1
|
Dopkins N, Fei T, Michael S, Liotta N, Guo K, Mickens KL, Barrett BS, Bendall ML, Dillon SM, Wilson CC, Santiago ML, Nixon DF. Endogenous retroelement expression in the gut microenvironment of people living with HIV-1. EBioMedicine 2024; 103:105133. [PMID: 38677181 PMCID: PMC11061259 DOI: 10.1016/j.ebiom.2024.105133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Endogenous retroelements (EREs), including human endogenous retroviruses (HERVs) and long interspersed nuclear elements (LINEs), comprise almost half of the human genome. Our previous studies of the interferome in the gut suggest potential mechanisms regarding how IFNb may drive HIV-1 gut pathogenesis. As ERE activity is suggested to partake in type 1 immune responses and is incredibly sensitive to viral infections, we sought to elucidate underlying interactions between ERE expression and gut dynamics in people living with HIV-1 (PLWH). METHODS ERE expression profiles from bulk RNA sequencing of colon biopsies and PBMC were compared between a cohort of PLWH not on antiretroviral therapy (ART) and uninfected controls. FINDINGS 59 EREs were differentially expressed in the colon of PLWH when compared to uninfected controls (padj <0.05 and FC ≤ -1 or ≥ 1) [Wald's Test]. Of these 59, 12 EREs were downregulated in PLWH and 47 were upregulated. Colon expression of the ERE loci LTR19_12p13.31 and L1FLnI_1q23.1s showed significant correlations with certain gut immune cell subset frequencies in the colon. Furthermore L1FLnI_1q23.1s showed a significant upregulation in peripheral blood mononuclear cells (PBMCs) of PLWH when compared to uninfected controls suggesting a common mechanism of differential ERE expression in the colon and PBMC. INTERPRETATION ERE activity has been largely understudied in genomic characterizations of human pathologies. We show that the activity of certain EREs in the colon of PLWH is deregulated, supporting our hypotheses that their underlying activity could function as (bio)markers and potential mediators of pathogenesis in HIV-1 reservoirs. FUNDING US NIH grants NCI CA260691 (DFN) and NIAID UM1AI164559 (DFN).
Collapse
Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Nicholas Liotta
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Kejun Guo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Kaylee L Mickens
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Brad S Barrett
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Stephanie M Dillon
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA
| | - Cara C Wilson
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Mario L Santiago
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| |
Collapse
|
2
|
Kyriakou E, Magiorkinis G. Interplay between endogenous and exogenous human retroviruses. Trends Microbiol 2023; 31:933-946. [PMID: 37019721 DOI: 10.1016/j.tim.2023.03.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 04/07/2023]
Abstract
In humans, retroviruses thrive more as symbionts than as parasites. Apart from the only two modern exogenous human retroviruses (human T-cell lymphotropic and immunodeficiency viruses; HTLV and HIV, respectively), ~8% of the human genome is occupied by ancient retroviral DNA [human endogenous retroviruses (HERVs)]. Here, we review the recent discoveries about the interactions between the two groups, the impact of infection by exogenous retroviruses on the expression of HERVs, the effect of HERVs on the pathogenicity of HIV and HTLV and on the severity of the diseases caused by them, and the antiviral protection that HERVs can allegedly provide to the host. Tracing the crosstalk between contemporary retroviruses and their endogenized ancestors will provide better understanding of the retroviral world.
Collapse
Affiliation(s)
- Eleni Kyriakou
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece.
| |
Collapse
|
3
|
Hokello J, Tyagi P, Dimri S, Sharma AL, Tyagi M. Comparison of the Biological Basis for Non-HIV Transmission to HIV-Exposed Seronegative Individuals, Disease Non-Progression in HIV Long-Term Non-Progressors and Elite Controllers. Viruses 2023; 15:1362. [PMID: 37376660 DOI: 10.3390/v15061362] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
HIV-exposed seronegative individuals (HESIs) are a small fraction of persons who are multiply exposed to human immunodeficiency virus (HIV), but do not exhibit serological or clinical evidence of HIV infection. In other words, they are groups of people maintaining an uninfected status for a long time, even after being exposed to HIV several times. The long-term non-progressors (LTNPs), on the other hand, are a group of HIV-infected individuals (approx. 5%) who remain clinically and immunologically stable for an extended number of years without combination antiretroviral therapy (cART). Meanwhile, elite controllers are comprise a much lower number (0.5%) of HIV-infected persons who spontaneously and durably control viremia to below levels of detection for at least 12 months, even when using the most sensitive assays, such as polymerase chain reaction (PCR) in the absence of cART. Despite the fact that there is no universal agreement regarding the mechanisms by which these groups of individuals are able to control HIV infection and/or disease progression, there is a general consensus that the mechanisms of protection are multifaceted and include genetic, immunological as well as viral factors. In this review, we analyze and compare the biological factors responsible for the control of HIV in these unique groups of individuals.
