1
|
Dow CT, Pierce ES, Sechi LA. Mycobacterium paratuberculosis: A HERV Turn-On for Autoimmunity, Neurodegeneration, and Cancer? Microorganisms 2024; 12:1890. [PMID: 39338563 PMCID: PMC11434025 DOI: 10.3390/microorganisms12091890] [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: 06/28/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that, over millions of years, became integrated into the human genome. While normally inactive, environmental stimuli such as infections have contributed to the transcriptional reactivation of HERV-promoting pathological conditions, including the development of autoimmunity, neurodegenerative disease and cancer. What infections trigger HERV activation? Mycobacterium avium subspecies paratuberculosis (MAP) is a pluripotent driver of human disease. Aside from granulomatous diseases, Crohn's disease, sarcoidosis and Blau syndrome, MAP is associated with autoimmune disease: type one diabetes (T1D), multiple sclerosis (MS), rheumatoid arthritis (RA) and autoimmune thyroiditis. MAP is also associated with Alzheimer's disease (AD) and Parkinson's disease (PD). Autoimmune diabetes, MS and RA are the diseases with the strongest MAP/HERV association. There are several other diseases associated with HERV activation, including diseases whose epidemiology and/or pathology would prompt speculation for a causal role of MAP. These include non-solar uveal melanoma, colon cancer, glioblastoma and amyotrophic lateral sclerosis (ALS). This article further points to MAP infection as a contributor to autoimmunity, neurodegenerative disease and cancer via the un-silencing of HERV. We examine the link between the ever-increasing number of MAP-associated diseases and the MAP/HERV intersection with these diverse medical conditions, and propose treatment opportunities based upon this association.
Collapse
Affiliation(s)
- Coad Thomas Dow
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - Leonardo A. Sechi
- Department of Biomedical Science, University of Sassari, 07100 Sassari, Italy;
- Azienda Ospedaliera Universitaria di Sassari, Viale San Pietro, 07100 Sassari, Italy
| |
Collapse
|
2
|
Chisca M, Larouche JD, Xing Q, Kassiotis G. Antibodies against endogenous retroviruses. Immunol Rev 2024. [PMID: 39152687 DOI: 10.1111/imr.13378] [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] [Indexed: 08/19/2024]
Abstract
The human genome harbors hundreds of thousands of integrations of ancient retroviruses, amassed over millions of years of evolution. To reduce further amplification in the genome, the host prevents transcription of these now endogenous retroviruses (ERVs) through epigenetic repression and, with evolutionary time, ERVs are incapacitated by accumulating mutations and deletions. However, several members of recently endogenized ERV groups still retain the capacity to produce viral RNA, retroviral proteins, and higher order structures, including virions. The retention of viral characteristics, combined with the reversible nature of epigenetic repression, particularly as seen in cancer, allow for immunologically unanticipated ERV expression, perceived by the adaptive immune system as a genuine retroviral infection, to which it has to respond. Accordingly, antibodies reactive with ERV antigens have been detected in diverse disorders and, occasionally, in healthy individuals. Although they are part of self, the retroviral legacy of ERV antigens, and association with and, possibly, causation of disease states may set them apart from typical self-antigens. Consequently, the pathogenic or, indeed, host-protective capacity of antibodies targeting ERV antigens is likely to be context-dependent. Here, we review the immunogenicity of typical ERV proteins, with emphasis on the antibody response and its potential disease implications.
Collapse
Affiliation(s)
- Mihaela Chisca
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | | | - Qi Xing
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| |
Collapse
|
3
|
Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye CJ, Dall'Era M, Yazdany J, Criswell LA, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. Cell-Specific Transposable Element and Gene Expression Analysis Across Systemic Lupus Erythematosus Phenotypes. ACR Open Rheumatol 2024. [PMID: 39143499 DOI: 10.1002/acr2.11713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/06/2024] [Accepted: 06/04/2024] [Indexed: 08/16/2024] Open
Abstract
OBJECTIVE There is an established yet unexplained link between interferon (IFN) and systemic lupus erythematosus (SLE). The expression of sequences derived from transposable elements (TEs) may contribute to SLE phenotypes, specifically production of type I IFNs and generation of autoantibodies. METHODS We profiled cell-sorted RNA-sequencing data (CD4+ T cells, CD14+ monocytes, CD19+ B cells, and natural killer cells) from peripheral blood mononuclear cells of 120 patients with SLE and quantified TE expression identifying 27,135 TEs. We tested for differential TE expression across 10 SLE phenotypes, including autoantibody production and disease activity. RESULTS We found 731 differentially expressed (DE) TEs across all SLE phenotypes that were mostly cell specific and phenotype specific. DE TEs were enriched for specific families and open reading frames of viral genes encoded in TE sequences. Increased expression of DE TEs was associated with genes involved in antiviral activity, such as LY6E, ISG15, and TRIM22, and pathways such as IFN signaling. CONCLUSION These findings suggest that expression of TEs contributes to activation of SLE-related mechanisms in a cell-specific manner, which can impact disease diagnostics and therapeutics.
Collapse
Affiliation(s)
- Zachary Cutts
- University of California, San Francisco, San Francisco
| | | | | | | | | | | | | | | | | | | | - John A Capra
- University of California, San Francisco, San Francisco
| | - Marina Sirota
- University of California, San Francisco, San Francisco
| | | |
Collapse
|
4
|
Chen M, Yang C, Zhai X, Wang C, Liu M, Zhang B, Guo X, Wang Y, Li H, Liu Y, Han J, Wang X, Li J, Jia L, Li L. Comprehensive Identification and Characterization of HML-9 Group in Chimpanzee Genome. Viruses 2024; 16:892. [PMID: 38932184 PMCID: PMC11209481 DOI: 10.3390/v16060892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Endogenous retroviruses (ERVs) are related to long terminal repeat (LTR) retrotransposons, comprising gene sequences of exogenous retroviruses integrated into the host genome and inherited according to Mendelian law. They are considered to have contributed greatly to the evolution of host genome structure and function. We previously characterized HERV-K HML-9 in the human genome. However, the biological function of this type of element in the genome of the chimpanzee, which is the closest living relative of humans, largely remains elusive. Therefore, the current study aims to characterize HML-9 in the chimpanzee genome and to compare the results with those in the human genome. Firstly, we report the distribution and genetic structural characterization of the 26 proviral elements and 38 solo LTR elements of HML-9 in the chimpanzee genome. The results showed that the distribution of these elements displayed a non-random integration pattern, and only six elements maintained a relatively complete structure. Then, we analyze their phylogeny and reveal that the identified elements all cluster together with HML-9 references and with those identified in the human genome. The HML-9 integration time was estimated based on the 2-LTR approach, and the results showed that HML-9 elements were integrated into the chimpanzee genome between 14 and 36 million years ago and into the human genome between 18 and 49 mya. In addition, conserved motifs, cis-regulatory regions, and enriched PBS sequence features in the chimpanzee genome were predicted based on bioinformatics. The results show that pathways significantly enriched for ERV LTR-regulated genes found in the chimpanzee genome are closely associated with disease development, including neurological and neurodevelopmental psychiatric disorders. In summary, the identification, characterization, and genomics of HML-9 presented here not only contribute to our understanding of the role of ERVs in primate evolution but also to our understanding of their biofunctional significance.
