1
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Fu Y, Wang Y, Zhang L, He T, Shi W, Guo X, Wang Y. SRSF3 Knockdown Inhibits Lipopolysaccharide-Induced Inflammatory Response in Macrophages. Curr Issues Mol Biol 2024; 46:6237-6247. [PMID: 38921043 PMCID: PMC11202707 DOI: 10.3390/cimb46060372] [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: 05/21/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 06/27/2024] Open
Abstract
Serine/arginine-rich splicing factor 3 (SRSF3), the smallest member of the SR protein family, serves multiple roles in RNA processing, including splicing, translation, and stability. Recent studies have shown that SRSF3 is implicated in several inflammatory diseases. However, its impact on macrophage inflammation remains unclear. Herein, we determined the expression of SRSF3 in inflammatory macrophages and found that the level of SRSF3 was increased in macrophages within atherosclerotic plaques, as well as in RAW-264.7 macrophages stimulated by lipopolysaccharides. Moreover, the downregulation of SRSF3 suppressed the levels of inflammatory cytokines by deactivating the nuclear factor κB (NFκB) pathway. Furthermore, the alternative splicing of myeloid differentiation protein 2 (MD2), a co-receptor of toll-like receptor 4 (TLR4), is regulated by SRSF3. The depletion of SRSF3 increased the level of the shorter MD2B splicing variants, which contributed to inflammatory inhibition in macrophages. In conclusion, our findings imply that SRSF3 regulates lipopolysaccharide-stimulated inflammation, in part by controlling the alternative splicing of MD2 mRNA in macrophages.
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Affiliation(s)
- Yu Fu
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China; (Y.W.); (L.Z.); (T.H.); (W.S.); (X.G.)
| | | | | | | | | | | | - Yingze Wang
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang 050018, China; (Y.W.); (L.Z.); (T.H.); (W.S.); (X.G.)
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2
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Li K, Wang WH, Wu JB, Xiao WH. β-hydroxybutyrate: A crucial therapeutic target for diverse liver diseases. Biomed Pharmacother 2023; 165:115191. [PMID: 37487440 DOI: 10.1016/j.biopha.2023.115191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
β-hydroxybutyrate (β-HB), the most abundant ketone body, is produced primarily in the liver and acts as a substitute energy fuel to provide energy to extrahepatic tissues in the event of hypoglycemia or glycogen depletion. We now have an improved understanding of β-HB as a signal molecule and epigenetic regulatory factor as a result of intensive research over the last ten years. Because β-HB regulates various physiological and pathological processes, it may have a potential role in the treatment of metabolic diseases. The liver is the most significant metabolic organ, and the part that β-HB plays in liver disorders is receiving increasing attention. In this review, we summarize the therapeutic effects of β-HB on liver diseases and its underlying mechanisms of action. Moreover, we explore the prospects of exogenous supplements and endogenous ketosis including fasting, caloric restriction (CR), ketogenic diet (KD), and exercise as adjuvant nutritional therapies to protect the liver from damage and provide insights and strategies for exploring the treatment of various liver diseases.
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Affiliation(s)
- Ke Li
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China
| | - Wen-Hong Wang
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China
| | - Jia-Bin Wu
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China
| | - Wei-Hua Xiao
- Key Lab of Exercise and Health Sciences of Ministry of Education, Shanghai University of Sport, Shanghai 200438, China; Shanghai Key Lab of Human Performance, Shanghai University of Sport, Shanghai 200438, China.
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3
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Lee FFY, Alper S. Alternative pre-mRNA splicing as a mechanism for terminating Toll-like Receptor signaling. Front Immunol 2022; 13:1023567. [PMID: 36531997 PMCID: PMC9755862 DOI: 10.3389/fimmu.2022.1023567] [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: 08/19/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
While inflammation induced by Toll-like receptor (TLR) signaling is required to combat infection, persistent inflammation can damage host tissues and contribute to a myriad of acute and chronic inflammatory disorders. Thus, it is essential not only that TLR signaling be activated in the presence of pathogens but that TLR signaling is ultimately terminated. One mechanism that limits persistent TLR signaling is alternative pre-mRNA splicing. In addition to encoding the canonical mRNAs that produce proteins that promote inflammation, many genes in the TLR signaling pathway also encode alternative mRNAs that produce proteins that are dominant negative inhibitors of signaling. Many of these negative regulators are induced by immune challenge, so production of these alternative isoforms represents a negative feedback loop that limits persistent inflammation. While these alternative splicing events have been investigated on a gene by gene basis, there has been limited systemic analysis of this mechanism that terminates TLR signaling. Here we review what is known about the production of negatively acting alternative isoforms in the TLR signaling pathway including how these inhibitors function, how they are produced, and what role they may play in inflammatory disease.
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Affiliation(s)
- Frank Fang Yao Lee
- Department of Immunology and Genomic Medicine and Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States,Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO, United States
| | - Scott Alper
- Department of Immunology and Genomic Medicine and Center for Genes, Environment, and Health, National Jewish Health, Denver, CO, United States,Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO, United States,*Correspondence: Scott Alper,
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4
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Li N, Li Y, Han X, Zhang J, Han J, Jiang X, Wang W, Xu Y, Xu Y, Fu Y, Si S. LXR agonist inhibits inflammation through regulating MyD88 mRNA alternative splicing. Front Pharmacol 2022; 13:973612. [PMID: 36313296 PMCID: PMC9614042 DOI: 10.3389/fphar.2022.973612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/22/2022] [Indexed: 12/02/2022] Open
Abstract
Liver X receptors (LXRs) are important regulators of cholesterol metabolism and inflammatory responses. LXR agonists exhibit potently anti-inflammatory effects in macrophages, which make them beneficial to anti-atherogenic therapy. In addition to transrepressive regulation by SUMOylation, LXRs can inhibit inflammation by various mechanisms through affecting multiple targets. In this study, we found that the classic LXR agonist T0901317 mediated numerous genes containing alternative splice sites, including myeloid differentiation factor 88 (MyD88), that contribute to inflammatory inhibition in RAW264.7 macrophages. Furthermore, T0901317 increased level of alternative splice short form of MyD88 mRNA by down-regulating expression of splicing factor SF3A1, leading to nuclear factor κB-mediated inhibition of inflammation. In conclusion, our results suggest for the first time that the LXR agonist T0901317 inhibits lipopolysaccharide-induced inflammation through regulating MyD88 mRNA alternative splicing involved in TLR4 signaling pathway.
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Affiliation(s)
- Ni Li
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Beijing, China
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Ni Li, ; Yu Fu, ; Shuyi Si,
| | - Yan Li
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang, Hebei
| | - Xiaowan Han
- State Key Laboratory of Bioactive Substances and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences, Beijing, China
| | - Jing Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiangxue Han
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinhai Jiang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weizhi Wang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yang Xu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanni Xu
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Fu
- College of Food Science and Biology, Hebei University of Science and Technology, Shijiazhuang, Hebei
- *Correspondence: Ni Li, ; Yu Fu, ; Shuyi Si,
| | - Shuyi Si
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Ni Li, ; Yu Fu, ; Shuyi Si,
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5
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Jusic A, Thomas PB, Wettinger SB, Dogan S, Farrugia R, Gaetano C, Tuna BG, Pinet F, Robinson EL, Tual-Chalot S, Stellos K, Devaux Y. Noncoding RNAs in age-related cardiovascular diseases. Ageing Res Rev 2022; 77:101610. [PMID: 35338919 DOI: 10.1016/j.arr.2022.101610] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/28/2022] [Accepted: 03/15/2022] [Indexed: 11/01/2022]
Abstract
Cardiovascular diseases (CVDs) are the leading cause of morbidity and mortality in the adult population worldwide and represent a severe economic burden and public health concern. The majority of human genes do not code for proteins. However, noncoding transcripts play important roles in ageing that significantly increases the risk for CVDs. Noncoding RNAs (ncRNAs) are critical regulators of multiple biological processes related to ageing such as oxidative stress, mitochondrial dysfunction and chronic inflammation. NcRNAs are also involved in pathophysiological developments within the cardiovascular system including arrhythmias, cardiac hypertrophy, fibrosis, myocardial infarction and heart failure. In this review article, we cover the roles of ncRNAs in cardiovascular ageing and disease as well as their potential therapeutic applications in CVDs.