Collapse
Affiliation(s)
- Joseph Hokello
- Department of Biology, Faculty of Science and Education, Busitema University, Tororo P.O. Box 236, Uganda
| | - Priya Tyagi
- Cherry Hill East High School, 1750 Kresson Rd, Cherry Hill, NJ 08003, USA
| | - Shelly Dimri
- George C. Marshall High School, Fairfax County Public Schools, 7731 Leesburg Pike, Falls Church, VA 22043, USA
| | | | - Mudit Tyagi
- Center for Translational Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| |
Collapse
|
4
|
Laine A, Wang X, Ni K, Smith SEB, Najjar R, Whitmore LS, Yacoub M, Bays A, Gale M, Mustelin T. Expression of Envelope Protein Encoded by Endogenous Retrovirus K102 in Rheumatoid Arthritis Neutrophils. Microorganisms 2023; 11:1310. [PMID: 37317284 PMCID: PMC10223813 DOI: 10.3390/microorganisms11051310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 05/13/2023] [Accepted: 05/14/2023] [Indexed: 06/16/2023] Open
Abstract
Many patients suffering from autoimmune diseases have autoantibodies against proteins encoded by genomic retroelements, suggesting that normal epigenetic silencing is insufficient to prevent the production of the encoded proteins for which immune tolerance appears to be limited. One such protein is the transmembrane envelope (Env) protein encoded by human endogenous retrovirus K (HERV-K). We reported recently that patients with rheumatoid arthritis (RA) have IgG autoantibodies that recognize Env. Here, we use RNA sequencing of RA neutrophils to analyze HERV-K expression and find that only two loci with an intact open-reading frame for Env, HERV-K102, and K108 are expressed, but only the former is increased in RA. In contrast, other immune cells express more K108 than K102. Patient autoantibodies recognized endogenously expressed Env in breast cancer cells and in RA neutrophils but not healthy controls. A monoclonal anti-Env antibody also detected Env on the surface of RA neutrophils but very little on the surface of other immune cells. We conclude that HERV-K102 is the locus that produces Env detectable on the surface of neutrophils in RA. The low levels of HERV-K108 transcripts may contribute only marginally to cell surface Env on neutrophils or other immune cells in some patients.
Collapse
Affiliation(s)
- Amanda Laine
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Xiaoxing Wang
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kathryn Ni
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sarah E. B. Smith
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Rayan Najjar
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Leanne S. Whitmore
- Center for Innate Immunity and Infectious Disease, Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Michael Yacoub
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Alison Bays
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Michael Gale
- Center for Innate Immunity and Infectious Disease, Department of Immunology, University of Washington, Seattle, WA 98195, USA
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Center for Innate Immunity and Infectious Disease, Department of Immunology, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
5
|
Khadjinova AI, Wang X, Laine A, Ukadike K, Eckert M, Stevens A, Bengtsson AA, Lood C, Mustelin T. Autoantibodies against the envelope proteins of endogenous retroviruses K102 and K108 in patients with systemic lupus erythematosus correlate with active disease. Clin Exp Rheumatol 2022; 40:1306-1312. [PMID: 34665695 PMCID: PMC10695298 DOI: 10.55563/clinexprheumatol/2kg1d8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/09/2021] [Indexed: 11/13/2022]
Abstract
OBJECTIVES To determine if patients with systemic lupus erythematosus (SLE), a disease characterised by elevated type I interferons reminiscent of anti-viral immunity, have expression of human endogenous retrovirus K (HERV-K) proviruses capable of producing envelope (Env) protein, as well as associated autoantibodies against the Env protein. METHODS ELISAs were conducted with recombinant Env protein and sera from SLE patients with active (n=60) or inactive (n=49) disease, healthy controls (n=47), other rheumatic disorders (n=59), as well as plasma from paediatric lupus patients with active (n=30) or inactive (n=30) disease, and 17 healthy children. Antibody reactivity was evaluated for correlations with clinical and laboratory parameters of the patients. Expression of HERV-K transcripts were profiled in SLE leukocytes by RNA-Seq. RESULTS Both adult and paediatric SLE patients had autoantibodies against HERV-K Env with higher titres than healthy controls or patients with Sjögren's syndrome, small- or large-vessel vasculitis, or psoriatic arthritis. Transcripts from only two HERV-K loci capable of producing Env, HERV-K102 and -K108, were detected among the 10 expressed loci in SLE patients. CONCLUSIONS Our data reveal that HERV-K proviruses are expressed in SLE and that the HERV-K-encoded Env protein elicits an immune response in patients, particularly during active disease.
