mouse lnc-EST12 negatively regulates anti-M.tb innate immunity through FUBP3.
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Affiliation(s)
- Qili Yao
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Yan Xie
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Dandan Xu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Zilu Qu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Jian Wu
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Yuanyuan Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Yuying Wei
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Huan Xiong
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China
| | - Xiao-Lian Zhang
- Hubei Province Key Laboratory of Allergy and Immunology, Department of Immunology, Wuhan University TaiKang Medical School (School of Basic Medical Sciences), Wuhan, China.
- State Key Laboratory of Virology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China.
- Department of Allergy, Zhongnan Hospital, Wuhan University, Wuhan, China.
- Wuhan Research Center for Infectious Diseases and Cancer, Chinese Academy of Medical Sciences, Wuhan, China.
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8
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Sun L, Zheng W, Sun Y, Xu T. Long non-coding RNA LTCONS7822 positively regulates innate immunity by targeting MITA in miiuy croaker (Miichthys miiuy). FISH & SHELLFISH IMMUNOLOGY 2022; 125:285-291. [PMID: 35595061 DOI: 10.1016/j.fsi.2022.05.027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/11/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Accumulated studies have shown that long non-coding RNA (lncRNA) is considered a critical regulatory factor in mammals, with a length greater than 200 nucleotides, and it can participate in gene imprinting, dose compensation, transcription enhancement, and antisense regulation. Most of the above studies are carried out in mammals, and there are very few studies on lncRNA of lower vertebrates. Here, we report a novel lncRNA, LTCONS7822, which can play a positive regulatory effect on antiviral immunity in miiuy croaker, Miichthys miiuy. Our results show that the levels of lncRNA LTCONS7822 were significantly increased after poly (I:C) stimulation. Further study, we found that lncRNA LTCONS7822 could positively regulate MITA at the post-transcriptional level. In addition, the dual-luciferase reporter assay analysis showed that the positive regulatory effect of lncRNA LTCONS7822 on NF-κB and IRF3 signaling pathways presented the dose and time-dependent manner. Western blotting experiments proved that lncRNA LTCONS7822 has a positive regulatory effect on MITA. Collectively, our study provided new information to enrich the immune regulation network of lncRNA in teleost fish.
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Affiliation(s)
- Lingping Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Yuena Sun
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China.
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources (Shanghai Ocean University), Ministry of Education, China; National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, China.
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9
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Emerging Role of LncRNAs in Autoimmune Lupus. Inflammation 2022; 45:937-948. [DOI: 10.1007/s10753-021-01607-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/11/2021] [Accepted: 12/05/2021] [Indexed: 12/13/2022]
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10
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Ren G, Xu L, Zhao J, Shao Y, Lu T, Zhang Q. Comparative transcriptome analysis of long non coding RNA (lncRNA) in RTG-2 cells infected by infectious hematopoietic necrosis virus. FISH & SHELLFISH IMMUNOLOGY 2022; 120:314-324. [PMID: 34890776 DOI: 10.1016/j.fsi.2021.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/09/2021] [Accepted: 12/05/2021] [Indexed: 06/13/2023]
Abstract
Infectious hematopoietic necrosis virus (IHNV) is the vital pathogen that has caused the great economic loss in salmonid fisheries. To date, there is limited information concerning the changes of lncRNAs in RTG-2 cells infected by IHNV. In this study, a comparative transcriptome analysis of lncRNAs was performed in RTG-2 cells with and without IHNV infection to determine their changes and the effects on IHNV infection. The results showed that IHNV infection significantly changed the expression levels of lncRNAs and mRNAs, including 3693 differentially expressed lncRNAs (DE-lncRNAs) and 3503 differentially expressed mRNAs (DE-mRNAs) respectively. These DE-lncRNAs and DE-mRNAs induced by IHNV were mostly associated with immune response, RNA processing, and viral diseases related pathways. Further analysis found that some DE-lncRNAs might participate in the regulation of extracellular matrix metabolism, apoptosis, lipid synthesis, autophagy, and immune responses referring to the functions of their target genes. Afterwards, 349 co-expression relationships were constructed by 223 DE-lncRNAs and 271 DE-mRNAs, of which LTCONS_00146935 was the pivotal node in the interaction networks, and was together with its target genes modulated the immune responses under the IHNV infection. RT-qPCR results showed that the changes of the selected immune-related DEGs were in consistent with the RNA-seq data, suggesting that the sequencing data was relatively reliable. In summary, this is the first study to determine the changes and interactions of lncRNA-mRNA in RTG-2 cells under the IHNV infection. The results provided the valuable information concerning the lncRNAs in salmonid fish, which will benefit for future study on uncovering the roles of lncRNAs-mRNAs during the viral infection.