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6
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Naler LB, Hsieh YP, Geng S, Zhou Z, Li L, Lu C. Epigenomic and transcriptomic analyses reveal differences between low-grade inflammation and severe exhaustion in LPS-challenged murine monocytes. Commun Biol 2022; 5:102. [PMID: 35091696 PMCID: PMC8799722 DOI: 10.1038/s42003-022-03035-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 01/05/2022] [Indexed: 12/28/2022] Open
Abstract
Emerging studies suggest that monocytes can be trained by bacterial endotoxin to adopt distinct memory states ranging from low-grade inflammation to immune exhaustion. While low-grade inflammation may contribute to the pathogenesis of chronic diseases, exhausted monocytes with pathogenic and immune-suppressive characteristics may underlie the pathogenesis of polymicrobial sepsis including COVID-19. However, detailed processes by which the dynamic adaption of monocytes occur remain poorly understood. Here we exposed murine bone-marrow derived monocytes to chronic lipopolysaccharide (LPS) stimulation at low-dose or high-dose, as well as a PBS control. The cells were profiled for genome-wide H3K27ac modification and gene expression. The gene expression of TRAM-deficient and IRAK-M-deficient monocytes with LPS exposure was also analyzed. We discover that low-grade inflammation preferentially utilizes the TRAM-dependent pathway of TLR4 signaling, and induces the expression of interferon response genes. In contrast, high dose LPS uniquely upregulates exhaustion signatures with metabolic and proliferative pathways. The extensive differences in the epigenomic landscape between low-dose and high-dose conditions suggest the importance of epigenetic regulations in driving differential responses. Our data provide potential targets for future mechanistic or therapeutic studies.
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Affiliation(s)
- Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Yuan-Pang Hsieh
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Shuo Geng
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Zirui Zhou
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Liwu Li
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA.
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA, USA.
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7
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An S, Li Y, Lin Y, Chu J, Su J, Chen Q, Wang H, Pan P, Zheng R, Li J, Jiang J, Ye L, Liang H. Genome-Wide Profiling Reveals Alternative Polyadenylation of Innate Immune-Related mRNA in Patients With COVID-19. Front Immunol 2021; 12:756288. [PMID: 34777369 PMCID: PMC8578971 DOI: 10.3389/fimmu.2021.756288] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/13/2021] [Indexed: 01/13/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has caused many deaths worldwide. To date, the mechanism of viral immune escape remains unclear, which is a great obstacle to developing effective clinical treatment. RNA processing mechanisms, including alternative polyadenylation (APA) and alternative splicing (AS), are crucial in the regulation of most human genes in many types of infectious diseases. Because the role of APA and AS in response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection remains unknown, we performed de novo identification of dynamic APA sites using a public dataset of human peripheral blood mononuclear cell (PBMC) RNA-Seq data in COVID-19 patients. We found that genes with APA were enriched in innate immunity -related gene ontology categories such as neutrophil activation, regulation of the MAPK cascade and cytokine production, response to interferon-gamma and the innate immune response. We also reported genome-wide AS events and enriched viral transcription-related categories upon SARS-CoV-2 infection. Interestingly, we found that APA events may give better predictions than AS in COVID-19 patients, suggesting that APA could act as a potential therapeutic target and novel biomarker in those patients. Our study is the first to annotate genes with APA and AS in COVID-19 patients and highlights the roles of APA variation in SARS-CoV-2 infection.
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Affiliation(s)
- Sanqi An
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Yueqi Li
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Yao Lin
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Jiemei Chu
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Jinming Su
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Qiuli Chen
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Hailong Wang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Peijiang Pan
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Ruili Zheng
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Jingyi Li
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China
| | - Junjun Jiang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Li Ye
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
| | - Hao Liang
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, China.,Guangxi Key Laboratory of AIDS Prevention and Treatment, School of Public Health, Guangxi Medical University, Nanning, China
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8
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Blake D, Lynch KW. The three as: Alternative splicing, alternative polyadenylation and their impact on apoptosis in immune function. Immunol Rev 2021; 304:30-50. [PMID: 34368964 DOI: 10.1111/imr.13018] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/13/2022]
Abstract
The latest advances in next-generation sequencing studies and transcriptomic profiling over the past decade have highlighted a surprising frequency of genes regulated by RNA processing mechanisms in the immune system. In particular, two control steps in mRNA maturation, namely alternative splicing and alternative polyadenylation, are now recognized to occur in the vast majority of human genes. Both have the potential to alter the identity of the encoded protein, as well as control protein abundance or even protein localization or association with other factors. In this review, we will provide a summary of the general mechanisms by which alternative splicing (AS) and alternative polyadenylation (APA) occur, their regulation within cells of the immune system, and their impact on immunobiology. In particular, we will focus on how control of apoptosis by AS and APA is used to tune cell fate during an immune response.
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Affiliation(s)
- Davia Blake
- Immunology Graduate Group and the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristen W Lynch
- Immunology Graduate Group and the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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9
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Robinson EK, Jagannatha P, Covarrubias S, Cattle M, Smaliy V, Safavi R, Shapleigh B, Abu-Shumays R, Jain M, Cloonan SM, Akeson M, Brooks AN, Carpenter S. Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2. eLife 2021; 10:69431. [PMID: 34047695 PMCID: PMC8260223 DOI: 10.7554/elife.69431] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/21/2021] [Indexed: 12/11/2022] Open
Abstract
Determining the layers of gene regulation within the innate immune response is critical to our understanding of the cellular responses to infection and dysregulation in disease. We identified a conserved mechanism of gene regulation in human and mouse via changes in alternative first exon (AFE) usage following inflammation, resulting in changes to the isoforms produced. Of these AFE events, we identified 95 unannotated transcription start sites in mice using a de novo transcriptome generated by long-read native RNA-sequencing, one of which is in the cytosolic receptor for dsDNA and known inflammatory inducible gene, Aim2. We show that this unannotated AFE isoform of Aim2 is the predominant isoform expressed during inflammation and contains an iron-responsive element in its 5′UTR enabling mRNA translation to be regulated by iron levels. This work highlights the importance of examining alternative isoform changes and translational regulation in the innate immune response and uncovers novel regulatory mechanisms of Aim2.
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Affiliation(s)
- Elektra K Robinson
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Pratibha Jagannatha
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States.,Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Matthew Cattle
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Valeriya Smaliy
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Rojin Safavi
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Barbara Shapleigh
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
| | - Robin Abu-Shumays
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Miten Jain
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Suzanne M Cloonan
- Division of Pulmonary and Critical Care Medicine, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, New York, United States
| | - Mark Akeson
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Angela N Brooks
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, United States
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, United States
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10
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Bernard EM, Fearns A, Bussi C, Santucci P, Peddie CJ, Lai RJ, Collinson LM, Gutierrez MG. M. tuberculosis infection of human iPSC-derived macrophages reveals complex membrane dynamics during xenophagy evasion. J Cell Sci 2020; 134:jcs252973. [PMID: 32938685 PMCID: PMC7710011 DOI: 10.1242/jcs.252973] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Xenophagy is an important cellular defence mechanism against cytosol-invading pathogens, such as Mycobacterium tuberculosis (Mtb). Activation of xenophagy in macrophages targets Mtb to autophagosomes; however, how Mtb is targeted to autophagosomes in human macrophages at a high spatial and temporal resolution is unknown. Here, we use human induced pluripotent stem cell-derived macrophages (iPSDMs) to study the human macrophage response to Mtb infection and the role of the ESX-1 type VII secretion system. Using RNA-seq, we identify ESX-1-dependent transcriptional responses in iPSDMs after infection with Mtb. This analysis revealed differential inflammatory responses and dysregulated pathways such as eukaryotic initiation factor 2 (eIF2) signalling and protein ubiquitylation. Moreover, live-cell imaging revealed that Mtb infection in human macrophages induces dynamic ESX-1-dependent, LC3B-positive tubulovesicular autophagosomes (LC3-TVS). Through a correlative live-cell and focused ion beam scanning electron microscopy (FIB SEM) approach, we show that upon phagosomal rupture, Mtb induces the formation of LC3-TVS, from which the bacterium is able to escape to reside in the cytosol. Thus, iPSDMs represent a valuable model for studying spatiotemporal dynamics of human macrophage-Mtb interactions, and Mtb is able to evade capture by autophagic compartments.