Collapse
Affiliation(s)
- Mingyue Chen
- National 111 Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering, Hubei University of Technology, Wuhan 430068, China;
| | - Caiqin Yang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiuli Zhai
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Chunlei Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Mengying Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Bohan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xing Guo
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- Department of Microbiology, School of Basic Medicine, Anhui Medical University, Hefei 230032, China
| | - Yanglan Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Hanping Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Yongjian Liu
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Xiaolin Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Jingyun Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lei Jia
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Sciences, Beijing 100071, China; (C.Y.); (X.Z.); (C.W.); (M.L.); (B.Z.); (X.G.); (Y.W.); (H.L.); (Y.L.); (J.H.); (X.W.); (J.L.)
| |
Collapse
|
5
|
Takahashi Ueda M. Retrotransposon-derived transcripts and their functions in immunity and disease. Genes Genet Syst 2024; 98:305-319. [PMID: 38199240 DOI: 10.1266/ggs.23-00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024] Open
Abstract
Retrotransposons, which account for approximately 42% of the human genome, have been increasingly recognized as "non-self" pathogen-associated molecular patterns (PAMPs) due to their virus-like sequences. In abnormal conditions such as cancer and viral infections, retrotransposons that are aberrantly expressed due to impaired epigenetic suppression display PAMPs, leading to their recognition by pattern recognition receptors (PRRs) of the innate immune system and triggering inflammation. This viral mimicry mechanism has been observed in various human diseases, including aging and autoimmune disorders. However, recent evidence suggests that retrotransposons possess highly regulated immune reactivity and play important roles in the development and function of the immune system. In this review, I discuss a wide range of retrotransposon-derived transcripts, their role as targets in immune recognition, and the diseases associated with retrotransposon activity. Furthermore, I explore the implications of chimeric transcripts formed between retrotransposons and known gene mRNAs, which have been previously underestimated, for the increase of immune-related gene isoforms and their influence on immune function. Retrotransposon-derived transcripts have profound and multifaceted effects on immune system function. The aim of this comprehensive review is to provide a better understanding of the complex relationship between retrotransposon transcripts and immune defense.
Collapse
Affiliation(s)
- Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University
| |
Collapse
|
6
|
Najjar R, Rogel N, Pineda JMB, Wang X, Tran M, Bays A, Mustelin T. Large overlap in neutrophil transcriptome between lupus and COVID-19 with limited lupus-specific gene expression. Lupus Sci Med 2024; 11:e001059. [PMID: 38302132 PMCID: PMC10831459 DOI: 10.1136/lupus-2023-001059] [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: 09/22/2023] [Accepted: 01/22/2024] [Indexed: 02/03/2024]
Abstract
OBJECTIVES To illuminate the poorly understood aetiology of SLE by comparing the gene expression profile of SLE neutrophils with that of neutrophils from patients infected by SARS-CoV-2, a disease (COVID-19) with well-defined antigens and a similar type I interferon response. METHODS RNA sequencing of neutrophils from patients with SLE (n=15) and healthy controls (n=12) was analysed for differential gene expression and modulated pathways. The same analyses were performed on a similar neutrophil dataset from patients with SARS-CoV-2 infection (n=30) and healthy controls (n=8). Next, we carried out comparative analyses to identify common and unique transcriptional changes between the two disease contexts, emphasising genes regulated in opposite directions. RESULTS We identified 372 differentially expressed genes in SLE neutrophils compared with healthy donor neutrophils (≥2 fold, p<0.05), 181 of which were concordant with transcriptional changes in SARS-CoV-2-infected individuals compared with their respective healthy controls. In contrast, 118 genes demonstrated statistically significant alterations exclusive to SLE, including 28 genes that were differentially expressed in opposite directions in the two diseases. CONCLUSIONS The substantial overlap between neutrophil responses in SLE and COVID-19 suggests that the unknown cause of SLE is functionally similar to a viral infection and drives a similar immune activation and type I interferon response. Conversely, the genes regulated in the opposite direction represent responses unique to SLE. These include tyrosylprotein sulfotransferase-1 and nucleic acid deaminases of the APOBEC family, which can catalyse cytosine-to-uridine editing of both RNA and DNA, and other RNA-modifying enzymes.
Collapse
Affiliation(s)
- Rayan Najjar
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Noga Rogel
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Xiaoxing Wang
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Megan Tran
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Alison Bays
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Tomas Mustelin
- Department of Medicine, University of Washington, Seattle, Washington, USA
| |
Collapse
|
7
|
Mantovani F, Kitsou K, Magiorkinis G. HERVs: Expression Control Mechanisms and Interactions in Diseases and Human Immunodeficiency Virus Infection. Genes (Basel) 2024; 15:192. [PMID: 38397182 PMCID: PMC10888493 DOI: 10.3390/genes15020192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/24/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the result of retroviral infections acquired millions of years ago; nowadays, they compose around 8% of human DNA. Multiple mechanisms have been employed for endogenous retroviral deactivation, rendering replication and retrotransposition defective, while some of them have been co-opted to serve host evolutionary advantages. A pleiad of mechanisms retains the delicate balance of HERV expression in modern humans. Thus, epigenetic modifications, such as DNA and histone methylation, acetylation, deamination, chromatin remodeling, and even post-transcriptional control are recruited. In this review, we aim to summarize the main HERV silencing pathways, revisit paradigms of human disease with a HERV component, and emphasize the human immunodeficiency virus (HIV) and HERV interactions during HIV infection.