Collapse
Affiliation(s)
- Anastasia I Khadjinova
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Xiaoxing Wang
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Amanda Laine
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Kennedy Ukadike
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Eckert
- Seattle Children's Hospital, Seattle, WA, USA
| | - Anne Stevens
- Seattle Children's Hospital and Seattle Children's Research Institute, Seattle, WA, and Jansen Research and Development LLC, Malvern, PA, USA
| | | | - Christian Lood
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, USA.
| |
Collapse
|
6
|
Bezerra RDS, Ximenez JPB, Giovanetti M, Zucherato VS, Bitencourt HT, Zimmermann A, Alcantara LCJ, Covas DT, Kashima S, Slavov SN. METAVIROME COMPOSITION OF BRAZILIAN BLOOD DONORS POSITIVE FOR THE ROUTINELY TESTED BLOOD-BORNE INFECTIONS. Virus Res 2022; 311:198689. [PMID: 35090996 DOI: 10.1016/j.virusres.2022.198689] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 12/14/2022]
Abstract
Viral metagenomics is widely applied to characterize emerging viral pathogens but it can also reveal the virome composition in health and disease. The evaluation of the virome in healthy blood donors can provide important knowledge on possible transfusion threats. Currently, there is still a paucity of information regarding the virome of blood donors who test positive for routinely tested blood-borne infections. Such analysis may reveal co-infections which in turn appear to be crucial for transfusion medicine and for patient management. The aim of this study was to evaluate the metavirome in blood donors who tested positive for routinely tested blood-borne infections, the information for which is important for transfusion medicine and blood donor management. For this purpose, we analyzed 18 blood donations obtained from HIV and HBV-infected blood donors from the Brazilian Amazon (Amapa state) and 11 HIV, HBV, HCV, syphilis and Chagas disease - positive blood donations obtained from blood donors sampled in South Brazil (Rio Grande do Sul state). We additionally included a control group of 20 blood donors obtained from Southeast Brazil (State of São Paulo). Samples were assembled in pools and sequenced by the Illumina NovaSeq 6000 platform. To link a given virus with geographic region or type of blood donor, we performed supervised machine learning classification (fingerprint analysis). The virome of both locations was predominantly composed of commensal viruses. However, in HBV-infected blood donors from the Brazilian Amazon, the Human Pegivirus-1 (HPgV-1) reads were prevailing, while in HIV-infected donors from the same location, the torque teno virus (TTV) reads expressive abundance. In blood donors from South Brazil, the most abundant reads were classified as Human endogenous retrovirus K (HERV-K). Putative emerging viruses like the Human gemykibivirus-2 (HuGkV-2) were exclusively identified in samples from the Brazilian Amazon. The fingerprint analysis demonstrated that the HERV-K, TTV-7, 13, and 15 were statistically important for the infected blood donors, while TTV-5, 12 and 20 were linked to geographic localization. Our study revealed differences in the viral composition among blood donors who tested positive for routinely tested blood-borne infections from two different Brazilian regions and indicated the presence of putative emerging viruses in samples obtained from the Amazon. Together our results show that the presence of specific commensal viruses may be related donor infection status but additional investigations including larger study groups and samples from other Brazilian regions are needed to confirm this hypothesis.
Collapse
Affiliation(s)
- Rafael Dos Santos Bezerra
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - João Paulo Bianchi Ximenez
- Department of Clinical Analysis, Toxicology and Food Science, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Marta Giovanetti
- Laboratory of Flaviviruses, Oswaldo Cruz Institute, Rio de Janeiro, Rio de Janeiro, Brazil;; Laboratory of Molecular and Cellular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Victoria Simionatto Zucherato
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | - Ana Zimmermann
- Hematology and Hemotherapy Service of Santa Maria, Hospital "Astrogildo de Azevedo" Santa Maria, Rio Grande do Sul, Brazil
| | - Luiz Carlos Júnior Alcantara
- Laboratory of Flaviviruses, Oswaldo Cruz Institute, Rio de Janeiro, Rio de Janeiro, Brazil;; Laboratory of Molecular and Cellular Genetics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Dimas Tadeu Covas
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil;; Biotechnology Unit (NUCEL), Butantan Institute, São Paulo, São Paulo, Brazil
| | - Simone Kashima
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil;; Biotechnology Unit (NUCEL), Butantan Institute, São Paulo, São Paulo, Brazil.
| |
Collapse
|
7
|
Wang X, Hefton A, Ni K, Ukadike KC, Bowen MA, Eckert M, Stevens A, Lood C, Mustelin T. Autoantibodies Against Unmodified and Citrullinated Human Endogenous Retrovirus K Envelope Protein in Patients With Rheumatoid Arthritis. J Rheumatol Suppl 2022; 49:26-35. [PMID: 34334364 PMCID: PMC8963793 DOI: 10.3899/jrheum.201492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2021] [Indexed: 01/03/2023]
Abstract
OBJECTIVE Autoantibodies against proteins encoded by human endogenous retrovirus K (HERV-K) have been reported in patients with rheumatoid arthritis (RA), but their relevance, if any, has remained unresolved. We revisited this question and tested if such autoantibodies may react with citrullinated epitopes on the envelope (Env) protein of HERV-K. METHODS Immunoblotting and ELISAs were conducted with unmodified Env protein and with Env citrullinated by protein arginine deiminase 4 (PAD4). Sera from 100 patients with RA, plasma from 32 patients with juvenile idiopathic arthritis (JIA), and healthy adult and pediatric controls were included. Antibody reactivity was evaluated for correlations with clinical and laboratory variables of the patients. RESULTS We replicated and expanded upon published data suggesting that patients with RA or JIA have autoantibodies against HERV-K Env, some with high titers. Anti-HERV-K antibodies correlated with cigarette smoking and with circulating myeloperoxidase-DNA complexes indicative of nonapoptotic neutrophil cell death. Further, most of the patients with RA, but not those with JIA, had autoantibodies that reacted more strongly with Env that was citrullinated by PAD4. These anticitrullinated Env autoantibodies correlated with seropositivity and tended to be higher in patients with erosive disease. CONCLUSION Our data suggest that anti-HERV-K immunity is elevated in RA and JIA and may have a connection with pathogenic protein citrullination in RA.