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Affiliation(s)
- Elliott M Bernard
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Antony Fearns
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Claudio Bussi
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Pierre Santucci
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Christopher J Peddie
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rachel J Lai
- Department of Medicine, Imperial College London, London W2 1PG, UK
| | - Lucy M Collinson
- Electron Microscopy Science Technology Platform, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Maximiliano G Gutierrez
- Host-Pathogen Interactions in Tuberculosis Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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11
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Farina AR, Cappabianca L, Sebastiano M, Zelli V, Guadagni S, Mackay AR. Hypoxia-induced alternative splicing: the 11th Hallmark of Cancer. J Exp Clin Cancer Res 2020; 39:110. [PMID: 32536347 PMCID: PMC7294618 DOI: 10.1186/s13046-020-01616-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Hypoxia-induced alternative splicing is a potent driving force in tumour pathogenesis and progression. In this review, we update currents concepts of hypoxia-induced alternative splicing and how it influences tumour biology. Following brief descriptions of tumour-associated hypoxia and the pre-mRNA splicing process, we review the many ways hypoxia regulates alternative splicing and how hypoxia-induced alternative splicing impacts each individual hallmark of cancer. Hypoxia-induced alternative splicing integrates chemical and cellular tumour microenvironments, underpins continuous adaptation of the tumour cellular microenvironment responsible for metastatic progression and plays clear roles in oncogene activation and autonomous tumour growth, tumor suppressor inactivation, tumour cell immortalization, angiogenesis, tumour cell evasion of programmed cell death and the anti-tumour immune response, a tumour-promoting inflammatory response, adaptive metabolic re-programming, epithelial to mesenchymal transition, invasion and genetic instability, all of which combine to promote metastatic disease. The impressive number of hypoxia-induced alternative spliced protein isoforms that characterize tumour progression, classifies hypoxia-induced alternative splicing as the 11th hallmark of cancer, and offers a fertile source of potential diagnostic/prognostic markers and therapeutic targets.
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Affiliation(s)
- Antonietta Rosella Farina
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Lucia Cappabianca
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Michela Sebastiano
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Veronica Zelli
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Stefano Guadagni
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Andrew Reay Mackay
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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12
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Werneck-Gomes H, Campolina-Silva GH, Maria BT, Barata MC, Mahecha GAB, Hess RA, Oliveira CA. Tumor-Associated Macrophages (TAM) are recruited to the aging prostate epithelial lesions and become intermingled with basal cells. Andrology 2020; 8:1375-1386. [PMID: 32157817 DOI: 10.1111/andr.12783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 02/13/2020] [Accepted: 03/09/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Prostate cancer remains one of the most common cancers in men. Macrophages are thought to be important regulators in cancers, and their potential involvement in prostate cancer should not be overlooked. Therefore, the association between macrophages and the pre-tumorous changes in prostate epithelium during aging deserves further investigation. OBJECTIVES We sought to investigate whether macrophages would be recruited into the prostate epithelium that display pathological lesions commonly found during aging. MATERIALS AND METHODS Prostates of aging rats, with and without treatment with a combination of testosterone and estradiol, were examined for premalignant and malignant epithelial lesions. For comparison, prostates of castrated rats were also investigated. RESULTS Intraepithelial macrophages were found restricted to areas of premalignant and malignant lesions. An unprecedented interaction between macrophages and basal cells was observed in the aging pathological lesions. The intraepithelial macrophages were associated with autophagy, in contrast to those found after castration. In prostate lesions, the intraepithelial macrophages had TAM phenotype (CD68+/iNOS+/CD206+/ARG+), denoting a possible involvement in cancer progression. However, M2 macrophages (CD68+/CD163+) were recruited into the epithelium after castration, possibly to phagocytize cells undergoing apoptosis. DISCUSSION AND CONCLUSION In conclusion, macrophages were recruited into the prostate epithelium and presented diverse phenotypes and morphology, consistent with changes reflected in the hormonal environment. Macrophages with the TAM phenotype were found restricted to areas of premalignant and malignant lesions in aging prostates, denoting a possible involvement in cancer progression. In contrast, M2 macrophages were found in the regressed epithelium after castration.
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Affiliation(s)
- Hipácia Werneck-Gomes
- Department of Morphology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Bruna T Maria
- Department of Morphology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria C Barata
- Department of Morphology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Germán A B Mahecha
- Department of Morphology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rex A Hess
- Department of Comparative Biosciences, University of Illinois, Urbana, IL, USA
| | - Cleida A Oliveira
- Department of Morphology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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13
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Liu E, Radmanesh B, Chung BH, Donnan MD, Yi D, Dadi A, Smith KD, Himmelfarb J, Li M, Freedman BS, Lin J. Profiling APOL1 Nephropathy Risk Variants in Genome-Edited Kidney Organoids with Single-Cell Transcriptomics. KIDNEY360 2020; 1:203-215. [PMID: 32656538 PMCID: PMC7351353 DOI: 10.34067/kid.0000422019] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND DNA variants in APOL1 associate with kidney disease, but the pathophysiologic mechanisms remain incompletely understood. Model organisms lack the APOL1 gene, limiting the degree to which disease states can be recapitulated. Here we present single-cell RNA sequencing (scRNA-seq) of genome-edited human kidney organoids as a platform for profiling effects of APOL1 risk variants in diverse nephron cell types. METHODS We performed footprint-free CRISPR-Cas9 genome editing of human induced pluripotent stem cells (iPSCs) to knock in APOL1 high-risk G1 variants at the native genomic locus. iPSCs were differentiated into kidney organoids, treated with vehicle, IFN-γ, or the combination of IFN-γ and tunicamycin, and analyzed with scRNA-seq to profile cell-specific changes in differential gene expression patterns, compared with isogenic G0 controls. RESULTS Both G0 and G1 iPSCs differentiated into kidney organoids containing nephron-like structures with glomerular epithelial cells, proximal tubules, distal tubules, and endothelial cells. Organoids expressed detectable APOL1 only after exposure to IFN-γ. scRNA-seq revealed cell type-specific differences in G1 organoid response to APOL1 induction. Additional stress of tunicamycin exposure led to increased glomerular epithelial cell dedifferentiation in G1 organoids. CONCLUSIONS Single-cell transcriptomic profiling of human genome-edited kidney organoids expressing APOL1 risk variants provides a novel platform for studying the pathophysiology of APOL1-mediated kidney disease.
