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Nichols C, Do-Thi VA, Peltier DC. Noncanonical microprotein regulation of immunity. Mol Ther 2024:S1525-0016(24)00324-1. [PMID: 38734902 DOI: 10.1016/j.ymthe.2024.05.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/19/2024] [Accepted: 05/09/2024] [Indexed: 05/13/2024] Open
Abstract
The immune system is highly regulated but, when dysregulated, suboptimal protective or overly robust immune responses can lead to immune-mediated disorders. The genetic and molecular mechanisms of immune regulation are incompletely understood, impeding the development of more precise diagnostics and therapeutics for immune-mediated disorders. Recently, thousands of previously unrecognized noncanonical microprotein genes encoded by small open reading frames have been identified. Many of these microproteins perform critical functions, often in a cell- and context-specific manner. Several microproteins are now known to regulate immunity; however, the vast majority are uncharacterized. Therefore, illuminating what is often referred to as the "dark proteome," may present opportunities to tune immune responses more precisely. Here, we review noncanonical microprotein biology, highlight recently discovered examples regulating immunity, and discuss the potential and challenges of modulating dysregulated immune responses by targeting microproteins.
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Affiliation(s)
- Cydney Nichols
- Morris Green Scholars Program, Department of Pediatrics, Riley Hospital for Children, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Van Anh Do-Thi
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Daniel C Peltier
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
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Yoshida M, Kwon AT, Qin XY, Nishimura H, Maeda S, Miyamoto Y, Yoshida Y, Hoshino Y, Suzuki H. Transcriptome analysis of long non-coding RNAs in Mycobacterium avium complex-infected macrophages. Front Immunol 2024; 15:1374437. [PMID: 38711507 PMCID: PMC11070510 DOI: 10.3389/fimmu.2024.1374437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 03/28/2024] [Indexed: 05/08/2024] Open
Abstract
Mycobacterium avium complex (MAC) is a non-tuberculous mycobacterium widely distributed in the environment. Even though MAC infection is increasing in older women and immunocompromised patients, to our knowledge there has been no comprehensive analysis of the MAC-infected host-cell transcriptome-and particularly of long non-coding RNAs (lncRNAs). By using in vitro-cultured primary mouse bone-marrow-derived macrophages (BMDMs) and Cap analysis of gene expression, we analyzed the transcriptional and kinetic landscape of macrophage genes, with a focus on lncRNAs, during MAC infection. MAC infection of macrophages induced the expression of immune/inflammatory response genes and other genes similar to those involved in M1 macrophage activation, consistent with previous reports, although Nos2 (M1 activation) and Arg1 (M2 activation) had distinct expression profiles. We identified 31 upregulated and 30 downregulated lncRNA promoters corresponding respectively to 18 and 26 lncRNAs. Upregulated lncRNAs were clustered into two groups-early and late upregulated-predicted to be associated with immune activation and the immune response to infection, respectively. Furthermore, an Ingenuity Pathway Analysis revealed canonical pathways and upstream transcription regulators associated with differentially expressed lncRNAs. Several differentially expressed lncRNAs reported elsewhere underwent expressional changes upon M1 or M2 preactivation and subsequent MAC infection. Finally, we showed that expressional change of lncRNAs in MAC-infected BMDMs was mediated by toll-like receptor 2, although there may be other mechanisms that sense MAC infection. We identified differentially expressed lncRNAs in MAC-infected BMDMs, revealing diverse features that imply the distinct roles of these lncRNAs in MAC infection and macrophage polarization.