Collapse
Affiliation(s)
- Xiaoxing Wang
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Amanda Hefton
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kathryn Ni
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Kennedy C. Ukadike
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Michael A. Bowen
- M.A. Bowen, PhD, Product and Process Development, Allogene Therapeutics, San Francisco, California
| | - Mary Eckert
- M. Eckert, BS, Seattle Children’s Research Institute, Seattle, Washington
| | - Anne Stevens
- A. Stevens, MD, Professor, Seattle Children’s Research Institute, Seattle, Division of Rheumatology, Department of Pediatrics, University of Washington, Seattle, Washington, and Janssen Research & Development, LLC, Wayne, Pennsylvania, USA
| | - Christian Lood
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| | - Tomas Mustelin
- X. Wang, PhD, A. Hefton, K. Ni, BS, K.C. Ukadike, MD, Acting Instructor, C. Lood, PhD, Associate Professor, T. Mustelin, MD, PhD, Professor, Division of Rheumatology, Department of Medicine, University of Washington, Seattle, Washington
| |
Collapse
|
8
|
Middlebrook EA, Stark DL, Cornwall DH, Kubinak JL, Potts WK. Deep Sequencing of MHC-Adapted Viral Lines Reveals Complex Recombinational Exchanges With Endogenous Retroviruses Leading to High-Frequency Variants. Front Genet 2021; 12:716623. [PMID: 34512727 PMCID: PMC8430262 DOI: 10.3389/fgene.2021.716623] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/05/2021] [Indexed: 12/03/2022] Open
Abstract
Experimental evolution (serial passage) of Friend virus complex (FVC) in mice demonstrates phenotypic adaptation to specific host major histocompatibility complex (MHC) genotypes. These evolved viral lines show increased fitness and virulence in their host-genotype-of-passage, but display fitness and virulence tradeoffs when infecting unfamiliar host MHC genotypes. Here, we deep sequence these viral lines in an attempt to discover the genetic basis of FVC adaptation. The principal prediction for genotype-specific adaptation is that unique mutations would rise to high frequency in viral lines adapted to each host MHC genotype. This prediction was not supported by our sequencing data as most observed high-frequency variants were present in each of our independently evolved viral lines. However, using a multi-variate approach to measure divergence between viral populations, we show that populations of replicate evolved viral lines from the same MHC congenic mouse strain were more similar to one another than to lines derived from different MHC congenic mouse strains, suggesting that MHC genotype does predictably act on viral evolution in our model. Sequence analysis also revealed rampant recombination with endogenous murine leukemia virus sequences (EnMuLVs) that are encoded within the BALB/c mouse genome. The highest frequency variants in all six lines contained a 12 bp insertion from a recombinant EnMuLV source, suggesting such recombinants were either being favored by selection or were contained in a recombinational hotspot. Interestingly, they did not reach fixation, as if they are low fitness. The amount of background mutations linked to FVC/EnMuLV variable sites indicated that FVC/EnMuLV recombinants had not reached mutation selection equilibrium and thus, that EnMuLV sequences are likely continuously introgressing into the replicating viral population. These discoveries raise the question: is the expression of EnMuLV sequences in mouse splenocytes that permit recombination with exogenous FVC a pathogen or host adaptation?
Collapse
Affiliation(s)
- Earl A. Middlebrook
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, NM, United States
| | - Derek L. Stark
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| | - Douglas H. Cornwall
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | - Jason L. Kubinak
- Department of Pathology, Microbiology and Immunology, University of South Carolina School of Medicine, Columbia, SC, United States
| | - Wayne K. Potts
- School of Biological Sciences, University of Utah, Salt Lake City, UT, United States
| |
Collapse
|
9
|
Römer C. Viruses and Endogenous Retroviruses as Roots for Neuroinflammation and Neurodegenerative Diseases. Front Neurosci 2021; 15:648629. [PMID: 33776642 PMCID: PMC7994506 DOI: 10.3389/fnins.2021.648629] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 02/05/2021] [Indexed: 12/15/2022] Open
Abstract
Many neurodegenerative diseases are associated with chronic inflammation in the brain and periphery giving rise to a continuous imbalance of immune processes. Next to inflammation markers, activation of transposable elements, including long intrespersed nuclear elements (LINE) elements and endogenous retroviruses (ERVs), has been identified during neurodegenerative disease progression and even correlated with the clinical severity of the disease. ERVs are remnants of viral infections in the human genome acquired during evolution. Upon activation, they produce transcripts and the phylogenetically youngest ones are still able to produce viral-like particles. In addition, ERVs can bind transcription factors and modulate immune response. Being between own and foreign, ERVs are reviewed in the context of viral infections of the central nervous system, in aging and neurodegenerative diseases. Moreover, this review tests the hypothesis that viral infection may be a trigger at the onset of neuroinflammation and that ERVs sustain the inflammatory imbalance by summarizing existing data of neurodegenerative diseases associated with viruses and/or ERVs.