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Affiliation(s)
- Esther Liu
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Behram Radmanesh
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Byungha H. Chung
- Division of Nephrology, Department of Medicine, Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Michael D. Donnan
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Dan Yi
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Amal Dadi
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Kelly D. Smith
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jonathan Himmelfarb
- Division of Nephrology, Department of Medicine, Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Mingyao Li
- Department of Biostatistics, Epidemiology, and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Benjamin S. Freedman
- Division of Nephrology, Department of Medicine, Kidney Research Institute, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jennie Lin
- Division of Nephrology and Hypertension, Department of Medicine, Feinberg Cardiovascular and Renal Research Institute, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Section of Nephrology, Jesse Brown Veterans Affairs Medical Center, Chicago, Illinois
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14
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de Bruin RG, Vogel G, Prins J, Duijs JMJG, Bijkerk R, van der Zande HJP, van Gils JM, de Boer HC, Rabelink TJ, van Zonneveld AJ, van der Veer EP, Richard S. Targeting the RNA-Binding Protein QKI in Myeloid Cells Ameliorates Macrophage-Induced Renal Interstitial Fibrosis. EPIGENOMES 2020; 4:epigenomes4010002. [PMID: 34968236 PMCID: PMC8594696 DOI: 10.3390/epigenomes4010002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 02/07/2023] Open
Abstract
In the pathophysiologic setting of acute and chronic kidney injury, the excessive activation and recruitment of blood-borne monocytes prompts their differentiation into inflammatory macrophages, a process that leads to progressive glomerulosclerosis and interstitial fibrosis. Importantly, this differentiation of monocytes into macrophages requires the meticulous coordination of gene expression at both the transcriptional and post-transcriptional level. The transcriptomes of these cells are ultimately determined by RNA-binding proteins such as QUAKING (QKI), that define their pre-mRNA splicing and mRNA transcript patterns. Using two mouse models, namely (1) quaking viable mice (qkv) and (2) the conditional deletion in the myeloid cell lineage using the lysozyme 2-Cre (QKIFL/FL;LysM-Cre mice), we demonstrate that the abrogation of QKI expression in the myeloid cell lineage reduces macrophage infiltration following kidney injury induced by unilateral urethral obstruction (UUO). The qkv and QKIFL/FL;LysM-Cre mice both showed significant diminished interstitial collagen deposition and fibrosis in the UUO-damaged kidney, as compared to wild-type littermates. We show that macrophages isolated from QKIFL/FL;LysM-Cre mice are associated with defects in pre-mRNA splicing. Our findings demonstrate that reduced expression of the alternative splice regulator QKI in the cells of myeloid lineage attenuates renal interstitial fibrosis, suggesting that inhibition of this splice regulator may be of therapeutic value for certain kidney diseases.
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Affiliation(s)
- Ruben G. de Bruin
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, QC H3T 1E2, Canada;
| | - Gillian Vogel
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, QC H3T 1E2, Canada;
| | - Jurrien Prins
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Jacques M. J. G. Duijs
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Roel Bijkerk
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Hendrik J. P. van der Zande
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Janine M. van Gils
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Hetty C. de Boer
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Ton J. Rabelink
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Anton Jan van Zonneveld
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
| | - Eric P. van der Veer
- Einthoven Laboratory for Experimental Vascular Medicine, Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, C7-36, PO Box 9600, 2300RC Leiden, The Netherlands; (R.G.d.B.); (J.P.); (J.M.J.G.D.); (R.B.); (H.J.P.v.d.Z.); (J.M.v.G.); (H.C.d.B.); (T.J.R.); (A.J.v.Z.)
- Correspondence: (E.P.v.d.V.); (S.R.)
| | - Stéphane Richard
- Segal Cancer Center, Lady Davis Institute for Medical Research and Gerald Bronfman Department of Oncology and Departments of Biochemistry, Human Genetics and Medicine, McGill University, Montréal, QC H3T 1E2, Canada;
- Correspondence: (E.P.v.d.V.); (S.R.)
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15
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Janssen WJ, Danhorn T, Harris C, Mould KJ, Lee FFY, Hedin BR, D'Alessandro A, Leach SM, Alper S. Inflammation-Induced Alternative Pre-mRNA Splicing in Mouse Alveolar Macrophages. G3 (BETHESDA, MD.) 2020; 10:555-567. [PMID: 31810980 PMCID: PMC7003074 DOI: 10.1534/g3.119.400935] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 11/26/2019] [Indexed: 12/16/2022]
Abstract
Alveolar macrophages serve as central orchestrators of inflammatory responses in the lungs, both initiating their onset and promoting their resolution. However, the mechanisms that program macrophages for these dynamic responses are not fully understood. Over 95% of all mammalian genes undergo alternative pre-mRNA splicing. While alternative splicing has been shown to regulate inflammatory responses in macrophages in vitro, it has not been investigated on a genome-wide scale in vivo Here we used RNAseq to investigate alternative pre-mRNA splicing in alveolar macrophages isolated from lipopolysaccharide (LPS)-treated mice during the peak of inflammation and during its resolution. We found that lung inflammation induced substantial alternative pre-mRNA splicing in alveolar macrophages. The number of changes in isoform usage was greatest at the peak of inflammation and involved multiple classes of alternative pre-mRNA splicing events. Comparative pathway analysis of inflammation-induced changes in alternative pre-mRNA splicing and differential gene expression revealed overlap of pathways enriched for immune responses such as chemokine signaling and cellular metabolism. Moreover, alternative pre-mRNA splicing of genes in metabolic pathways differed in tissue resident vs. recruited (blood monocyte-derived) alveolar macrophages and corresponded to changes in core metabolism, including a switch to Warburg-like metabolism in recruited macrophages with increased glycolysis and decreased flux through the tricarboxylic acid cycle.
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Affiliation(s)
- William J Janssen
- Department of Medicine
- Division of Pulmonary Sciences and Critical Care Medicine, and
| | | | - Chelsea Harris
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
| | - Kara J Mould
- Department of Medicine
- Division of Pulmonary Sciences and Critical Care Medicine, and
| | - Frank Fang-Yao Lee
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
| | - Brenna R Hedin
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO, 80045
| | - Sonia M Leach
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
| | - Scott Alper
- Center for Genes, Environment and Health, and
- Department of Biomedical Research, National Jewish Health, Denver, CO, 80206
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, 80045
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16
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Liu B, Lindner P, Jirmo AC, Maus U, Illig T, DeLuca DS. A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. BMC Bioinformatics 2020; 21:28. [PMID: 31992182 PMCID: PMC6986093 DOI: 10.1186/s12859-020-3366-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/14/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Despite the significant contribution of transcriptomics to the fields of biological and biomedical research, interpreting long lists of significantly differentially expressed genes remains a challenging step in the analysis process. Gene set enrichment analysis is a standard approach for summarizing differentially expressed genes into pathways or other gene groupings. Here, we explore an alternative approach to utilizing gene sets from curated databases. We examine the method of deriving custom gene sets which may be relevant to a given experiment using reference data sets from previous transcriptomics studies. We call these data-derived gene sets, "gene signatures" for the biological process tested in the previous study. We focus on the feasibility of this approach in analyzing immune-related processes, which are complicated in their nature but play an important role in the medical research. RESULTS We evaluate several statistical approaches to detecting the activity of a gene signature in a target data set. We compare the performance of the data-derived gene signature approach with comparable GO term gene sets across all of the statistical tests. A total of 61 differential expression comparisons generated from 26 transcriptome experiments were included in the analysis. These experiments covered eight immunological processes in eight types of leukocytes. The data-derived signatures were used to detect the presence of immunological processes in the test data with modest accuracy (AUC = 0.67). The performance for GO and literature based gene sets was worse (AUC = 0.59). Both approaches were plagued by poor specificity. CONCLUSIONS When investigators seek to test specific hypotheses, the data-derived signature approach can perform as well, if not better than standard gene-set based approaches for immunological signatures. Furthermore, the data-derived signatures can be generated in the cases that well-defined gene sets are lacking from pathway databases and also offer the opportunity for defining signatures in a cell-type specific manner. However, neither the data-derived signatures nor standard gene-sets can be demonstrated to reliably provide negative predictions for negative cases. We conclude that the data-derived signature approach is a useful and sometimes necessary tool, but analysts should be weary of false positives.