Collapse
Affiliation(s)
| | | | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (F.M.); (K.K.)
| |
Collapse
|
8
|
Cutts Z, Patterson S, Maliskova L, Taylor KE, Ye C, Dall'Era M, Yazdany J, Criswell L, Fragiadakis GK, Langelier C, Capra JA, Sirota M, Lanata CM. Cell-Specific Transposable Element Gene Expression Analysis Identifies Associations with Systemic Lupus Erythematosus Phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.27.567477. [PMID: 38076936 PMCID: PMC10705239 DOI: 10.1101/2023.11.27.567477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
There is an established yet unexplained link between interferon (IFN) and systemic lupus erythematosus (SLE). The expression of sequences derived from transposable elements (TEs) may contribute to production of type I IFNs and generation of autoantibodies. We profiled cell-sorted RNA-seq data (CD4+ T cells, CD14+ monocytes, CD19+ B cells, and NK cells) from PBMCs of 120 SLE patients and quantified TE expression identifying 27,135 TEs. We tested for differential TE expression across 10 SLE phenotypes including autoantibody production and disease activity and discovered 731 differentially expressed (DE) TEs whose effects were mostly cell-specific and phenotype-specific. DE TEs were enriched for specific families and viral genes encoded in TE sequences. Increased expression of DE TEs was associated with genes involved in antiviral activity such as LY6E, ISG15, TRIM22 and pathways such as interferon signaling. These findings suggest that expression of TEs contributes to activation of SLE-related mechanisms in a cell-specific manner, which can impact disease diagnostics and therapeutics.
Collapse
|
9
|
Vylegzhanina AV, Bespalov IA, Novototskaya-Vlasova KA, Hall BM, Gleiberman AS, Yu H, Leontieva OV, Leonova KI, Kurnasov OV, Osterman AL, Dy GK, Komissarov AA, Vasilieva E, Gehlhausen J, Iwasaki A, Ambrosone CB, Tsuji T, Matsuzaki J, Odunsi K, Andrianova EL, Gudkov AV. Cancer Relevance of Circulating Antibodies Against LINE-1 Antigens in Humans. CANCER RESEARCH COMMUNICATIONS 2023; 3:2256-2267. [PMID: 37870410 PMCID: PMC10631453 DOI: 10.1158/2767-9764.crc-23-0289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/16/2023] [Accepted: 10/13/2023] [Indexed: 10/24/2023]
Abstract
Long interspersed nuclear element-1 (LINE-1 or L1), the most abundant family of autonomous retrotransposons occupying over 17% of human DNA, is epigenetically silenced in normal tissues by the mechanisms involving p53 but is frequently derepressed in cancer, suggesting that L1-encoded proteins may act as tumor-associated antigens recognized by the immune system. In this study, we established an immunoassay to detect circulating autoantibodies against L1 proteins in human blood. Using this assay in >2,800 individuals with or without cancer, we observed significantly higher IgG titers against L1-encoded ORF1p and ORF2p in patients with lung, pancreatic, ovarian, esophageal, and liver cancers than in healthy individuals. Remarkably, elevated levels of anti-ORF1p-reactive IgG were observed in patients with cancer with disease stages 1 and 2, indicating that the immune response to L1 antigens can occur in the early phases of carcinogenesis. We concluded that the antibody response against L1 antigens could contribute to the diagnosis and determination of immunoreactivity of tumors among cancer types that frequently escape early detection. SIGNIFICANCE The discovery of autoantibodies against antigens encoded by L1 retrotransposons in patients with five poorly curable cancer types has potential implications for the detection of an ongoing carcinogenic process and tumor immunoreactivity.
Collapse
Affiliation(s)
| | | | | | | | | | - Han Yu
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | | | | | - Oleg V. Kurnasov
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Andrei L. Osterman
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Grace K. Dy
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Alexey A. Komissarov
- I.V. Davydovsky Clinical City Hospital, Moscow, Russia
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | - Elena Vasilieva
- I.V. Davydovsky Clinical City Hospital, Moscow, Russia
- A.I. Yevdokimov Moscow State University of Medicine and Dentistry, Moscow, Russia
| | | | - Akiko Iwasaki
- Yale University, New Haven, Connecticut
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | | | - Takemasa Tsuji
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, Illinois
| | - Junko Matsuzaki
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, Illinois
| | - Kunle Odunsi
- University of Chicago Medicine Comprehensive Cancer Center, Chicago, Illinois
| | | | - Andrei V. Gudkov
- Genome Protection, Inc., Buffalo, New York
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| |
Collapse
|
10
|
Liu Y, Ma YH, Yang JW, Man JW, Wang HB, Li Y, Liang C, Cao JL, Chen SY, Li KP, Yang L. Rethinking neutrophil extracellular traps. Int Immunopharmacol 2023; 124:110834. [PMID: 37625368 DOI: 10.1016/j.intimp.2023.110834] [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: 05/17/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 08/27/2023]
Abstract
Neutrophils are a major subset of leukocytes in human circulating blood. In some circumstances, neutrophils release neutrophil extracellular traps (NETs). lnitially, NETs were considered to have a strong antibacterial capacity. However, currently, NETs have been shown to have a pivotal impact on various diseases. Different stimulators induce the production of different types of NETs, and their biological functions and modes of clearance do not appear to be the same. In this review, we will discuss several important issues related to NETs in order to better understand the relationship between NETs and diseases, as well as how to utilize the characteristics of NETs for disease treatment.