Collapse
Affiliation(s)
- Christine Römer
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, The Berlin Institute for Medical Systems Biology, Berlin, Germany
| |
Collapse
|
10
|
Casseb J, Janini LM, Barros Kanzaki LI, Lopes LR, Paiva AM. Is the human T-cell lymphotropic virus type 2 in the process of endogenization into the human genome? J Virus Erad 2020; 6:100009. [PMID: 33294211 PMCID: PMC7695812 DOI: 10.1016/j.jve.2020.100009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/27/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
Human T-cell lymphotropic virus type 2 (HTLV-2) infection has been shown to be endemic among intravenous drug users in parts of North America, Europe and Southeast Asia and in a number of Amerindian populations. Despite a 65% genetic similarity and common host humoral response, the human T-cell lymphotropic viruses type 1 (HTLV-1) and 2 display different mechanisms of host interaction and capacity for disease development. While HTLV-1 pathogenicity is well documented, HTLV-2 etiology in human disease is not clearly established. From an evolutionary point of view, its introduction and integration into the germ cell chromosomes of host species could be considered as the final stage of parasitism and evasion from host immunity. The extraordinary abundance of endogenous viral sequences in all vertebrate species genomes, including the hominid family, provides evidence of this invasion. Some of these gene sequences still retain viral characteristics and the ability to replicate and hence are potentially able to elicit responses from the innate and adaptive host immunity, which could result in beneficial or pathogenic effects. Taken together, this data may indicate that HTLV-2 is more likely to progress towards endogenization as has happened to the human endogenous retroviruses millions of years ago. Thus, this intimate association (HTLV-2/human genome) may provide protection from the immune system with better adaptation and low pathogenicity.
Collapse
Affiliation(s)
- Jorge Casseb
- Institute of Tropical Medicine of Sao Paulo - University of Sao Paulo, Laboratory of Medical Investigation LIM-56 / Faculty of Medicine -USP, Brazil
| | - Luiz Mario Janini
- Discipline of Microbiology, Department of Microbiology, Immunology and Parasitology, Federal University of Sao Paulo - Unifesp, Sao Paulo, SP, Brazil
| | - Luis Isamu Barros Kanzaki
- Laboratory of Bioprospection, Department of Pharmacy, Faculty of Health. Sciences, University of Brasilia, DF, Brazil
| | - Luciano Rodrigo Lopes
- Bioinformatics and Biomedical Data Science Division, Health Informatics Department, Federal University of Sao Paulo - Unifesp, São Paulo, SP, Brazil
| | - Arthur Maia Paiva
- Institute of Tropical Medicine of Sao Paulo - University of Sao Paulo, Laboratory of Medical Investigation LIM-56 / Faculty of Medicine -USP, Brazil.,University Hospital Alberto Antunes / Federal University of Alagoas, Brazil
| |
Collapse
|
11
|
Srinivasachar Badarinarayan S, Shcherbakova I, Langer S, Koepke L, Preising A, Hotter D, Kirchhoff F, Sparrer KMJ, Schotta G, Sauter D. HIV-1 infection activates endogenous retroviral promoters regulating antiviral gene expression. Nucleic Acids Res 2020; 48:10890-10908. [PMID: 33021676 PMCID: PMC7641743 DOI: 10.1093/nar/gkaa832] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 12/13/2022] Open
Abstract
Although endogenous retroviruses (ERVs) are known to harbor cis-regulatory elements, their role in modulating cellular immune responses remains poorly understood. Using an RNA-seq approach, we show that several members of the ERV9 lineage, particularly LTR12C elements, are activated upon HIV-1 infection of primary CD4+ T cells. Intriguingly, HIV-1-induced ERVs harboring transcription start sites are primarily found in the vicinity of immunity genes. For example, HIV-1 infection activates LTR12C elements upstream of the interferon-inducible genes GBP2 and GBP5 that encode for broad-spectrum antiviral factors. Reporter assays demonstrated that these LTR12C elements drive gene expression in primary CD4+ T cells. In line with this, HIV-1 infection triggered the expression of a unique GBP2 transcript variant by activating a cryptic transcription start site within LTR12C. Furthermore, stimulation with HIV-1-induced cytokines increased GBP2 and GBP5 expression in human cells, but not in macaque cells that naturally lack the GBP5 gene and the LTR12C element upstream of GBP2. Finally, our findings suggest that GBP2 and GBP5 have already been active against ancient viral pathogens as they suppress the maturation of the extinct retrovirus HERV-K (HML-2). In summary, our findings uncover how human cells can exploit remnants of once-infectious retroviruses to regulate antiviral gene expression.