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Affiliation(s)
- Bin Liu
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Patrick Lindner
- Institute of Technical Chemistry, Leibniz University of Hannover, Callinstraße 5, Hannover, 30167 Germany
| | - Adan Chari Jirmo
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Department of Pediatric Pneumology,Allergology and Neonatology, Hannover Medical School, Carl-Neuberg-Straße 1, Hannover, 30625 Germany
| | - Ulrich Maus
- Division of Experimental Pneumology, Hannover Medical School, Feodor-Lynen-Straße 21, Hannover, 30625 Germany
| | - Thomas Illig
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
- Hannover Unified Biobank, Hannover Medical School, Feodor-Lynen-Straße, Hannover, 30625 Germany
| | - David S. DeLuca
- Hannover Medical School, Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research, Carl-Neuberg-Straße, Hannover, 30625 Germany
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17
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Genome-wide meta-analysis associates GPSM1 with type 2 diabetes, a plausible gene involved in skeletal muscle function. J Hum Genet 2020; 65:411-420. [PMID: 31959871 DOI: 10.1038/s10038-019-0720-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 12/20/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022]
Abstract
Genome-wide association studies (GWASs) have identified many genetic variations associated with type 2 diabetes mellitus (T2DM) in Asians, but understanding the functional genetic variants that influence traits is often a complex process. In this study, fine mapping and other analytical strategies were performed to investigate the effects of G protein signaling modulator 1 (GPSM1) on insulin resistance in skeletal muscle. A total of 128 single-nucleotide polymorphisms (SNPs) within GPSM1 were analysed in 21,897 T2DM cases and 32,710 healthy controls from seven GWASs. The SNP rs28539249 in intron 9 of GPSM1 showed a nominally significant association with T2DM in Asians (OR = 1.07, 95% CI = 1.04-1.10, P < 10-4). The GPSM1 mRNA was increased in skeletal muscle and correlated with T2DM traits across obese mice model. An eQTL for the cis-acting regulation of GPSM1 expression in human skeletal muscle was identified for rs28539249, and the increased GPSM1 expression related with T2DM traits within GEO datasets. Another independent Asian cohort showed that rs28539249 is associated with the skeletal muscle expression of CACFD1, GTF3C5, SARDH, and FAM163B genes, which are functionally enriched for endoplasmic reticulum stress (ERS) and unfolded protein response (UPR) pathways. Moreover, rs28539249 locus was predicted to disrupt regulatory regions in human skeletal muscle with enriched epigenetic marks and binding affinity for CTCF. Supershift EMSA assays followed luciferase assays demonstrated the CTCF specifically binding to rs28539249-C allele leading to decreased transcriptional activity. Thus, the post-GWAS annotation confirmed the Asian-specific association of genetic variant in GPSM1 with T2DM, suggesting a role for the variant in the regulation in skeletal muscle.
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18
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Spliceosome protein Eftud2 promotes colitis-associated tumorigenesis by modulating inflammatory response of macrophage. Mucosal Immunol 2019; 12:1164-1173. [PMID: 31278373 DOI: 10.1038/s41385-019-0184-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 06/11/2019] [Accepted: 06/12/2019] [Indexed: 02/04/2023]
Abstract
Alternative splicing (AS) of mRNA is known to be involved in regulation of immune cell differentiation and activation. Elongation factor Tu GTP binding domain containing 2 (Eftud2) is an AS factor to potentially modulate innate immune response in macrophages. In this study, we investigate its involvement in the pathogenesis of colitis-associated cancer (CAC). Using an established mouse model of CAC, we show that Eftud2 is constantly overexpressed in the colonic tissues as well as infiltrating macrophages. Myeloid-specific knockout of Eftud2 remarkably suppresses chronic intestinal inflammation and tumorigenesis, which is associated with decreased production of inflammatory cytokines and tumorigenic factors. Repression of colonic inflammation and colorectal tumor development in Eftud2-deficient mice is due to the impaired activation of NF-κB signaling in LPS-challenged macrophages. Furthermore, the alteration of Eftud2-mediated AS involving the components of TLR4-NF-κB cascades underlies the impairment of NF-κB activation. Overall, these findings provide new insights into the tight link between inflammation and cancer and modulation of AS in innate immune signals may be a potentially therapeutic avenue for CAC treatment.
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19
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Liu H, Lorenzini PA, Zhang F, Xu S, Wong MSM, Zheng J, Roca X. Alternative splicing analysis in human monocytes and macrophages reveals MBNL1 as major regulator. Nucleic Acids Res 2019; 46:6069-6086. [PMID: 29771377 PMCID: PMC6159523 DOI: 10.1093/nar/gky401] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/01/2018] [Indexed: 12/11/2022] Open
Abstract
We report the detailed transcriptomic profiles of human innate myeloid cells using RNA sequencing. Monocytes migrate from blood into infected or wounded tissue to differentiate into macrophages, and control inflammation via phagocytosis or cytokine secretion. We differentiated culture primary monocytes with either GM- or M-CSF to obtain pro- or anti-inflammatory macrophages, and respectively activated them with either LPS/IFNγ or anti-inflammatory cytokines. We also treated the THP-1 monocytic cell line with PMA and similar cytokines to mimic differentiation and activation. We detected thousands of expression and alternative-splicing changes during monocyte-to-macrophage differentiation and activation, and a net increase in exon inclusion. MBNL1 knockdown phenocopies several alternative-splicing changes and strongly impairs PMA differentiation, suggesting functional defects in monocytes from Myotonic Dystrophy patients. This study provides general insights into alternative splicing in the monocyte–macrophage lineage, whose future characterization will elucidate their contribution to immune functions, which are altered in immunodeficiencies, autoimmunity, atherosclerosis and cancer.
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Affiliation(s)
- Hongfei Liu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Paolo A Lorenzini
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore.,Nanyang Institute of Technology in Health and Medicine, Interdisciplinary Graduate School (IGS), Nanyang Technological University, 637551 Singapore
| | - Fan Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 637551 Singapore
| | - Shaohai Xu
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Mei Su M Wong
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
| | - Jie Zheng
- School of Computer Science and Engineering, Nanyang Technological University, 637551 Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 637551 Singapore
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20
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Ding W, Li D, Zhang P, Shi L, Dai H, Li Y, Bao X, Wang Y, Zhang H, Deng L. Mutual editing of alternative splicing between breast cancer cells and macrophages. Oncol Rep 2019; 42:629-656. [PMID: 31233192 PMCID: PMC6609318 DOI: 10.3892/or.2019.7200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 06/06/2019] [Indexed: 01/06/2023] Open
Abstract
Breast cancer is a highly heterogeneous disease and numerous secreted factors may differentially contribute to a macrophage phenotype whose extensive infiltration is generally regarded as indicative of an unfavorable outcome. How different breast tumor cells and macrophage cells interplay or influence each other on the alternative splicing (AS) level have not been characterized. Here, we exploited one previous study, which investigated the interplay between macrophages and estrogen receptor-positive (ER+) breast cancer and triple-negative breast cancer (TNBC) at the transcriptional level, to investigate the tumor-macrophage crosstalk at the AS level. In the present study, it was demonstrated that biological processes such as DNA damage and DNA repair were significantly affected both in ER+ breast cancer and TNBC by co-culturing with macrophages, whereas biological pathways altered in macrophages co-cultured with tumor cells depended on the breast cancer type. Specifically, biological processes altered in macrophages co-cultured with ER+ breast cancer were enriched in RNA processing and translation-related pathways whereas biological processes altered in macrophages co-cultured with TNBC were mainly enriched in protein transport pathways. We also analyzed the sequence features of skip exons among different conditions. In addition, putative splicing factors which were responsible for the altered AS profile in each condition were identified. The findings of the present study revealed significant tumor-macrophage crosstalk at the AS level which may facilitate the development of new therapeutic strategies for cancer.
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Affiliation(s)
- Wanbao Ding
- Key Laboratory of Tumor Immunological Prevention and Treatment, Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Dongdong Li
- Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Peixian Zhang
- Key Laboratory of Tumor Immunological Prevention and Treatment, Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Lan Shi
- Key Laboratory of Tumor Immunological Prevention and Treatment, Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Hui Dai
- Key Laboratory of Tumor Immunological Prevention and Treatment, Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Yan Li
- Key Laboratory of Tumor Immunological Prevention and Treatment, Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Xin Bao
- Key Laboratory of Tumor Immunological Prevention and Treatment, Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Yue Wang
- Department of Breast Cancer, Third Affiliated Hospital, Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Honglei Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, P.R. China
| | - Lei Deng
- Key Laboratory of Tumor Immunological Prevention and Treatment, Department of Oncology, Yan'an Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
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21
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Affiliation(s)
- Ziad Mallat
- From the Department of Medicine, Division of Cardiovascular Medicine, University of Cambridge, United Kingdom; and Institut National de la Santé et de la Recherche Médicale, Paris, France.