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Affiliation(s)
- Guangming Ren
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China; State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Liming Xu
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Jingzhuang Zhao
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Yizhi Shao
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China
| | - Tongyan Lu
- Department of Aquatic Animal Diseases and Control, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Key Laboratory of Aquatic Animal Diseases and Immune Technology of Heilongjiang Province, Harbin, 150070, China; Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, 430223, China.
| | - Qiya Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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11
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Yang Y, Liu S, He C, Chen Z, Lyu T, Zeng L, Wang L, Zhang F, Chen H, Zhao RC. Long Non-coding RNA Regulation of Mesenchymal Stem Cell Homeostasis and Differentiation: Advances, Challenges, and Perspectives. Front Cell Dev Biol 2021; 9:711005. [PMID: 34368161 PMCID: PMC8339964 DOI: 10.3389/fcell.2021.711005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 06/21/2021] [Indexed: 12/25/2022] Open
Abstract
Given the self-renewal, multi-differentiation, immunoregulatory, and tissue maintenance properties, mesenchymal stem cells (MSCs) are promising candidates for stem cell-based therapies. Breakthroughs have been made in uncovering MSCs as key contributors to homeostasis and the regenerative repair of tissues and organs derived from three germ layers. MSC differentiation into specialized cell types is sophisticatedly regulated, and accumulating evidence suggests long non-coding RNAs (lncRNAs) as the master regulators of various biological processes including the maintenance of homeostasis and multi-differentiation functions through epigenetic, transcriptional, and post-translational mechanisms. LncRNAs are ubiquitous and generally referred to as non-coding transcripts longer than 200 bp. Most lncRNAs are evolutionary conserved and species-specific; however, the weak conservation of their sequences across species does not affect their diverse biological functions. Although numerous lncRNAs have been annotated and studied, they are nevertheless only the tip of the iceberg; the rest remain to be discovered. In this review, we characterize MSC functions in homeostasis and highlight recent advances on the functions and mechanisms of lncRNAs in regulating MSC homeostasis and differentiation. We also discuss the current challenges and perspectives for understanding the roles of lncRNAs in MSC functions in homeostasis, which could help develop promising targets for MSC-based therapies.
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Affiliation(s)
- Yanlei Yang
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,Beijing Key Laboratory (No. BZO381), School of Basic Medicine, Center of Excellence in Tissue Engineering, Peking Union Medical College Hospital, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Suying Liu
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Chengmei He
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Zhilei Chen
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Taibiao Lyu
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Liuting Zeng
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Li Wang
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Fengchun Zhang
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Hua Chen
- Key Laboratory of the Ministry of Education, Department of Rheumatology and Clinical Immunology, Clinical Immunology Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Robert Chunhua Zhao
- Beijing Key Laboratory (No. BZO381), School of Basic Medicine, Center of Excellence in Tissue Engineering, Peking Union Medical College Hospital, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.,School of Life Sciences, Shanghai University, Shanghai, China
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12
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Wei S, Chen Y, Huang L, Ma H, Qi L, Wang Q, Sun M, Zhang X, Sha Z. Analysis of lncRNA and mRNA expression profiles in peripheral blood leukocytes of the half-smooth tongue sole (Cynoglossus semilaevis) treated with chitosan oligosaccharide. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 120:104043. [PMID: 33621610 DOI: 10.1016/j.dci.2021.104043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
