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Zhou T, Pan J, Yan C, Yuan J, Song H, Han Y. Unveiling shared biomarkers and therapeutic targets between systemic lupus erythematosus and heart failure through bioinformatics analysis. Front Med (Lausanne) 2024; 11:1402010. [PMID: 38912340 PMCID: PMC11190381 DOI: 10.3389/fmed.2024.1402010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Accepted: 05/21/2024] [Indexed: 06/25/2024] Open
Abstract
Background Systemic lupus erythematosus (SLE) is frequently accompanied by various complications, with cardiovascular diseases being particularly concerning due to their high mortality rate. Although there is clinical evidence suggesting a potential correlation between SLE and heart failure (HF), the underlying shared mechanism is not fully understood. Therefore, it is imperative to explore the potential mechanisms and shared therapeutic targets between SLE and HF. Methods The SLE and HF datasets were downloaded from the NCBI Gene Expression Omnibus database. Differentially expressed genes (DEGs) in both SLE and HF were performed using "limma" R package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genes (KEGG) analyses were conducted to analyze the enriched functions and pathways of DEGs in both SLE and HF datasets. Protein-Protein Interaction network (PPI) and the molecular complex detection (MCODE) plugins in the Cytoscape software were performed to identify the shared hub genes between SLE and HF datasets. R package "limma" was utilized to validate the expression of hub genes based on SLE (GSE122459) and HF (GSE196656) datasets. CIBERSORT algorithm was utilized to analyze the immune cell infiltration of SLE and HF samples based on SLE (GSE112087) and HF (GSE116250) datasets. A weighted gene co-expression network analysis (WGCNA) network was established to further validate the hub genes based on HF dataset (GSE116250). Molecular biology techniques were conducted to validate the hub genes. Results 999 shared DGEs were identified between SLE and HF datasets, which were mainly enriched in pathways related to Th17 cell differentiation. 5 shared hub genes among the common DGEs between SLE and HF datasets were screened and validated, including HSP90AB1, NEDD8, RPLP0, UBB, and UBC. Additionally, 5 hub genes were identified in the central part of the MEbrown module, showing the strongest correlation with dilated cardiomyopathy. HSP90AB1 and UBC were upregulated in failing hearts compared to non-failing hearts, while UBB, NEDD8, and RPLP0 did not show significant changes. Conclusion HSP90AB1 and UBC are closely related to the co-pathogenesis of SLE and HF mediated by immune cell infiltration. They serve as promising molecular markers and potential therapeutic targets for the treatment of SLE combined with HF.
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Affiliation(s)
- Ting Zhou
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Jing Pan
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Chenghui Yan
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Jing Yuan
- Department of Cardiology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haixu Song
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
| | - Yaling Han
- State Key Laboratory of Frigid Zone Cardiovascular Disease, Cardiovascular Research Institute and Department of Cardiology, General Hospital of Northern Theater Command, Shenyang, China
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2
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Duarte RRR, Pain O, Bendall ML, de Mulder Rougvie M, Marston JL, Selvackadunco S, Troakes C, Leung SK, Bamford RA, Mill J, O'Reilly PF, Srivastava DP, Nixon DF, Powell TR. Integrating human endogenous retroviruses into transcriptome-wide association studies highlights novel risk factors for major psychiatric conditions. Nat Commun 2024; 15:3803. [PMID: 38778015 PMCID: PMC11111684 DOI: 10.1038/s41467-024-48153-z] [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: 04/05/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are repetitive elements previously implicated in major psychiatric conditions, but their role in aetiology remains unclear. Here, we perform specialised transcriptome-wide association studies that consider HERV expression quantified to precise genomic locations, using RNA sequencing and genetic data from 792 post-mortem brain samples. In Europeans, we identify 1238 HERVs with expression regulated in cis, of which 26 represent expression signals associated with psychiatric disorders, with ten being conditionally independent from neighbouring expression signals. Of these, five are additionally significant in fine-mapping analyses and thus are considered high confidence risk HERVs. These include two HERV expression signatures specific to schizophrenia risk, one shared between schizophrenia and bipolar disorder, and one specific to major depressive disorder. No robust signatures are identified for autism spectrum conditions or attention deficit hyperactivity disorder in Europeans, or for any psychiatric trait in other ancestries, although this is likely a result of relatively limited statistical power. Ultimately, our study highlights extensive HERV expression and regulation in the adult cortex, including in association with psychiatric disorder risk, therefore providing a rationale for exploring neurological HERV expression in complex neuropsychiatric traits.
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Affiliation(s)
- Rodrigo R R Duarte
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA.
| | - Oliver Pain
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Matthew L Bendall
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | | | - Jez L Marston
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Sashika Selvackadunco
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC London Neurodegenerative Diseases Brain Bank, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Szi Kay Leung
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rosemary A Bamford
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Paul F O'Reilly
- Department of Genetics and Genomic Sciences, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Deepak P Srivastava
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Douglas F Nixon
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA
- Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Timothy R Powell
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
- Division of Infectious Diseases, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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3
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Guo X, Zhao Y, You F. Identification and characterization of endogenous retroviruses upon SARS-CoV-2 infection. Front Immunol 2024; 15:1294020. [PMID: 38646531 PMCID: PMC11026653 DOI: 10.3389/fimmu.2024.1294020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 03/14/2024] [Indexed: 04/23/2024] Open
Abstract
Endogenous retroviruses (ERVs) derived from the long terminal repeat (LTR) family of transposons constitute a significant portion of the mammalian genome, with origins tracing back to ancient viral infections. Despite comprising approximately 8% of the human genome, the specific role of ERVs in the pathogenesis of COVID-19 remains unclear. In this study, we conducted a genome-wide identification of ERVs in human peripheral blood mononuclear cells (hPBMCs) and primary lung epithelial cells from monkeys and mice, both infected and uninfected with SARS-CoV-2. We identified 405, 283, and 206 significantly up-regulated transposable elements (TEs) in hPBMCs, monkeys, and mice, respectively. This included 254, 119, 68, and 28 ERVs found in hPBMCs from severe and mild COVID-19 patients, monkeys, and transgenic mice expressing the human ACE2 receptor (hACE2) and infected with SARS-CoV-2. Furthermore, analysis using the Genomic Regions Enrichment of Annotations Tool (GREAT) revealed certain parental genomic sequences of these up-regulated ERVs in COVID-19 patients may be involved in various biological processes, including histone modification and viral replication. Of particular interest, we identified 210 ERVs specifically up-regulated in the severe COVID-19 group. The genes associated with these differentially expressed ERVs were enriched in processes such as immune response activation and histone modification. HERV1_I-int: ERV1:LTR and LTR7Y: ERV1:LTR were highlighted as potential biomarkers for evaluating the severity of COVID-19. Additionally, validation of our findings using RT-qPCR in Bone Marrow-Derived Macrophages (BMDMs) from mice infected by HSV-1 and VSV provided further support to our results. This study offers insights into the expression patterns and potential roles of ERVs following viral infection, providing a valuable resource for future studies on ERVs and their interaction with SARS-CoV-2.