Collapse
Affiliation(s)
- Yi Liu
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Yu-Hua Ma
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Jian-Wei Yang
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Jiang-Wei Man
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Hua-Bin Wang
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Yi Li
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Cheng Liang
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Jin-Long Cao
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Si-Yu Chen
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Kun-Peng Li
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China
| | - Li Yang
- Department of Urology, The Second Hospital of Lanzhou University, Gansu Province Clinical Research Center for Urology, Second Clinical School Lanzhou University, China.
| |
Collapse
|
11
|
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: 3] [Impact Index Per Article: 3.0] [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
|
12
|
Wang D, Yang D, Yang L, Diao L, Zhang Y, Li Y, Wang H, Ren J, Cheng L, Tan Q, Zhang R, Han X, Zhang X, Wang B, Li D, Chen M, Hermjakob H, Li Y, LaBaer J, Zhou Z, Yu X. Human Autoantigen Atlas: Searching for the Hallmarks of Autoantigens. J Proteome Res 2023. [PMID: 37183442 DOI: 10.1021/acs.jproteome.2c00799] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Understanding autoimmunity to endogenous proteins is crucial in diagnosing and treating autoimmune diseases. In this work, we developed a user-friendly AAgAtlas portal (http://biokb.ncpsb.org.cn/aagatlas_portal/index.php#), which can be used to search for 8045 non-redundant autoantigens (AAgs) and 47 post-translationally modified AAgs against 1073 human diseases that are prioritized by a credential score developed by multisource evidence. Using AAgAtlas, the immunogenic properties of human AAgs was systematically elucidated according to their genetic, biophysical, cytological, expression profile, and evolutionary characteristics. The results indicated that human AAgs are evolutionally conserved in protein sequence and enriched in three hydrophilic and polar amino acid residues (K, D, and E) that are located at the protein surface. AAgs are enriched in proteins that are involved in nucleic acid binding, transferase, and the cytoskeleton. Genome, transcriptome, and proteome analyses further indicated that AAb production is associated with gene variance and abnormal protein expression related to the pathological activities of different tumors. Collectively, our data outlines the hallmarks of human AAgs that facilitate the understanding of humoral autoimmunity and the identification of biomarkers of human diseases.
Collapse
Affiliation(s)
- Dan Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Dong Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Liuhui Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Lihong Diao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuqi Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hongye Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jing Ren
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Linlin Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Qiaoyun Tan
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China
| | - Ran Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaohong Han
- Clinical Pharmacology Research Center, Peking Union Medical College Hospital, State Key Laboratory of Complex Severe and Rare Diseases, NMPA Key Laboratory for Clinical Research and Evaluation of Drug, Beijing Key Laboratory of Clinical PK & PD Investigation for Innovative Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xiaohan Zhang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
- College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Bingwei Wang
- College of Medicine and Integrated Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Dong Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Meng Chen
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Henning Hermjakob
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Yongzhe Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Joshua LaBaer
- The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Zhou Zhou
- Department of Laboratory Medicine, National Center for Cardiovascular Diseases and Fuwai Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100037, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| |
Collapse
|
13
|
Vinuesa CG, Grenov A, Kassiotis G. Innate virus-sensing pathways in B cell systemic autoimmunity. Science 2023; 380:478-484. [PMID: 37141353 DOI: 10.1126/science.adg6427] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Although all multicellular organisms have germ line-encoded innate receptors to sense pathogen-associated molecular patterns, vertebrates also evolved adaptive immunity based on somatically generated antigen receptors on B and T cells. Because randomly generated antigen receptors may also react with self-antigens, tolerance checkpoints operate to limit but not completely prevent autoimmunity. These two systems are intricately linked, with innate immunity playing an instrumental role in the induction of adaptive antiviral immunity. In this work, we review how inborn errors of innate immunity can instigate B cell autoimmunity. Increased nucleic acid sensing, often resulting from defects in metabolizing pathways or retroelement control, can break B cell tolerance and converge into TLR7-, cGAS-STING-, or MAVS-dominant signaling pathways. The resulting syndromes span a spectrum that ranges from chilblain and systemic lupus to severe interferonopathies.
Collapse
Affiliation(s)
- Carola G Vinuesa
- The Francis Crick Institute, London, UK
- China Centre for Personalised Immunology, Renji Hospital, Shanghai, China
| | | | - George Kassiotis
- The Francis Crick Institute, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| |
Collapse
|
14
|
Abstract
Our defenses against infection rely on the ability of the immune system to distinguish invading pathogens from self. This task is exceptionally challenging, if not seemingly impossible, in the case of retroviruses that have integrated almost seamlessly into the host. This review examines the limits of innate and adaptive immune responses elicited by endogenous retroviruses and other retroelements, the targets of immune recognition, and the consequences for host health and disease. Contrary to theoretical expectation, endogenous retroelements retain substantial immunogenicity, which manifests most profoundly when their epigenetic repression is compromised, contributing to autoinflammatory and autoimmune disease and age-related inflammation. Nevertheless, recent evidence suggests that regulated immune reactivity to endogenous retroelements is integral to immune system development and function, underpinning cancer immunosurveillance, resistance to infection, and responses to the microbiota. Elucidation of the interaction points with endogenous retroelements will therefore deepen our understanding of immune system function and contribution to disease.
Collapse
Affiliation(s)
- George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, United Kingdom;
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, United Kingdom
| |
Collapse
|
15
|
Daradoumis J, Ragonnaud E, Skandorff I, Nielsen KN, Bermejo AV, Andersson AM, Schroedel S, Thirion C, Neukirch L, Holst PJ. An Endogenous Retrovirus Vaccine Encoding an Envelope with a Mutated Immunosuppressive Domain in Combination with Anti-PD1 Treatment Eradicates Established Tumours in Mice. Viruses 2023; 15:v15040926. [PMID: 37112906 PMCID: PMC10141008 DOI: 10.3390/v15040926] [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: 02/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Endogenous retroviruses (ERVs) account for 8% of our genome, and, although they are usually silent in healthy tissues, they become reactivated and expressed in pathological conditions such as cancer. Several studies support a functional role of ERVs in tumour development and progression, specifically through their envelope (Env) protein, which contains a region described as an immunosuppressive domain (ISD). We have previously shown that targeting of the murine ERV (MelARV) Env using virus-like vaccine (VLV) technology, consisting of an adenoviral vector encoding virus-like particles (VLPs), induces protection against small tumours in mice. Here, we investigate the potency and efficacy of a novel MelARV VLV with a mutated ISD (ISDmut) that can modify the properties of the adenoviral vaccine-encoded Env protein. We show that the modification of the vaccine's ISD significantly enhanced T-cell immunogenicity in both prime and prime-boost vaccination regimens. The modified VLV in combination with an α-PD1 checkpoint inhibitor (CPI) exhibited excellent curative efficacy against large established colorectal CT26 tumours in mice. Furthermore, only ISDmut-vaccinated mice that survived CT26 challenge were additionally protected against rechallenge with a triple-negative breast cancer cell line (4T1), showing that our modified VLV provides cross-protection against different tumour types expressing ERV-derived antigens. We envision that translating these findings and technology into human ERVs (HERVs) could provide new treatment opportunities for cancer patients with unmet medical needs.