Long noncoding RNAs (lncRNAs) play a multifaceted role in transcriptional regulation and are important regulators of immune function. Scarce information is available regarding lncRNAs in fish. Peripheral blood mononuclear cells participate in the immune response of fish and aid resistance to infection with pathogenic microorganisms. Chitosan oligosaccharide can improve cellular and humoral immunity to enhance disease resistance in fish. In this study, we obtained peripheral blood leukocytes from half-smooth tongue sole and studied the effect of chitosan oligosaccharide on the lncRNA-mRNA expression profile of these cells using high-throughput sequencing and bioinformatics techniques. A total of 609 differentially expressed mRNAs and 50 differentially expressed lncRNAs were identified. The GO term enrichment analysis of the differentially expressed genes was annotated by 220 GO terms, 137 biological processes, 18 cellular components, and 65 molecular functions. Sixteen KEGG pathways, including immune signaling pathways, metabolism, and genetic information processing, were significantly enriched in differentially expressed genes. Thirty-six differentially expressed lncRNAs and 32 differentially expressed mRNAs produced a coexpression network containing 90 relationship pairs. The prediction of lncRNA target genes revealed 244 lncRNAs that potentially cis-regulated 294 differentially expressed mRNAs. qPCR verified that the expression levels of 17 differentially expressed lncRNAs and 15 differentially expressed mRNAs were consistent with the RNA-Seq results. Among them, 6 lncRNAs and 7 mRNAs were differentially expressed genes obtained from the prediction and analysis of lncRNA target genes, and 8 lncRNAs and 4 mRNAs were differentially expressed genes that participated in the construction of the coexpression network. In peripheral blood leukocytes after chitosan oligosaccharide treatment, as well as in peripheral blood and spleen after Vibrio anguillarum stimulation, lncRNAs and mRNAs showed significant differential expression. The results indicated that they may be related to the immune response, providing novel reference information for further research on the role of lncRNAs in immune regulation in half-smooth tongue sole.
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Affiliation(s)
- Shu Wei
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Yadong Chen
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China; Key Laboratory for Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China
| | - Lin Huang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Hui Ma
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Longjiang Qi
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Qian Wang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Mengjie Sun
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Xue Zhang
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China
| | - Zhenxia Sha
- Institute of Biomedical Engineering, College of Life Sciences, Qingdao University, Qingdao, 266071, China; Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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13
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Zhang Y, Chang J, Jiang W, Ye X, Zhang S. Long non-coding RNA CASC9/microRNA-590-3p axis participates in lutein-mediated suppression of breast cancer cell proliferation. Oncol Lett 2021; 22:544. [PMID: 34084220 PMCID: PMC8161424 DOI: 10.3892/ol.2021.12805] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/23/2021] [Indexed: 12/16/2022] Open
Abstract
Previous studies have shown that lutein can inhibit the proliferation of breast cancer cells. However, the mechanism of lutein inhibiting the proliferation of breast cancer cells remains unclear. The present study aimed to determine whether the long non-coding RNA (lncRNA) Cancer Susceptibility 9 (CASC9)/microRNA (miR)-590-3p axis participates in the antiproliferative effects of lutein via lncRNA microarray hybridization, reverse transcription-quantitative PCR, dual-luciferase reporter and MTT assays. The results demonstrated that CASC9 was the most significantly downregulated lncRNA in MCF7 cells treated with lutein. miR-590-3p was identified as the target of CASC9. In addition, lutein downregulated CASC9 expression and upregulated miR-590-3p expression in dose- and time-dependent manners, respectively. CASC9 knockdown or overexpression of miR-590-3p inhibited the proliferation of breast cancer cells. Notably, simultaneous transfection with miR-590-3p mimics and CASC9 small interfering RNA increased the potency of lutein in inhibiting the proliferation of breast cancer cells. Taken together, these results suggest that the CASC9/miR-590-3p axis participates in the antiproliferative effects of lutein on breast cancer.