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22
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Shi J, Xue C, Liu W, Zhang H. Differentiation of Human-Induced Pluripotent Stem Cells to Macrophages for Disease Modeling and Functional Genomics. ACTA ACUST UNITED AC 2018; 48:e74. [PMID: 30537374 DOI: 10.1002/cpsc.74] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Macrophages play important roles in many diseases. We describe a protocol and the associated resources for the differentiation of human induced pluripotent stem cell-derived macrophages (IPSDM) and their applications in understanding human macrophage physiology and relevant diseases. The protocol uses an embryoid body-based approach with a combination of serum-free condition for hematopoiesis specification, followed by adherent culture with serum and M-CSF for myeloid expansion and macrophage maturation. The protocol produced an almost pure culture of CD45+ /CD18+ macrophages yielding up to 2 × 107 cells per 6-well plate of iPSCs within 24 days, demonstrating high efficiency, purity, and scalability. The IPSDM and monocyte-derived macrophages (HMDM) cultured in the same medium were compared at morphological, functional and transcriptomic levels by RNA-sequencing. IPSDM and HMDM showed broadly similar profiles of coding transcriptome, alternative splicing events, and long noncoding RNAs, with advantages and successful applications in disease modeling using patients-derived and CRISPR-edited iPSC lines. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jianting Shi
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Chenyi Xue
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Wen Liu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Hanrui Zhang
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
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23
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Chen Y, Ouyang X, Hoque R, Garcia-Martinez I, Yousaf MN, Tonack S, Offermanns S, Dubuquoy L, Louvet A, Mathurin P, Massey V, Schnabl B, Bataller RA, Mehal WZ. β-Hydroxybutyrate protects from alcohol-induced liver injury via a Hcar2-cAMP dependent pathway. J Hepatol 2018; 69:687-696. [PMID: 29705237 PMCID: PMC6098974 DOI: 10.1016/j.jhep.2018.04.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/03/2018] [Accepted: 04/04/2018] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Sterile inflammation resulting in alcoholic hepatitis (AH) occurs unpredictably after many years of excess alcohol intake. The factors responsible for the development of AH are not known but mitochondrial damage with loss of mitochondrial function are common features. Hcar2 is a G-protein coupled receptor which is activated by β-hydroxybutyrate (BHB). We aimed to determine the relevance of the BHB-Hcar2 pathway in alcoholic liver disease. METHODS We tested if loss of BHB production can result in increased liver inflammation. We further tested if BHB supplementation is protective in AH through interaction with Hcar2, and analyzed the immune and cellular basis for protection. RESULTS Humans with AH have reduced hepatic BHB, and inhibition of BHB production in mice aggravated ethanol-induced AH, with higher plasma alanine aminotransferase levels, increased steatosis and greater neutrophil influx. Conversely supplementation of BHB had the opposite effects with reduced alanine aminotransferase levels, reduced steatosis and neutrophil influx. This therapeutic effect of BHB is dependent on the receptor Hcar2. BHB treatment increased liver Il10 transcripts, and promoted the M2 phenotype of intrahepatic macrophages. BHB also increased the transcriptional level of M2 related genes in vitro bone marrow derived macrophages. This skewing towards M2 related genes is dependent on lower mitochondrial membrane potential (Δψ) induced by BHB. CONCLUSIONS Collectively, our data shows that BHB production during excess alcohol consumption has an anti-inflammatory and hepatoprotective role through an Hcar2 dependent pathway. This introduces the concept of metabolite-based therapy for AH. LAY SUMMARY Alcoholic hepatitis is a life-threatening condition with no approved therapy that occurs unexpectedly in people who consume excess alcohol. The liver makes many metabolites, and we demonstrate that loss of one such metabolite β-hydroxybutyrate occurs in patients with alcoholic hepatitis. This loss can increase alcohol-induced liver injury, and β-hydroxybutyrate can protect from alcohol-induced liver injury via a receptor on liver macrophages. This opens the possibility of metabolite-based therapy for alcoholic hepatitis.
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Affiliation(s)
- Yonglin Chen
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xinshou Ouyang
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Rafaz Hoque
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Irma Garcia-Martinez
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Muhammad Nadeem Yousaf
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Sarah Tonack
- Max-Planck-Institute for Heart and Lung Research, Department of Pharmacology, Ludwigstr. 43, 61231 Bad Nauheim, Germany; Medical Faculty, J.W. Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | - Stefan Offermanns
- Max-Planck-Institute for Heart and Lung Research, Department of Pharmacology, Ludwigstr. 43, 61231 Bad Nauheim, Germany; Medical Faculty, J.W. Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany
| | | | - Alexandre Louvet
- Service des Maladies de l'appareil digestif, Hôpital Huriez, Lille, France; Unité INSERM 995, Faculté de Médecine, Lille, France
| | - Philippe Mathurin
- Service des Maladies de l'appareil digestif, Hôpital Huriez, Lille, France; Unité INSERM 995, Faculté de Médecine, Lille, France
| | - Veronica Massey
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Ramon Alberola Bataller
- Division of Gastroenterology, Hepatology and Nutrition, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Wajahat Zafar Mehal
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT 06520, USA; USA West Haven Veterans Medical Center, West Haven, CT 06516, USA.
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24
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Orekhov AN, Pushkarsky T, Oishi Y, Nikiforov NG, Zhelankin AV, Dubrovsky L, Makeev VJ, Foxx K, Jin X, Kruth HS, Sobenin IA, Sukhorukov VN, Zakiev ER, Kontush A, Le Goff W, Bukrinsky M. HDL activates expression of genes stimulating cholesterol efflux in human monocyte-derived macrophages. Exp Mol Pathol 2018; 105:202-207. [PMID: 30118702 DOI: 10.1016/j.yexmp.2018.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 08/09/2018] [Accepted: 08/13/2018] [Indexed: 12/24/2022]
Abstract
High density lipoproteins (HDL) are key components of reverse cholesterol transport pathway. HDL removes excessive cholesterol from peripheral cells, including macrophages, providing protection from cholesterol accumulation and conversion into foam cells, which is a key event in pathogenesis of atherosclerosis. The mechanism of cellular cholesterol efflux stimulation by HDL involves interaction with the ABCA1 lipid transporter and ensuing transfer of cholesterol to HDL particles. In this study, we looked for additional proteins contributing to HDL-dependent cholesterol efflux. Using RNAseq, we analyzed mRNAs induced by HDL in human monocyte-derived macrophages and identified three genes, fatty acid desaturase 1 (FADS1), insulin induced gene 1 (INSIG1), and the low-density lipoprotein receptor (LDLR), expression of which was significantly upregulated by HDL. We individually knocked down these genes in THP-1 cells using gene silencing by siRNA, and measured cellular cholesterol efflux to HDL. Knock down of FADS1 did not significantly change cholesterol efflux (p = 0.70), but knockdown of INSIG1 and LDLR resulted in highly significant reduction of the efflux to HDL (67% and 75% of control, respectively, p < 0.001). Importantly, the suppression of cholesterol efflux was independent of known effects of these genes on cellular cholesterol content, as cells were loaded with cholesterol using acetylated LDL. These results indicate that HDL particles stimulate expression of genes that enhance cellular cholesterol transfer to HDL.