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Dopkins N, Nixon DF. Activation of human endogenous retroviruses and its physiological consequences. Nat Rev Mol Cell Biol 2024; 25:212-222. [PMID: 37872387 DOI: 10.1038/s41580-023-00674-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Human endogenous retroviruses (HERVs) are abundant sequences that persist within the human genome as remnants of ancient retroviral infections. These sequences became fixed and accumulate mutations or deletions over time. HERVs have affected human evolution and physiology by providing a unique repertoire of coding and non-coding sequences to the genome. In healthy individuals, HERVs participate in immune responses, formation of syncytiotrophoblasts and cell-fate specification. In this Review, we discuss how endogenized retroviral motifs and regulatory sequences have been co-opted into human physiology and how they are tightly regulated. Infections and mutations can derail this regulation, leading to differential HERV expression, which may contribute to pathologies including neurodegeneration, pathological inflammation and oncogenesis. Emerging evidence demonstrates that HERVs are crucial to human health and represent an understudied facet of many diseases, and we therefore argue that investigating their fundamental properties could improve existing therapies and help develop novel therapeutic strategies.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
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5
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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.
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Affiliation(s)
- Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University
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6
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Link VM, Subramanian P, Cheung F, Han KL, Stacy A, Chi L, Sellers BA, Koroleva G, Courville AB, Mistry S, Burns A, Apps R, Hall KD, Belkaid Y. Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans. Nat Med 2024; 30:560-572. [PMID: 38291301 PMCID: PMC10878979 DOI: 10.1038/s41591-023-02761-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 12/11/2023] [Indexed: 02/01/2024]
Abstract
Nutrition has broad impacts on all physiological processes. However, how nutrition affects human immunity remains largely unknown. Here we explored the impact of a dietary intervention on both immunity and the microbiota by performing a post hoc analysis of a clinical trial in which each of the 20 participants sequentially consumed vegan or ketogenic diets for 2 weeks ( NCT03878108 ). Using a multiomics approach including multidimensional flow cytometry, transcriptomic, proteomic, metabolomic and metagenomic datasets, we assessed the impact of each diet, and dietary switch, on host immunity and the microbiota. Our data revealed that overall, a ketogenic diet was associated with a significant upregulation of pathways and enrichment in cells associated with the adaptive immune system. In contrast, a vegan diet had a significant impact on the innate immune system, including upregulation of pathways associated with antiviral immunity. Both diets significantly and differentially impacted the microbiome and host-associated amino acid metabolism, with a strong downregulation of most microbial pathways following ketogenic diet compared with baseline and vegan diet. Despite the diversity of participants, we also observed a tightly connected network between datasets driven by compounds associated with amino acids, lipids and the immune system. Collectively, this work demonstrates that in diverse participants 2 weeks of controlled dietary intervention is sufficient to significantly and divergently impact host immunity, which could have implications for precision nutritional interventions. ClinicalTrials.gov registration: NCT03878108 .
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Affiliation(s)
- Verena M Link
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA.
| | - Poorani Subramanian
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Foo Cheung
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Kyu Lee Han
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
- Center for Cellular Engineering, Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, USA
| | - Apollo Stacy
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Liang Chi
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Brian A Sellers
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Galina Koroleva
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Amber B Courville
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shreni Mistry
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew Burns
- NIAID Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Richard Apps
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA
| | - Kevin D Hall
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| | - Yasmine Belkaid
- Metaorganism Immunity Section, Laboratory of Host Immunity and Microbiome, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
- NIH Center for Human Immunology, National Institutes of Health, Bethesda, MD, USA.
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7
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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.
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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.)
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8
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Ali MJ. Fungal microbiome (mycobiome) and virome of the lacrimal sac in patients with PANDO: the lacriome paper 5. Br J Ophthalmol 2024; 108:317-322. [PMID: 36270766 DOI: 10.1136/bjo-2022-322433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/12/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE To study the fungal microbiome (mycobiome) and the virome of the lacrimal sacs in patients with primary acquired nasolacrimal duct obstruction (PANDO). METHODS A prospective study was performed on 10 consecutive samples of the lacrimal sac contents obtained from patients with PANDO. The samples were obtained from the lacrimal sacs under endoscopy guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform (NOVASEQ 6000). The fungal internal transcript spacer analysis was performed using the PIPITS v2.7 . The viral taxonomy profiling was performed using Kraken2 against the virus database. RESULTS The taxonomic hit distribution across the lacrimal sac samples showed rich fungal diversity (4 phyla, 12 classed, 21 families and 26 genera). The major phyla were Ascomycota and Basidiomycota, and the key genera identified were Alternaria, Hyphopichia, Malassezia, Aspergillus and Epicoccum. The virome analysis identified 13 phyla, 15 classes and 27 families. The viruses were commonly from the families Poxviridae, Retroviridae, Siphoviridae and Myoviridae, Poxviridae being the most prevalent family. The BeAn 58058 virus, a member of the Poxviridae family, was the most abundant in all the samples. CONCLUSION The present study is the first whole metagenome sequencing exclusively of the fungal microbiome and virome from the lacrimal sacs of patients with PANDO. The lacrimal sacs harbour diverse fungal and viral communities with distinct ecosystem dynamics. Further studies of their functions and interactions with the hosts would provide valuable insights.