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Affiliation(s)
- Mitsunori Yoshida
- Department of Mycobacteriology, National Institute of Infectious Diseases, Higashi-Murayama, Tokyo, Japan
| | - Andrew Taejun Kwon
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Xian-Yang Qin
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Hajime Nishimura
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Shiori Maeda
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Yuji Miyamoto
- Department of Mycobacteriology, National Institute of Infectious Diseases, Higashi-Murayama, Tokyo, Japan
| | - Yasuhiro Yoshida
- Department of Immunology and Parasitology, University of Occupational and Environmental Health, Kita-Kyushu, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, National Institute of Infectious Diseases, Higashi-Murayama, Tokyo, Japan
| | - Harukazu Suzuki
- Laboratory for Cellular Function Conversion Technology, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
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Sabikunnahar B, Caldwell S, Varnum S, Hogan T, Lahue KG, Rathkolb B, Gerlini R, Dragano NRV, Aguilar‐Pimentel A, Irmler M, Sanz‐Moreno A, da Silva‐Buttkus P, Beckers J, Wolf E, Gailus‐Durner V, Fuchs H, Hrabe de Angelis M, Ather JL, Poynter ME, Krementsov DN. LncRNA U90926 is dispensable for the development of obesity-associated phenotypes in vivo. Physiol Rep 2024; 12:e15901. [PMID: 38171546 PMCID: PMC10764201 DOI: 10.14814/phy2.15901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Obesity is a global health problem characterized by excessive fat accumulation, driven by adipogenesis and lipid accumulation. Long non-coding RNAs (lncRNAs) have recently been implicated in regulating adipogenesis and adipose tissue function. Mouse lncRNA U90926 was previously identified as a repressor of in vitro adipogenesis in 3T3-L1 preadipocytes. Consequently, we hypothesized that, in vivo, U90926 may repress adipogenesis, and hence its deletion would increase weight gain and adiposity. We tested the hypothesis by applying U90926-deficient (U9-KO) mice to a high-throughput phenotyping pipeline. Compared with WT, U9-KO mice showed no major differences across a wide range of behavioral, neurological, and other physiological parameters. In mice fed a standard diet, we have found no differences in obesity-related phenotypes, including weight gain, fat mass, and plasma concentrations of glucose, insulin, triglycerides, and free fatty acids, in U9-KO mice compared to WT. U90926 deficiency lacked a major effect on white adipose tissue morphology and gene expression profile. Furthermore, in mice fed a high-fat diet, we found increased expression of U90926 in adipose tissue stromal vascular cell fraction, yet observed no effect of U90926 deficiency on weight gain, fat mass, adipogenesis marker expression, and immune cell infiltration into the adipose tissue. These data suggest that the U90926 lacks an essential role in obesity-related phenotypes and adipose tissue biology in vivo.
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Affiliation(s)
- Bristy Sabikunnahar
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Sydney Caldwell
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Stella Varnum
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Tyler Hogan
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Karolyn G. Lahue
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
| | - Birgit Rathkolb
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- Institute of Molecular Animal Breeding and Biotechnology, Gene CenterLudwig‐Maximilians‐University MünchenMunichGermany
| | - Raffaele Gerlini
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Nathalia R. V. Dragano
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
| | - Antonio Aguilar‐Pimentel
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Martin Irmler
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Adrián Sanz‐Moreno
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Patricia da Silva‐Buttkus
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Johannes Beckers
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- TUM School of Life SciencesTechnische Universität MünchenFreisingGermany
| | - Eckhard Wolf
- Institute of Molecular Animal Breeding and Biotechnology, Gene CenterLudwig‐Maximilians‐University MünchenMunichGermany
| | - Valerie Gailus‐Durner
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Helmut Fuchs
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
| | - Martin Hrabe de Angelis
- Institute of Experimental Genetics and German Mouse ClinicHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes Research (DZD)NeuherbergGermany
- TUM School of Life SciencesTechnische Universität MünchenFreisingGermany
| | | | | | - Dimitry N. Krementsov
- Department of Biomedical and Health SciencesUniversity of VermontBurlingtonVermontUSA