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Affiliation(s)
- Alexander N Orekhov
- Institute of General Pathology and Pathophysiology, Moscow, Russia; Institute for Atherosclerosis Research, Skolkovo Innovative Center, Moscow, Russia
| | - Tatiana Pushkarsky
- The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Yumiko Oishi
- Department of Cellular and Molecular Medicine, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Nikita G Nikiforov
- Institute of General Pathology and Pathophysiology, Moscow, Russia; Laboratory of Medical Genetics, Institute of Experimental Cardiology, National Medical Research Center of Cardiology, Moscow, Russia; Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Andrey V Zhelankin
- Laboratory of postgenomic research, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Larisa Dubrovsky
- The George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Vsevolod J Makeev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Scientific Center "Kurchatov Institute", Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia; Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow, Region, Russia; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kathy Foxx
- Kalen Biomedical LLC, Montgomery Village, MD, USA
| | - Xueting Jin
- Experimental Atherosclerosis Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Howard S Kruth
- Experimental Atherosclerosis Section, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Igor A Sobenin
- Institute of General Pathology and Pathophysiology, Moscow, Russia; Laboratory of Medical Genetics, Institute of Experimental Cardiology, National Medical Research Center of Cardiology, Moscow, Russia
| | - Vasily N Sukhorukov
- Institute of General Pathology and Pathophysiology, Moscow, Russia; Sorbonne Université, Inserm, Institute of Cardiometabolism and Nutrition (ICAN), UMR_S1166, Hôpital de la Pitié, Paris, France
| | - Emile R Zakiev
- Institute of General Pathology and Pathophysiology, Moscow, Russia; Sorbonne Université, Inserm, Institute of Cardiometabolism and Nutrition (ICAN), UMR_S1166, Hôpital de la Pitié, Paris, France
| | - Anatol Kontush
- Sorbonne Université, Inserm, Institute of Cardiometabolism and Nutrition (ICAN), UMR_S1166, Hôpital de la Pitié, Paris, France
| | - Wilfried Le Goff
- Sorbonne Université, Inserm, Institute of Cardiometabolism and Nutrition (ICAN), UMR_S1166, Hôpital de la Pitié, Paris, France
| | - Michael Bukrinsky
- The George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
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25
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de Bruin RG, Rabelink TJ, van Zonneveld AJ, van der Veer EP. Emerging roles for RNA-binding proteins as effectors and regulators of cardiovascular disease. Eur Heart J 2018; 38:1380-1388. [PMID: 28064149 DOI: 10.1093/eurheartj/ehw567] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/02/2016] [Indexed: 12/18/2022] Open
Abstract
The cardiovascular system comprises multiple cell types that possess the capacity to modulate their phenotype in response to acute or chronic injury. Transcriptional and post-transcriptional mechanisms play a key role in the regulation of remodelling and regenerative responses to damaged cardiovascular tissues. Simultaneously, insufficient regulation of cellular phenotype is tightly coupled with the persistence and exacerbation of cardiovascular disease. Recently, RNA-binding proteins such as Quaking, HuR, Muscleblind, and SRSF1 have emerged as pivotal regulators of these functional adaptations in the cardiovascular system by guiding a wide-ranging number of post-transcriptional events that dramatically impact RNA fate, including alternative splicing, stability, localization and translation. Moreover, homozygous disruption of RNA-binding protein genes is commonly associated with cardiac- and/or vascular complications. Here, we summarize the current knowledge on the versatile role of RNA-binding proteins in regulating the transcriptome during phenotype switching in cardiovascular health and disease. We also detail existing and potential DNA- and RNA-based therapeutic approaches that could impact the treatment of cardiovascular disease in the future.
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Affiliation(s)
- Ruben G de Bruin
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Ton J Rabelink
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Anton Jan van Zonneveld
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
| | - Eric P van der Veer
- Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands.,Division of Nephrology, Department of Internal Medicine, Leiden University Medical Center, Albinusdreef 2, Leiden 2300RC, The Netherlands
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26
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Affiliation(s)
- Jennie Lin
- From the Division of Nephrology and Hypertension, Department of Medicine (J.L.) and Feinberg Cardiovascular Research Institute (J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; and Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (K.M.)
| | - Kiran Musunuru
- From the Division of Nephrology and Hypertension, Department of Medicine (J.L.) and Feinberg Cardiovascular Research Institute (J.L.), Northwestern University Feinberg School of Medicine, Chicago, IL; and Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia (K.M.)
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27
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Lin J, Musunuru K. From Genotype to Phenotype: A Primer on the Functional Follow-up of Genome-Wide Association Studies in Cardiovascular Disease. CIRCULATION. GENOMIC AND PRECISION MEDICINE 2018; 11:e001946. [PMID: 29915816 PMCID: PMC6003539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Genome-wide association studies (GWASs) have implicated many human genomic loci in the development of complex traits. The loci identified by these studies are potentially involved in novel pathways that contribute to disease pathophysiology. However, eventual therapeutic targeting of these pathways relies on bridging the gap between genetic association and function, a task that first requires validation of causal genetic variants, casual genes, and directionality of effect. Executing this task requires basic knowledge of interpreting GWAS results and prioritizing candidates for further study, in addition to understanding the experimental methods available for evaluating candidate variants. Here we review the basic genetic principles of genome-wide association studies, the computational and experimental tools used for identifying causal variants and genes, and salient illustrative examples of how cardiovascular loci have undergone functional investigation.
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Affiliation(s)
- Jennie Lin
- Division of Nephrology and Hypertension, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL
- Feinberg Cardiovascular Research Institute, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Kiran Musunuru
- Division of Cardiovascular Medicine, Department of Medicine, Cardiovascular Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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28
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Zhang H, Xue C, Wang Y, Shi J, Zhang X, Li W, Nunez S, Foulkes AS, Lin J, Hinkle CC, Yang W, Morrisey EE, Rader DJ, Li M, Reilly MP. Deep RNA Sequencing Uncovers a Repertoire of Human Macrophage Long Intergenic Noncoding RNAs Modulated by Macrophage Activation and Associated With Cardiometabolic Diseases. J Am Heart Assoc 2017; 6:JAHA.117.007431. [PMID: 29133519 PMCID: PMC5721798 DOI: 10.1161/jaha.117.007431] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Background Sustained and dysfunctional macrophage activation promotes inflammatory cardiometabolic disorders, but the role of long intergenic noncoding RNA (lincRNA) in human macrophage activation and cardiometabolic disorders is poorly defined. Through transcriptomics, bioinformatics, and selective functional studies, we sought to elucidate the lincRNA landscape of human macrophages. Methods and Results We used deep RNA sequencing to assemble the lincRNA transcriptome of human monocyte‐derived macrophages at rest and following stimulation with lipopolysaccharide and IFN‐γ (interferon γ) for M1 activation and IL‐4 (interleukin 4) for M2 activation. Through de novo assembly, we identified 2766 macrophage lincRNAs, including 861 that were previously unannotated. The majority (≈85%) was nonsyntenic or was syntenic but not annotated as expressed in mouse. Many macrophage lincRNAs demonstrated tissue‐enriched transcription patterns (21.5%) and enhancer‐like chromatin signatures (60.9%). Macrophage activation, particularly to the M1 phenotype, markedly altered the lincRNA expression profiles, revealing 96 lincRNAs differentially expressed, suggesting potential roles in regulating macrophage inflammatory functions. A subset of lincRNAs overlapped genomewide association study loci for cardiometabolic disorders. MacORIS (macrophage‐enriched obesity‐associated lincRNA serving as a repressor of IFN‐γ signaling), a macrophage‐enriched lincRNA not expressed in mouse macrophages, harbors variants associated with central obesity. Knockdown of MacORIS, which is located in the cytoplasm, enhanced IFN‐γ–induced JAK2 (Janus kinase 2) and STAT1 (signal transducer and activator of transcription 1) phosphorylation in THP‐1 macrophages, suggesting a potential role as a repressor of IFN‐γ signaling. Induced pluripotent stem cell–derived macrophages recapitulated the lincRNA transcriptome of human monocyte‐derived macrophages and provided a high‐fidelity model with which to study lincRNAs in human macrophage biology, particularly those not conserved in mouse. Conclusions High‐resolution transcriptomics identified lincRNAs that form part of the coordinated response during macrophage activation, including specific macrophage lincRNAs associated with human cardiometabolic disorders that modulate macrophage inflammatory functions.