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Affiliation(s)
- Mohammad Javed Ali
- Govindram Seksaria Institute of Dacryology, LV Prasad Eye Institute, Hyderabad, India
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9
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Shen J, Wen X, Xing X, Fozza C, Sechi LA. Endogenous retroviruses Suppressyn and Syncytin-2 as innovative prognostic biomarkers in Acute Myeloid Leukemia. Front Cell Infect Microbiol 2024; 13:1339673. [PMID: 38274728 PMCID: PMC10808309 DOI: 10.3389/fcimb.2023.1339673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction Emerging evidence has proven that human endogenous retroviruses (HERVs) play a critical role in the pathogenesis of Acute Myeloid Leukemia (AML), whereas the specific HERVs influencing the prognosis of AML patients have yet to be fully understood. Methods In this study, a systematic exploration was achieved to identify potential prognostic HERVs for AML, sourced from TCGA and GTEx database. Differential analysis and functional enrichment studies were conducted using GO, KEGG, GSEA, and GSVA. The ESTIMATE algorithm was applied to explore the immune infiltration of HERVs in AML. A prognostic risk-score model was evaluated with predicted yearly accuracy using ROC analysis. Results Two HERVs Suppressyn and Syncytin-2, were identified as promising prognostic biomarkers, with high discrimination ability based on ROC analysis between AML and healthy cohorts from TCGA. Their expression was notably higher in AML patients compared to those in healthy individuals but correlates with favorable clinical outcomes in sub-groups such as white race, lower WBC counts, favorable and intermediate risks, and NPM1 or IDH1 mutation. Suppressyn and Syncytin-2 participated in immune-related pathways and exhibited correlations with multiple immune infiltration cells, such as T cells, mast cells, and tumor-associated macrophages. Finally, we developed a prognostic risk-scoring model combining Suppressyn and Syncytin-2, where a high risk-score is associated with better prognosis. Discussion Collectively, our findings revealed that Suppressyn and Syncytin-2 may act as valuable diagnostic and prognostic biomarkers for individuals with AML, while highlighting links between HERV activation, immunogenicity, and future therapeutic targets.
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Affiliation(s)
- Jiaxin Shen
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Hematology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Xiaofen Wen
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Xueyang Xing
- Department of Hematology, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
| | - Claudio Fozza
- Department of Medicine and Pharmacy, University of Sassari, Sassari, Italy
| | - Leonardo Antonio Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- SC of Microbiology and Virology, Azienda Ospedaliera Universitaria (AOU) of Sassari, Sassari, Italy
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10
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Li C, Qian Q, Yan C, Lu M, Li L, Li P, Fan Z, Lei W, Shang K, Wang P, Wang J, Lu T, Huang Y, Yang H, Wei H, Han J, Xiao J, Chen F. HervD Atlas: a curated knowledgebase of associations between human endogenous retroviruses and diseases. Nucleic Acids Res 2024; 52:D1315-D1326. [PMID: 37870452 PMCID: PMC10767980 DOI: 10.1093/nar/gkad904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
Human endogenous retroviruses (HERVs), as remnants of ancient exogenous retrovirus infected and integrated into germ cells, comprise ∼8% of the human genome. These HERVs have been implicated in numerous diseases, and extensive research has been conducted to uncover their specific roles. Despite these efforts, a comprehensive source of HERV-disease association still needs to be added. To address this gap, we introduce the HervD Atlas (https://ngdc.cncb.ac.cn/hervd/), an integrated knowledgebase of HERV-disease associations manually curated from all related published literature. In the current version, HervD Atlas collects 60 726 HERV-disease associations from 254 publications (out of 4692 screened literature), covering 21 790 HERVs (21 049 HERV-Terms and 741 HERV-Elements) belonging to six types, 149 diseases and 610 related/affected genes. Notably, an interactive knowledge graph that systematically integrates all the HERV-disease associations and corresponding affected genes into a comprehensive network provides a powerful tool to uncover and deduce the complex interplay between HERVs and diseases. The HervD Atlas also features a user-friendly web interface that allows efficient browsing, searching, and downloading of all association information, research metadata, and annotation information. Overall, the HervD Atlas is an essential resource for comprehensive, up-to-date knowledge on HERV-disease research, potentially facilitating the development of novel HERV-associated diagnostic and therapeutic strategies.
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Affiliation(s)
- Cuidan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Qiheng Qian
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenghao Yan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingming Lu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Lin Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Pan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuojing Fan
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
| | - Wenyan Lei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kang Shang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Peihan Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianyi Lu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuting Huang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Hongwei Yang
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Haobin Wei
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingwan Han
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing100101, China
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11
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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.
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12
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Chilosi M, Doglioni C, Ravaglia C, Piciucchi S, Dubini A, Stefanizzi L, Poletti V. COVID-19. Biology, pathophysiology, and immunology: a pathologist view. Pathologica 2023; 115:248-256. [PMID: 38054899 DOI: 10.32074/1591-951x-954] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 12/07/2023] Open
Abstract
Even if the SARS-CoV-2 pandemic has been declared over, several risks and clinical problems remain to be faced, including long-COVID sequelae and possible outbreaks of pathogenic variants. Intense research on COVID-19 has provided in these few years a striking amount of data covering different fields and disciplines, which can help to provide a knowledge shield against new potential infective spreads, and may also potentially be applied to other fields of medicine, including oncology and neurology. Nevertheless, areas of uncertainty still remain regarding the pathogenic mechanisms that subtend the multifaceted manifestations of the disease. To better clarify the pathogenesis of the disease, a systematic multidisciplinary evaluation of the many mechanisms involved in COVID-19 is mandatory, including clinical, physiological, radiological, immunological and pathological studies. In COVID-19 syndrome the pathological studies have been mainly performed on autopsy cases, and only a few studies are available on biopsies. Nevertheless, these studies have provided relevant information that can substantially contribute to decipher the complex scenario characterizing the different forms of COVID-19 and long-COVID-19. In this review the data provided by pathological investigations are recapitulated and discussed, in the light of different hypothesis and data provided by clinical, physiological and immunological data.
