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John K, Huntress I, Smith E, Chou H, Tollison TS, Covarrubias S, Crisci E, Carpenter S, Peng X. Human long noncoding RNA, VILMIR, is induced by major respiratory viral infections and modulates the host interferon response. bioRxiv 2024:2024.03.25.586578. [PMID: 38585942 PMCID: PMC10996554 DOI: 10.1101/2024.03.25.586578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic datasets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus inducible lncRNA modulator of interferon response (VILMIR), that was consistently upregulated after in vitro influenza infection across multiple human epithelial cell lines and influenza A virus subtypes. VILMIR was also upregulated after SARS-CoV-2 and RSV infections in vitro. We experimentally confirmed the response of VILMIR to influenza infection and interferon-beta (IFN-β) treatment in the A549 human epithelial cell line and found the expression of VILMIR was robustly induced by IFN-β treatment in a dose and time-specific manner. Single cell RNA-seq analysis of bronchoalveolar lavage fluid (BALF) samples from COVID-19 patients uncovered that VILMIR was upregulated across various cell types including at least five immune cells. The upregulation of VILMIR in immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-β treatment. Finally, we found that knockdown of VILMIR expression reduced the magnitude of host transcriptional responses to IFN-β treatment in A549 cells. Together, our results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation.
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Affiliation(s)
- Kristen John
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC
- Genetics & Genomics Graduate Program, North Carolina State University, Raleigh, NC
| | - Ian Huntress
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC
| | - Ethan Smith
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC
| | - Hsuan Chou
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC
| | - Tammy S. Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC
| | - Sergio Covarrubias
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Elisa Crisci
- Department of Population Health and Pathobiology, North Carolina State University College of Veterinary Medicine, Raleigh, NC
| | - Susan Carpenter
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC
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Walsh ES, Tollison TS, Brochu HN, Shaw BI, Diveley KR, Chou H, Law L, Kirk AD, Gale M, Peng X. Single-Cell-Based High-Throughput Ig and TCR Repertoire Sequencing Analysis in Rhesus Macaques. J Immunol 2022; 208:762-771. [PMID: 34987112 PMCID: PMC8820446 DOI: 10.4049/jimmunol.2100824] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/17/2021] [Indexed: 02/03/2023]
Abstract
Recent advancements in microfluidics and high-throughput sequencing technologies have enabled recovery of paired H and L chains of Igs and VDJ and VJ chains of TCRs from thousands of single cells simultaneously in humans and mice. Despite rhesus macaques being one of the most well-studied model organisms for the human adaptive immune response, high-throughput single-cell immune repertoire sequencing assays are not yet available due to the complexity of these polyclonal receptors. We used custom primers that capture all known rhesus macaque Ig and TCR isotypes and chains that are fully compatible with a commercial solution for single-cell immune repertoire profiling. Using these rhesus-specific assays, we sequenced Ig and TCR repertoires in >60,000 cells from cryopreserved rhesus PBMCs, splenocytes, and FACS-sorted B and T cells. We were able to recover every Ig isotype and TCR chain, measure clonal expansion in proliferating T cells, and pair Ig and TCR repertoires with gene expression profiles of the same single cells. Our results establish the ability to perform high-throughput immune repertoire analysis in rhesus macaques at the single-cell level.
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Affiliation(s)
- Evan S. Walsh
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Tammy S. Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
| | - Hayden N. Brochu
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Brian I. Shaw
- Department of Surgery, Duke University, Durham, NC 27710
| | - Kayleigh R. Diveley
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Genetics Graduate Program, North Carolina State University, Raleigh, NC 27695
| | - Hsuan Chou
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607
| | - Lynn Law
- Department of Immunology, University of Washington, Seattle, WA 98109
| | - Allan D. Kirk
- Department of Surgery, Duke University, Durham, NC 27710
| | - Michael Gale
- Department of Immunology, University of Washington, Seattle, WA 98109,Center for Innate Immunity and Immune Diseases, University of Washington, Seattle, WA 98109,Washington National Primate Research Center, University of Washington, Seattle, WA 98121
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC 27607,Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC 27695,Bioinformatics Research Center, North Carolina State University, Raleigh, NC 27695
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Jiang D, Sun W, Wu T, Zou M, Vasamsetti SB, Zhang X, Zhao Y, Phillippi JA, Sawalha AH, Tavakoli S, Dutta P, Florentin J, Chan SY, Tollison TS, Di Wu, Cui J, Huntress I, Peng X, Finkel T, Li G. Post-GWAS functional analysis identifies CUX1 as a regulator of p16 INK4a and cellular senescence. Nat Aging 2022; 2:140-154. [PMID: 37117763 PMCID: PMC10154215 DOI: 10.1038/s43587-022-00177-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 12/21/2021] [Indexed: 04/30/2023]
Abstract
Accumulation of senescent cells with age is an important driver of aging and age-related diseases. However, the mechanisms and signaling pathways that regulate senescence remain elusive. In this report, we performed post-genome-wide association studies (GWAS) functional studies on the CDKN2A/B locus, a locus known to be associated with multiple age-related diseases and overall human lifespan. We demonstrate that transcription factor CUX1 (Cut-Like Homeobox 1) specifically binds to an atherosclerosis-associated functional single-nucleotide polymorphism (fSNP) (rs1537371) within the locus and regulates the CDKN2A/B-encoded proteins p14ARF, p15INK4b and p16INK4a and the antisense noncoding RNA in the CDK4 (INK4) locus (ANRIL) in endothelial cells (ECs). Endothelial CUX1 expression correlates with telomeric length and is induced by both DNA-damaging agents and oxidative stress. Moreover, induction of CUX1 expression triggers both replicative and stress-induced senescence via activation of p16INK4a expression. Thus, our studies identify CUX1 as a regulator of p16INK4a-dependent endothelial senescence and a potential therapeutic target for atherosclerosis and other age-related diseases.
