1
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Montano C, Flores-Arenas C, Carpenter S. LncRNAs, nuclear architecture and the immune response. Nucleus 2024; 15:2350182. [PMID: 38738760 PMCID: PMC11093052 DOI: 10.1080/19491034.2024.2350182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024] Open
Abstract
Long noncoding RNAs (LncRNAs) are key regulators of gene expression and can mediate their effects in both the nucleus and cytoplasm. Some of the best-characterized lncRNAs are localized within the nucleus, where they modulate the nuclear architecture and influence gene expression. In this review, we discuss the role of lncRNAs in nuclear architecture in the context of their gene regulatory functions in innate immunity. Here, we discuss various approaches to functionally characterize nuclear-localized lncRNAs and the challenges faced in the field.
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Affiliation(s)
- Christy Montano
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Flores-Arenas
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Susan Carpenter
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
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2
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Leask MP, Crișan TO, Ji A, Matsuo H, Köttgen A, Merriman TR. The pathogenesis of gout: molecular insights from genetic, epigenomic and transcriptomic studies. Nat Rev Rheumatol 2024; 20:510-523. [PMID: 38992217 DOI: 10.1038/s41584-024-01137-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2024] [Indexed: 07/13/2024]
Abstract
The pathogenesis of gout involves a series of steps beginning with hyperuricaemia, followed by the deposition of monosodium urate crystal in articular structures and culminating in an innate immune response, mediated by the NLRP3 inflammasome, to the deposited crystals. Large genome-wide association studies (GWAS) of serum urate levels initially identified the genetic variants with the strongest effects, mapping mainly to genes that encode urate transporters in the kidney and gut. Other GWAS highlighted the importance of uncommon genetic variants. More recently, genetic and epigenetic genome-wide studies have revealed new pathways in the inflammatory process of gout, including genetic associations with epigenomic modifiers. Epigenome-wide association studies are also implicating epigenomic remodelling in gout, which perhaps regulates the responsiveness of the innate immune system to monosodium urate crystals. Notably, genes implicated in gout GWAS do not include those encoding components of the NLRP3 inflammasome itself, but instead include genes encoding molecules involved in its regulation. Knowledge of the molecular mechanisms underlying gout has advanced through the translation of genetic associations into specific molecular mechanisms. Notable examples include ABCG2, HNF4A, PDZK1, MAF and IL37. Current genetic studies are dominated by participants of European ancestry; however, studies focusing on other population groups are discovering informative population-specific variants associated with gout.
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Affiliation(s)
- Megan P Leask
- Department of Physiology, University of Otago, Dunedin, Aotearoa, New Zealand
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tania O Crișan
- Department of Medical Genetics, "Iuliu Haţieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Aichang Ji
- Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama, Japan
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Faculty of Medicine and Medical Center - University of Freiburg, Freiburg, Germany
| | - Tony R Merriman
- Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Microbiology and Immunology, University of Otago, Dunedin, Aotearoa, New Zealand.
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3
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Bechtold V, Smolen KK, Burny W, de Angelis SP, Delandre S, Essaghir A, Marchant A, Ndour C, Taton M, van der Most R, Willems F, Didierlaurent AM. Functional and epigenetic changes in monocytes from adults immunized with an AS01-adjuvanted vaccine. Sci Transl Med 2024; 16:eadl3381. [PMID: 39083587 DOI: 10.1126/scitranslmed.adl3381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 03/25/2024] [Accepted: 06/10/2024] [Indexed: 08/02/2024]
Abstract
The adjuvant AS01 plays a key role in the immunogenicity of several approved human vaccines with demonstrated high efficacy. Its adjuvant effect relies on activation of the innate immune system. However, specific effects of AS01-adjuvanted vaccines on innate cell function and epigenetic remodeling, as described for Bacille Calmette-Guérin (BCG) and influenza vaccines, are still unknown. We assessed the long-term functional and epigenetic changes in circulating monocytes and dendritic cells induced by a model vaccine containing hepatitis B surface antigen and AS01 in healthy adults (NCT01777295). The AS01-adjuvanted vaccine, but not an Alum-adjuvanted vaccine, increased the number of circulating monocytes and their expression of human leukocyte antigen (HLA)-DR, which correlated with the magnitude of the memory CD4+ T cell response. Single-cell analyses revealed epigenetic alterations in monocyte and dendritic cell subsets, affecting accessibility of transcription factors involved in cell functions including activator protein-1 (AP-1), GATA, C/EBP, and interferon regulatory factor. The functional changes were characterized by a reduced proinflammatory response to Toll-like receptor activation and an improved response to interferon-γ, a cytokine critical for the adjuvant's mode of action. Epigenetic changes were most evident shortly after the second vaccine dose in CD14+ monocytes, for which accessibility differences of some transcription factors could persist for up to 6 months postvaccination. Together, we show that reprogramming of monocyte subsets occurs after vaccination with an AS01-adjuvanted vaccine, an effect that may contribute to the impact of vaccination beyond antigen-specific protection.
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Affiliation(s)
| | - Kinga K Smolen
- GSK, Rixensart, 1330, Belgium
- Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Faculty of Medicine, Université libre de Bruxelles (ULB), Brussels, 1070, Belgium
| | | | | | | | | | - Arnaud Marchant
- Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Faculty of Medicine, Université libre de Bruxelles (ULB), Brussels, 1070, Belgium
| | - Cheikh Ndour
- Business and Decision Life Sciences c/o GSK, Rixensart, 1330, Belgium
| | - Martin Taton
- Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Faculty of Medicine, Université libre de Bruxelles (ULB), Brussels, 1070, Belgium
| | | | - Fabienne Willems
- Institute for Medical Immunology and ULB Center for Research in Immunology (U-CRI), Faculty of Medicine, Université libre de Bruxelles (ULB), Brussels, 1070, Belgium
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Kim HY, Kang YJ, Kim DH, Jang J, Lee SJ, Kim G, Koh HB, Ko YE, Shin HM, Lee H, Yoo TH, Lee WW. Uremic toxin indoxyl sulfate induces trained immunity via the AhR-dependent arachidonic acid pathway in end-stage renal disease (ESRD). eLife 2024; 12:RP87316. [PMID: 38980302 PMCID: PMC11233136 DOI: 10.7554/elife.87316] [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] [Indexed: 07/10/2024] Open
Abstract
Trained immunity is the long-term functional reprogramming of innate immune cells, which results in altered responses toward a secondary challenge. Despite indoxyl sulfate (IS) being a potent stimulus associated with chronic kidney disease (CKD)-related inflammation, its impact on trained immunity has not been explored. Here, we demonstrate that IS induces trained immunity in monocytes via epigenetic and metabolic reprogramming, resulting in augmented cytokine production. Mechanistically, the aryl hydrocarbon receptor (AhR) contributes to IS-trained immunity by enhancing the expression of arachidonic acid (AA) metabolism-related genes such as arachidonate 5-lipoxygenase (ALOX5) and ALOX5 activating protein (ALOX5AP). Inhibition of AhR during IS training suppresses the induction of IS-trained immunity. Monocytes from end-stage renal disease (ESRD) patients have increased ALOX5 expression and after 6 days training, they exhibit enhanced TNF-α and IL-6 production to lipopolysaccharide (LPS). Furthermore, healthy control-derived monocytes trained with uremic sera from ESRD patients exhibit increased production of TNF-α and IL-6. Consistently, IS-trained mice and their splenic myeloid cells had increased production of TNF-α after in vivo and ex vivo LPS stimulation compared to that of control mice. These results provide insight into the role of IS in the induction of trained immunity, which is critical during inflammatory immune responses in CKD patients.
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Affiliation(s)
- Hee Young Kim
- Department of Microbiology and Immunology, Seoul National University College of MedicineSeoulRepublic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul National University College of MedicineSeoulRepublic of Korea
| | - Yeon Jun Kang
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of MedicineSeoulRepublic of Korea
| | - Dong Hyun Kim
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of MedicineSeoulRepublic of Korea
| | - Jiyeon Jang
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of MedicineSeoulRepublic of Korea
| | - Su Jeong Lee
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of MedicineSeoulRepublic of Korea
| | - Gwanghun Kim
- Department of Biomedical Sciences, College of Medicine and BK21Plus Biomedical Science Project, Seoul National University College of MedicineSeoulRepublic of Korea
| | - Hee Byung Koh
- Department of Internal Medicine, College of Medicine, Yonsei UniversitySeoulRepublic of Korea
| | - Ye Eun Ko
- Department of Internal Medicine, College of Medicine, Yonsei UniversitySeoulRepublic of Korea
| | - Hyun Mu Shin
- Department of Biomedical Sciences, College of Medicine and BK21Plus Biomedical Science Project, Seoul National University College of MedicineSeoulRepublic of Korea
- Wide River Institute of Immunology, Seoul National UniversityHongcheonRepublic of Korea
| | - Hajeong Lee
- Division of Nephrology, Department of Internal Medicine, Seoul National University HospitalSeoulRepublic of Korea
| | - Tae-Hyun Yoo
- Division of Nephrology, Department of Internal Medicine, Yonsei University College of MedicineSeoulRepublic of Korea
| | - Won-Woo Lee
- Department of Microbiology and Immunology, Seoul National University College of MedicineSeoulRepublic of Korea
- Institute of Endemic Diseases, Seoul National University Medical Research Center, Seoul National University College of MedicineSeoulRepublic of Korea
- Laboratory of Autoimmunity and Inflammation (LAI), Department of Biomedical Sciences, and BK21Plus Biomedical Science Project, Seoul National University College of MedicineSeoulRepublic of Korea
- Seoul National University Cancer Research Institute; Ischemic/Hypoxic Disease Institute, Seoul National University Medical Research Center, Seoul National University Hospital Biomedical Research InstituteSeoulRepublic of Korea
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5
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Khan H, Bhargava V, Elkins KL. Francisella tularensis Live Vaccine Strain training of murine alveolar and bone marrow-derived macrophages. Microbiol Spectr 2024:e0002824. [PMID: 38940590 DOI: 10.1128/spectrum.00028-24] [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: 01/04/2024] [Accepted: 05/28/2024] [Indexed: 06/29/2024] Open
Abstract
Traditionally, successful vaccines rely on specific adaptive immunity by activating lymphocytes with an attenuated pathogen, or pathogen subunit, to elicit heightened responses upon subsequent exposures. However, recent work with Mycobacterium tuberculosis and other pathogens has identified a role for "trained" monocytes in protection through memory-like but non-specific immunity. Here, we used an in vitro co-culture approach to study the potential role of trained macrophages, including lung alveolar macrophages, in immune responses to the Live Vaccine Strain (LVS) of Francisella tularensis. F. tularensis is an intracellular bacterium that replicates within mammalian macrophages and causes respiratory as well as systemic disease. We vaccinated mice with F. tularensis LVS and then obtained lung alveolar macrophages, or derived macrophages from bone marrow. LVS infected and replicated comparably in both types of macrophages, whether naïve or from LVS-vaccinated mice. LVS-infected macrophages were then co-cultured with either naïve splenocytes, splenocytes from mice vaccinated intradermally, or splenocytes from mice vaccinated intravenously. For the first time, we show that immune (but not naïve) splenocytes controlled bacterial replication within alveolar macrophages, similar to previous results using bone marrow-derived macrophage. However, no differences in control of intramacrophage bacterial replication were found between co-cultures with naïve macrophages or macrophages from LVS-vaccinated mice; furthermore, nitric oxide levels and interferon-gamma production in supernatants were largely comparable across all conditions. Thus, in the context of in vitro co-cultures, the data do not support development of trained macrophages in bone marrow or lungs of mice vaccinated with LVS intradermally or intravenously. IMPORTANCE The discovery of non-specific "trained immunity" in monocytes has generated substantial excitement. However, to date, training has been studied with relatively few microbes (e.g., Mycobacterium bovis Bacille Calmette-Guérin, a live attenuated intracellular bacterium used as a vaccine) and microbial substances (e.g., LPS), and it remains unclear whether training during infection is common. We previously demonstrated that vaccination of mice with Francisella tularensis Live Vaccine Strain (LVS), another live attenuated intracellular bacterium, protected against challenge with the unrelated bacterium Listeria monocytogenes. The present study therefore tested whether LVS vaccination engenders trained macrophages that contributed to this protection. To do so, we used a previous in vitro co-culture approach with murine bone marrow-derived macrophages to expand and study lung alveolar macrophages. We demonstrated that alveolar macrophages can be productively infected and employed to characterize interactions with LVS-immune lymphocytes. However, we find no evidence that either bone marrow-derived or alveolar macrophages are trained by LVS vaccination.