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Affiliation(s)
- Yuxia Zhang
- Department of Biochemistry and Molecular Biology, Shangqiu Medical College, Shangqiu, Henan 476100, P.R. China
| | - Jingzhi Chang
- Department of Biochemistry and Molecular Biology, Shangqiu Medical College, Shangqiu, Henan 476100, P.R. China
| | - Weiwei Jiang
- Department of Medical College, Shangqiu Institute of Technology, Shangqiu, Henan 476400, P.R. China
| | - Xin Ye
- Department of Biochemistry and Molecular Biology, Shangqiu Medical College, Shangqiu, Henan 476100, P.R. China
| | - Shanfeng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450001, P.R. China
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14
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Khan S, Masood M, Gaur H, Ahmad S, Syed MA. Long non-coding RNA: An immune cells perspective. Life Sci 2021; 271:119152. [PMID: 33548285 DOI: 10.1016/j.lfs.2021.119152] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 01/14/2021] [Accepted: 01/24/2021] [Indexed: 02/08/2023]
Abstract
Long non-coding RNAs (lncRNAs) were considered as accumulated genetic waste until they were found to be gene expression regulators by highly sensitive modern genomics platforms. It is a huge class of non-coding transcripts with an arbitrary length of >200 nucleotides, which has gained much attention in the past few years. Increasing evidence from several experimental studies unraveled the expression of lncRNA linked to immune response and disease progression. However, only a small number of lncRNAs have robust evidence of their function. Differential expression of lncRNAs in different immune cells is also evident. In this review, we focused on how lncRNAs expression assist in shaping immune cells (Macrophages, Dendritic cells, NK cells, T cells, B cells, eosinophils, neutrophils, and microglial cells) function and their response to the diseased conditions. Emerging evidence revealed lncRNAs may serve as key regulators in the innate and adaptive immune response system. So, the molecular mechanism insight into the function of lncRNAs in immune response may contribute to the development of potential therapeutic targets for various disease treatments. Therefore, it is imperative to explore the expression of lncRNAs and understand its relevance associated with the immune system.
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Affiliation(s)
- Salman Khan
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Mohammad Masood
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India
| | - Harshita Gaur
- Department of Life Sciences, University of Glasgow, United Kingdom
| | - Shaniya Ahmad
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
| | - Mansoor Ali Syed
- Department of Biotechnology, Jamia Millia Islamia, New Delhi, India.
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15
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Luo D, Liu F, Zhang J, Shao Q, Tao W, Xiao R, Dai W, Ding C, Qian K. Comprehensive Analysis of LncRNA-mRNA Expression Profiles and the ceRNA Network Associated with Pyroptosis in LPS-Induced Acute Lung Injury. J Inflamm Res 2021; 14:413-428. [PMID: 33628043 PMCID: PMC7898231 DOI: 10.2147/jir.s297081] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 01/22/2021] [Indexed: 12/11/2022] Open
Abstract
Purpose To explore the molecular mechanism and search for candidate lncRNA and mRNA associated with pyroptosis in the gene expression profile of LPS-induced acute lung injury (ALI). Methods We investigated lncRNA and mRNA expression in lipopolysaccharide (LPS)-induced ALI at an early stage. RNA sequencing (RNA-Seq) was carried out to analyze lncRNA and mRNA expression profiles between the LPS-induced and control groups. We used bioinformatics analysis to predict target genes of early differential lncRNAs among obtained the differential mRNAs. Results A total of 78 lncRNAs and 248 mRNAs were upregulated at 2 hours and downregulated at 9 hours, and 21 lncRNAs and 107 mRNAs were downregulated at 2 and upregulated at 9 hours in early ALI models. We predicted 7 cis-and trans-regulated target genes of the top 20 lncRNAs. Gene Ontology (GO) analysis indicated that the target genes for the screened lncRNAs were most enriched in three-terms: regulation of protein serine/threonine kinase activity, pertussis, and cellular response to LPS. Additionally, target genes of lncRNAs were the top three enriched in pertussis, osteoclast differentiation, and cAMP signaling pathways with Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. We also identified vital mRNAs and lncRNAs. Protein-protein interaction (PPI) network analysis suggested that Tnf, Jun, and Atf3 were the top three key genes. Hub lncRNA4344 (NONRATT004344.2) and cis-regulated target mRNA (NLRP3) were validated in vitro. Finally, luciferase assay results confirmed that lncRNA4344 sponged miR‐138-5p to promote pyroptosis in inflammatory responses to LPS‐induced acute lung injury by targeting NLRP3. Conclusion Based on analysis of lncRNA and mRNA expression profiles by RNA-Seq and experimental verification, this study is the first to reveal that lncRNA4344 sponged miR‐138-5p to promote pyroptosis in inflammatory responses of LPS‐induced acute lung injury by targeting NLRP3. These newly identified lncRNA, miRNA, and mRNA might be novel potential targets for early treatment and prevention in early ALI.