Collapse
Affiliation(s)
- Joana Daradoumis
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Emeline Ragonnaud
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Isabella Skandorff
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | - Amaia Vergara Bermejo
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Anne-Marie Andersson
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | | | | | - Lasse Neukirch
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
- Department of Biomedical Sciences, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Peter Johannes Holst
- Department of Immunology and Microbiology, The Panum Institute, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
- InProTher, Bioinnovation Institute, COBIS, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| |
Collapse
|
16
|
Ng KW, Boumelha J, Enfield KSS, Almagro J, Cha H, Pich O, Karasaki T, Moore DA, Salgado R, Sivakumar M, Young G, Molina-Arcas M, de Carné Trécesson S, Anastasiou P, Fendler A, Au L, Shepherd STC, Martínez-Ruiz C, Puttick C, Black JRM, Watkins TBK, Kim H, Shim S, Faulkner N, Attig J, Veeriah S, Magno N, Ward S, Frankell AM, Al Bakir M, Lim EL, Hill MS, Wilson GA, Cook DE, Birkbak NJ, Behrens A, Yousaf N, Popat S, Hackshaw A, Hiley CT, Litchfield K, McGranahan N, Jamal-Hanjani M, Larkin J, Lee SH, Turajlic S, Swanton C, Downward J, Kassiotis G. Antibodies against endogenous retroviruses promote lung cancer immunotherapy. Nature 2023; 616:563-573. [PMID: 37046094 PMCID: PMC10115647 DOI: 10.1038/s41586-023-05771-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 01/30/2023] [Indexed: 04/14/2023]
Abstract
B cells are frequently found in the margins of solid tumours as organized follicles in ectopic lymphoid organs called tertiary lymphoid structures (TLS)1,2. Although TLS have been found to correlate with improved patient survival and response to immune checkpoint blockade (ICB), the underlying mechanisms of this association remain elusive1,2. Here we investigate lung-resident B cell responses in patients from the TRACERx 421 (Tracking Non-Small-Cell Lung Cancer Evolution Through Therapy) and other lung cancer cohorts, and in a recently established immunogenic mouse model for lung adenocarcinoma3. We find that both human and mouse lung adenocarcinomas elicit local germinal centre responses and tumour-binding antibodies, and further identify endogenous retrovirus (ERV) envelope glycoproteins as a dominant anti-tumour antibody target. ERV-targeting B cell responses are amplified by ICB in both humans and mice, and by targeted inhibition of KRAS(G12C) in the mouse model. ERV-reactive antibodies exert anti-tumour activity that extends survival in the mouse model, and ERV expression predicts the outcome of ICB in human lung adenocarcinoma. Finally, we find that effective immunotherapy in the mouse model requires CXCL13-dependent TLS formation. Conversely, therapeutic CXCL13 treatment potentiates anti-tumour immunity and synergizes with ICB. Our findings provide a possible mechanistic basis for the association of TLS with immunotherapy response.
Collapse
Affiliation(s)
- Kevin W Ng
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Jesse Boumelha
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK
| | - Katey S S Enfield
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Jorge Almagro
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
| | - Hongui Cha
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Oriol Pich
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Takahiro Karasaki
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
| | - David A Moore
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Cellular Pathology, University College London Hospitals, London, UK
| | - Roberto Salgado
- Department of Pathology, ZAS Hospitals, Antwerp, Belgium
- Division of Research, Peter MacCallum Cancer Centre, Melbourne, Queensland, Australia
| | - Monica Sivakumar
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - George Young
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- Bioinformatics and Biostatistics Facility, The Francis Crick Institute, London, UK
| | | | | | | | - Annika Fendler
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Lewis Au
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Scott T C Shepherd
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
| | - Carlos Martínez-Ruiz
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Clare Puttick
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - James R M Black
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Hyemin Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seohee Shim
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Nikhil Faulkner
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Jan Attig
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK
| | - Selvaraju Veeriah
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Neil Magno
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Sophia Ward
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Advanced Sequencing Facility, The Francis Crick Institute, London, UK
| | - Alexander M Frankell
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mark S Hill
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Daniel E Cook
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Axel Behrens
- Adult Stem Cell Laboratory, The Francis Crick Institute, London, UK
- Cancer Stem Cell Laboratory, Institute of Cancer Research, London, UK
- Division of Cancer, Department of Surgery and Cancer, Imperial College, London, UK
- CRUK Convergence Science Centre, Imperial College, London, UK
| | - Nadia Yousaf
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Lung Unit, The Royal Marsden Hospital, London, UK
| | - Sanjay Popat
- Lung Unit, The Royal Marsden Hospital, London, UK
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Allan Hackshaw
- Cancer Research UK and University College London Cancer Trials Centre, London, UK
| | - Crispin T Hiley
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Kevin Litchfield
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Tumour Immunogenomics and Immunosurveillance Laboratory, University College London Cancer Institute, London, UK
| | - Nicholas McGranahan
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Genome Evolution Research Group, Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Metastasis Laboratory, University College London Cancer Institute, London, UK
- Department of Oncology, University College London Hospitals, London, UK
| | - James Larkin
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Se-Hoon Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute of Health Sciences and Technology, Sungkyunkwan University, Seoul, Republic of Korea
| | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Units, The Royal Marsden Hospital, London, UK
- Melanoma and Kidney Cancer Team, The Institute of Cancer Research, London, UK
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Department of Oncology, University College London Hospitals, London, UK.
| | - Julian Downward
- Oncogene Biology Laboratory, The Francis Crick Institute, London, UK.