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Affiliation(s)
- Hamda Khan
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Varunika Bhargava
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
| | - Karen L Elkins
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, USA
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6
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Wang Z, Liu Y, Hu J, You X, Yang J, Zhang Y, Liu Q, Yang D. Tissue-resident trained immunity in hepatocytes protects against septic liver injury in zebrafish. Cell Rep 2024; 43:114324. [PMID: 38850536 DOI: 10.1016/j.celrep.2024.114324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 04/25/2024] [Accepted: 05/22/2024] [Indexed: 06/10/2024] Open
Abstract
Trained immunity is classically characterized by long-term functional reprogramming of innate immune cells to combat infectious diseases. Infection-induced organ injury is a common clinical severity phenotype of sepsis. However, whether the induction of trained immunity plays a role in protecting septic organ injury remains largely unknown. Here, through establishing an in vivo β-glucan training and lipopolysaccharide (LPS) challenge model in zebrafish larvae, we observe that induction of trained immunity could inhibit pyroptosis of hepatocytes to alleviate septic liver injury, with an elevated trimethyl-histone H3 lysine 4 (H3K4me3) modification that targets mitophagy-related genes. Moreover, we identify a C-type lectin domain receptor in zebrafish, named DrDectin-1, which is revealed as the orchestrator in gating H3K4me3 rewiring-mediated mitophagy activation and alleviating pyroptosis-engaged septic liver injury in vivo. Taken together, our results uncover tissue-resident trained immunity in maintaining liver homeostasis at the whole-animal level and offer an in vivo model to efficiently integrate trained immunity for immunotherapies.
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Affiliation(s)
- Zhuang Wang
- State Key Laboratory of Bioreactor Engineering, Laboratory for Aquatic Animal Diseases, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanyuan Liu
- State Key Laboratory of Bioreactor Engineering, Laboratory for Aquatic Animal Diseases, East China University of Science and Technology, Shanghai 200237, China
| | - Jing Hu
- State Key Laboratory of Bioreactor Engineering, Laboratory for Aquatic Animal Diseases, East China University of Science and Technology, Shanghai 200237, China
| | - Xinwei You
- State Key Laboratory of Bioreactor Engineering, Laboratory for Aquatic Animal Diseases, East China University of Science and Technology, Shanghai 200237, China
| | - Jin Yang
- State Key Laboratory of Bioreactor Engineering, Laboratory for Aquatic Animal Diseases, East China University of Science and Technology, Shanghai 200237, China
| | - Yuanxing Zhang
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Qin Liu
- State Key Laboratory of Bioreactor Engineering, Laboratory for Aquatic Animal Diseases, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China
| | - Dahai Yang
- State Key Laboratory of Bioreactor Engineering, Laboratory for Aquatic Animal Diseases, East China University of Science and Technology, Shanghai 200237, China; Shanghai Engineering Research Center of Maricultured Animal Vaccines, Shanghai 200237, China.
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7
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Montano C, Covarrubias S, Malekos E, Katzman S, Carpenter S. Identification and Functional Characterization of lncRNAs involved in Human Monocyte-to-Macrophage Differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599925. [PMID: 38979363 PMCID: PMC11230152 DOI: 10.1101/2024.06.20.599925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Long noncoding RNAs (lncRNAs) make up the largest portion of RNA produced from the human genome, but only a small fraction have any ascribed functions. Although the role of protein-coding genes in macrophage biology has been studied extensively, our understanding of the role played by lncRNAs in this context is still in its early stages. There are over 20,000 lncRNAs in the human genome therefore, attempting to select a lncRNA to characterize functionally can be a challenge. Here we describe two approaches to identify and functionally characterize lncRNAs involved in monocyte-to-macrophage differentiation. The first involves the use of RNA-seq to infer possible functions and the second involves a high throughput functional screen. We examine the advantages and disadvantages of these methodologies and the pipelines for validation that assist in determining functional lncRNAs.
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Affiliation(s)
- Christy Montano
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, California, USA
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, California, USA
| | - Eric Malekos
- Department of Biomolecular Engineering, University of California Santa Cruz, California, USA
| | - Sol Katzman
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, California, USA
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, California, USA
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8
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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [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: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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9
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Criado M, Silva M, Mendívil P, Molina E, Pérez V, Benavides J, Elguezabal N, Gutiérrez-Expósito D. No Evidence of Neutrophil Response Modulation in Goats after Immunization against Paratuberculosis with a Heat-Inactivated Vaccine. Animals (Basel) 2024; 14:1694. [PMID: 38891741 PMCID: PMC11171245 DOI: 10.3390/ani14111694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Neutrophils are believed to play a role in the initial stages of paratuberculosis, and it has recently been demonstrated that vaccination can modulate their function via priming or through epigenetic and metabolic reprogramming (training). Modulation of the neutrophil response against Mycobacterium avium subspecies paratuberculosis (Map) through vaccination has been demonstrated in a rabbit model but not in ruminants. Therefore, in the present work, the effect of vaccination on the response of caprine neutrophils against Map was studied. Neutrophils were isolated from non-vaccinated (n = 7) and Gudair®-vaccinated goat kids (n = 7), before vaccination and 30 days post-vaccination. Then, several neutrophil functions were quantified ex vivo: cell-free and anchored neutrophil extracellular trap (NET) release, phagocytosis, and the differential expression of several cytokines and TLR2. The induction of cell-free NETosis and TLR2 expression by Map is reported for the first time. However, vaccination showed no significant effect on any of the functions studied. This suggests that the protection conferred by Gudair® vaccination is based on mechanisms that are independent of the neutrophil function modulation. Further research into the impact of alternative vaccination strategies or the paratuberculosis infection stage on ruminant neutrophil function could provide valuable insights into its role in paratuberculosis.
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Affiliation(s)
- Miguel Criado
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Marta Silva
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Pedro Mendívil
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Elena Molina
- Departamento de Sanidad Animal, NEIKER-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 48160 Derio, Spain; (E.M.); (N.E.)
| | - Valentín Pérez
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Julio Benavides
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
| | - Natalia Elguezabal
- Departamento de Sanidad Animal, NEIKER-BRTA, Instituto Vasco de Investigación y Desarrollo Agrario, 48160 Derio, Spain; (E.M.); (N.E.)
| | - Daniel Gutiérrez-Expósito
- Departamento de Sanidad Animal, Instituto de Ganadería de Montaña (IGM) CSIC-ULE, Ctra León-Vega de Infanzones, 24346 León, Spain; (M.S.); (P.M.); (V.P.); (J.B.); (D.G.-E.)
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
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10
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Cao R, Thatavarty A, King KY. Forged in the fire: Lasting impacts of inflammation on hematopoietic progenitors. Exp Hematol 2024; 134:104215. [PMID: 38580008 DOI: 10.1016/j.exphem.2024.104215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/26/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
Quiescence and differentiation of hematopoietic stem and progenitor cells (HSPC) can be modified by systemic inflammatory cues. Such cues can not only yield short-term changes in HSPCs such as in supporting emergency granulopoiesis but can also promote lasting influences on the HSPC compartment. First, inflammation can be a driver for clonal expansion, promoting clonal hematopoiesis for certain mutant clones, reducing overall clonal diversity, and reshaping the composition of the HSPC pool with significant health consequences. Second, inflammation can generate lasting cell-autonomous changes in HSPCs themselves, leading to changes in the epigenetic state, metabolism, and function of downstream innate immune cells. This concept, termed "trained immunity," suggests that inflammatory stimuli can alter subsequent immune responses leading to improved innate immunity or, conversely, autoimmunity. Both of these concepts have major implications in human health. Here we reviewed current literature about the lasting effects of inflammation on the HSPC compartment and opportunities for future advancement in this fast-developing field.
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Affiliation(s)
- Ruoqiong Cao
- Department of Pediatrics - Division of Infectious Disease, Texas Children's Hospital, Baylor College of Medicine, Houston, TX; Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Apoorva Thatavarty
- Department of Pediatrics - Division of Infectious Disease, Texas Children's Hospital, Baylor College of Medicine, Houston, TX; Graduate Program in Genetics and Genomics, Baylor College of Medicine, Houston, Texas; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX
| | - Katherine Y King
- Department of Pediatrics - Division of Infectious Disease, Texas Children's Hospital, Baylor College of Medicine, Houston, TX; Graduate Program in Immunology and Microbiology, Baylor College of Medicine, Houston, TX; Medical Scientist Training Program, Baylor College of Medicine, Houston, TX; Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX.
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11
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Sharma S, Houfani AA, Foster LJ. Pivotal functions and impact of long con-coding RNAs on cellular processes and genome integrity. J Biomed Sci 2024; 31:52. [PMID: 38745221 PMCID: PMC11092263 DOI: 10.1186/s12929-024-01038-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Recent advances in uncovering the mysteries of the human genome suggest that long non-coding RNAs (lncRNAs) are important regulatory components. Although lncRNAs are known to affect gene transcription, their mechanisms and biological implications are still unclear. Experimental research has shown that lncRNA synthesis, subcellular localization, and interactions with macromolecules like DNA, other RNAs, or proteins can all have an impact on gene expression in various biological processes. In this review, we highlight and discuss the major mechanisms through which lncRNAs function as master regulators of the human genome. Specifically, the objective of our review is to examine how lncRNAs regulate different processes like cell division, cell cycle, and immune responses, and unravel their roles in maintaining genomic architecture and integrity.
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Affiliation(s)
- Siddhant Sharma
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Aicha Asma Houfani
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada.
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12
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Blériot C, Dunsmore G, Alonso-Curbelo D, Ginhoux F. A temporal perspective for tumor-associated macrophage identities and functions. Cancer Cell 2024; 42:747-758. [PMID: 38670090 DOI: 10.1016/j.ccell.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/13/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024]
Abstract
Cancer is a progressive disease that can develop and evolve over decades, with inflammation playing a central role at each of its stages, from tumor initiation to metastasis. In this context, macrophages represent well-established bridges reciprocally linking inflammation and cancer via an array of diverse functions that have spurred efforts to classify them into subtypes. Here, we discuss the intertwines between macrophages, inflammation, and cancer with an emphasis on temporal dynamics of macrophage diversity and functions in pre-malignancy and cancer. By instilling temporal dynamism into the more static classic view of tumor-associated macrophage biology, we propose a new framework to better contextualize their significance in the inflammatory processes that precede and result from the onset of cancer and shape its evolution.
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Affiliation(s)
- Camille Blériot
- Gustave Roussy, INSERM, Villejuif, France; Institut Necker des Enfants Malades (INEM), INSERM, CNRS, Université Paris Cité, Paris, France
| | | | - Direna Alonso-Curbelo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
| | - Florent Ginhoux
- Gustave Roussy, INSERM, Villejuif, France; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore, Singapore; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, Shanghai, China; Translational Immunology Institute, SingHealth Duke-NUS, Singapore, Singapore.