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Affiliation(s)
- Deqiang Luo
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China.,Department of Intensive Care Unit, The Fifth People's Hospital of Shangrao City, Shangrao, 334000, People's Republic of China
| | - Fen Liu
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Jianguo Zhang
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Qiang Shao
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Wenqiang Tao
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Rui Xiao
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Wei Dai
- Department of Intensive Care Unit, The Fifth People's Hospital of Shangrao City, Shangrao, 334000, People's Republic of China
| | - Chengzhi Ding
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
| | - Kejian Qian
- Department of Intensive Care Unit, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi Province, 330000, People's Republic of China
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16
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Li W, Hua R, Wang M, Zhang D, Zhu J, Zhang S, Yang Y, Cheng J, Zhou H, Zhang J, He J. H19 gene polymorphisms and Wilms tumor risk in Chinese children: a four-center case-control study. Mol Genet Genomic Med 2021; 9:e1584. [PMID: 33403826 PMCID: PMC8077085 DOI: 10.1002/mgg3.1584] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/05/2020] [Accepted: 12/15/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Wilms tumor is the most common pediatric renal cancer. However, genetic bases behind Wilms tumor remain largely unknown. H19 is a critical maternally imprinted gene. Previous studies indicated that single nucleotide polymorphisms (SNPs) in the H19 can modify the risk of several human malignancies. Epigenetic errors at the H19 locus lead to biallelic silencing in Wilms tumors. Genetic variations in the H19 may be related to Wilms tumor susceptibility. METHODS We conducted a four-center study to investigate whether H19 SNP was a predisposing factor to Wilms tumor. Three polymorphisms in the H19 (rs2839698 G > A, rs3024270 C > G, rs217727 G > A) were genotyped in 355 cases and 1070 cancer-free controls, using Taqman method. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated to evaluate the strength of the associations. RESULTS We found that all of these three polymorphisms were significantly associated with Wilms tumor risk alterations. The rs2839698 G > A polymorphism (AG vs. GG: adjusted OR = 0.74, 95% CI = 0.57-0.96, p = 0.024; AA vs. GG: adjusted OR = 1.52, 95% CI = 1.05-2.22, p = 0.027), the rs3024270 C > G polymorphism (CG vs. CC: adjusted OR = 0.61, 95% CI = 0.46-0.81, p = 0.0007; and the rs217727 polymorphism (AG vs. GG: adjusted OR = 0.76, 95% CI = 0.58-0.99, p = 0.035). The Carriers of 1, 2, and 1-2 risk genotypes were inclined to develop Wilms tumor compared with those without risk genotype (adjusted OR = 1.36, 95% CI = 1.02-1.80, p = 0.037; adjusted OR = 1.84, 95% CI = 1.27-2.67, p = 0.001; adjusted OR = 1.50, 95% CI = 1.17-1.92, p = 0.002, respectively). The stratified analysis further revealed that rs2839698 AA, rs217727 AA, and 1-2 risk genotypes could strongly increase Wilms tumor risk among children above 18 months of age, males, and with clinical stage I+II disease. CONCLUSION Our findings indicate that genetic variations in the H19 may confer Wilms tumor risk.