| | - George Kassiotis
- Retroviral Immunology Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
| |
Collapse
|
17
|
Russ E, Mikhalkevich N, Iordanskiy S. Expression of Human Endogenous Retrovirus Group K (HERV-K) HML-2 Correlates with Immune Activation of Macrophages and Type I Interferon Response. Microbiol Spectr 2023; 11:e0443822. [PMID: 36861980 PMCID: PMC10100713 DOI: 10.1128/spectrum.04438-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/30/2023] [Indexed: 03/03/2023] Open
Abstract
Human endogenous retroviruses (HERVs) comprise about 8.3% of the human genome and are capable of producing RNA molecules that can be sensed by pattern recognition receptors, leading to the activation of innate immune response pathways. The HERV-K (HML-2) subgroup is the youngest HERV clade with the highest degree of coding competence. Its expression is associated with inflammation-related diseases. However, the precise HML-2 loci, stimuli, and signaling pathways involved in these associations are not well understood or defined. To elucidate HML-2 expression on a locus-specific level, we used the retroelement sequencing tools TEcount and Telescope to analyze publicly available transcriptome sequencing (RNA-seq) and chromatin immunoprecipitation (ChIP) sequencing data sets of macrophages treated with a wide range of agonists. We found that macrophage polarization significantly correlates with modulation of the expression of specific HML-2 proviral loci. Further analysis demonstrated that the provirus HERV-K102, located in an intergenic region of locus 1q22, constituted the majority of the HML-2 derived transcripts following pro-inflammatory (M1) polarization and was upregulated explicitly in response to interferon gamma (IFN-γ) signaling. We found that signal transducer and activator of transcription 1 and interferon regulatory factor 1 interact with a solo long terminal repeat (LTR) located upstream of HERV-K102, termed LTR12F, following IFN-γ signaling. Using reporter constructs, we demonstrated that LTR12F is critical for HERV-K102 upregulation by IFN-γ. In THP1-derived macrophages, knockdown of HML-2 or knockout of MAVS, an adaptor of RNA-sensing pathways, significantly downregulated genes containing interferon-stimulated response elements (ISREs) in their promoters, suggesting an intermediate role of HERV-K102 in the switch from IFN-γ signaling to the activation of type I interferon expression and, therefore, in a positive feedback loop to enhance pro-inflammatory signaling. IMPORTANCE The human endogenous retrovirus group K subgroup, HML-2, is known to be elevated in a long list of inflammation-associated diseases. However, a clear mechanism for HML-2 upregulation in response to inflammation has not been defined. In this study, we identify a provirus of the HML-2 subgroup, HERV-K102, which is significantly upregulated and constitutes the majority of the HML-2 derived transcripts in response to pro-inflammatory activation of macrophages. Moreover, we identify the mechanism of HERV-K102 upregulation and demonstrate that HML-2 expression enhances interferon-stimulated response element activation. We also demonstrate that this provirus is elevated in vivo and correlates with interferon gamma signaling activity in cutaneous leishmaniasis patients. This study provides key insights into the HML-2 subgroup and suggests that it may participate in enhancing pro-inflammatory signaling in macrophages and probably other immune cells.
Collapse
Affiliation(s)
- Eric Russ
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
- Graduate Program of Cellular and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Natallia Mikhalkevich
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland, USA
| | - Sergey Iordanskiy
- Department of Pharmacology & Molecular Therapeutics, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
- Armed Forces Radiobiology Research Institute, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| |
Collapse
|
18
|
Gómez-Bañuelos E, Fava A, Andrade F. An update on autoantibodies in systemic lupus erythematosus. Curr Opin Rheumatol 2023; 35:61-67. [PMID: 36695053 PMCID: PMC9881844 DOI: 10.1097/bor.0000000000000922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
PURPOSE OF REVIEW Autoantibodies are cornerstone biomarkers in systemic lupus erythematosus (SLE), an autoimmune disease characterized by autoantibody-mediated tissue damage. Autoantibodies can inform about disease susceptibility, clinical course, outcomes and the cause of SLE. Identifying pathogenic autoantibodies in SLE, however, remains a significant challenge. This review summarizes recent advances in the field of autoantibodies in SLE. RECENT FINDINGS High-throughput technologies and innovative hypothesis have been applied to identify autoantibodies linked to pathogenic pathways in SLE. This work has led to the discovery of functional autoantibodies targeting key components is SLE pathogenesis (e.g. DNase1L3, cytokines, extracellular immunoregulatory receptors), as well as the identification of endogenous retroelements and interferon-induced proteins as sources of autoantigens in SLE. Others have reinvigorated the study of mitochondria, which has antigenic parallels with bacteria, as a trigger of autoantibodies in SLE, and identified faecal IgA to nuclear antigens as potential biomarkers linking gut permeability and microbial translocation in SLE pathogenesis. Recent studies showed that levels of autoantibodies against dsDNA, C1q, chromatin, Sm and ribosomal P may serve as biomarkers of proliferative lupus nephritis, and identified novel autoantibodies to several unique species of Ro52 overexpressed by SLE neutrophils. SUMMARY Autoantibodies hold promise as biomarkers of pathogenic mechanisms in SLE.
Collapse
Affiliation(s)
- Eduardo Gómez-Bañuelos
- Division of Rheumatology, The Johns Hopkins University School of Medicine. Baltimore, MD, 21224. U.S.A
| | - Andrea Fava
- Division of Rheumatology, The Johns Hopkins University School of Medicine. Baltimore, MD, 21224. U.S.A
| | - Felipe Andrade
- Division of Rheumatology, The Johns Hopkins University School of Medicine. Baltimore, MD, 21224. U.S.A
| |
Collapse
|
19
|
Endogenous Retroviruses as Modulators of Innate Immunity. Pathogens 2023; 12:pathogens12020162. [PMID: 36839434 PMCID: PMC9963469 DOI: 10.3390/pathogens12020162] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/11/2023] [Accepted: 01/16/2023] [Indexed: 01/21/2023] Open
Abstract
Endogenous retroviruses (ERVs), or LTR retrotransposons, are a class of transposable elements that are highly represented in mammalian genomes. Human ERVs (HERVs) make up roughly 8.3% of the genome and over the course of evolution, HERV elements underwent positive selection and accrued mutations that rendered them non-infectious; thereby, the genome could co-opt them into constructive roles with important biological functions. In the past two decades, with the help of advances in sequencing technology, ERVs are increasingly considered to be important components of the innate immune response. While typically silenced, expression of HERVs can be induced in response to traumatic, toxic, or infection-related stress, leading to a buildup of viral transcripts and under certain circumstances, proteins, including functionally active reverse transcriptase and viral envelopes. The biological activity of HERVs in the context of the innate immune response can be based on the functional effect of four major viral components: (1) HERV LTRs, (2) HERV-derived RNAs, (3) HERV-derived RNA:DNA duplexes and cDNA, and (4) HERV-derived proteins and ribonucleoprotein complexes. In this review, we will discuss the implications of HERVs in all four contexts in relation to innate immunity and their association with various pathological disease states.