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13
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Hoffmann MH, Kirchner H, Krönke G, Riemekasten G, Bonelli M. Inflammatory tissue priming: novel insights and therapeutic opportunities for inflammatory rheumatic diseases. Ann Rheum Dis 2024:ard-2023-224092. [PMID: 38702177 DOI: 10.1136/ard-2023-224092] [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: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
Due to optimised treatment strategies and the availability of new therapies during the last decades, formerly devastating chronic inflammatory diseases such as rheumatoid arthritis or systemic sclerosis (SSc) have become less menacing. However, in many patients, even state-of-the-art treatment cannot induce remission. Moreover, the risk for flares strongly increases once anti-inflammatory therapy is tapered or withdrawn, suggesting that underlying pathological processes remain active even in the absence of overt inflammation. It has become evident that tissues have the ability to remember past encounters with pathogens, wounds and other irritants, and to react more strongly and/or persistently to the next occurrence. This priming of the tissue bears a paramount role in defence from microbes, but on the other hand drives inflammatory pathologies (the Dr Jekyll and Mr Hyde aspect of tissue adaptation). Emerging evidence suggests that long-lived tissue-resident cells, such as fibroblasts, macrophages, long-lived plasma cells and tissue-resident memory T cells, determine inflammatory tissue priming in an interplay with infiltrating immune cells of lymphoid and myeloid origin, and with systemically acting factors such as cytokines, extracellular vesicles and antibodies. Here, we review the current state of science on inflammatory tissue priming, focusing on tissue-resident and tissue-occupying cells in arthritis and SSc, and reflect on the most promising treatment options targeting the maladapted tissue response during these diseases.
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Affiliation(s)
| | - Henriette Kirchner
- Institute for Human Genetics, Epigenetics and Metabolism Lab, University of Lübeck, Lübeck, Germany
| | - Gerhard Krönke
- Department of Rheumatology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Gabriela Riemekasten
- Department of Rheumatology and Clinical Immunology, University of Lübeck, Lübeck, Germany
| | - Michael Bonelli
- Division of Rheumatology, Department of Internal Medicine III, Medical University of Vienna, Vienna, Austria
- Ludwig Boltzmann Institute for Arthritis and Rehabilitation, Vienna, Austria
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14
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Scholz R, Brösamle D, Yuan X, Beyer M, Neher JJ. Epigenetic control of microglial immune responses. Immunol Rev 2024; 323:209-226. [PMID: 38491845 DOI: 10.1111/imr.13317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/02/2024] [Indexed: 03/18/2024]
Abstract
Microglia, the major population of brain-resident macrophages, are now recognized as a heterogeneous population comprising several cell subtypes with different (so far mostly supposed) functions in health and disease. A number of studies have performed molecular characterization of these different microglial activation states over the last years making use of "omics" technologies, that is transcriptomics, proteomics and, less frequently, epigenomics profiling. These approaches offer the possibility to identify disease mechanisms, discover novel diagnostic biomarkers, and develop new therapeutic strategies. Here, we focus on epigenetic profiling as a means to understand microglial immune responses beyond what other omics methods can offer, that is, revealing past and present molecular responses, gene regulatory networks and potential future response trajectories, and defining cell subtype-specific disease relevance through mapping non-coding genetic variants. We review the current knowledge in the field regarding epigenetic regulation of microglial identity and function, provide an exemplary analysis that demonstrates the advantages of performing joint transcriptomic and epigenomic profiling of single microglial cells and discuss how comprehensive epigenetic analyses may enhance our understanding of microglial pathophysiology.
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Affiliation(s)
- Rebekka Scholz
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Desirée Brösamle
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Xidi Yuan
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Marc Beyer
- Immunogenomics & Neurodegeneration, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Systems Medicine, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Platform for Single Cell Genomics and Epigenomics, German Center for Neurodegenerative Diseases (DZNE) and University of Bonn and West German Genome Center, Bonn, Germany
| | - Jonas J Neher
- Biomedical Center (BMC), Biochemistry, Faculty of Medicine, LMU Munich, Munich, Germany
- Neuroimmunology and Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
- Department of Cellular Neurology, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
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15
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Vuscan P, Kischkel B, Joosten LAB, Netea MG. Trained immunity: General and emerging concepts. Immunol Rev 2024; 323:164-185. [PMID: 38551324 DOI: 10.1111/imr.13326] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/11/2024] [Indexed: 05/18/2024]
Abstract
Over the past decade, compelling evidence has unveiled previously overlooked adaptive characteristics of innate immune cells. Beyond their traditional role in providing short, non-specific protection against pathogens, innate immune cells can acquire antigen-agnostic memory, exhibiting increased responsiveness to secondary stimulation. This long-term de-facto innate immune memory, also termed trained immunity, is mediated through extensive metabolic rewiring and epigenetic modifications. While the upregulation of trained immunity proves advantageous in countering immune paralysis, its overactivation contributes to the pathogenesis of autoinflammatory and autoimmune disorders. In this review, we present the latest advancements in the field of innate immune memory followed by a description of the fundamental mechanisms underpinning trained immunity generation and different cell types that mediate it. Furthermore, we explore its implications for various diseases and examine current limitations and its potential therapeutic targeting in immune-related disorders.
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Affiliation(s)
- Patricia Vuscan
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Brenda Kischkel
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
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16
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Mishra B, Ivashkiv LB. Interferons and epigenetic mechanisms in training, priming and tolerance of monocytes and hematopoietic progenitors. Immunol Rev 2024; 323:257-275. [PMID: 38567833 PMCID: PMC11102283 DOI: 10.1111/imr.13330] [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: 01/27/2024] [Accepted: 03/11/2024] [Indexed: 05/18/2024]
Abstract
Training and priming of innate immune cells involve preconditioning by PAMPs, DAMPs, and/or cytokines that elicits stronger induction of inflammatory genes upon secondary challenge. Previous models distinguish training and priming based upon whether immune activation returns to baseline prior to secondary challenge. Tolerance is a protective mechanism whereby potent stimuli induce refractoriness to secondary challenge. Training and priming are important for innate memory responses that protect against infection, efficacy of vaccines, and maintaining innate immune cells in a state of readiness; tolerance prevents toxicity from excessive immune activation. Dysregulation of these processes can contribute to pathogenesis of autoimmune/inflammatory conditions, post-COVID-19 hyperinflammatory states, or sepsis-associated immunoparalysis. Training, priming, and tolerance regulate similar "signature" inflammatory genes such as TNF, IL6, and IL1B and utilize overlapping epigenetic mechanisms. We review how interferons (IFNs), best known for activating JAK-STAT signaling and interferon-stimulated genes, also play a key role in regulating training, priming, and tolerance via chromatin-mediated mechanisms. We present new data on how monocyte-to-macrophage differentiation modulates IFN-γ-mediated priming, affects regulation of AP-1 and CEBP activity, and attenuates superinduction of inflammatory genes. We present a "training-priming continuum" model that integrates IFN-mediated priming into current concepts about training and tolerance and proposes a central role for STAT1 and IRF1.
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Affiliation(s)
- Bikash Mishra
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, New York, USA
| | - Lionel B Ivashkiv
- HSS Research Institute and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, New York, USA
- Immunology and Microbial Pathogenesis Program, Weill Cornell Medicine, New York, New York, USA
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
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17
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Daccache JA, Naik S. Inflammatory Memory in Chronic Skin Disease. JID INNOVATIONS 2024; 4:100277. [PMID: 38708420 PMCID: PMC11068922 DOI: 10.1016/j.xjidi.2024.100277] [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: 01/03/2024] [Revised: 03/01/2024] [Accepted: 03/11/2024] [Indexed: 05/07/2024] Open
Abstract
Inflammation is a hallmark of remitting-relapsing dermatological diseases. Although a large emphasis has been placed on adaptive immune cells as mediators of relapse, evidence in epithelial and innate immune biology suggests that disease memory is widespread. In this study, we bring to the fore the concept of inflammatory memory or nonspecific training of long-lived cells in the skin, highlighting the epigenetic and other mechanisms that propagate memory at the cellular level. We place these findings in the context of psoriasis, a prototypic flaring disease known to have localized memory, and underscore the importance of targeting memory to limit disease flares.
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Affiliation(s)
| | - Shruti Naik
- Department of Pathology, NYU Langone Health, New York, New York, USA
- Ronald O. Perelman Department of Dermatology, NYU Langone Health, New York, New York, USA
- Department of Medicine, NYU Langone Health, New York, New York, USA
- Perlmutter Cancer Center, NYU Langone Health, New York, New York, USA
- Colton Center for Autoimmunity, NYU Langone Health, New York, New York, USA
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18
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López-Collazo E, del Fresno C. Endotoxin tolerance and trained immunity: breaking down immunological memory barriers. Front Immunol 2024; 15:1393283. [PMID: 38742111 PMCID: PMC11089161 DOI: 10.3389/fimmu.2024.1393283] [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: 02/28/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
For decades, innate immune cells were considered unsophisticated first responders, lacking the adaptive memory of their T and B cell counterparts. However, mounting evidence demonstrates the surprising complexity of innate immunity. Beyond quickly deploying specialized cells and initiating inflammation, two fascinating phenomena - endotoxin tolerance (ET) and trained immunity (TI) - have emerged. ET, characterized by reduced inflammatory response upon repeated exposure, protects against excessive inflammation. Conversely, TI leads to an enhanced response after initial priming, allowing the innate system to mount stronger defences against subsequent challenges. Although seemingly distinct, these phenomena may share underlying mechanisms and functional implications, blurring the lines between them. This review will delve into ET and TI, dissecting their similarities, differences, and the remaining questions that warrant further investigation.
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Affiliation(s)
- Eduardo López-Collazo
- The Innate Immune Response Group, Hospital la Paz Institute for Health Research (IdiPAZ), La Paz University Hospital, Madrid, Spain
- Tumour Immunology Laboratory, IdiPAZ, La Paz University Hospital, Madrid, Spain
- Centro de Investigación Biomédica en Red (CIBER), Respiratory Diseases (CIBRES), Madrid, Spain
| | - Carlos del Fresno
- The Innate Immune Response Group, Hospital la Paz Institute for Health Research (IdiPAZ), La Paz University Hospital, Madrid, Spain
- Immunomodulation Laboratory, IdiPAZ, La Paz University Hospital, Madrid, Spain
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19
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Dhaka B, Zimmerli M, Hanhart D, Moser M, Guillen-Ramirez H, Mishra S, Esposito R, Polidori T, Widmer M, García-Pérez R, Julio MKD, Pervouchine D, Melé M, Chouvardas P, Johnson R. Functional identification of cis-regulatory long noncoding RNAs at controlled false discovery rates. Nucleic Acids Res 2024; 52:2821-2835. [PMID: 38348970 PMCID: PMC11014264 DOI: 10.1093/nar/gkae075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 01/15/2024] [Accepted: 01/26/2024] [Indexed: 03/09/2024] Open
Abstract
A key attribute of some long noncoding RNAs (lncRNAs) is their ability to regulate expression of neighbouring genes in cis. However, such 'cis-lncRNAs' are presently defined using ad hoc criteria that, we show, are prone to false-positive predictions. The resulting lack of cis-lncRNA catalogues hinders our understanding of their extent, characteristics and mechanisms. Here, we introduce TransCistor, a framework for defining and identifying cis-lncRNAs based on enrichment of targets amongst proximal genes. TransCistor's simple and conservative statistical models are compatible with functionally defined target gene maps generated by existing and future technologies. Using transcriptome-wide perturbation experiments for 268 human and 134 mouse lncRNAs, we provide the first large-scale survey of cis-lncRNAs. Known cis-lncRNAs are correctly identified, including XIST, LINC00240 and UMLILO, and predictions are consistent across analysis methods, perturbation types and independent experiments. We detect cis-activity in a minority of lncRNAs, primarily involving activators over repressors. Cis-lncRNAs are detected by both RNA interference and antisense oligonucleotide perturbations. Mechanistically, cis-lncRNA transcripts are observed to physically associate with their target genes and are weakly enriched with enhancer elements. In summary, TransCistor establishes a quantitative foundation for cis-lncRNAs, opening a path to elucidating their molecular mechanisms and biological significance.