Collapse
Affiliation(s)
| | - Irina Shcherbakova
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Simon Langer
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Lennart Koepke
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Andrea Preising
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | | | - Gunnar Schotta
- Molecular Biology Division, Biomedical Center, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| |
Collapse
|
12
|
Mustelin T, Ukadike KC. How Retroviruses and Retrotransposons in Our Genome May Contribute to Autoimmunity in Rheumatological Conditions. Front Immunol 2020; 11:593891. [PMID: 33281822 PMCID: PMC7691656 DOI: 10.3389/fimmu.2020.593891] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/19/2020] [Indexed: 12/14/2022] Open
Abstract
More than 200 human disorders include various manifestations of autoimmunity. The molecular events that lead to these diseases are still incompletely understood and their causes remain largely unknown. Numerous potential triggers of autoimmunity have been proposed over the years, but very few of them have been conclusively confirmed or firmly refuted. Viruses have topped the lists of suspects for decades, and it seems that many viruses, including those of the Herpesviridae family, indeed can influence disease initiation and/or promote exacerbations by a number of mechanisms that include prolonged anti-viral immunity, immune subverting factors, and mechanisms, and perhaps “molecular mimicry”. However, no specific virus has yet been established as being truly causative. Here, we discuss a different, but perhaps mechanistically related possibility, namely that retrotransposons or retroviruses that infected us in the past and left a lasting copy of themselves in our genome still can provoke an escalating immune response that leads to autoimmune disease. Many of these loci still encode for retroviral proteins that have retained some, or all, of their original functions. Importantly, these endogenous proviruses cannot be eliminated by the immune system the way it can eliminate exogenous viruses. Hence, if not properly controlled, they may drive a frustrated and escalating chronic, or episodic, immune response to the point of a frank autoimmune disorder. Here, we discuss the evidence and the proposed mechanisms, and assess the therapeutic options that emerge from the current understanding of this field.
Collapse
Affiliation(s)
- Tomas Mustelin
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| | - Kennedy C Ukadike
- Division of Rheumatology, Department of Medicine, University of Washington, Seattle, WA, United States
| |
Collapse
|
13
|
Curty G, Beckerle GA, Iñiguez LP, Furler RL, de Carvalho PS, Marston JL, Champiat S, Heymann JJ, Ormsby CE, Reyes-Terán G, Soares MA, Nixon DF, Bendall ML, Leal FE, de Mulder Rougvie M. Human Endogenous Retrovirus Expression Is Upregulated in the Breast Cancer Microenvironment of HIV Infected Women: A Pilot Study. Front Oncol 2020; 10:553983. [PMID: 33194615 PMCID: PMC7649802 DOI: 10.3389/fonc.2020.553983] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
In people living with HIV (PLWH), chronic inflammation can lead to cancer initiation and progression, besides driving a dysregulated and diminished immune responsiveness. HIV infection also leads to increased transcription of Human Endogenous Retroviruses (HERVs), which could increase an inflammatory environment and create a tumor growth suppressive environment with high expression of pro-inflammatory cytokines. In order to determine the impact of HIV infection to HERV expression on the breast cancer microenvironment, we sequenced total RNA from formalin-fixed paraffin-embedded (FFPE) breast cancer samples of women HIV-negative and HIV-positive for transcriptome and retrotranscriptome analyses. We performed RNA extraction from FFPE samples, library preparation and total RNA sequencing (RNA-seq). The RNA-seq analysis shows 185 differentially expressed genes: 181 host genes (178 upregulated and three downregulated) and four upregulated HERV transcripts in HIV-positive samples. We also explored the impact of HERV expression in its neighboring breast cancer development genes (BRCA1, CCND1, NBS1/NBN, RAD50, KRAS, PI3K/PIK3CA) and in long non-coding RNA expression (AC060780.1, also known as RP11-242D8.1). We found a significant positive association of HERV expression with RAD50 and with AC060780.1, which suggest a possible role of HERV in regulating breast cancer genes from PLWH with breast cancer. In addition, we found immune system, extracellular matrix organization and metabolic signaling genes upregulated in HIV-positive breast cancer. In conclusion, our findings provide evidence of transcriptional and retrotranscriptional changes in breast cancer from PLWH compared to non-HIV breast cancer, including dysregulation of HERVs, suggesting an indirect effect of the virus on the breast cancer microenvironment.