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Affiliation(s)
- Marco Chilosi
- Department of Pathology, Pederzoli Hospital, Peschiera del Garda, Italy
| | - Claudio Doglioni
- Department of Pathology, San Raffaele Scientific Institute. Milan, Italy
| | - Claudia Ravaglia
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Sara Piciucchi
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | | | | | - Venerino Poletti
- Department of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
- Department of Pathology, Ospedale GB Morgagni, Forlì, Italy
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13
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Luqman-Fatah A, Miyoshi T. Human LINE-1 retrotransposons: impacts on the genome and regulation by host factors. Genes Genet Syst 2023; 98:121-154. [PMID: 36436935 DOI: 10.1266/ggs.22-00038] [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] [Indexed: 11/25/2022] Open
Abstract
Genome sequencing revealed that nearly half of the human genome is comprised of transposable elements. Although most of these elements have been rendered inactive due to mutations, full-length intact long interspersed element-1 (LINE-1 or L1) copies retain the ability to mobilize through RNA intermediates by a so-called "copy-and-paste" mechanism, termed retrotransposition. L1 is the only known autonomous mobile genetic element in the genome, and its retrotransposition contributes to inter- or intra-individual genetic variation within the human population. However, L1 retrotransposition also poses a threat to genome integrity due to gene disruption and chromosomal instability. Moreover, recent studies suggest that aberrant L1 expression can impact human health by causing diseases such as cancer and chronic inflammation that might lead to autoimmune disorders. To counteract these adverse effects, the host cells have evolved multiple layers of defense mechanisms at the epigenetic, RNA and protein levels. Intriguingly, several host factors have also been reported to facilitate L1 retrotransposition, suggesting that there is competition between negative and positive regulation of L1 by host factors. Here, we summarize the known host proteins that regulate L1 activity at different stages of the replication cycle and discuss how these factors modulate disease-associated phenotypes caused by L1.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University
- Department of Stress Response, Radiation Biology Center, Graduate School of Biostudies, Kyoto University
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14
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Yoth M, Maupetit-Méhouas S, Akkouche A, Gueguen N, Bertin B, Jensen S, Brasset E. Reactivation of a somatic errantivirus and germline invasion in Drosophila ovaries. Nat Commun 2023; 14:6096. [PMID: 37773253 PMCID: PMC10541861 DOI: 10.1038/s41467-023-41733-5] [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: 12/15/2022] [Accepted: 09/15/2023] [Indexed: 10/01/2023] Open
Abstract
Most Drosophila transposable elements are LTR retrotransposons, some of which belong to the genus Errantivirus and share structural and functional characteristics with vertebrate endogenous retroviruses. Like endogenous retroviruses, it is unclear whether errantiviruses retain some infectivity and transposition capacity. We created conditions where control of the Drosophila ZAM errantivirus through the piRNA pathway was abolished leading to its de novo reactivation in somatic gonadal cells. After reactivation, ZAM invaded the oocytes and severe fertility defects were observed. While ZAM expression persists in the somatic gonadal cells, the germline then set up its own adaptive genomic immune response by producing piRNAs against the constantly invading errantivirus, restricting invasion. Our results suggest that although errantiviruses are continuously repressed by the piRNA pathway, they may retain their ability to infect the germline and transpose, thus allowing them to efficiently invade the germline if they are expressed.
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Affiliation(s)
- Marianne Yoth
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | | | - Abdou Akkouche
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Nathalie Gueguen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France
| | - Benjamin Bertin
- LIMAGRAIN EUROPE, Centre de recherche, 63720, Chappes, France
| | - Silke Jensen
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
| | - Emilie Brasset
- iGReD, Université Clermont Auvergne, CNRS, INSERM, Faculté de Médecine, 63000, Clermont-Ferrand, France.
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15
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Liu J, Min S, Kim D, Park J, Park E, Pei S, Koh Y, Shin DY, Byun JM, Ko M, Yoon SS, Hong J. Pharmacological GLUT3 salvage augments the efficacy of vitamin C-induced TET2 restoration in acute myeloid leukemia. Leukemia 2023; 37:1638-1648. [PMID: 37393342 DOI: 10.1038/s41375-023-01954-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 05/19/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
Vitamin C has been demonstrated to regulate hematopoietic stem cell frequencies and leukemogenesis by augmenting and restoring Ten-Eleven Translocation-2 (TET2) function, potentially acting as a promising adjunctive therapeutic agent for leukemia. However, glucose transporter 3 (GLUT3) deficiency in acute myeloid leukemia (AML) impedes vitamin C uptake and abolishes the clinical benefit of vitamin C. In this study, we aimed to investigate the therapeutic value of GLUT3 restoration in AML. In vitro GLUT3 restoration was conducted with the transduction of GLUT3-overexpressing lentivirus or the pharmacological salvage with 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) treatment to OCI-AML3, a naturally GLUT3-deficient AML cell line. The effects of GLUT3 salvage were further confirmed in patient-derived primary AML cells. Upregulation of GLUT3 expression made AML cells successfully augment TET2 activity and enhanced the vitamin C-induced anti-leukemic effect. Pharmacological GLUT3 salvage has the potential to overcome GLUT3 deficiency in AML and improves the antileukemic effect of vitamin C treatments.
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Affiliation(s)
- Jun Liu
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Suji Min
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dongchan Kim
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jihyun Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunchae Park
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Shanshan Pei
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Youngil Koh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Yeop Shin
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ja Min Byun
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Myunggon Ko
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| | - Sung-Soo Yoon
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junshik Hong
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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16
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Xu L, Yang Y, Li Y, Lu Y, Gao C, Bian X, Liu Z, Sun Q. Characterizing the Pathogenicity and Immunogenicity of Simian Retrovirus Subtype 8 (SRV-8) Using SRV-8-Infected Cynomolgus Monkeys. Viruses 2023; 15:1538. [PMID: 37515223 PMCID: PMC10384433 DOI: 10.3390/v15071538] [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: 06/06/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Simian retrovirus subtype 8 (SRV-8) infections have been reported in cynomolgus monkeys (Macaca fascicularis) in China and America, but its pathogenicity and immunogenicity are rarely reported. In this work, the SRV-8-infected monkeys were identified from the monkeys with anemia, weight loss, and diarrhea. To clarify the impact of SRV-8 infection on cynomolgus monkeys, infected monkeys were divided into five groups according to disease progression. Hematoxylin (HE) staining and viral loads analysis showed that SRV-8 mainly persisted in the intestine and spleen, causing tissue damage. Additionally, the dynamic variations of blood routine indexes, innate and adaptive immunity, and the transcriptomic changes in peripheral blood cells were analyzed during SRV-8 infection. Compared to uninfected animals, red blood cells, hemoglobin, and white blood cells were reduced in SRV-8-infected monkeys. The percentage of immune cell populations was changed after SRV-8 infection. Furthermore, the number of hematopoietic stem cells decreased significantly during the early stages of SRV-8 infection, and returned to normal levels after antibody-mediated viral clearance. Finally, global transcriptomic analysis in PBMCs from SRV-8-infected monkeys revealed distinct gene expression profiles across different disease stages. In summary, SRV-8 infection can cause severe pathogenicity and immune disturbance in cynomolgus monkeys, and it might be responsible for fatal virus-associated immunosuppressive syndrome.