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Affiliation(s)
- Bhavya Dhaka
- School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
| | - Marc Zimmerli
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Daniel Hanhart
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Mario B Moser
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Hugo Guillen-Ramirez
- School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Sanat Mishra
- Indian Institute of Science Education and Research, Mohali, India
| | - Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Maro Widmer
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
| | - Raquel García-Pérez
- Department of Life Sciences, Barcelona Supercomputing Centre, Barcelona 08034, Spain
| | - Marianna Kruithof-de Julio
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Dmitri Pervouchine
- Center for Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Marta Melé
- Department of Life Sciences, Barcelona Supercomputing Centre, Barcelona 08034, Spain
| | - Panagiotis Chouvardas
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern 3010, Switzerland
- Department for BioMedical Research, University of Bern, Bern 3008, Switzerland
- FutureNeuro SFI Research Centre, University College Dublin, Dublin D04 V1W8, Ireland
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20
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Ge T, Brickner JH. Inheritance of epigenetic transcriptional memory. Curr Opin Genet Dev 2024; 85:102174. [PMID: 38430840 PMCID: PMC10947848 DOI: 10.1016/j.gde.2024.102174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/23/2024] [Accepted: 02/06/2024] [Indexed: 03/05/2024]
Abstract
Epigenetic memory allows organisms to stably alter their transcriptional program in response to developmental or environmental stimuli. Such transcriptional programs are mediated by heritable regulation of the function of enhancers and promoters. Memory involves read-write systems that enable self-propagation and mitotic inheritance of cis-acting epigenetic marks to induce stable changes in transcription. Also, in response to environmental cues, cells can induce epigenetic transcriptional memory to poise inducible genes for faster induction in the future. Here, we discuss modes of epigenetic inheritance and the molecular basis of epigenetic transcriptional memory.
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Affiliation(s)
- Tiffany Ge
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA.
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21
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Chen J, Jamaiyar A, Wu W, Hu Y, Zhuang R, Sausen G, Cheng HS, de Oliveira Vaz C, Pérez-Cremades D, Tzani A, McCoy MG, Assa C, Eley S, Randhawa V, Lee K, Plutzky J, Hamburg NM, Sabatine MS, Feinberg MW. Deficiency of lncRNA MERRICAL abrogates macrophage chemotaxis and diabetes-associated atherosclerosis. Cell Rep 2024; 43:113815. [PMID: 38428421 PMCID: PMC11006532 DOI: 10.1016/j.celrep.2024.113815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 01/18/2024] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
Diabetes-associated atherosclerosis involves excessive immune cell recruitment and plaque formation. However, the mechanisms remain poorly understood. Transcriptomic analysis of the aortic intima in Ldlr-/- mice on a high-fat, high-sucrose-containing (HFSC) diet identifies a macrophage-enriched nuclear long noncoding RNA (lncRNA), MERRICAL (macrophage-enriched lncRNA regulates inflammation, chemotaxis, and atherosclerosis). MERRICAL expression increases by 249% in intimal lesions during progression. lncRNA-mRNA pair genomic mapping reveals that MERRICAL positively correlates with the chemokines Ccl3 and Ccl4. MERRICAL-deficient macrophages exhibit lower Ccl3 and Ccl4 expression, chemotaxis, and inflammatory responses. Mechanistically, MERRICAL guides the WDR5-MLL1 complex to activate CCL3 and CCL4 transcription via H3K4me3 modification. MERRICAL deficiency in HFSC diet-fed Ldlr-/- mice reduces lesion formation by 74% in the aortic sinus and 86% in the descending aorta by inhibiting leukocyte recruitment into the aortic wall and pro-inflammatory responses. These findings unveil a regulatory mechanism whereby a macrophage-enriched lncRNA potently inhibits chemotactic responses, alleviating lesion progression in diabetes.
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Affiliation(s)
- Jingshu Chen
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anurag Jamaiyar
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Winona Wu
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yi Hu
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rulin Zhuang
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Cardiovascular Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai 200120, China
| | - Grasiele Sausen
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Henry S Cheng
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Camila de Oliveira Vaz
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Daniel Pérez-Cremades
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Physiology, University of Valencia and INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Aspasia Tzani
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Michael G McCoy
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Carmel Assa
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Samuel Eley
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vinay Randhawa
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Kwangwoon Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Jorge Plutzky
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Naomi M Hamburg
- Evans Department of Medicine and Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA
| | - Marc S Sabatine
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mark W Feinberg
- Cardiovascular Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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22
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Ma H, Yang Y, Nie T, Yan R, Si Y, Wei J, Li M, Liu H, Ye W, Zhang H, Cheng L, Zhang L, Lv X, Luo L, Xu Z, Zhang X, Lei Y, Zhang F. Disparate macrophage responses are linked to infection outcome of Hantan virus in humans or rodents. Nat Commun 2024; 15:438. [PMID: 38200007 PMCID: PMC10781751 DOI: 10.1038/s41467-024-44687-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Hantaan virus (HTNV) is asymptomatically carried by rodents, yet causes lethal hemorrhagic fever with renal syndrome in humans, the underlying mechanisms of which remain to be elucidated. Here, we show that differential macrophage responses may determine disparate infection outcomes. In mice, late-phase inactivation of inflammatory macrophage prevents cytokine storm syndrome that usually occurs in HTNV-infected patients. This is attained by elaborate crosstalk between Notch and NF-κB pathways. Mechanistically, Notch receptors activated by HTNV enhance NF-κB signaling by recruiting IKKβ and p65, promoting inflammatory macrophage polarization in both species. However, in mice rather than humans, Notch-mediated inflammation is timely restrained by a series of murine-specific long noncoding RNAs transcribed by the Notch pathway in a negative feedback manner. Among them, the lnc-ip65 detaches p65 from the Notch receptor and inhibits p65 phosphorylation, rewiring macrophages from the pro-inflammation to the pro-resolution phenotype. Genetic ablation of lnc-ip65 leads to destructive HTNV infection in mice. Thus, our findings reveal an immune-braking function of murine noncoding RNAs, offering a special therapeutic strategy for HTNV infection.
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Affiliation(s)
- Hongwei Ma
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
- Department of Anaesthesiology & Critical Care Medicine, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Yongheng Yang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710038, China
| | - Rong Yan
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Yue Si
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Jing Wei
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
- Shaanxi Provincial Centre for Disease Control and Prevention, Xi'an, Shaanxi, 710054, China
| | - Mengyun Li
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - He Liu
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Wei Ye
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Hui Zhang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Linfeng Cheng
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Liang Zhang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Xin Lv
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Limin Luo
- Department of Infectious Disease, Air Force Hospital of Southern Theatre Command, Guangzhou, Guangdong, 510602, China
| | - Zhikai Xu
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
| | - Xijing Zhang
- Department of Anaesthesiology & Critical Care Medicine, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
| | - Yingfeng Lei
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
| | - Fanglin Zhang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
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23
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Fok ET, Moorlag SJCFM, Negishi Y, Groh LA, Dos Santos JC, Gräwe C, Monge VV, Craenmehr DDD, van Roosmalen M, da Cunha Jolvino DP, Migliorini LB, Neto AS, Severino P, Vermeulen M, Joosten LAB, Netea MG, Fanucchi S, Mhlanga MM. A chromatin-regulated biphasic circuit coordinates IL-1β-mediated inflammation. Nat Genet 2024; 56:85-99. [PMID: 38092881 DOI: 10.1038/s41588-023-01598-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/26/2023] [Indexed: 12/23/2023]
Abstract
Inflammation is characterized by a biphasic cycle consisting initially of a proinflammatory phase that is subsequently resolved by anti-inflammatory processes. Interleukin-1β (IL-1β) is a master regulator of proinflammation and is encoded within the same topologically associating domain (TAD) as IL-37, which is an anti-inflammatory cytokine that opposes the function of IL-1β. Within this TAD, we identified a long noncoding RNA called AMANZI, which negatively regulates IL-1β expression and trained immunity through the induction of IL37 transcription. We found that the activation of IL37 occurs through the formation of a dynamic long-range chromatin contact that leads to the temporal delay of anti-inflammatory responses. The common variant rs16944 present in AMANZI augments this regulatory circuit, predisposing individuals to enhanced proinflammation or immunosuppression. Our work illuminates a chromatin-mediated biphasic circuit coordinating expression of IL-1β and IL-37, thereby regulating two functionally opposed states of inflammation from within a single TAD.
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Affiliation(s)
- Ezio T Fok
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
- Lemba Therapeutics, Nijmegen, the Netherlands
| | - Simone J C F M Moorlag
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yutaka Negishi
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Laszlo A Groh
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jéssica Cristina Dos Santos
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
| | | | | | | | - David Pablo da Cunha Jolvino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
- Australian and New Zealand Intensive Care Research Centre, Monash University, Melbourne, Victoria, Australia
| | - Letícia Busato Migliorini
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Ary Serpa Neto
- Department of Critical Care Medicine, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Patricia Severino
- Albert Einstein Research and Education Institute, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University, Nijmegen, the Netherlands
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Musa M Mhlanga
- Department of Cell Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands.
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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24
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Fang XH, Li ZJ, Liu CY, Mor G, Liao AH. Macrophage memory: Types, mechanisms, and its role in health and disease. Immunology 2024; 171:18-30. [PMID: 37702350 DOI: 10.1111/imm.13697] [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: 02/14/2023] [Accepted: 09/05/2023] [Indexed: 09/14/2023] Open
Abstract
On the basis of the mechanisms of action and characteristics of immune effects, immunity is commonly categorized into innate and adaptive immunity. Adaptive immunity is associated with the response to non-self-entities and is characterized by high specificity and memory properties. In contrast, innate immunity has traditionally been considered devoid of memory characteristics. However, an increasing number of studies have sought to challenge this conventional immunological dogma and shown that innate immune cells exhibit a more robust and rapid response to secondary stimulation, thus providing evidence of the immunological memory in innate immunity. Macrophages, which are among the most important innate immune cells, can also acquire memory phenotype that facilitates the mediation of recall responses. Macrophage memory is a relatively new concept that is revolutionizing our understanding of macrophage biology and immunological memory and could lead to a new class of vaccines and immunotherapies. In this review, we describe the characteristics and mechanisms of macrophage memory, as well as its essential roles in various diseases.
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Affiliation(s)
- Xu-Hui Fang
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Zhi-Jing Li
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Chun-Yan Liu
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
| | - Gil Mor
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
- C.S. Mott Center for Human Growth and Development, Wayne State University School of Medicine, Detroit, Michigan, USA
| | - Ai-Hua Liao
- Institute of Reproductive Health, Center for Reproductive Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P.R. China
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25
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Li W, Lv Y, Sun Y. Roles of non-coding RNA in megakaryocytopoiesis and thrombopoiesis: new target therapies in ITP. Platelets 2023; 34:2157382. [PMID: 36550091 DOI: 10.1080/09537104.2022.2157382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Noncoding RNAs (ncRNAs) are a group of RNA molecules that cannot encode proteins, and a better understanding of the complex interaction networks coordinated by ncRNAs will provide a theoretical basis for the development of therapeutics targeting the regulatory effects of ncRNAs. Platelets are produced upon the differentiation of hematopoietic stem cells into megakaryocytes, 1011 per day, and are renewed every 8-9 days. The process of thrombopoiesis is affected by multiple factors, in which ncRNAs also exert a significant regulatory role. This article reviewed the regulatory roles of ncRNAs, mainly microRNAs (miRNAs), circRNAs (circular RNAs), and long non-coding RNAs (lncRNAs), in thrombopoiesis in recent years as well as their roles in primary immune thrombocytopenia (ITP).
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Affiliation(s)
- Wuquan Li
- College of Pharmacy, Binzhou Medical University, Yantai, China
| | - Yan Lv
- College of Life Science, Yantai University, Yantai, China
| | - Yeying Sun
- College of Pharmacy, Binzhou Medical University, Yantai, China
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26
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Riksen NP, Bekkering S, Mulder WJM, Netea MG. Trained immunity in atherosclerotic cardiovascular disease. Nat Rev Cardiol 2023; 20:799-811. [PMID: 37322182 DOI: 10.1038/s41569-023-00894-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2023] [Indexed: 06/17/2023]
Abstract
Trained immunity, also known as innate immune memory, is a persistent hyper-responsive functional state of innate immune cells. Accumulating evidence implicates trained immunity as an underlying mechanism of chronic inflammation in atherosclerotic cardiovascular disease. In this context, trained immunity is induced by endogenous atherosclerosis-promoting factors, such as modified lipoproteins or hyperglycaemia, causing broad metabolic and epigenetic reprogramming of the myeloid cell compartment. In addition to traditional cardiovascular risk factors, lifestyle factors, including unhealthy diets, sedentary lifestyle, sleep deprivation and psychosocial stress, as well as inflammatory comorbidities, have been shown to activate trained immunity-like mechanisms in bone marrow haematopoietic stem cells. In this Review, we discuss the molecular and cellular mechanisms of trained immunity, its systemic regulation through haematopoietic progenitor cells in the bone marrow, and the activation of these mechanisms by cardiovascular disease risk factors. We also highlight other trained immunity features that are relevant for atherosclerotic cardiovascular disease, including the diverse cell types that show memory characteristics and transgenerational inheritance of trained immunity traits. Finally, we propose potential strategies for the therapeutic modulation of trained immunity to manage atherosclerotic cardiovascular disease.