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Affiliation(s)
- Wenya Li
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Rui‐Xi Hua
- Department of OncologyThe First Affiliated Hospital of Sun Yat‐sen UniversityGuangzhouChina
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Mi Wang
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
| | - Da Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jinhong Zhu
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
- Department of Clinical LaboratoryBiobankHarbin Medical University Cancer HospitalHarbinChina
| | - Songyang Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Yang Yang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jiwen Cheng
- Department of Pediatric Surgerythe Second Affiliated Hospital of Xi'an Jiaotong UniversityXi'anChina
| | - Haixia Zhou
- Department of HematologyThe Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical UniversityWenzhouChina
| | - Jiao Zhang
- Department of Pediatric SurgeryThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Jing He
- Department of Pediatric SurgeryGuangzhou Institute of PediatricsGuangdong Provincial Key Laboratory of Research in Structural Birth Defect DiseaseGuangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouChina
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Idlett-Ali S, Liechty K, Xu J. Upregulation of long noncoding RNA growth arrest-specific 5 mediates pro-inflammatory mechanisms of diabetic wound healing impairment. DERMATOLOGY JOURNAL 2021; 1:8-10. [PMID: 35464754 PMCID: PMC9027011 DOI: 10.46439/derma.1.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Unresolved inflammatory processes contribute to impaired healing in diabetic wounds, with increasing evidence implicating persistent pro-inflammatory macrophage polarization as a driver of chronic inflammation and delayed wound closure. Previous investigations aimed to uncover the role of regulatory RNAs in macrophage polarization and to understand how aberrant expression patterns contribute to wound healing impairment, with the goal of identifying novel therapeutic targets for promoting normal wound healing progression. In the Journal of Investigative Dermatology, Hu et al. reveal a role of the tumor suppressor, long noncoding RNA (lncRNA) Growth Arrest-Specific 5 (GAS5), in regulating macrophage polarization. Of note, their findings suggest that hyperglycemia induces overexpression of GAS5 which subsequently results in a greater production of the pro-inflammatory macrophage phenotype. Knockdown of GAS5 in diabetic wounds normalized healing time, highlighting the potential therapeutic value of targeting GAS5 for enhanced wound healing progression.
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Affiliation(s)
- Shaquia Idlett-Ali
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Colorado, Denver-Anschutz Medical Campus and Children’s Hospital of Colorado, Aurora, Colorado 80045, USA
| | - Kenneth Liechty
- Laboratory for Fetal and Regenerative Biology, Department of Surgery, University of Colorado, Denver-Anschutz Medical Campus and Children’s Hospital of Colorado, Aurora, Colorado 80045, USA
| | - Junwang Xu
- Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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18
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Interferon-Mediated Long Non-Coding RNA Response in Macrophages in the Context of HIV. Int J Mol Sci 2020; 21:ijms21207741. [PMID: 33086748 PMCID: PMC7589721 DOI: 10.3390/ijms21207741] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/07/2023] Open
Abstract
Interferons play a critical role in the innate immune response against a variety of pathogens, such as HIV-1. Recent studies have shown that long non-coding genes are part of a reciprocal feedforward/feedback relationship with interferon expression. They presumably contribute to the cell type specificity of the interferon response, such as the phenotypic and functional transition of macrophages throughout the immune response. However, no comprehensive understanding exists today about the IFN–lncRNA interplay in macrophages, also a sanctuary for latent HIV-1. Therefore, we completed a poly-A+ RNAseq analysis on monocyte-derived macrophages (MDMs) treated with members of all three types of IFNs (IFN-α, IFN-ε, IFN-γ or IFN-λ) and on macrophages infected with HIV-1, revealing an extensive non-coding IFN and/or HIV-1 response. Moreover, co-expression correlation with mRNAs was used to identify important (long) non-coding hub genes within IFN- or HIV-1-associated gene clusters. This study identified and prioritized IFN related hub lncRNAs for further functional validation.
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19
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Macrophage Long Non-Coding RNAs in Pathogenesis of Cardiovascular Disease. Noncoding RNA 2020; 6:ncrna6030028. [PMID: 32664594 PMCID: PMC7549353 DOI: 10.3390/ncrna6030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 12/21/2022] Open
Abstract
Chronic inflammation is inextricably linked to cardiovascular disease (CVD). Macrophages themselves play important roles in atherosclerosis, as well as acute and chronic heart failure. Although the role of macrophages in CVD pathophysiology is well-recognized, little is known regarding the precise mechanisms influencing their function in these contexts. Long non-coding RNAs (lncRNAs) have emerged as significant regulators of macrophage function; as such, there is rising interest in understanding how these nucleic acids influence macrophage signaling, cell fate decisions, and activity in health and disease. In this review, we summarize current knowledge regarding lncRNAs in directing various aspects of macrophage function in CVD. These include foam cell formation, Toll-like receptor (TLR) and NF-kβ signaling, and macrophage phenotype switching. This review will provide a comprehensive understanding concerning previous, ongoing, and future studies of lncRNAs in macrophage functions and their importance in CVD.