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Affiliation(s)
- Libing Xu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yunpeng Yang
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yandong Li
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yong Lu
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Changshan Gao
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xinyan Bian
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zongping Liu
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Qiang Sun
- Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China
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17
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Qiao J, Zhang SX, Chang MJ, Zhao R, Song S, Hao JW, Wang C, Hu JX, Gao C, Wang CH, Li XF. Deep stratification by transcriptome molecular characters for precision treatment of patients with systemic lupus erythematosus. Rheumatology (Oxford) 2023; 62:2574-2584. [PMID: 36308437 DOI: 10.1093/rheumatology/keac625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 07/20/2023] Open
Abstract
OBJECTIVES To leverage the high clinical heterogeneity of systemic lupus erythematosus (SLE), we developed and validated a new stratification scheme by integrating genome-scale transcriptomic profiles to identify patient subtypes sharing similar transcriptomic markers and drug targets. METHODS A normalized compendium of transcription profiles was created from peripheral blood mononuclear cells (PBMCs) of 1046 SLE patients and 86 healthy controls (HCs), covering an intersection of 13 689 genes from six microarray datasets. Upregulated differentially expressed genes were subjected to functional and network analysis in which samples were grouped using unsupervised clustering to identify patient subtypes. Then, clustering stability was evaluated by the stratification of six integrated RNA-sequencing datasets using the same method. Finally, the Xgboost classifier was applied to the independent datasets to identify factors associated with treatment outcomes. RESULTS Based on 278 upregulated DEGs of the transcript profiles, SLE patients were classified into three subtypes (subtype A-C) each with distinct molecular and cellular signatures. Neutrophil activation-related pathways were markedly activated in subtype A (named NE-driving), whereas lymphocyte and IFN-related pathways were more enriched in subtype B (IFN-driving). As the most severe subtype, subtype C [NE-IFN-dual-driving (Dual-driving)] shared functional mechanisms with both NE-driving and IFN-driving, which was closely associated with clinical features and could be used to predict the responses of treatment. CONCLUSION We developed the largest cohesive SLE transcriptomic compendium for deep stratification using the most comprehensive microarray and RNA sequencing datasets to date. This result could guide future design of molecular diagnosis and the development of stratified therapy for SLE patients.
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Affiliation(s)
- Jun Qiao
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Sheng-Xiao Zhang
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Min-Jing Chang
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision, Shanxi Medical University, Taiyuan, China
| | - Rong Zhao
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Shan Song
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Jia-Wei Hao
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Can Wang
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
- Shanxi Key Laboratory of Big Data for Clinical Decision, Shanxi Medical University, Taiyuan, China
| | - Jing-Xi Hu
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Chong Gao
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Cai-Hong Wang
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
| | - Xiao-Feng Li
- Department of Rheumatology, Second Hospital of Shanxi Medical University, Taiyuan, China
- Ministry of Education, Key Laboratory of Cellular Physiology at Shanxi Medical University, Taiyuan, China
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18
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Li Z, Wang Q, Lv N, Xu G, Yang X, Zhu B. Genome-wide identification of endogenous retrovirus elements and their active transcription in mink genome. MLIFE 2023; 2:201-208. [PMID: 38817617 PMCID: PMC10989824 DOI: 10.1002/mlf2.12074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/12/2023] [Accepted: 05/15/2023] [Indexed: 06/01/2024]
Abstract
Mammalian endogenous retroviruses (ERVs) are ancient retroviruses that have been integrated into genomes. ERVs were believed to be inactive until the discovery of ERV transcription in the mouse genome. However, the transcription level and function of ERV elements in mammalian genomes are not well understood. In this study, we performed the first genome-wide scanning of ERV loci in the American mink (Neogale vison) genome (NeoERV) followed by transcriptomic analysis to detect actively transcribed NeoERV elements. A total of 365,791 NeoERV loci were identified, and161,205 (44%) of these loci were found to be actively transcribed based on transcriptomic data from three types of tissues (amygdala, trachea and lung). More than one third of the actively transcribed NeoERV loci were tissue-specific. Furthermore, some of the active loci were associated with host gene transcription, and the level of NeoERV transcription was positively correlated with that of host genes, specifically when active loci were located in overlapped gene regions. An in-depth analysis of the envelope protein coding env gene showed that, in general, its transcription level was higher than that of NeoERVs, which is believed to be associated with host immunity.
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Affiliation(s)
- Zheng Li
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qing Wang
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jiangxi Science and Technology Normal UniversityNanchangChina
| | - Na Lv
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
| | - Guojin Xu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
| | - Xuemei Yang
- Beijing Pediatric Research InstituteBeijingChina
| | - Baoli Zhu
- CAS Key Laboratory of Pathogen Microbiology and ImmunologyInstitute of Microbiology, Chinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
- Jinan Microecological Biomedicine Shandong LaboratoryJinanChina
- Department of Pathogenic Biology, School of Basic Medical SciencesSouthwest Medical UniversityLuzhouChina
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19
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Felley-Bosco E. Exploring the Expression of the «Dark Matter» of the Genome in Mesothelioma for Potentially Predictive Biomarkers for Prognosis and Immunotherapy. Cancers (Basel) 2023; 15:cancers15112969. [PMID: 37296931 DOI: 10.3390/cancers15112969] [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: 05/21/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Recent high-throughput RNA sequencing technologies have confirmed that a large part of the non-coding genome is transcribed. The priority for further investigations is nevertheless generally given in cancer to coding sequences, due to the obvious interest of finding therapeutic targets. In addition, several RNA-sequencing pipelines eliminate repetitive sequences, which are difficult to analyze. In this review, we shall focus on endogenous retroviruses. These sequences are remnants of ancestral germline infections by exogenous retroviruses. These sequences represent 8% of human genome, meaning four-fold the fraction of the genome encoding for proteins. These sequences are generally mostly repressed in normal adult tissues, but pathological conditions lead to their de-repression. Specific mesothelioma-associated endogenous retrovirus expression and their association to clinical outcome is discussed.