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Affiliation(s)
- Niels P Riksen
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Siroon Bekkering
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Willem J M Mulder
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- Department for Genomics and Immunoregulation, University of Bonn, Bonn, Germany
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27
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Chakraborty S, Singh A, Wang L, Wang X, Sanborn MA, Ye Z, Maienschein-Cline M, Mukhopadhyay A, Ganesh BB, Malik AB, Rehman J. Trained immunity of alveolar macrophages enhances injury resolution via KLF4-MERTK-mediated efferocytosis. J Exp Med 2023; 220:e20221388. [PMID: 37615937 PMCID: PMC10450795 DOI: 10.1084/jem.20221388] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 05/19/2023] [Accepted: 08/02/2023] [Indexed: 08/25/2023] Open
Abstract
Recent studies suggest that training of innate immune cells such as tissue-resident macrophages by repeated noxious stimuli can heighten host defense responses. However, it remains unclear whether trained immunity of tissue-resident macrophages also enhances injury resolution to counterbalance the heightened inflammatory responses. Here, we studied lung-resident alveolar macrophages (AMs) prechallenged with either the bacterial endotoxin or with Pseudomonas aeruginosa and observed that these trained AMs showed greater resilience to pathogen-induced cell death. Transcriptomic analysis and functional assays showed greater capacity of trained AMs for efferocytosis of cellular debris and injury resolution. Single-cell high-dimensional mass cytometry analysis and lineage tracing demonstrated that training induces an expansion of a MERTKhiMarcohiCD163+F4/80low lung-resident AM subset with a proresolving phenotype. Reprogrammed AMs upregulated expression of the efferocytosis receptor MERTK mediated by the transcription factor KLF4. Adoptive transfer of these trained AMs restricted inflammatory lung injury in recipient mice exposed to lethal P. aeruginosa. Thus, our study has identified a subset of tissue-resident trained macrophages that prevent hyperinflammation and restore tissue homeostasis following repeated pathogen challenges.
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Affiliation(s)
- Sreeparna Chakraborty
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL, USA
| | - Abhalaxmi Singh
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Li Wang
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Xinge Wang
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL, USA
- Department of Biomedical Engineering, University of Illinois College of Medicine, Chicago, IL, USA
| | - Mark A. Sanborn
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Zijing Ye
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | | | - Amitabha Mukhopadhyay
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Balaji B. Ganesh
- Research Resources Center, University of Illinois Chicago, Chicago, Illinois, USA
| | - Asrar B. Malik
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
| | - Jalees Rehman
- Department of Biochemistry and Molecular Genetics, University of Illinois College of Medicine, Chicago, IL, USA
- Department of Pharmacology and Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL, USA
- Division of Cardiology, Department of Medicine, University of Illinois College of Medicine, Chicago, IL, USA
- Department of Biomedical Engineering, University of Illinois College of Medicine, Chicago, IL, USA
- University of Illinois Cancer Center, Chicago, IL, USA
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28
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Robinson KA, Akbar N, Baidžajevas K, Choudhury RP. Trained immunity in diabetes and hyperlipidemia: Emerging opportunities to target cardiovascular complications and design new therapies. FASEB J 2023; 37:e23231. [PMID: 37779347 PMCID: PMC10947360 DOI: 10.1096/fj.202301078r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Some metabolic diseases, such as diabetes and hyperlipidemia, are associated with a state of inflammation, which adversely affects cardiovascular health. Emerging evidence suggests that long-term hyperactivation of innate immune cells and their bone marrow progenitors, termed trained immunity, functions to accelerate atherosclerosis and its complications in cardiometabolic diseases. This review will focus on how trained immunity is established, particularly through metabolic and epigenetic reprogramming, to cause persistent and deleterious changes in immune cell function, even after the original stimulus has been corrected or removed. Understanding the mechanisms driving maladaptive trained immunity and its fundamental contribution to cardiovascular disease might enable the development of novel disease-modifying therapeutics for the reduction in cardiovascular risk in diabetes, hyperlipidemia, and related cardiometabolic states.
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Affiliation(s)
- Katherine A. Robinson
- Division of Cardiovascular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Naveed Akbar
- Division of Cardiovascular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Kajus Baidžajevas
- Division of Cardiovascular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
| | - Robin P. Choudhury
- Division of Cardiovascular Medicine, Radcliffe Department of MedicineUniversity of OxfordOxfordUK
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29
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Zheng G, Zhu Y, Xu L, Chen S, Zhang X, Li W, Chen W, Zhou Y, Gu W. LncRNA MACC1-AS1 associates with DDX5 to modulate MACC1 transcription in breast cancer cells. iScience 2023; 26:107642. [PMID: 37664587 PMCID: PMC10474461 DOI: 10.1016/j.isci.2023.107642] [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: 08/18/2022] [Revised: 03/31/2023] [Accepted: 08/11/2023] [Indexed: 09/05/2023] Open
Abstract
MACC1 is a master oncogene involved in multiple aspects of cancer metastasis in a broad variety of tumors. However, the molecular mechanism by which MACC1 transcription is regulated remains unclear. Here, we show that in breast cancer cells, lncRNA MACC1-AS1 serves as a cis-factor to up-regulate MACC1 transcription and this regulation increases the cell proliferation potential. Mechanistically, MACC1-AS1 forms a complex with DEAD-Box helicase 5 (DDX5) and simultaneously interacts with the distal region of the MACC1 promoter. The interaction allows its associated DDX5 to spatially contact the MACC1 core promoter and shift from MACC1-AS1 to the core promoter. Moreover, binding of DDX5 to the core promoter results in local recruitment of the transcription factor SP-1, thus enhancing MACC1 transcription. Our findings reveal a molecular mechanism by which MACC1-AS1 cis-regulates MACC1 transcription by interacting with the distal promoter region and delivering DDX5 to the core-promoter of the gene.
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Affiliation(s)
- Guiyu Zheng
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Yanmei Zhu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Liqun Xu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Shaoying Chen
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Xiaona Zhang
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Wei Li
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Weibin Chen
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Yanchun Zhou
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
| | - Wei Gu
- Department of Pathophysiology, Key Immunopathology Laboratory of Guangdong Province, Shantou University Medical College, Shantou, Guangdong Province 515041, China
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30
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Al B, Suen TK, Placek K, Netea MG. Innate (learned) memory. J Allergy Clin Immunol 2023; 152:551-566. [PMID: 37385546 DOI: 10.1016/j.jaci.2023.06.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023]
Abstract
With the growing body of evidence, it is now clear that not only adaptive immune cells but also innate immune cells can mount a more rapid and potent nonspecific immune response to subsequent exposures. This process is known as trained immunity or innate (learned) immune memory. This review discusses the different immune and nonimmune cell types of the central and peripheral immune systems that can develop trained immunity. This review highlights the intracellular signaling and metabolic and epigenetic mechanisms underlying the formation of innate immune memory. Finally, this review explores the health implications together with the potential therapeutic interventions harnessing trained immunity.
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Affiliation(s)
- Burcu Al
- Department of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn
| | - Tsz K Suen
- Department of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn
| | - Katarzyna Placek
- Department of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn
| | - Mihai G Netea
- Department of Molecular Immunology and Cell Biology, Life and Medical Sciences Institute, University of Bonn; Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen.
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31
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Sun H, Gao W, Chen R, Chen S, Gu X, Wang F, Li Q. CircRNAs in BALF exosomes and plasma as diagnostic biomarkers in patients with acute respiratory distress syndrome caused by severe pneumonia. Front Cell Infect Microbiol 2023; 13:1194495. [PMID: 37674577 PMCID: PMC10477665 DOI: 10.3389/fcimb.2023.1194495] [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: 03/27/2023] [Accepted: 06/29/2023] [Indexed: 09/08/2023] Open
Abstract
Background The transcriptomic studies targeting circular RNAs (circRNAs) in bronchoalveolar lavage fluid (BALF) exosomes of acute respiratory distress syndrome (ARDS) patients caused by severe pneumonia have rarely been reported. This study aimed to screen and validate abnormally expressed circRNAs in exosomes from BALF of patients with ARDS caused by severe pneumonia and then evaluate the diagnostic values of these circRNAs for ARDS. Method BALF was collected from four patients with ARDS caused by severe pneumonia and four healthy subjects. CircRNA expression profile was obtained by microarray analysis in BALF exosomes of the discovery cohort. The differentially expressed circRNAs in BALF exosomes were verified by real-time quantitative PCR (RT-qPCR) and underwent competitive endogenous RNA (ceRNA) network construction and functional enrichment analysis. Results A total of 629 circRNAs were differentially expressed in BALF exosomes between ARDS patients and healthy subjects. Nine differentially expressed circRNAs were validated by RT-qPCR, and seven were consistent with the results of microarray analysis. CeRNA network analysis was performed for hsa_circRNA_002809, hsa_circRNA_042882, and hsa_circRNA_104034. Functional enrichment analysis showed that the target genes were mainly associated with hypoxia-induced damage, inflammatory response, and the HIF-1 signaling pathway. Hsa_circRNA_042882 and hsa_circRNA_104034 can be regarded as promising diagnostic biomarkers for patients with ARDS caused by severe pneumonia, with remarkable sensitivity and specificity of the area under the curve of 0.8050 and 1 or 0.835 and 0.799, respectively. Conclusion This study obtained circRNA expression profiles of ARDS patients, and hsa_circRNA_042882 and hsa_circRNA_104034 were regarded as promising diagnostic biomarkers for patients with ARDS caused by severe pneumonia.
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Affiliation(s)
- He Sun
- *Correspondence: Qiang Li, ; Feilong Wang, ; He Sun,
| | | | | | | | | | - Feilong Wang
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Qiang Li
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
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32
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Tehrani SSH, Kogan A, Mikulski P, Jansen LET. Remembering foods and foes: emerging principles of transcriptional memory. Cell Death Differ 2023:10.1038/s41418-023-01200-6. [PMID: 37563261 DOI: 10.1038/s41418-023-01200-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Transcriptional memory is characterized by a primed cellular state, induced by an external stimulus that results in an altered expression of primed genes upon re-exposure to the inducing signal. Intriguingly, the primed state is heritably maintained across somatic cell divisions even after the initial stimulus and target gene transcription cease. This phenomenon is widely observed across various organisms and appears to enable cells to retain a memory of external signals, thereby adapting to environmental changes. Signals range from nutrient supplies (food) to a variety of stress signals, including exposure to pathogens (foes), leading to long-term memory such as in the case of trained immunity in plants and mammals. Here, we review these priming phenomena and our current understanding of transcriptional memory. We consider different mechanistic models for how memory can work and discuss existing evidence for potential carriers of memory. Key molecular signatures include: the poising of RNA polymerase II machinery, maintenance of histone marks, as well as alterations in nuclear positioning and long-range chromatin interactions. Finally, we discuss the potential adaptive roles of transcriptional memory in the organismal response to its environment from nutrient sensing to trained immunity.
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Affiliation(s)
- Sahar S H Tehrani
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Anna Kogan
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK
| | - Pawel Mikulski
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
| | - Lars E T Jansen
- Department of Biochemistry, University of Oxford, OX1 3QU, Oxford, UK.