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Holt EA, Waytashek CM, Sessions KJ, Asarian L, Lahue KG, Usherwood EJ, Teuscher C, Krementsov DN. Host Genetic Variation Has a Profound Impact on Immune Responses Mediating Control of Viral Load in Chronic Gammaherpesvirus Infection. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1526-1539. [PMID: 37819784 PMCID: PMC10841120 DOI: 10.4049/jimmunol.2300294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/14/2023] [Indexed: 10/13/2023]
Abstract
Chronic infection with the gammaherpesvirus EBV is a risk factor for several autoimmune diseases, and poor control of EBV viral load and enhanced anti-EBV responses elevate this risk further. However, the role of host genetic variation in the regulation of immune responses to chronic gammaherpesvirus infection and control of viral replication remains unclear. To address this question, we infected C57BL/6J (B6) and genetically divergent wild-derived inbred PWD/PhJ (PWD) mice with murine gammaherpesvirus-68 (MHV-68), a gammaherpesvirus similar to EBV, and determined the effect of latent gammaherpesvirus infection on the CD4 T cell transcriptome. Chronic MHV-68 infection of B6 mice resulted in a dramatic upregulation of genes characteristic of a cytotoxic Th cell phenotype, including Gzmb, Cx3cr1, Klrg1, and Nkg7, a response that was highly muted in PWD mice. Flow cytometric analyses revealed an expansion of CX3CR1+KLRG1+ cytotoxic Th cell-like cells in B6 but not PWD mice. Analysis of MHV-68 replication demonstrated that in spite of muted adaptive responses, PWD mice had superior control of viral load in lymphoid tissue, despite an absence of a defect in MHV-68 in vitro replication in PWD macrophages. Depletion of NK cells in PWD mice, but not B6 mice, resulted in elevated viral load, suggesting genotype-dependent NK cell involvement in MHV-68 control. Taken together, our findings demonstrate that host genetic variation can regulate control of gammaherpesvirus replication through disparate immunological mechanisms, resulting in divergent long-term immunological sequelae during chronic infection.
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Affiliation(s)
- Emily A. Holt
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Courtney M. Waytashek
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Katherine J. Sessions
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Loredana Asarian
- Department of Medicine, Vermont Center for Immunology and Infectious Diseases, Larner College of Medicine, The University of Vermont, Burlington, VT 05405, USA
| | - Karolyn G Lahue
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
| | - Edward J. Usherwood
- Department of Microbiology and Immunology, The Geisel School of Medicine at Dartmouth College, Lebanon, NH 03756, USA
| | - Cory Teuscher
- Department of Medicine, Vermont Center for Immunology and Infectious Diseases, Larner College of Medicine, The University of Vermont, Burlington, VT 05405, USA
| | - Dimitry N. Krementsov
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA
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Zhang L, Tang M, Diao H, Xiong L, Yang X, Xing S. LncRNA-encoded peptides: unveiling their significance in cardiovascular physiology and pathology-current research insights. Cardiovasc Res 2023; 119:2165-2178. [PMID: 37517040 DOI: 10.1093/cvr/cvad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/17/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), which are RNA transcripts exceeding 200 nucleotides were believed to lack any protein-coding capacity. But advancements in -omics technology have revealed that some lncRNAs have small open reading frames (sORFs) that can be translated by ribosomes to encode peptides, some of which have important biological functions. These encoded peptides subserve important biological functions by interacting with their targets to modulate transcriptional or signalling axes, thereby enhancing or suppressing cardiovascular disease (CVD) occurrence and progression. In this review, we summarize what is known about the research strategy of lncRNA-encoded peptides, mainly comprising predictive websites/tools and experimental methods that have been widely used for prediction, identification, and validation. More importantly, we have compiled a list of lncRNA- encoded peptides, with a focus on those that play significant roles in cardiovascular physiology and pathology, including ENSRNOT (RNO)-sORF6/RNO-sORF7/RNO-sORF8, dwarf open reading frame (DOWRF), myoregulin (NLN), etc. Additionally, we have outlined the functions and mechanisms of these peptides in cardiovascular physiology and pathology, such as cardiomyocyte hypertrophy, myocardial contraction, myocardial infarction, and vascular remodelling. Finally, an overview of the existing challenges and potential future developments in the realm of lncRNA-encoded peptides was provided, with consideration given to prospective avenues for further research. Given that many lncRNA-encoded peptides have not been functionally annotated yet, their application in CVD diagnosis and treatment still requires further research.