Collapse
Affiliation(s)
- Gislaine Curty
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Greta A Beckerle
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Luis P Iñiguez
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Robert L Furler
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | | | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Stephane Champiat
- Drug Development Department (DITEP), Gustave Roussy, Paris-Saclay University, Villejuif, France
| | - Jonas J Heymann
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Christopher E Ormsby
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Center for Research in Infectious Diseases (CIENI), National Institute of Respiratory Diseases (INER), Mexico City, Mexico
| | - Marcelo A Soares
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Fabio E Leal
- Oncovirology Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Miguel de Mulder Rougvie
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| |
Collapse
|
14
|
Comprehensive Analysis of HERV Transcriptome in HIV+ Cells: Absence of HML2 Activation and General Downregulation of Individual HERV Loci. Viruses 2020; 12:v12040481. [PMID: 32340287 PMCID: PMC7232394 DOI: 10.3390/v12040481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 04/20/2020] [Accepted: 04/20/2020] [Indexed: 01/08/2023] Open
Abstract
Human endogenous retrovirus (HERV) expression is currently studied for its possible activation by HIV infection. In this context, the HERV-K(HML2) group is the most investigated: it has been proposed that HIV-1 infection can prompt HML2 transcription, and that HML2 proteins can affect HIV-1 replication, either complementing HIV or possibly influencing antiretroviral therapy. However, little information is available on the expression of other HERV groups in HIV infection. In the present study, we used a bioinformatics pipeline to investigate the transcriptional modulation of approximately 3250 well-characterized HERV loci, comparing their expression in a public RNA-seq profile, including a HIV-1-infected and a control T cell culture. In our pilot study, we found approximately 200 HERV loci belonging to 35 HERV groups that were expressed in one or both conditions, with transcripts per million (TPM) values from 1 to >500. Intriguingly, HML2 elements constituted only the 3% of expressed HERV loci, and in most cases (160) HERV expression was downregulated in the HIV-infected culture, showing from a 1- to 14-fold decrease as compared to uninfected cells. HERV transcriptome has been inferred de novo and employed to predict a total of about 950 HERV open reading frames (ORFs). These have been validated according to the coding potential and estimated abundance of the corresponding transcripts, leading to a set of 57 putative proteins potentially encoded by 23 HERV loci. Analysis showed that some individual loci have a coding potential that deserves further investigation. Among them, a HML6 provirus at locus 19q13.43 was predicted to produce a transcript showing the highest TPM among HERV-derived transcripts, being upregulated in HIV+ cells and inferred to produce Gag and Env puteins with possible biological activity.
Collapse
|
15
|
Gray LR, Jackson RE, Jackson PEH, Bekiranov S, Rekosh D, Hammarskjöld ML. HIV-1 Rev interacts with HERV-K RcREs present in the human genome and promotes export of unspliced HERV-K proviral RNA. Retrovirology 2019; 16:40. [PMID: 31842941 PMCID: PMC6916052 DOI: 10.1186/s12977-019-0505-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Accepted: 12/07/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The HERV-K (HML-2) viruses are the youngest of the human endogenous retroviruses. They are present as several almost complete proviral copies and numerous fragments in the human genome. Many HERV-K proviruses express a regulatory protein Rec, which binds to an element present in HERV-K mRNAs called the RcRE. This interaction is necessary for the nucleo-cytoplasmic export and expression of HERV-K mRNAs that retain introns and plays a role analogous to that of Rev and the RRE in HIV replication. There are over 900 HERV-K RcREs distributed throughout the human genome. Thus, it was of interest to determine if Rev could functionally interact with selected RcRE elements that map either to HERV-K proviruses or human gene regions. This interaction would have the potential to alter the expression of both HERV-K mRNAs and cellular mRNAs during HIV-1 infection. RESULTS In this study we employed a combination of RNAseq, bioinformatics and cell-based functional assays. Potential RcREs were identified through a number of bioinformatic approaches. They were then tested for their ability to promote export and translation of a reporter mRNA with a retained intron in conjunction with Rev or Rec. Some of the selected elements functioned well with either Rev, Rec or both, whereas some showed little or no function. Rev function on individual RcREs varied and was also dependent on the Rev sequence. We also performed RNAseq on total and cytoplasmic RNA isolated from SupT1 cells expressing HIV Rev, with or without Tat, or HERV-K Rec. Proviral mRNA from three HERV-K loci (4p16.1b, 22q11.23 and most significantly 3q12.3) accumulated in the cytoplasm in the presence of Rev or Tat and Rev, but not Rec. Consistent with this, the 3' RcRE from 3q12.3 functioned well with HIV-Rev in our reporter assay. In contrast, this RcRE showed little or no function with Rec. CONCLUSIONS The HIV Rev protein can functionally interact with many RcREs present in the human genome, depending on the RcRE sequence, as well as the Rev sequence. This leads to export of some of the HERV-K proviral mRNAs and also has the potential to change the expression of non-viral genes.