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33
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Lei Y, Meng Q, Hong F, Zhao M, Gao X. Pan-cancer survey of lncRNA rewiring and functional alternation in tumor-infiltrating T cell by scLNC. Cancer Lett 2023:216319. [PMID: 37468058 DOI: 10.1016/j.canlet.2023.216319] [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: 04/27/2023] [Revised: 06/27/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Long non-coding RNAs (lncRNAs) have been reported to involve in diverse biological processes, including tumor immunity. Since lncRNAs are expressed with high cell-type specificity, investigation of lncRNAs at the single-cell level will unveil the cell-type-specific functions of lncRNAs. However, at the single-cell level, a systematic pan-cancer analysis of lncRNA functions in tumor immune microenvironments (TIMEs) remains lacking. Here, we performed pan-cancer single-cell profiling of lncRNA functions in TIMEs and developed a tool, scLNC, tailored for lncRNA functional characterization at the single-cell level. scLNC enabled the comparison of lncRNA function from the levels of lncRNA-mRNA pairs, lncRNA regulatory unit activity and unit function in a cell-type-specific manner. Applying scLNC, our analysis depicted the cross-tumor and tumor-specific lncRNA regulatory profiles in the T cell subtypes and revealed the new regulatory units that lncRNAs established in tumor-infiltrating T cells, particularly in the tumor-enriched T cells. We further characterized the activity and functional alternations of lncRNAs through their regulatory units. Overall, our findings suggested that lncRNAs played an important role in the regulation of cytokine production, cell activation and migration in tumor-enriched T cells and further in immunotherapy.
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Affiliation(s)
- Yang Lei
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Qianqian Meng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Fang Hong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Mengyu Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China
| | - Xin Gao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, 300020, China.
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Natarajan P, Shrinivas K, Chakraborty AK. A model for cis-regulation of transcriptional condensates and gene expression by proximal lncRNAs. Biophys J 2023; 122:2757-2772. [PMID: 37277993 PMCID: PMC10397817 DOI: 10.1016/j.bpj.2023.05.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 05/01/2023] [Accepted: 05/31/2023] [Indexed: 06/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) perform several important functions in cells including cis-regulation of transcription. Barring a few specific cases, the mechanisms underlying transcriptional regulation by lncRNAs remain poorly understood. Transcriptional proteins can form condensates via phase separation at protein-binding loci (BL) on the genome (e.g., enhancers and promoters). lncRNA-coding genes are present at loci in close genomic proximity of these BL and these RNAs can interact with transcriptional proteins via attractive heterotypic interactions mediated by their net charge. Motivated by these observations, we propose that lncRNAs can dynamically regulate transcription in cis via charge-based heterotypic interactions with transcriptional proteins in condensates. To study the consequences of this mechanism, we developed and studied a dynamical phase-field model. We find that proximal lncRNAs can promote condensate formation at the BL. Vicinally localized lncRNA can migrate to the BL to attract more protein because of favorable interaction free energies. However, increasing the distance beyond a threshold leads to a sharp decrease in protein recruitment to the BL. This finding could potentially explain why genomic distances between lncRNA-coding genes and protein-coding genes are conserved across metazoans. Finally, our model predicts that lncRNA transcription can fine-tune transcription from neighboring condensate-controlled genes, repressing transcription from highly expressed genes and enhancing transcription of genes expressed at a low level. This nonequilibrium effect can reconcile conflicting reports that lncRNAs can enhance or repress transcription from proximal genes.
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Affiliation(s)
- Pradeep Natarajan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts
| | - Krishna Shrinivas
- NSF-Simons Center for Mathematical & Statistical Analysis of Biology, Harvard University, Cambridge, Massachusetts
| | - Arup K Chakraborty
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts; Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts; Institute of Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, Massachusetts; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts; Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts.
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35
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Zhang W, Zhao J, Deng L, Ishimwe N, Pauli J, Wu W, Shan S, Kempf W, Ballantyne MD, Kim D, Lyu Q, Bennett M, Rodor J, Turner AW, Lu YW, Gao P, Choi M, Warthi G, Kim HW, Barroso MM, Bryant WB, Miller CL, Weintraub NL, Maegdefessel L, Miano JM, Baker AH, Long X. INKILN is a Novel Long Noncoding RNA Promoting Vascular Smooth Muscle Inflammation via Scaffolding MKL1 and USP10. Circulation 2023; 148:47-67. [PMID: 37199168 PMCID: PMC10330325 DOI: 10.1161/circulationaha.123.063760] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
BACKGROUND Activation of vascular smooth muscle cell (VSMC) inflammation is vital to initiate vascular disease. The role of human-specific long noncoding RNAs in VSMC inflammation is poorly understood. METHODS Bulk RNA sequencing in differentiated human VSMCs revealed a novel human-specific long noncoding RNA called inflammatory MKL1 (megakaryoblastic leukemia 1) interacting long noncoding RNA (INKILN). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation as well as human atherosclerosis and abdominal aortic aneurysm. The transcriptional regulation of INKILN was verified through luciferase reporter and chromatin immunoprecipitation assays. Loss-of-function and gain-of-function studies and multiple RNA-protein and protein-protein interaction assays were used to uncover a mechanistic role of INKILN in the VSMC proinflammatory gene program. Bacterial artificial chromosome transgenic mice were used to study INKILN expression and function in ligation injury-induced neointimal formation. RESULTS INKILN expression is downregulated in contractile VSMCs and induced in human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-κB (nuclear factor kappa B) site within its proximal promoter. INKILN activates proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-κB pathway. INKILN depletion blocks interleukin-1β-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1 and the luciferase activity of an NF-κB reporter. Furthermore, INKILN knockdown enhances MKL1 ubiquitination through reduced physical interaction with the deubiquitinating enzyme USP10 (ubiquitin-specific peptidase 10). INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in bacterial artificial chromosome transgenic mice. CONCLUSIONS These findings elucidate an important pathway of VSMC inflammation involving an INKILN/MKL1/USP10 regulatory axis. Human bacterial artificial chromosome transgenic mice offer a novel and physiologically relevant approach for investigating human-specific long noncoding RNAs under vascular disease conditions.
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Affiliation(s)
- Wei Zhang
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Jinjing Zhao
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Lin Deng
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Nestor Ishimwe
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Jessica Pauli
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany
| | - Wen Wu
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Shengshuai Shan
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Wolfgang Kempf
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany
| | | | - David Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Qing Lyu
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Matthew Bennett
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Julie Rodor
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Adam W. Turner
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Yao Wei Lu
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Ping Gao
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Mihyun Choi
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - Ganesh Warthi
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Ha Won Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Margarida M Barroso
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
| | - William B. Bryant
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Clint L. Miller
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Neal L. Weintraub
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Lars Maegdefessel
- Department for Vascular and Endovascular Surgery, Klinikum rechts der Isar, Technical University Munich, Germany
- German Center for Cardiovascular Research (DZHK, partner site Munich), Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Joseph M. Miano
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
| | - Andrew H Baker
- Centre for Cardiovascular Science University of Edinburgh, Edinburgh, Scotland
| | - Xiaochun Long
- Vascular Biology Center, Medical College of Georgia at Augusta University, Augusta, GA, USA
- Department of Molecular and Cellular Physiology, Albany Medical College, Albany, NY, USA
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36
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Gil N, Perry RBT, Mukamel Z, Tuck A, Bühler M, Ulitsky I. Complex regulation of Eomes levels mediated through distinct functional features of the Meteor long non-coding RNA locus. Cell Rep 2023; 42:112569. [PMID: 37256750 PMCID: PMC10320833 DOI: 10.1016/j.celrep.2023.112569] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/07/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are implicated in a plethora of cellular processes, but an in-depth understanding of their functional features or their mechanisms of action is currently lacking. Here we study Meteor, a lncRNA transcribed near the gene encoding EOMES, a pleiotropic transcription factor implicated in various processes throughout development and in adult tissues. Using a wide array of perturbation techniques, we show that transcription elongation through the Meteor locus is required for Eomes activation in mouse embryonic stem cells, with Meteor repression linked to a change in the subpopulation primed to differentiate to the mesoderm lineage. We further demonstrate that a distinct functional feature of the locus-namely, the underlying DNA element-is required for suppressing Eomes expression following neuronal differentiation. Our results demonstrate the complex regulation that can be conferred by a single locus and emphasize the importance of careful selection of perturbation techniques when studying lncRNA loci.
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Affiliation(s)
- Noa Gil
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Ben-Tov Perry
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Zohar Mukamel
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Alex Tuck
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Igor Ulitsky
- Department of Immunology and Regenerative Biology and Department of Molecular Neuroscience, Weizmann Institute of Science, Rehovot 76100, Israel.
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37
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Mattick JS, Amaral PP, Carninci P, Carpenter S, Chang HY, Chen LL, Chen R, Dean C, Dinger ME, Fitzgerald KA, Gingeras TR, Guttman M, Hirose T, Huarte M, Johnson R, Kanduri C, Kapranov P, Lawrence JB, Lee JT, Mendell JT, Mercer TR, Moore KJ, Nakagawa S, Rinn JL, Spector DL, Ulitsky I, Wan Y, Wilusz JE, Wu M. Long non-coding RNAs: definitions, functions, challenges and recommendations. Nat Rev Mol Cell Biol 2023; 24:430-447. [PMID: 36596869 PMCID: PMC10213152 DOI: 10.1038/s41580-022-00566-8] [Citation(s) in RCA: 426] [Impact Index Per Article: 426.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 01/05/2023]
Abstract
Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
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Affiliation(s)
- John S Mattick
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia.
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia.
| | - Paulo P Amaral
- INSPER Institute of Education and Research, São Paulo, Brazil
| | - Piero Carninci
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Human Technopole, Milan, Italy
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamics Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Dermatology, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Ling-Ling Chen
- CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Runsheng Chen
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Caroline Dean
- John Innes Centre, Norwich Research Park, Norwich, UK
| | - Marcel E Dinger
- School of Biotechnology and Biomolecular Sciences, UNSW, Sydney, NSW, Australia
- UNSW RNA Institute, UNSW, Sydney, NSW, Australia
| | - Katherine A Fitzgerald
- Division of Innate Immunity, Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | | | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Osaka, Japan
| | - Maite Huarte
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra, Pamplona, Spain
| | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Chandrasekhar Kanduri
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Philipp Kapranov
- Institute of Genomics, School of Medicine, Huaqiao University, Xiamen, China
| | - Jeanne B Lawrence
- Department of Neurology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Jeannie T Lee
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua T Mendell
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, TX, USA
- Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Timothy R Mercer
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, QLD, Australia
| | - Kathryn J Moore
- Department of Medicine, New York University Grossman School of Medicine, New York, NY, USA
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO, USA
- BioFrontiers Institute, University of Colorado Boulder, Boulder, CO, USA
- Howard Hughes Medical Institute, University of Colorado Boulder, Boulder, CO, USA
| | - David L Spector
- Cold Spring Harbour Laboratory, Cold Spring Harbour, NY, USA
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Yue Wan
- Laboratory of RNA Genomics and Structure, Genome Institute of Singapore, A*STAR, Singapore, Singapore
- Department of Biochemistry, National University of Singapore, Singapore, Singapore
| | - Jeremy E Wilusz
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mian Wu
- Translational Research Institute, Henan Provincial People's Hospital, Academy of Medical Science, Zhengzhou University, Zhengzhou, China
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Xu H, Lin S, Zhou Z, Li D, Zhang X, Yu M, Zhao R, Wang Y, Qian J, Li X, Li B, Wei C, Chen K, Yoshimura T, Wang JM, Huang J. New genetic and epigenetic insights into the chemokine system: the latest discoveries aiding progression toward precision medicine. Cell Mol Immunol 2023:10.1038/s41423-023-01032-x. [PMID: 37198402 DOI: 10.1038/s41423-023-01032-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Over the past thirty years, the importance of chemokines and their seven-transmembrane G protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine interactions with receptors trigger signaling pathway activity to form a network fundamental to diverse immune processes, including host homeostasis and responses to disease. Genetic and nongenetic regulation of both the expression and structure of chemokines and receptors conveys chemokine functional heterogeneity. Imbalances and defects in the system contribute to the pathogenesis of a variety of diseases, including cancer, immune and inflammatory diseases, and metabolic and neurological disorders, which render the system a focus of studies aiming to discover therapies and important biomarkers. The integrated view of chemokine biology underpinning divergence and plasticity has provided insights into immune dysfunction in disease states, including, among others, coronavirus disease 2019 (COVID-19). In this review, by reporting the latest advances in chemokine biology and results from analyses of a plethora of sequencing-based datasets, we outline recent advances in the understanding of the genetic variations and nongenetic heterogeneity of chemokines and receptors and provide an updated view of their contribution to the pathophysiological network, focusing on chemokine-mediated inflammation and cancer. Clarification of the molecular basis of dynamic chemokine-receptor interactions will help advance the understanding of chemokine biology to achieve precision medicine application in the clinic.