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Affiliation(s)
- Li Zhang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
- Hongqiao International Institute of Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200336, China
| | - Mi Tang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Haoyang Diao
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Liling Xiong
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Xiao Yang
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
| | - Shasha Xing
- Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, 1617 Riyue Street, Qingyang District, Chengdu 611731, China
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Graham ML, Li M, Gong AY, Deng S, Jin K, Wang S, Chen XM. Cryptosporidium parvum hijacks a host's long noncoding RNA U90926 to evade intestinal epithelial cell-autonomous antiparasitic defense. Front Immunol 2023; 14:1205468. [PMID: 37346046 PMCID: PMC10280636 DOI: 10.3389/fimmu.2023.1205468] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 05/16/2023] [Indexed: 06/23/2023] Open
Abstract
Cryptosporidium is a zoonotic apicomplexan parasite that infects the gastrointestinal epithelium and other mucosal surfaces in humans. It is an important opportunistic pathogen in AIDS patients and a leading cause of infectious diarrhea and diarrheal-related death in children worldwide. The intestinal epithelial cells provide the first line of defense against Cryptosporidium infection and play a central role in activating and regulating the host's antiparasitic response. Increasing evidence suggests that long noncoding RNAs (lncRNAs) participate in host-pathogen interactions and play a regulatory role in the pathogenesis of diseases but the underlying molecular mechanisms are not fully understood. We previously identified a panel of host lncRNAs that are upregulated in murine intestinal epithelial cells following Cryptosporidium infection, including U90926. We demonstrate here that U90926 is acting in a pro-parasitic manner in regulating intestinal epithelial cell-autonomous antiparasitic defense. Inhibition of U90926 resulted in a decreased infection burden of the parasite while overexpression of U90926 showed an increase in infection burden in cultured murine intestinal epithelial cells. Induction of U90926 suppressed transcription of epithelial defense genes involved in controlling Cryptosporidium infection through epigenetic mechanisms. Specifically, transcription of Aebp1, which encodes the Aebp1 protein, a potent modulator of inflammation and NF-κB signaling, was suppressed by U90926. Gain- or loss-of-function of Aebp1 in the host's epithelial cells caused reciprocal alterations in the infection burden of the parasite. Interestingly, Cryptosporidium carries the Cryptosporidium virus 1 (CSpV1), a double-stranded (ds) RNA virus coding two dsRNA fragments, CSpV1-dsRdRp and CSpV1-dsCA. Both CSpV1-dsRdRp and CSpV1-dsCA can be delivered into infected cells as previously reported. We found that cells transfected with in vitro transcribed CSpV1-dsCA or CSpV1-dsRdRp displayed an increased level of U90926, suggesting that CSpV1 is involved in the upregulation of U90926 during Cryptosporidium infection. Our study highlights a new strategy by Cryptosporidium to hijack a host lncRNA to suppress epithelial cell-autonomous antiparasitic defense and allow for a robust infection.
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Affiliation(s)
- Marion L. Graham
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
| | - Min Li
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States
| | - Ai-Yu Gong
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
| | - Silu Deng
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
- Department of Medical Microbiology and Immunology, Creighton University School of Medicine, Omaha, NE, United States
| | - Kehua Jin
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Hubei University of Science and Technology, Xianning, Hubei, China
| | - Shuhong Wang
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
| | - Xian-Ming Chen
- Department of Microbial Pathogens and Immunity, Rush University Medical Center, Chicago, IL, United States
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