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Affiliation(s)
- Emanuela Felley-Bosco
- Laboratory of Molecular Oncology, Department of Thoracic Surgery, Zürich University Hospital, 8091 Zurich, Switzerland
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20
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Ishihara S. Detection of long terminal repeat loci derived from endogenous retrovirus in junglefowl using whole-genome sequencing. Sci Rep 2023; 13:7380. [PMID: 37149699 PMCID: PMC10164170 DOI: 10.1038/s41598-023-34520-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/03/2023] [Indexed: 05/08/2023] Open
Abstract
Endogenous retroviruses (ERVs) are genetic elements present in the genome that retain traces of past viral infections. Characterization of ERVs can provide crucial insights into avian evolution. This study aimed to identify novel long terminal repeat (LTR) loci derived from ERVs (ERV-LTRs) absent in the reference genome using whole-genome sequencing data of red junglefowl, gray junglefowl, Ceylon junglefowl, and green junglefowl. In total, 835 ERV-LTR loci were identified across the four Gallus species. The numbers of ERV-LTRs loci detected in red junglefowl and its subspecies gray junglefowl, Ceylon junglefowl, and green junglefowl were 362, 216, 193, and 128, respectively. The phylogenetic tree was congruent with previously reported trees, suggesting the potential for inferring relationships among past junglefowl populations from the identified ERV-LTR loci. Of the detected loci, 306 ERV-LTRs were identified near or within the genes, and some were associated with cell adhesion. The detected ERV-LTR sequences were classified as endogenous avian retrovirus family, avian leukosis virus subgroup E, Ovex-1, and murine leukemia virus-related ERVs. In addition, the sequence of the EAV family was divided into four patterns by combining the U3, R, and U5 regions. These findings contribute to a more comprehensive understanding of the characteristics of junglefowl ERVs.
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Affiliation(s)
- Shinya Ishihara
- Department of Animal Science, Nippon Veterinary and Life Science University, 1-7-1 Kyonancho, Musashino, Tokyo, 180-8602, Japan.
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21
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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.
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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
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22
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Liu J, Min S, Kim D, Park J, Park E, Koh Y, Shin DY, Kim TK, Byun JM, Yoon SS, Hong J. Epigenetic priming improves salvage chemotherapy in diffuse large B-cell lymphoma via endogenous retrovirus-induced cGAS-STING activation. Clin Epigenetics 2023; 15:75. [PMID: 37138342 PMCID: PMC10155448 DOI: 10.1186/s13148-023-01493-x] [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: 01/15/2023] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
BACKGROUND Although most patients with diffuse large B-cell lymphoma (DLBCL) achieve complete remission after first-line rituximab-containing immunochemotherapy, up to 40% of patients relapse and require salvage therapy. Among those patients, a substantial proportion remain refractory to salvage therapy due to insufficient efficacy or intolerance of toxicities. A hypomethylating agent, 5-azacytidine, showed a chemosensitizing effect when primed before chemotherapy in lymphoma cell lines and newly diagnosed DLBCL patients. However, its potential to improve outcomes of salvage chemotherapy in DLBCL has not been investigated. RESULTS In this study, we demonstrated the mechanism of 5-azacytidine priming as a chemosensitizer in a platinum-based salvage regimen. This chemosensitizing effect was associated with endogenous retrovirus (ERV)-induced viral mimicry responses via the cGAS-STING axis. We found deficiency of cGAS impaired the chemosensitizing effect of 5-azacytidine. Furthermore, combining vitamin C and 5-azacytidine to synergistically activate STING could be a potential remedy for insufficient priming induced by 5-azacytidine alone. CONCLUSIONS Taken together, the chemosensitizing effect of 5-azacytidine could be exploited to overcome the limitations of the current platinum-containing salvage chemotherapy in DLBCL and the status of cGAS-STING has the potential to predict the efficacy of 5-azacytidine priming.
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Affiliation(s)
- Jun Liu
- College of Medicine, Zhejiang University, Hangzhou, China
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Suji Min
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dongchan Kim
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jihyun Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Eunchae Park
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Youngil Koh
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong-Yeop Shin
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Tae Kon Kim
- Division of Hematology/Oncology, Department of Internal Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Ja Min Byun
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung-Soo Yoon
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Junshik Hong
- Center for Medical Innovation, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
- Department of Internal Medicine, Seoul National University Hospital, Seoul National University College of Medicine, 101 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea.
- Biomedical Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
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23
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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24
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Johnson E, Salari K, Yang S. SETDB1: A perspective into immune cell function and cancer immunotherapy. Immunology 2023; 169:3-12. [PMID: 36524435 PMCID: PMC10121739 DOI: 10.1111/imm.13619] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 12/11/2022] [Indexed: 12/23/2022] Open
Abstract
Oncogene SET Domain Bifurcated 1 (SETDB1)/ESET, an H3K9 methyltransferase, was originally discovered over two decades ago; however, its function in the immune response was not first reported until 2011. SETDB1 immune functions include B cell maturation, T cell activity regulation, and immune escape in cancer cells. In B lymphocytes, SETDB1 mediates the transition from pro-B to pre-B cells and represses endogenous retroviruses (ERV) to encourage B cell lineage differentiation and maturation. SETDB1 alters T cell function by methylating IL-2 and IL-17 promoters and mediating T cell lineage commitment and development. In addition, SETDB1 plays a critical role in ERV silencing within a variety of immune cells, which can indirectly weaken the immune response. Although SETDB1 is critical for normal immune cell function, overexpression in cancer cells negatively impacts immune cell fights against cancer through decreased tumour immunogenicity. Within cancer cells, SETDB1 overexpression represses production and infiltration of antitumour immune cells, mediates immune escape through TE and ERV silencing, represses the type I interferon pathway, and interferes in immune checkpoint blockade (ICB) outcomes by regulation of PD-L1 expression and IFN signalling. In this review, we further discuss the immunological mechanisms of SETDB1 in normal and cancerous cells and its implications in cancer immunotherapy.