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Affiliation(s)
- Hanli Xu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Shuye Lin
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China
| | - Ziyun Zhou
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Duoduo Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xiting Zhang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Muhan Yu
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Ruoyi Zhao
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Yiheng Wang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Junru Qian
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Xinyi Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Bohan Li
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Chuhan Wei
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China
| | - Keqiang Chen
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Teizo Yoshimura
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Ji Ming Wang
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA
| | - Jiaqiang Huang
- College of Life Sciences and Bioengineering, School of Physical Science and Engineering, Beijing Jiaotong University, 3 ShangyuanCun, Haidian District, 100044, Beijing, P.R. China.
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, 101149, Beijing, China.
- Laboratory of Cancer Innovation, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.
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Ma H, Hu T, Tao W, Tong J, Han Z, Herndler-Brandstetter D, Wei Z, Liu R, Zhou T, Liu Q, Xu X, Zhang K, Zhou R, Cho JH, Li HB, Huang H, Flavell RA, Zhu S. A lncRNA from an inflammatory bowel disease risk locus maintains intestinal host-commensal homeostasis. Cell Res 2023; 33:372-388. [PMID: 37055591 PMCID: PMC10156687 DOI: 10.1038/s41422-023-00790-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 02/10/2023] [Indexed: 04/15/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are known to have complex, genetically influenced etiologies, involving dysfunctional interactions between the intestinal immune system and the microbiome. Here, we characterized how the RNA transcript from an IBD-associated long non-coding RNA locus ("CARINH-Colitis Associated IRF1 antisense Regulator of Intestinal Homeostasis") protects against IBD. We show that CARINH and its neighboring gene coding for the transcription factor IRF1 together form a feedforward loop in host myeloid cells. The loop activation is sustained by microbial factors, and functions to maintain the intestinal host-commensal homeostasis via the induction of the anti-inflammatory factor IL-18BP and anti-microbial factors called guanylate-binding proteins (GBPs). Extending these mechanistic insights back to humans, we demonstrate that the function of the CARINH/IRF1 loop is conserved between mice and humans. Genetically, the T allele of rs2188962, the most probable causal variant of IBD within the CARINH locus from the human genetics study, impairs the inducible expression of the CARINH/IRF1 loop and thus increases genetic predisposition to IBD. Our study thus illustrates how an IBD-associated lncRNA maintains intestinal homeostasis and protects the host against colitis.
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Affiliation(s)
- Hongdi Ma
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Taidou Hu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Wanyin Tao
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Jiyu Tong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Zili Han
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | | | - Zheng Wei
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Ruize Liu
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Tingyue Zhou
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Qiuyuan Liu
- The Key Laboratory of Digestive Diseases of Anhui Province, Department of Gastroenterology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Xuemei Xu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Kaiguang Zhang
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Rongbin Zhou
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Judy H Cho
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Hua-Bing Li
- Shanghai Institute of Immunology, Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai, China.
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
| | - Richard A Flavell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA.
- Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT, USA.
| | - Shu Zhu
- Department of Digestive Disease, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- Institute of Immunology, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
- School of Data Science, University of Science and Technology of China, Hefei, Anhui, China.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, Anhui, China.
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Tao X, Li S, Chen G, Wang J, Xu S. Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination. Int J Mol Sci 2023; 24:ijms24065562. [PMID: 36982636 PMCID: PMC10054671 DOI: 10.3390/ijms24065562] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes of action. Thus, it is very important to choose appropriate research methodologies when investigating lncRNAs with biological significance. Multiple reviews to date have summarized the mechanisms of lncRNA biogenesis, their localization, their functions in gene regulation at multiple levels, and also their potential applications. However, little has been reviewed on the leading strategies for lncRNA research. Here, we generalize a basic and systemic mind map for lncRNA research and discuss the mechanisms and the application scenarios of ‘up-to-date’ techniques as applied to molecular function studies of lncRNAs. Taking advantage of documented lncRNA research paradigms as examples, we aim to provide an overview of the developing techniques for elucidating lncRNA interactions with genomic DNA, proteins, and other RNAs. In the end, we propose the future direction and potential technological challenges of lncRNA studies, focusing on techniques and applications.
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Affiliation(s)
- Xiaoyuan Tao
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Sujuan Li
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Guang Chen
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Jian Wang
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Shengchun Xu
- Xianghu Laboratory, Hangzhou 311231, China
- Central Laboratory, State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Correspondence:
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Lajqi T, Köstlin-Gille N, Bauer R, Zarogiannis SG, Lajqi E, Ajeti V, Dietz S, Kranig SA, Rühle J, Demaj A, Hebel J, Bartosova M, Frommhold D, Hudalla H, Gille C. Training vs. Tolerance: The Yin/Yang of the Innate Immune System. Biomedicines 2023; 11:biomedicines11030766. [PMID: 36979747 PMCID: PMC10045728 DOI: 10.3390/biomedicines11030766] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
For almost nearly a century, memory functions have been attributed only to acquired immune cells. Lately, this paradigm has been challenged by an increasing number of studies revealing that innate immune cells are capable of exhibiting memory-like features resulting in increased responsiveness to subsequent challenges, a process known as trained immunity (known also as innate memory). In contrast, the refractory state of endotoxin tolerance has been defined as an immunosuppressive state of myeloid cells portrayed by a significant reduction in the inflammatory capacity. Both training as well tolerance as adaptive features are reported to be accompanied by epigenetic and metabolic alterations occurring in cells. While training conveys proper protection against secondary infections, the induction of endotoxin tolerance promotes repairing mechanisms in the cells. Consequently, the inappropriate induction of these adaptive cues may trigger maladaptive effects, promoting an increased susceptibility to secondary infections—tolerance, or contribute to the progression of the inflammatory disorder—trained immunity. This review aims at the discussion of these opposing manners of innate immune and non-immune cells, describing the molecular, metabolic and epigenetic mechanisms involved and interpreting the clinical implications in various inflammatory pathologies.
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Affiliation(s)
- Trim Lajqi
- Department of Neonatology, Heidelberg University Children’s Hospital, D-69120 Heidelberg, Germany
- Correspondence: (T.L.); (C.G.)
| | - Natascha Köstlin-Gille
- Department of Neonatology, Heidelberg University Children’s Hospital, D-69120 Heidelberg, Germany
- Department of Neonatology, University of Tübingen, D-72076 Tübingen, Germany
| | - Reinhard Bauer
- Institute of Molecular Cell Biology, Jena University Hospital, D-07745 Jena, Germany
| | - Sotirios G. Zarogiannis
- Department of Physiology, School of Health Sciences, Faculty of Medicine, University of Thessaly, GR-41500 Larissa, Greece
| | - Esra Lajqi
- Department of Radiation Oncology, Heidelberg University Hospital, D-69120 Heidelberg, Germany
| | - Valdrina Ajeti
- Department of Pharmacy, Alma Mater Europaea—Campus College Rezonanca, XK-10000 Pristina, Kosovo
| | - Stefanie Dietz
- Department of Neonatology, Heidelberg University Children’s Hospital, D-69120 Heidelberg, Germany
- Department of Neonatology, University of Tübingen, D-72076 Tübingen, Germany
| | - Simon A. Kranig
- Department of Neonatology, Heidelberg University Children’s Hospital, D-69120 Heidelberg, Germany
| | - Jessica Rühle
- Department of Neonatology, University of Tübingen, D-72076 Tübingen, Germany
| | - Ardian Demaj
- Faculty of Medical Sciences, University of Tetovo, MK-1200 Tetova, North Macedonia
| | - Janine Hebel
- Department of Neonatology, University of Tübingen, D-72076 Tübingen, Germany
| | - Maria Bartosova
- Center for Pediatric and Adolescent Medicine Heidelberg, University of Heidelberg, D-69120 Heidelberg, Germany
| | - David Frommhold
- Klinik für Kinderheilkunde und Jugendmedizin, D-87700 Memmingen, Germany
| | - Hannes Hudalla
- Department of Neonatology, Heidelberg University Children’s Hospital, D-69120 Heidelberg, Germany
| | - Christian Gille
- Department of Neonatology, Heidelberg University Children’s Hospital, D-69120 Heidelberg, Germany
- Correspondence: (T.L.); (C.G.)
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Yeo SJ, Ying C, Fullwood MJ, Tergaonkar V. Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains. Trends Genet 2023; 39:217-232. [PMID: 36642680 DOI: 10.1016/j.tig.2022.12.003] [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: 08/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.
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Affiliation(s)
- Samuel Jianjie Yeo
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Singapore 308232, Singapore
| | - Chen Ying
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Pathology and the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore.
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Abstract
The principle of trained immunity represents innate immune memory due to sustained, mainly epigenetic, changes triggered by endogenous or exogenous stimuli in bone marrow (BM) progenitors (central trained immunity) and their innate immune cell progeny, thereby triggering elevated responsiveness against secondary stimuli. BM progenitors can respond to microbial and sterile signals, thereby possibly acquiring trained immunity-mediated long-lasting alterations that may shape the fate and function of their progeny, for example, neutrophils. Neutrophils, the most abundant innate immune cell population, are produced in the BM from committed progenitor cells in a process designated granulopoiesis. Neutrophils are the first responders against infectious or inflammatory challenges and have versatile functions in immunity. Together with other innate immune cells, neutrophils are effectors of peripheral trained immunity. However, given the short lifetime of neutrophils, their ability to acquire immunological memory may lie in the central training of their BM progenitors resulting in generation of reprogrammed, that is, "trained", neutrophils. Although trained immunity may have beneficial effects in infection or cancer, it may also mediate detrimental outcomes in chronic inflammation. Here, we review the emerging research area of trained immunity with a particular emphasis on the role of neutrophils and granulopoiesis.
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Affiliation(s)
- Lydia Kalafati
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - Aikaterini Hatzioannou
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
| | - George Hajishengallis
- Department of Basic and Translational Sciences, School of Dental Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany
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Yang J, Zhang J, Yang Q, Huang X, Yan Z, Wang P, Gao X, Li J, Li N, Gao Y, Gun S. LncRNA EN-90756 promotes CPB2-induced proliferation and inhibits apoptosis in IPEC-J2 cells by affecting the JAK-STAT signaling pathway activation. Front Microbiol 2023; 13:1082025. [PMID: 36713226 PMCID: PMC9879603 DOI: 10.3389/fmicb.2022.1082025] [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: 11/11/2022] [Accepted: 12/28/2022] [Indexed: 01/14/2023] Open
Abstract
Background Long non-coding RNAs (lncRNAs), as key regulators, are closely associated with the development of a variety of disease. However, the mechanisms by which lncRNAs regulate Clostridium perfringens type C induced piglet diarrhea are unclear. Methods In the present study, we explored the expression and characterization of lncRNAs in a C. perfringens beta2 (CPB2) toxin-treated intestinal porcine epithelial cell line-J2 (IPEC-J2) using RNA-sequencing (RNA-seq). Results A total of 6,558 lncRNAs were identified, of which 49 lncRNAs were significantly differentially expressed between the control and CPB2 groups. Functional enrichment analysis showed that the target genes of differentially expressed lncRNA EN-90756 were mainly associated with defense response to virus, and negative regulation of apoptotic process. LncRNA EN-90756 was significantly up-regulated in IPEC-J2 cells at different time points after CPB2 treatment. Functionally, knockdown of lncRNA EN-90756 might regulate the proliferation and apoptosis of IPEC-J2 cells by affecting the Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathway. LncRNA EN-90756 may be involved in CPB2 toxin-induced piglet diarrhea by regulating the expression of its target gene MX1 (encoding MX dynamin like GTPase 1). Conclusion Long non-coding RNA EN-90756 affected the antiviral ability of IPEC-J2 cells by regulating the expression of MX1. Meanwhile, lncRNA EN-90756 might regulate cell proliferation and apoptosis by affecting JAK-STAT signaling pathway activation. These findings provide novel perspectives and directions for further exploration of the regulatory mechanisms of lncRNAs on CPB2 toxin-induced diarrhea in piglets.