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Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27. Int J Mol Sci 2019; 20:ijms20246207. [PMID: 31835347 PMCID: PMC6941108 DOI: 10.3390/ijms20246207] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/04/2019] [Accepted: 12/06/2019] [Indexed: 12/20/2022] Open
Abstract
Macrophages play an essential role in the immune system. Recent studies have shown that long non-coding RNAs (lncRNAs) can regulate genes encoding products involved in the immune response. Interleukin (IL)-27 is a member of the IL-6/IL-12 family of cytokines with broad anti-viral effects that inhibits human immunodeficiency virus (HIV) type-1 and herpes simplex virus (HSV). However, little is known about the role of lncRNAs in macrophages affected by IL-27. Therefore, we investigated the expression profiles of mRNA and lncRNA in human monocyte-derived macrophages (MDMs) regulated by IL-27. Monocytes were differentiated in the presence of macrophage-colony stimulatory factor (M-CSF)- or human AB serum with or without IL-27, and these cells were the subject for the profile analysis using RNA-Seq. We identified 146 lncRNAs (including 88 novel ones) and 434 coding genes were differentially regulated by IL-27 in both M-CSF- and AB serum-induced macrophages. Using weighted gene co-expression network analysis, we obtained four modules. The immune system, cell cycle, and regulation of complement cascade pathways were enriched in different modules. The network of mRNAs and lncRNAs in the pathways suggest that lncRNAs might regulate immune activity in macrophages. This study provides potential insight into the roles of lncRNA in macrophages regulated by IL-27.
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Rizzacasa B, Amati F, Romeo F, Novelli G, Mehta JL. Epigenetic Modification in Coronary Atherosclerosis. J Am Coll Cardiol 2019; 74:1352-1365. [DOI: 10.1016/j.jacc.2019.07.043] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 07/15/2019] [Indexed: 02/06/2023]
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Liu X, Lu Y, Zhu J, Liu M, Xie M, Ye M, Li M, Wang S, Ming Z, Tong Q, Liu F, Zhou R. A Long Noncoding RNA, Antisense IL-7, Promotes Inflammatory Gene Transcription through Facilitating Histone Acetylation and Switch/Sucrose Nonfermentable Chromatin Remodeling. THE JOURNAL OF IMMUNOLOGY 2019; 203:1548-1559. [PMID: 31383742 DOI: 10.4049/jimmunol.1900256] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 07/08/2019] [Indexed: 12/16/2022]
Abstract
Long noncoding RNAs are important regulators of gene expression in innate immune responses. Antisense IL-7 (IL-7-AS) is a newly discovered long noncoding RNA in human and mouse that has been reported to regulate the expression of IL-6. However, the potential function of IL-7-AS in innate immune system is not fully understood. In this study, we found that the expression of IL-7-AS is primarily dependent on the NF-κB and MAPK signaling pathways in macrophages and intestinal epithelial cells. Functionally, IL-7-AS promotes the expression of several inflammatory genes, including CCL2, CCL5, CCL7, and IL-6, in cells in response to LPS. Specifically, IL-7-AS physically interacts with p300 to regulate histone acetylation levels around the promoter regions of these gene loci. Moreover, IL-7-AS and p300 complex modulate the assembly of SWI/SNF complex to the promoters. IL-7-AS regulates chemotaxis activity of monocytes to intestine epithelial cells with involvement of CCL2. Therefore, our data indicate a new promoting role for NF-κB/MAPK-responsive IL-7-AS in the transcriptional regulation of inflammatory genes in the innate immune system although modulation of histone acetylation around the promoters of related genes.