Collapse
|
20
|
Endogenous retroelements as alarms for disruptions to cellular homeostasis. Trends Cancer 2023; 9:55-68. [PMID: 36216729 DOI: 10.1016/j.trecan.2022.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/28/2022] [Accepted: 09/07/2022] [Indexed: 11/05/2022]
Abstract
Endogenous retroelements are DNA sequences which can duplicate and move to new locations in the genome. Actively moving endogenous retroelements can be disruptive to the host, and their expression is therefore often repressed. Interestingly, drugs that disrupt the repression of endogenous retroelements show promise for treating cancer. Expressed endogenous retroelements can activate innate immune receptors that activate the antiviral response, potentially leading to the death of cancer cells. We discuss disruptions to cellular processes which can lead to activation of the antiviral state from endogenous retroelements, and present the 'fire alarm hypothesis', where we argue that endogenous retroelements act as alarms for disruptions to these cellular processes. Furthermore, we discuss the properties of endogenous retroelements which make them suitable as alarms.
Collapse
|
21
|
Rangel SC, da Silva MD, da Silva AL, dos Santos JDMB, Neves LM, Pedrosa A, Rodrigues FM, Trettel CDS, Furtado GE, de Barros MP, Bachi ALL, Romano CM, Nali LHDS. Human endogenous retroviruses and the inflammatory response: A vicious circle associated with health and illness. Front Immunol 2022; 13:1057791. [PMID: 36518758 PMCID: PMC9744114 DOI: 10.3389/fimmu.2022.1057791] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 11/24/2022] Open
Abstract
Human Endogenous Retroviruses (HERVs) are derived from ancient exogenous retroviral infections that have infected our ancestors' germline cells, underwent endogenization process, and were passed throughout the generations by retrotransposition and hereditary transmission. HERVs comprise 8% of the human genome and are critical for several physiological activities. Yet, HERVs reactivation is involved in pathological process as cancer and autoimmune diseases. In this review, we summarize the multiple aspects of HERVs' role within the human genome, as well as virological and molecular aspects, and their fusogenic property. We also discuss possibilities of how the HERVs are possibly transactivated and participate in modulating the inflammatory response in health conditions. An update on their role in several autoimmune, inflammatory, and aging-related diseases is also presented.
Collapse
Affiliation(s)
- Sara Coelho Rangel
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | | | - Amanda Lopes da Silva
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
| | | | - Lucas Melo Neves
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Ana Pedrosa
- CNC-Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, (3004-504), Coimbra, Portugal
| | | | - Caio dos Santos Trettel
- Interdisciplinary Program in Health Sciences, Institute of Physical Activity Sciences and Sports (ICAFE), Cruzeiro do Sul University, São Paulo, Brazil
| | - Guilherme Eustáquio Furtado
- Polytechnic Institute of Coimbra, Applied Research Institute, Rua da Misericórdia, Lagar dos Cortiços – S. Martinho do Bispo, Coimbra, Portugal
| | - Marcelo Paes de Barros
- Interdisciplinary Program in Health Sciences, Institute of Physical Activity Sciences and Sports (ICAFE), Cruzeiro do Sul University, São Paulo, Brazil
| | - André Luis Lacerda Bachi
- UNISA Research Center, Universidade Santo Amaro, Post-Graduation in Health Sciences, São Paulo, Brazil
| | - Camila Malta Romano
- Laboratório de Virologia, Instituto de Medicina Tropical de São Paulo, Universidade de São Paulo, São Paulo, Brazil
- Hospital das Clínicas HCFMUSP (LIM52), Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | | |
Collapse
|
22
|
Takahashi T, Stoiljkovic M, Song E, Gao XB, Yasumoto Y, Kudo E, Carvalho F, Kong Y, Park A, Shanabrough M, Szigeti-Buck K, Liu ZW, Kristant A, Zhang Y, Sulkowski P, Glazer PM, Kaczmarek LK, Horvath TL, Iwasaki A. LINE-1 activation in the cerebellum drives ataxia. Neuron 2022; 110:3278-3287.e8. [PMID: 36070749 PMCID: PMC9588660 DOI: 10.1016/j.neuron.2022.08.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 06/29/2022] [Accepted: 08/05/2022] [Indexed: 02/06/2023]
Abstract
Dysregulation of long interspersed nuclear element 1 (LINE-1, L1), a dominant class of transposable elements in the human genome, has been linked to neurodegenerative diseases, but whether elevated L1 expression is sufficient to cause neurodegeneration has not been directly tested. Here, we show that the cerebellar expression of L1 is significantly elevated in ataxia telangiectasia patients and strongly anti-correlated with the expression of epigenetic silencers. To examine the role of L1 in the disease etiology, we developed an approach for direct targeting of the L1 promoter for overexpression in mice. We demonstrated that L1 activation in the cerebellum led to Purkinje cell dysfunctions and degeneration and was sufficient to cause ataxia. Treatment with a nucleoside reverse transcriptase inhibitor blunted ataxia progression by reducing DNA damage, attenuating gliosis, and reversing deficits of molecular regulators for calcium homeostasis in Purkinje cells. Our study provides the first direct evidence that L1 activation can drive neurodegeneration.
Collapse
Affiliation(s)
- Takehiro Takahashi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Milan Stoiljkovic
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Xiao-Bing Gao
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yuki Yasumoto
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Eriko Kudo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Fernando Carvalho
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Yong Kong
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Annsea Park
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Marya Shanabrough
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Klara Szigeti-Buck
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Zhong-Wu Liu
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Ashley Kristant
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Yalan Zhang
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Parker Sulkowski
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Peter M Glazer
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Leonard K Kaczmarek
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Tamas L Horvath
- Department of Comparative Medicine and Yale Center for Molecular and Systems Metabolism, Yale University School of Medicine, New Haven, CT 06510, USA.