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Affiliation(s)
- Jiaojiao Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Juanli Zhang
- College of Life Sciences and Technology, Longdong University, Qingyang, China
| | - Qiaoli Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoyu Huang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Zunqiang Yan
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Pengfei Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaoli Gao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jie Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Na Li
- Jilin Rongtai Agricultural Development Co., Ltd., Changchun, China
| | - Yi Gao
- Jilin Rongtai Agricultural Development Co., Ltd., Changchun, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China,Gansu Research Center for Swine Production Engineering and Technology, Lanzhou, China,*Correspondence: Shuangbao Gun,
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Zhang W, Zhao J, Deng L, Ishimwe N, Pauli J, Wu W, Shan S, Kempf W, Ballantyne MD, Kim D, Lyu Q, Bennett M, Rodor J, Turner AW, Lu YW, Gao P, Choi M, Warthi G, Kim HW, Barroso MM, Bryant WB, Miller CL, Weintraub NL, Maegdefessel L, Miano JM, Baker AH, Long X. INKILN is a novel long noncoding RNA promoting vascular smooth muscle inflammation via scaffolding MKL1 and USP10. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.07.522948. [PMID: 36711681 PMCID: PMC9881896 DOI: 10.1101/2023.01.07.522948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background Activation of vascular smooth muscle cells (VSMCs) inflammation is vital to initiate vascular disease. However, the role of human-specific long noncoding RNAs (lncRNAs) in VSMC inflammation is poorly understood. Methods Bulk RNA-seq in differentiated human VSMCs revealed a novel human-specific lncRNA called IN flammatory M K L1 I nteracting L ong N oncoding RNA ( INKILN ). INKILN expression was assessed in multiple in vitro and ex vivo models of VSMC phenotypic modulation and human atherosclerosis and abdominal aortic aneurysm (AAA) samples. The transcriptional regulation of INKILN was determined through luciferase reporter system and chromatin immunoprecipitation assay. Both loss- and gain-of-function approaches and multiple RNA-protein and protein-protein interaction assays were utilized to uncover the role of INKILN in VSMC proinflammatory gene program and underlying mechanisms. Bacterial Artificial Chromosome (BAC) transgenic (Tg) mice were utilized to study INKLIN expression and function in ligation injury-induced neointimal formation. Results INKILN expression is downregulated in contractile VSMCs and induced by human atherosclerosis and abdominal aortic aneurysm. INKILN is transcriptionally activated by the p65 pathway, partially through a predicted NF-κB site within its proximal promoter. INKILN activates the proinflammatory gene expression in cultured human VSMCs and ex vivo cultured vessels. Mechanistically, INKILN physically interacts with and stabilizes MKL1, a key activator of VSMC inflammation through the p65/NF-κB pathway. INKILN depletion blocks ILIβ-induced nuclear localization of both p65 and MKL1. Knockdown of INKILN abolishes the physical interaction between p65 and MKL1, and the luciferase activity of an NF-κB reporter. Further, INKILN knockdown enhances MKL1 ubiquitination, likely through the reduced physical interaction with the deubiquitinating enzyme, USP10. INKILN is induced in injured carotid arteries and exacerbates ligation injury-induced neointimal formation in BAC Tg mice. Conclusions These findings elucidate an important pathway of VSMC inflammation involving an INKILN /MKL1/USP10 regulatory axis. Human BAC Tg mice offer a novel and physiologically relevant approach for investigating human-specific lncRNAs under vascular disease conditions.
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Maheshwari A. Innate Immune Memory in Macrophages. NEWBORN (CLARKSVILLE, MD.) 2023; 2:60-79. [PMID: 37206580 PMCID: PMC10193650 DOI: 10.5005/jp-journals-11002-0058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Macrophages have been recognized as the primary mediators of innate immunity starting from embryonic/fetal development. Macrophage-mediated defenses may not be as antigen-specific as adaptive immunity, but increasing information suggests that these responses do strengthen with repeated immunological triggers. The concept of innate memory in macrophages has been described as "trained immunity" or "innate immune memory (IIM)." As currently understood, this cellular memory is rooted in epigenetic and metabolic reprogramming. The recognition of IIM may be particularly important in the fetus and the young neonate who are yet to develop protective levels of adaptive immunity, and could even be of preventive/therapeutic importance in many disorders. There may also be a possibility of therapeutic enhancement with targeted vaccination. This article presents a review of the properties, mechanisms, and possible clinical significance of macrophage-mediated IIM.
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Affiliation(s)
- Akhil Maheshwari
- Founding Chairman, Global Newborn Society, Clarksville, Maryland, United States of America
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Wang J, Liu YM, Hu J, Chen C. Trained immunity in monocyte/macrophage: Novel mechanism of phytochemicals in the treatment of atherosclerotic cardiovascular disease. Front Pharmacol 2023; 14:1109576. [PMID: 36895942 PMCID: PMC9989041 DOI: 10.3389/fphar.2023.1109576] [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: 11/29/2022] [Accepted: 01/27/2023] [Indexed: 02/23/2023] Open
Abstract
Atherosclerosis (AS) is the pathology of atherosclerotic cardiovascular diseases (ASCVD), characterized by persistent chronic inflammation in the vessel wall, in which monocytes/macrophages play a key role. It has been reported that innate immune system cells can assume a persistent proinflammatory state after short stimulation with endogenous atherogenic stimuli. The pathogenesis of AS can be influenced by this persistent hyperactivation of the innate immune system, which is termed trained immunity. Trained immunity has also been implicated as a key pathological mechanism, leading to persistent chronic inflammation in AS. Trained immunity is mediated via epigenetic and metabolic reprogramming and occurs in mature innate immune cells and their bone marrow progenitors. Natural products are promising candidates for novel pharmacological agents that can be used to prevent or treat cardiovascular diseases (CVD). A variety of natural products and agents exhibiting antiatherosclerotic abilities have been reported to potentially interfere with the pharmacological targets of trained immunity. This review describes in as much detail as possible the mechanisms involved in trained immunity and how phytochemicals of this process inhibit AS by affecting trained monocytes/macrophages.
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Affiliation(s)
- Jie Wang
- Guang'anmen Hospital, China Academy of Chinese Medicine Sciences, Beijing, China
| | - Yong-Mei Liu
- Guang'anmen Hospital, China Academy of Chinese Medicine Sciences, Beijing, China
| | - Jun Hu
- Guang'anmen Hospital, China Academy of Chinese Medicine Sciences, Beijing, China
| | - Cong Chen
- Guang'anmen Hospital, China Academy of Chinese Medicine Sciences, Beijing, China
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Li Y, Yu H, Feng J. Role of chemokine-like factor 1 as an inflammatory marker in diseases. Front Immunol 2023; 14:1085154. [PMID: 36865551 PMCID: PMC9971601 DOI: 10.3389/fimmu.2023.1085154] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
Immunoinflammatory mechanisms have been incrementally found to be involved in the pathogenesis of multiple diseases, with chemokines being the main drivers of immune cell infiltration in the inflammatory response. Chemokine-like factor 1 (CKLF1), a novel chemokine, is highly expressed in the human peripheral blood leukocytes and exerts broad-spectrum chemotactic and pro-proliferative effects by activating multiple downstream signaling pathways upon binding to its functional receptors. Furthermore, the relationship between CKLF1 overexpression and various systemic diseases has been demonstrated in both in vivo and in vitro experiments. In this context, it is promising that clarifying the downstream mechanism of CKLF1 and identifying its upstream regulatory sites can yield new strategies for targeted therapeutics of immunoinflammatory diseases.
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Affiliation(s)
- Yutong Li
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiyang Yu
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Juan Feng
- Department of Neurology, Shengjing Hospital of China Medical University, Shenyang, China
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Kloc M, Kubiak JZ, Zdanowski R, Ghobrial RM. Memory Macrophages. Int J Mol Sci 2022; 24:ijms24010038. [PMID: 36613481 PMCID: PMC9819859 DOI: 10.3390/ijms24010038] [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: 12/01/2022] [Revised: 12/12/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
Immunological memory is a crucial part of the immune defense that allows organisms to respond against previously encountered pathogens or other harmful factors. Immunological memory is based on the establishment of epigenetic modifications of the genome. The ability to memorize encounters with pathogens and other harmful factors and mount enhanced defense upon subsequent encounters is an evolutionarily ancient mechanism operating in all animals and plants. However, the term immunological memory is usually restricted to the organisms (invertebrates and vertebrates) possessing the immune system. The mammalian immune system, with innate and adaptive branches, is the most sophisticated among vertebrates. The concept of innate memory and memory macrophages is relatively new and thus understudied. We introduce the concept of immunological memory and describe types of memory in different species and their evolutionary status. We discuss why the traditional view of innate immune cells as the first-line defenders is too restrictive and how the innate immune cells can accumulate and retain immunologic memory. We describe how the initial priming leads to chromatin remodeling and epigenetic changes, which allow memory macrophage formation. We also summarize what is currently known about the mechanisms underlying development of memory macrophages; their molecular and metabolic signature and surface markers; and how they may contribute to immune defense, diseases, and organ transplantation.
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Affiliation(s)
- Malgorzata Kloc
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
- Department of Genetics, MD Anderson Cancer Center, The University of Texas, Houston, TX 77030, USA
- Correspondence:
| | - Jacek Z. Kubiak
- Dynamics and Mechanics of Epithelia Group, Faculty of Medicine, Institute of Genetics and Development of Rennes, University of Rennes, CNRS, UMR 6290, 35043 Rennes, France
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Robert Zdanowski
- Laboratory of Molecular Oncology and Innovative Therapies, Military Institute of Medicine National Research Institute, Szaserow 128, 04-141 Warsaw, Poland
| | - Rafik M. Ghobrial
- The Houston Methodist Research Institute, Transplant Immunology, Houston, TX 77030, USA
- Department of Surgery, The Houston Methodist Hospital, Houston, TX 77030, USA
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50
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Sun B, Sherrin M, Roy R. Unscheduled epigenetic modifications cause genome instability and sterility through aberrant R-loops following starvation. Nucleic Acids Res 2022; 51:84-98. [PMID: 36504323 PMCID: PMC9841415 DOI: 10.1093/nar/gkac1155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
During starvation, organisms modify both gene expression and metabolism to adjust to the energy stress. We previously reported that Caenorhabditis elegans lacing AMP-activated protein kinase (AMPK) exhibit transgenerational reproductive defects associated with abnormally elevated trimethylated histone H3 at lysine 4 (H3K4me3) levels in the germ line following recovery from acute starvation. Here, we show that these H3K4me3 marks are significantly increased at promoters, driving aberrant transcription elongation resulting in the accumulation of R-loops in starved AMPK mutants. DNA-RNA immunoprecipitation followed by high-throughput sequencing (DRIP-seq) analysis demonstrated that a significant proportion of the genome was affected by R-loop formation. This was most pronounced in the promoter-transcription start site regions of genes, in which the chromatin was modified by H3K4me3. Like H3K4me3, the R-loops were also found to be heritable, likely contributing to the transgenerational reproductive defects typical of these mutants following starvation. Strikingly, AMPK mutant germ lines show considerably more RAD-51 (the RecA recombinase) foci at sites of R-loop formation, potentially sequestering them from their roles at meiotic breaks or at sites of induced DNA damage. Our study reveals a previously unforeseen role of AMPK in maintaining genome stability following starvation. The downstream effects of R-loops on DNA damage sensitivity and germline stem cell integrity may account for inappropriate epigenetic modification that occurs in numerous human disorders, including various cancers.
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Affiliation(s)
- Bing Sun
- To whom correspondence should be addressed.
| | - McLean Sherrin
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada
| | - Richard Roy
- Correspondence may also be addressed to Richard Roy. Tel: +1 514 398 6437;
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