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Affiliation(s)
- Xu Liu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China.,Department of Biochemistry and Molecular Biology, Medical College, Hubei Minzu University, Enshi 445000, Hubei, People's Republic of China
| | - Yajing Lu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China.,Department of Endocrinology, Institute of Geriatric Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430077, Hubei, People's Republic of China
| | - Jie Zhu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Mingjia Liu
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Minghong Xie
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Mengling Ye
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Mingxuan Li
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Shuhong Wang
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Zhenping Ming
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China
| | - Qiang Tong
- Department of Gastrointestinal Surgery Section, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, People's Republic of China; and
| | - Feng Liu
- School of Computer Sciences, Wuhan University, Wuhan 430072, Hubei, People's Republic of China
| | - Rui Zhou
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan 430071, Hubei, People's Republic of China;
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Hennessy EJ, van Solingen C, Scacalossi KR, Ouimet M, Afonso MS, Prins J, Koelwyn GJ, Sharma M, Ramkhelawon B, Carpenter S, Busch A, Chernogubova E, Matic LP, Hedin U, Maegdefessel L, Caffrey BE, Hussein MA, Ricci EP, Temel RE, Garabedian MJ, Berger JS, Vickers KC, Kanke M, Sethupathy P, Teupser D, Holdt LM, Moore KJ. The long noncoding RNA CHROME regulates cholesterol homeostasis in primate. Nat Metab 2019; 1:98-110. [PMID: 31410392 PMCID: PMC6691505 DOI: 10.1038/s42255-018-0004-9] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The human genome encodes thousands of long non-coding RNAs (lncRNAs), the majority of which are poorly conserved and uncharacterized. Here we identify a primate-specific lncRNA (CHROME), elevated in the plasma and atherosclerotic plaques of individuals with coronary artery disease, that regulates cellular and systemic cholesterol homeostasis. LncRNA CHROME expression is influenced by dietary and cellular cholesterol via the sterol-activated liver X receptor transcription factors, which control genes mediating responses to cholesterol overload. Using gain- and loss-of-function approaches, we show that CHROME promotes cholesterol efflux and HDL biogenesis by curbing the actions of a set of functionally related microRNAs that repress genes in those pathways. CHROME knockdown in human hepatocytes and macrophages increases levels of miR-27b, miR-33a, miR-33b and miR-128, thereby reducing expression of their overlapping target gene networks and associated biologic functions. In particular, cells lacking CHROME show reduced expression of ABCA1, which regulates cholesterol efflux and nascent HDL particle formation. Collectively, our findings identify CHROME as a central component of the non-coding RNA circuitry controlling cholesterol homeostasis in humans.
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Affiliation(s)
- Elizabeth J. Hennessy
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Coen van Solingen
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Kaitlyn R. Scacalossi
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Mireille Ouimet
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Milessa S. Afonso
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Jurrien Prins
- Department of Internal Medicine (Nephrology), Einthoven
Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center,
Leiden, The Netherlands
| | - Graeme J. Koelwyn
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Monika Sharma
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Bhama Ramkhelawon
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology,
University of California, Santa Cruz, California, USA
| | - Albert Busch
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
- Department of Vascular and Endovascular Surgery, Klinikum
Rechts der Isar, Technical University Munich, Munich, Germany
| | | | - Ljubica Perisic Matic
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
| | - Ulf Hedin
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
| | - Lars Maegdefessel
- Department of Molecular Medicine and Surgery, Karolinska
Institute, Stockholm, Sweden
- Department of Vascular and Endovascular Surgery, Klinikum
Rechts der Isar, Technical University Munich, Munich, Germany
| | | | - Maryem A. Hussein
- Department of Microbiology, New York University School of
Medicine, New York, New York, USA
| | - Emiliano P. Ricci
- INSERM U1111, Centre International de Recherche en
Infectiologie, Ecole Normale Supérieure de Lyon, Université de Lyon,
Lyon, France
| | - Ryan E. Temel
- Saha Cardiovascular Research Center, University of
Kentucky, Lexington, Kentucky, USA
| | - Michael J. Garabedian
- Department of Microbiology, New York University School of
Medicine, New York, New York, USA
| | - Jeffrey S. Berger
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
| | - Kasey C. Vickers
- Department of Medicine, Vanderbilt University Medical
Center, Nashville, Tenessee, USA
| | - Matthew Kanke
- Department of Biomedical Sciences, College of Veterinary
Medicine, Cornell University Ithaca, New York, USA
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary
Medicine, Cornell University Ithaca, New York, USA
| | - Daniel Teupser
- Institute of Laboratory Medicine,
Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lesca M. Holdt
- Institute of Laboratory Medicine,
Ludwig-Maximilians-University Munich, Munich, Germany
| | - Kathryn J. Moore
- Department of Medicine, Leon H. Charney Division of
Cardiology, New York University School of Medicine, New York, New York, USA
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