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Affiliation(s)
- Eleanor Johnson
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Kiarash Salari
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Shujie Yang
- Department of Pathology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Holden Comprehensive Cancer Center, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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25
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Bodmer W, Golubovskaya V. Cancer Immunotherapy: Where Next? Cancers (Basel) 2023; 15:cancers15082358. [PMID: 37190286 DOI: 10.3390/cancers15082358] [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: 03/23/2023] [Revised: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/17/2023] Open
Abstract
The fundamental problem of dealing with cancer is that cancer cells are so like normal cells that it is very hard to find differences that can be a basis for treatment without severe side effects. The key to successful cancer immunotherapy will be based on a very careful choice of cancer targets that are sufficiently cancer specific not to cause serious side effects. There are two fundamentally different ways to deploy the immune system for such cancer treatments. One is to increase the efficacy of the cancer patient's own immune system so that it attacks these differences. This has been achieved by "checkpoint blocking" which is very successful but only with a relatively small proportion of cancers. Secondly, one can produce antibodies, or T cells, whose specificity is directed against proteins expressed differentially in cancers. CART cell treatments have proved very effective for some blood cancers but not so far for common solid tumours. Humanised, unmodified monoclonal antibodies have been used extensively for the treatment of certain adenocarcinomas with modest success. However, using antibodies together with the body's own immune system to treat cancers by engineering monoclonal antibodies that are directed at both a target antigen on the cancer cell surface and also against T cells shows promise for the development of novel immunotherapies. Genes can be found which are expressed highly in some cancers but with a low or absent expression on normal tissues and so are good novel targets. It is so far, only immune-based killing that can kill bystander target negative cells, which is essential for successful treatment since hardly ever will all the cells in a cancer express any desired target. We conclude that, while there still may be many hurdles in the way, engineered bispecific T cell attracting monoclonal antibody-mediated killing of cancer cells may be the most promising approach for achieving novel effective cancer immunotherapies.
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Affiliation(s)
- Walter Bodmer
- Weatherall Institute of Molecular Medicine, Department of Oncology, University of Oxford, Oxford OX3 9DS, UK
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26
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Hamann MV, Adiba M, Lange UC. Confounding factors in profiling of locus-specific human endogenous retrovirus (HERV) transcript signatures in primary T cells using multi-study-derived datasets. BMC Med Genomics 2023; 16:68. [PMID: 37013607 PMCID: PMC10068191 DOI: 10.1186/s12920-023-01486-y] [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: 01/17/2023] [Accepted: 03/11/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERV) are repetitive sequence elements and a substantial part of the human genome. Their role in development has been well documented and there is now mounting evidence that dysregulated HERV expression also contributes to various human diseases. While research on HERV elements has in the past been hampered by their high sequence similarity, advanced sequencing technology and analytical tools have empowered the field. For the first time, we are now able to undertake locus-specific HERV analysis, deciphering expression patterns, regulatory networks and biological functions of these elements. To do so, we inevitable rely on omics datasets available through the public domain. However, technical parameters inevitably differ, making inter-study analysis challenging. We here address the issue of confounding factors for profiling locus-specific HERV transcriptomes using datasets from multiple sources. METHODS We collected RNAseq datasets of CD4 and CD8 primary T cells and extracted HERV expression profiles for 3220 elements, resembling most intact, near full-length proviruses. Looking at sequencing parameters and batch effects, we compared HERV signatures across datasets and determined permissive features for HERV expression analysis from multiple-source data. RESULTS We could demonstrate that considering sequencing parameters, sequencing-depth is most influential on HERV signature outcome. Sequencing samples deeper broadens the spectrum of expressed HERV elements. Sequencing mode and read length are secondary parameters. Nevertheless, we find that HERV signatures from smaller RNAseq datasets do reliably reveal most abundantly expressed HERV elements. Overall, HERV signatures between samples and studies overlap substantially, indicating a robust HERV transcript signature in CD4 and CD8 T cells. Moreover, we find that measures of batch effect reduction are critical to uncover genic and HERV expression differences between cell types. After doing so, differences in the HERV transcriptome between ontologically closely related CD4 and CD8 T cells became apparent. CONCLUSION In our systematic approach to determine sequencing and analysis parameters for detection of locus-specific HERV expression, we provide evidence that analysis of RNAseq datasets from multiple studies can aid confidence of biological findings. When generating de novo HERV expression datasets we recommend increased sequence depth ( > = 100 mio reads) compared to standard genic transcriptome pipelines. Finally, batch effect reduction measures need to be implemented to allow for differential expression analysis.
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Affiliation(s)
| | - Maisha Adiba
- Leibniz Institute of Virology (LIV), Hamburg, Germany
| | - Ulrike C Lange
- Leibniz Institute of Virology (LIV), Hamburg, Germany.
- Institute for Infection Research and Vaccine Development, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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27
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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.
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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
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28
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Elbasir A, Ye Y, Schäffer DE, Hao X, Wickramasinghe J, Tsingas K, Lieberman PM, Long Q, Morris Q, Zhang R, Schäffer AA, Auslander N. A deep learning approach reveals unexplored landscape of viral expression in cancer. Nat Commun 2023; 14:785. [PMID: 36774364 PMCID: PMC9922274 DOI: 10.1038/s41467-023-36336-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Accepted: 01/25/2023] [Indexed: 02/13/2023] Open
Abstract
About 15% of human cancer cases are attributed to viral infections. To date, virus expression in tumor tissues has been mostly studied by aligning tumor RNA sequencing reads to databases of known viruses. To allow identification of divergent viruses and rapid characterization of the tumor virome, we develop viRNAtrap, an alignment-free pipeline to identify viral reads and assemble viral contigs. We utilize viRNAtrap, which is based on a deep learning model trained to discriminate viral RNAseq reads, to explore viral expression in cancers and apply it to 14 cancer types from The Cancer Genome Atlas (TCGA). Using viRNAtrap, we uncover expression of unexpected and divergent viruses that have not previously been implicated in cancer and disclose human endogenous viruses whose expression is associated with poor overall survival. The viRNAtrap pipeline provides a way forward to study viral infections associated with different clinical conditions.