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| |
Collapse
|
23
|
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
|
24
|
Lu-Culligan A, Tabachnikova A, Pérez-Then E, Tokuyama M, Lee HJ, Lucas C, Silva Monteiro V, Miric M, Brache V, Cochon L, Muenker MC, Mohanty S, Huang J, Kang I, Dela Cruz C, Farhadian S, Campbell M, Yildirim I, Shaw AC, Ma S, Vermund SH, Ko AI, Omer SB, Iwasaki A. No evidence of fetal defects or anti-syncytin-1 antibody induction following COVID-19 mRNA vaccination. PLoS Biol 2022; 20:e3001506. [PMID: 35609110 PMCID: PMC9129011 DOI: 10.1371/journal.pbio.3001506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/05/2022] [Indexed: 12/13/2022] Open
Abstract
The impact of Coronavirus Disease 2019 (COVID-19) mRNA vaccination on pregnancy and fertility has become a major topic of public interest. We investigated 2 of the most widely propagated claims to determine (1) whether COVID-19 mRNA vaccination of mice during early pregnancy is associated with an increased incidence of birth defects or growth abnormalities; and (2) whether COVID-19 mRNA-vaccinated human volunteers exhibit elevated levels of antibodies to the human placental protein syncytin-1. Using a mouse model, we found that intramuscular COVID-19 mRNA vaccination during early pregnancy at gestational age E7.5 did not lead to differences in fetal size by crown-rump length or weight at term, nor did we observe any gross birth defects. In contrast, injection of the TLR3 agonist and double-stranded RNA mimic polyinosinic-polycytidylic acid, or poly(I:C), impacted growth in utero leading to reduced fetal size. No overt maternal illness following either vaccination or poly(I:C) exposure was observed. We also found that term fetuses from these murine pregnancies vaccinated prior to the formation of the definitive placenta exhibit high circulating levels of anti-spike and anti-receptor-binding domain (anti-RBD) antibodies to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) consistent with maternal antibody status, indicating transplacental transfer in the later stages of pregnancy after early immunization. Finally, we did not detect increased levels of circulating anti-syncytin-1 antibodies in a cohort of COVID-19 vaccinated adults compared to unvaccinated adults by ELISA. Our findings contradict popular claims associating COVID-19 mRNA vaccination with infertility and adverse neonatal outcomes.
Collapse
Affiliation(s)
- Alice Lu-Culligan
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Alexandra Tabachnikova
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | | | - Maria Tokuyama
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, Canada
| | - Hannah J. Lee
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Carolina Lucas
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Valter Silva Monteiro
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Marija Miric
- Two Oceans in Health, Santo Domingo, Dominican Republic
| | - Vivian Brache
- Biomedical Research Department, Profamilia, Santo Domingo, Dominican Republic
| | - Leila Cochon
- Biomedical Research Department, Profamilia, Santo Domingo, Dominican Republic
| | - M. Catherine Muenker
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Subhasis Mohanty
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Jiefang Huang
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Insoo Kang
- Section of Rheumatology, Allergy and Immunology, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Charles Dela Cruz
- Section of Pulmonary and Critical Care Medicine, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Shelli Farhadian
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Melissa Campbell
- Section of Pediatric Infectious Diseases, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Inci Yildirim
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Section of Pediatric Infectious Diseases, Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Albert C. Shaw
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Shuangge Ma
- Department of Biostatistics, Yale University, New Haven, Connecticut, United States of America
| | - Sten H. Vermund
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Saad B. Omer
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Section of Infectious Diseases, Department of Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Akiko Iwasaki
- Department of Immunobiology, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular and Developmental Biology, New Haven, Connecticut, United States of America
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
| |
Collapse
|
25
|
Müller MD, Holst PJ, Nielsen KN. A Systematic Review of Expression and Immunogenicity of Human Endogenous Retroviral Proteins in Cancer and Discussion of Therapeutic Approaches. Int J Mol Sci 2022; 23:1330. [PMID: 35163254 PMCID: PMC8836156 DOI: 10.3390/ijms23031330] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections that have become fixed in the human genome. While HERV genes are typically silenced in healthy somatic cells, there are numerous reports of HERV transcription and translation across a wide spectrum of cancers, while T and B cell responses against HERV proteins have been detected in cancer patients. This review systematically categorizes the published evidence on the expression of and adaptive immune response against specific HERVs in distinct cancer types. A systematic literature search was performed using Medical Search Headings (MeSH) in the PubMed/Medline database. Papers were included if they described the translational activity of HERVs. We present multiple tables that pair the protein expression of specific HERVs and cancer types with information on the quality of the evidence. We find that HERV-K is the most investigated HERV. HERV-W (syncytin-1) is the second-most investigated, while other HERVs have received less attention. From a therapeutic perspective, HERV-K and HERV-E are the only HERVs with experimental demonstration of effective targeted therapies, but unspecific approaches using antiviral and demethylating agents in combination with chemo- and immunotherapies have also been investigated.
Collapse
Affiliation(s)
- Mikkel Dons Müller
- Institute of Immunology and Microbiology, University of Copenhagen, Blegdamsvej 3, 2200 Copenhagen N, Denmark;
| | | | | |
Collapse
|
26
|
Zhang S, Zhan L, Li X, Yang Z, Luo Y, Zhao H. Preclinical and clinical progress for HDAC as a putative target for epigenetic remodeling and functionality of immune cells. Int J Biol Sci 2021; 17:3381-3400. [PMID: 34512154 PMCID: PMC8416716 DOI: 10.7150/ijbs.62001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 07/26/2021] [Indexed: 11/17/2022] Open
Abstract
Genetic changes are difficult to reverse; thus, epigenetic aberrations, including changes in DNA methylation, histone modifications, and noncoding RNAs, with potential reversibility, have attracted attention as pharmaceutical targets. The current paradigm is that histone deacetylases (HDACs) regulate gene expression via deacetylation of histone and nonhistone proteins or by forming corepressor complexes with transcription factors. The emergence of epigenetic tools related to HDACs can be used as diagnostic and therapeutic markers. HDAC inhibitors that block specific or a series of HDACs have proven to be a powerful therapeutic treatment for immune-related diseases. Here, we summarize the various roles of HDACs and HDAC inhibitors in the development and function of innate and adaptive immune cells and their implications for various diseases and therapies.
Collapse
Affiliation(s)
- Sijia Zhang
- Institute of Cerebrovascular Disease Research, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Lingjun Zhan
- Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences, Beijing, China
| | - Xue Li
- Institute of Cerebrovascular Disease Research, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Zhenhong Yang
- Institute of Cerebrovascular Disease Research, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Yumin Luo
- Institute of Cerebrovascular Disease Research, Xuanwu Hospital of Capital Medical University, Beijing, China.,Beijing Geriatric Medical Research Center and National Clinical Research Center for Geriatric Disorders, Beijing, China.,Beijing Institute for Brain Disorders, Capital Medical University, Beijing, China
| | - Haiping Zhao
- Institute of Cerebrovascular Disease Research, Xuanwu Hospital of Capital Medical University, Beijing, China.,Beijing Geriatric Medical Research Center and National Clinical Research Center for Geriatric Disorders, Beijing, China
| |
Collapse
|