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Affiliation(s)
- Danli Jiang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Wei Sun
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Ting Wu
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Meijuan Zou
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology, Nanjing Medical University, Nanjing, China
| | - Sathish Babu Vasamsetti
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Xiaoyu Zhang
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yihan Zhao
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Julie A Phillippi
- Department of Cardiothoracic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Amr H Sawalha
- Departments of Pediatrics Medicine, and Immunology & Lupus Center of Excellence, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Sina Tavakoli
- Departments of Radiology and Medicine, University of Pittsburgh, UPMC Presbyterian Hospital, Pittsburg, PA, USA
| | - Partha Dutta
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Jonathan Florentin
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Stephen Y Chan
- Center for Pulmonary Vascular Biology and Medicine, Pittsburgh Heart, Lung, Blood, and Vascular Medicine Institute, University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Tammy S Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
| | - Di Wu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Division of Oral and Craniofacial Health Sciences, Adam School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Jing Cui
- Department of Medicine, Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Ian Huntress
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
- Bioinformatics Graduate Program, North Carolina State University, Raleigh, NC, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University College of Veterinary Medicine, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Toren Finkel
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Gang Li
- Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.
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Liu C, Hufnagel K, O'Connell CM, Goonetilleke N, Mokashi N, Waterboer T, Tollison TS, Peng X, Wiesenfeld HC, Hillier SL, Zheng X, Darville T. Reduced Endometrial Ascension and Enhanced Reinfection Associated with IgG Antibodies to Specific Chlamydia trachomatis Proteins in Women at Risk for Chlamydia. J Infect Dis 2021; 225:846-855. [PMID: 34610131 DOI: 10.1093/infdis/jiab496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/28/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Previous research revealed antibodies targeting Chlamydia trachomatis (CT) elementary bodies was not associated with reduced endometrial or incident infection in CT-exposed women. However, data on the role of CT protein-specific antibodies in protection are limited. METHODS A whole-proteome CT array screening serum pools from CT-exposed women identified 121 immunoprevalent proteins. Individual sera were probed using a focused array. IgG antibody frequencies and endometrial or incident infection relationships were examined using Wilcoxon Rank sum test. The impact of breadth and magnitude of protein-specific IgGs on ascension and incident infection were examined using multivariable stepwise logistic regression. Complementary RNA-sequencing quantified CT gene transcripts in cervical swabs from infected women. RESULTS IgG to Pgp3 and CT005 were associated with reduced endometrial infection; anti-CT443, -CT486 and -CT123 were associated with increased incident infection. Increased breadth of protein recognition did not however predict protection from endometrial or incident infection. mRNAs for immunoprevalent CT proteins were highly abundant in the cervix. CONCLUSIONS Protein-specific CT antibodies are not sufficient to protect against ascending or incident infection but broad recognition of CT proteins by IgG correlates with cervical CT gene transcript abundance, suggesting CT protein abundance correlates with immunogenicity and signifies their potential as vaccine candidates.
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Affiliation(s)
- Chuwen Liu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Katrin Hufnagel
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany
| | - Catherine M O'Connell
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nilu Goonetilleke
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Neha Mokashi
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Tim Waterboer
- Division of Infections and Cancer Epidemiology, German Cancer Research Center (Deutsches Krebsforschungszentrum, DKFZ), Heidelberg, Germany
| | - Tammy S Tollison
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Xinxia Peng
- Department of Molecular Biomedical Sciences, North Carolina State University, Raleigh, North Carolina, USA.,Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Harold C Wiesenfeld
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Pittsburgh School of Medicine, The Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Sharon L Hillier
- Department of Obstetrics, Gynecology and Reproductive Sciences, The University of Pittsburgh School of Medicine, The Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA
| | - Xiaojing Zheng
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Toni Darville
- Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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