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Affiliation(s)
- Hanrui Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY
| | - Chenyi Xue
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY
| | - Ying Wang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY
| | - Jianting Shi
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY
| | - Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY
| | - Wenjun Li
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Sara Nunez
- Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA
| | - Andrea S Foulkes
- Department of Mathematics and Statistics, Mount Holyoke College, South Hadley, MA
| | - Jennie Lin
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Christine C Hinkle
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Wenli Yang
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA
| | - Edward E Morrisey
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA.,Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA
| | - Daniel J Rader
- Division of Translational Medicine and Human Genetics, Departments of Genetics and Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY .,Irving Institute for Clinical and Translational Research, Columbia University, New York, NY
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29
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Zhang H, Reilly MP. Human Induced Pluripotent Stem Cell-Derived Macrophages for Unraveling Human Macrophage Biology. Arterioscler Thromb Vasc Biol 2017; 37:2000-2006. [PMID: 28982665 DOI: 10.1161/atvbaha.117.309195] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/12/2017] [Indexed: 12/21/2022]
Abstract
Despite a substantial appreciation for the critical role of macrophages in cardiometabolic diseases, understanding of human macrophage biology has been hampered by the lack of reliable and scalable models for cellular and genetic studies. Human induced pluripotent stem cell (iPSC)-derived macrophages (IPSDM), as an unlimited source of subject genotype-specific cells, will undoubtedly play an important role in advancing our understanding of the role of macrophages in human diseases. In this review, we summarize current literature in the differentiation and characterization of IPSDM at phenotypic, functional, and transcriptomic levels. We emphasize the progress in differentiating iPSC to tissue resident macrophages, and in understanding the ontogeny of in vitro differentiated IPSDM that resembles primitive hematopoiesis, rather than adult definitive hematopoiesis. We review the application of IPSDM in modeling both Mendelian genetic disorders and host-pathogen interactions. Finally, we highlighted the potential areas of research using IPSDM in functional validation of coronary artery disease loci in genome-wide association studies, functional genomic analyses, drug testing, and cell therapeutics in cardiovascular diseases.
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Affiliation(s)
- Hanrui Zhang
- From the Division of Cardiology, Department of Medicine (H.Z., M.P.R.) and Irving Institute for Clinical and Translational Research (M.P.R.), Columbia University Medical Center, New York, NY.
| | - Muredach P Reilly
- From the Division of Cardiology, Department of Medicine (H.Z., M.P.R.) and Irving Institute for Clinical and Translational Research (M.P.R.), Columbia University Medical Center, New York, NY.
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30
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Dron JS, Ho R, Hegele RA. Recent Advances in the Genetics of Atherothrombotic Disease and Its Determinants. Arterioscler Thromb Vasc Biol 2017; 37:e158-e166. [DOI: 10.1161/atvbaha.117.309934] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jacqueline S. Dron
- From the Department of Biochemistry (J.S.D, R.H., R.A.H.), Robarts Research Institute (J.S.D., R.H., R.A.H.), and Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Rosettia Ho
- From the Department of Biochemistry (J.S.D, R.H., R.A.H.), Robarts Research Institute (J.S.D., R.H., R.A.H.), and Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Robert A. Hegele
- From the Department of Biochemistry (J.S.D, R.H., R.A.H.), Robarts Research Institute (J.S.D., R.H., R.A.H.), and Department of Medicine (R.A.H.), Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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31
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Xue C, Zhang X, Zhang H, Ferguson JF, Wang Y, Hinkle CC, Li M, Reilly MP. De novo RNA sequence assembly during in vivo inflammatory stress reveals hundreds of unannotated lincRNAs in human blood CD14 + monocytes and in adipose tissue. Physiol Genomics 2017; 49:287-305. [PMID: 28389524 PMCID: PMC5495909 DOI: 10.1152/physiolgenomics.00001.2017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/20/2017] [Accepted: 04/04/2017] [Indexed: 12/29/2022] Open
Abstract
Long intergenic noncoding RNAs (lincRNAs) have emerged as key regulators of cellular functions and physiology. Yet functional lincRNAs often have low, context-specific and tissue-specific expression. We hypothesized that many human monocyte and adipose lincRNAs would be absent in current public annotations due to lincRNA tissue specificity, modest sequencing depth in public data, limitations of transcriptome assembly algorithms, and lack of dynamic physiological contexts. Deep RNA sequencing (RNA-Seq) was performed in peripheral blood CD14+ monocytes (monocytes; average ~247 million reads per sample) and adipose tissue (average ~378 million reads per sample) collected before and after human experimental endotoxemia, an in vivo inflammatory stress, to identify tissue-specific and clinically relevant lincRNAs. Using a stringent filtering pipeline, we identified 109 unannotated lincRNAs in monocytes and 270 unannotated lincRNAs in adipose. Most unannotated lincRNAs are not conserved in rodents and are tissue specific, while many have features of regulated expression and are enriched in transposable elements. Specific subsets have enhancer RNA characteristics or are expressed only during inflammatory stress. A subset of unannotated lincRNAs was validated and replicated for their presence and inflammatory induction in independent human samples and for their monocyte and adipocyte origins. Through interrogation of public genome-wide association data, we also found evidence of specific disease association for selective unannotated lincRNAs. Our findings highlight the critical need to perform deep RNA-Seq in a cell-, tissue-, and context-specific manner to annotate the full repertoire of human lincRNAs for a complete understanding of lincRNA roles in dynamic cell functions and in human disease.
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Affiliation(s)
- Chenyi Xue
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Xuan Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Hanrui Zhang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Jane F Ferguson
- Vanderbilt Translational and Clinical Cardiovascular Research Center, Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ying Wang
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York
| | - Christine C Hinkle
- Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Mingyao Li
- Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania; and
| | - Muredach P Reilly
- Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, New York; .,Irving Institute for Clinical and Translational Research, Columbia University, New York, New York
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Lurier EB, Dalton D, Dampier W, Raman P, Nassiri S, Ferraro NM, Rajagopalan R, Sarmady M, Spiller KL. Transcriptome analysis of IL-10-stimulated (M2c) macrophages by next-generation sequencing. Immunobiology 2017; 222:847-856. [PMID: 28318799 DOI: 10.1016/j.imbio.2017.02.006] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 02/15/2017] [Indexed: 01/23/2023]
Abstract
Alternatively activated "M2" macrophages are believed to function during late stages of wound healing, behaving in an anti-inflammatory manner to mediate the resolution of the pro-inflammatory response caused by "M1" macrophages. However, the differences between two main subtypes of M2 macrophages, namely interleukin-4 (IL-4)-stimulated "M2a" macrophages and IL-10-stimulated "M2c" macrophages, are not well understood. M2a macrophages are characterized by their ability to inhibit inflammation and contribute to the stabilization of angiogenesis. However, the role and temporal profile of M2c macrophages in wound healing are not known. Therefore, we performed next generation sequencing (RNA-seq) to identify biological functions and gene expression signatures of macrophages polarized in vitro with IL-10 to the M2c phenotype in comparison to M1 and M2a macrophages and an unactivated control (M0). We then explored the expression of these gene signatures in a publicly available data set of human wound healing. RNA-seq analysis showed that hundreds of genes were upregulated in M2c macrophages compared to the M0 control, with thousands of alternative splicing events. Following validation by Nanostring, 39 genes were found to be upregulated by M2c macrophages compared to the M0 control, and 17 genes were significantly upregulated relative to the M0, M1, and M2a phenotypes (using an adjusted p-value cutoff of 0.05 and fold change cutoff of 1.5). Many of the identified M2c-specific genes are associated with angiogenesis, matrix remodeling, and phagocytosis, including CD163, MMP8, TIMP1, VCAN, SERPINA1, MARCO, PLOD2, PCOCLE2 and F5. Analysis of the macrophage-conditioned media for secretion of matrix-remodeling proteins showed that M2c macrophages secreted higher levels of MMP7, MMP8, and TIMP1 compared to the other phenotypes. Interestingly, temporal gene expression analysis of a publicly available microarray data set of human wound healing showed that M2c-related genes were upregulated at early times after injury, similar to M1-related genes, while M2a-related genes appeared at later stages or were downregulated after injury. While further studies are required to confirm the timing and role of M2c macrophages in vivo, these results suggest that M2c macrophages may function at early stages of wound healing. Identification of markers of the M2c phenotype will allow more detailed investigations into the role of M2c macrophages in vivo.
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Affiliation(s)
- Emily B Lurier
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - Donald Dalton
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - Will Dampier
- Department of Microbiology and Immunology, Drexel University College of Medicine, 245 N Broad St. Philadelphia, PA, 19107, USA
| | - Pichai Raman
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA; Deparment of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Sina Nassiri
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - Nicole M Ferraro
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA
| | - Ramakrishan Rajagopalan
- Deparment of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Mahdi Sarmady
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kara L Spiller
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Philadelphia, PA, 19104, USA.
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