Collapse
Affiliation(s)
- Laurie R Gray
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Rachel E Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Patrick E H Jackson
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, 22908, USA
| | - Stefan Bekiranov
- Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, 22908, USA
| | - David Rekosh
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA
| | - Marie-Louise Hammarskjöld
- Myles H. Thaler Center for AIDS and Human Retrovirus Research and the Department of Microbiology, Immunology, Cancer Biology, University of Virginia, Charlottesville, 22908, USA.
| |
Collapse
|
16
|
Kaplan MH, Kaminski M, Estes JM, Gitlin SD, Zahn J, Elder JT, Tejasvi T, Gensterblum E, Sawalha AH, McGowan JP, Dosik MH, Direskeneli H, Direskeneli GS, Adebamowo SN, Adebamowo CA, Sajadi M, Contreras-Galindo R. Structural variation of centromeric endogenous retroviruses in human populations and their impact on cutaneous T-cell lymphoma, Sézary syndrome, and HIV infection. BMC Med Genomics 2019; 12:58. [PMID: 31046767 PMCID: PMC6498702 DOI: 10.1186/s12920-019-0505-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 04/15/2019] [Indexed: 12/16/2022] Open
Abstract
Background Human Endogenous Retroviruses type K HML-2 (HK2) are integrated into 117 or more areas of human chromosomal arms while two newly discovered HK2 proviruses, K111 and K222, spread extensively in pericentromeric regions, are the first retroviruses discovered in these areas of our genome. Methods We use PCR and sequencing analysis to characterize pericentromeric K111 proviruses in DNA from individuals of diverse ethnicities and patients with different diseases. Results We found that the 5′ LTR-gag region of K111 proviruses is missing in certain individuals, creating pericentromeric instability. K111 deletion (−/− K111) is seen in about 15% of Caucasian, Asian, and Middle Eastern populations; it is missing in 2.36% of African individuals, suggesting that the −/− K111 genotype originated out of Africa. As we identified the −/−K111 genotype in Cutaneous T-cell lymphoma (CTCL) cell lines, we studied whether the −/−K111 genotype is associated with CTCL. We found a significant increase in the frequency of detection of the −/−K111 genotype in Caucasian patients with severe CTCL and/or Sézary syndrome (n = 35, 37.14%), compared to healthy controls (n = 160, 15.6%) [p = 0.011]. The −/−K111 genotype was also found to vary in HIV-1 infection. Although Caucasian healthy individuals have a similar frequency of detection of the −/− K111 genotype, Caucasian HIV Long-Term Non-Progressors (LTNPs) and/or elite controllers, have significantly higher detection of the −/−K111 genotype (30.55%; n = 36) than patients who rapidly progress to AIDS (8.5%; n = 47) [p = 0.0097]. Conclusion Our data indicate that pericentromeric instability is associated with more severe CTCL and/or Sézary syndrome in Caucasians, and appears to allow T-cells to survive lysis by HIV infection. These findings also provide new understanding of human evolution, as the −/−K111 genotype appears to have arisen out of Africa and is distributed unevenly throughout the world, possibly affecting the severity of HIV in different geographic areas. Electronic supplementary material The online version of this article (10.1186/s12920-019-0505-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Mark H Kaplan
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Mark Kaminski
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Judith M Estes
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Scott D Gitlin
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Joseph Zahn
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - James T Elder
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Trilokraj Tejasvi
- Division of Dermatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.,Ann Arbor Veterans Affairs Hospital, Ann Arbor, MI, 48105, USA
| | - Elizabeth Gensterblum
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Joseph Patrick McGowan
- Division of Infectious Diseases, The Feinstein Institute for Medical research, Manhasset, NY, 11030, USA
| | | | - Haner Direskeneli
- Division of Rheumatology, School of Medicine, Marmara University, Istanbul, Turkey
| | | | - Sally N Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Clement A Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.,Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Mohammad Sajadi
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Rafael Contreras-Galindo
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA. .,Hormel Institute, University of Minnesota, Austin, MN, 55912, USA.
| |
Collapse
|
17
|
Douville RN, Nath A. Human Endogenous Retrovirus-K and TDP-43 Expression Bridges ALS and HIV Neuropathology. Front Microbiol 2017; 8:1986. [PMID: 29075249 PMCID: PMC5641584 DOI: 10.3389/fmicb.2017.01986] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 09/27/2017] [Indexed: 12/12/2022] Open
Abstract
Despite the repetitive association of endogenous retroviruses in human disease, the mechanisms behind their pathological contributions remain to be resolved. Here we discuss how neuronal human endogenous retrovirus-K (HERV-K) expression in human immunodeficiency virus (HIV)-infected individuals is a distinct pathological aspect of HIV-associated neurological conditions, such as HIV encephalitis and HIV-associated neurocognitive disorders. Enhanced neuronal HERV-K levels were observed in the majority of HIV-infected individuals, and to a higher degree in brain tissue marked by HIV replication. Moreover, we highlight an important neuropathological overlap between amyotrophic lateral sclerosis and HIV encephalitis, that being the formation of neurotoxic TDP-43 deposits in neurons. Herein, we argue for enhanced transdisciplinary research in the field of ERV biology, using an example of how HERV-K expression has novel mechanistic and therapeutic implications for HIV neuropathology.
Collapse
Affiliation(s)
- Renée N Douville
- Department of Biology, University of Winnipeg, Winnipeg, MB, Canada.,Department of Immunology, University of Manitoba, Winnipeg, MB, Canada
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|