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Affiliation(s)
| | - Ying Ye
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Daniel E Schäffer
- The Wistar Institute, Philadelphia, PA, 19104, USA.,Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Xue Hao
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | | | - Konstantinos Tsingas
- The Wistar Institute, Philadelphia, PA, 19104, USA.,University of Pennsylvania, Philadelphia, PA, USA
| | | | - Qi Long
- University of Pennsylvania, Philadelphia, PA, USA
| | - Quaid Morris
- Computational and Systems Biology, Sloan Kettering Institute, New York City, NY, 10065, USA
| | - Rugang Zhang
- The Wistar Institute, Philadelphia, PA, 19104, USA
| | - Alejandro A Schäffer
- Cancer Data Science Laboratory (CDSL), National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
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29
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Endogenous Retroviruses as Modulators of Innate Immunity. Pathogens 2023; 12:pathogens12020162. [PMID: 36839434 PMCID: PMC9963469 DOI: 10.3390/pathogens12020162] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [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.
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30
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Alldredge J, Kumar V, Nguyen J, Sanders BE, Gomez K, Jayachandran K, Zhang J, Schwarz J, Rahmatpanah F. Endogenous Retrovirus RNA Expression Differences between Race, Stage and HPV Status Offer Improved Prognostication among Women with Cervical Cancer. Int J Mol Sci 2023; 24:1492. [PMID: 36675007 PMCID: PMC9864224 DOI: 10.3390/ijms24021492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/29/2022] [Accepted: 12/31/2022] [Indexed: 01/15/2023] Open
Abstract
Endogenous human retroviruses (ERVs) are remnants of exogenous retroviruses that have integrated into the human genome. Using publicly available RNA-seq data from 63 cervical cancer patients, we investigated the expression of ERVs in cervical cancers. Four aspects of cervical cancer were investigated: patient ancestral background, tumor HPV type, tumor stage and patient survival. Between the racial subgroups, 74 ERVs were significantly differentially expressed, with Black Americans having 30 upregulated and 44 downregulated (including MER21C, HERV9-int, and HERVH-int) ERVs when compared to White Americans. We found that 3313 ERVs were differentially expressed between HPV subgroups, including MER41A, HERVH-int and HERVK9. There were 28 downregulated (including MLT1D and HERVH-int) and 61 upregulated (including MER41A) ERVs in locally advanced-stage compared to early-stage samples. Tissue microarrays of cervical cancer patients were used to investigate the protein expression of ERVs with protein coding potential (i.e., HERVK and ERV3). Significant differences in protein expression of ERV3 (p = 0.000905) were observed between early-stage and locally advanced-stage tumors. No significant differential expression at the protein level was found for HERVK7 (p = 0.243). We also investigated a prognostic model, supplementing a baseline prediction model using FIGO stage, age and HPV positivity with ERVs data. The expression levels of all ERVs in the HERVd were input into a Lasso-Cox proportional hazards model, developing a predictive 67-ERV panel. When ERVs expression levels were supplemented with the clinical data, a significant increase in prognostic power (p = 9.433 × 10-15) relative to that obtained with the clinical parameters alone (p = 0.06027) was observed. In summary, ERV RNA expression in cervical cancer tumors is significantly different among racial cohorts, HPV subgroups and disease stages. The combination of the expression of certain ERVs in cervical cancers with clinical factors significantly improved prognostication compared to clinical factors alone; therefore, ERVs may serve as future prognostic biomarkers and therapeutic targets. Novelty and Impact: When endogenous retroviral (ERV) expression signatures were combined with currently employed clinical prognosticators of relapse of cervical cancer, the combination outperformed prediction models based on clinical prognosticators alone. ERV expression signatures in tumor biopsies may therefore be useful to help identify patients at greater risk of recurrence. The novel ERV expression signatures or adjacent genes possibly impacted by ERV expression described here may also be targets for the development of future therapeutic interventions.
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Affiliation(s)
- Jill Alldredge
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Vinay Kumar
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - James Nguyen
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Brooke E. Sanders
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Karina Gomez
- Department of Obstetrics and Gynecology, University of Colorado, Aurora, CO 80045, USA
| | - Kay Jayachandran
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Jin Zhang
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63108, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Julie Schwarz
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA
- Institute for Informatics, Washington University School of Medicine, St. Louis, MO 63108, USA
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Farah Rahmatpanah
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
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31
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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.
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32
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Fan TJ, Cui J. Human Endogenous Retroviruses in Diseases. Subcell Biochem 2023; 106:403-439. [PMID: 38159236 DOI: 10.1007/978-3-031-40086-5_15] [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: 01/03/2024]
Abstract
Human endogenous retroviruses (HERVs), which are conserved sequences of ancient retroviruses, are widely distributed in the human genome. Although most HERVs have been rendered inactive by evolution, some have continued to exhibit important cytological functions. HERVs in the human genome perform dual functions: on the one hand, they are involved in important physiological processes such as placental development and immune regulation; on the other hand, their aberrant expression is closely associated with the pathological processes of several diseases, such as cancers, autoimmune diseases, and viral infections. HERVs can also regulate a variety of host cellular functions, including the expression of protein-coding genes and regulatory elements that have evolved from HERVs. Here, we present recent research on the roles of HERVs in viral infections and cancers, including the dysregulation of HERVs in various viral infections, HERV-induced epigenetic modifications of histones (such as methylation and acetylation), and the potential mechanisms of HERV-mediated antiviral immunity. We also describe therapies to improve the efficacy of vaccines and medications either by directly or indirectly targeting HERVs, depending on the HERV.
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Affiliation(s)
- Tian-Jiao Fan
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China.
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33
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Nocturne G, Mariette X. Interferon signature in systemic autoimmune diseases: what does it mean? RMD Open 2022; 8:rmdopen-2022-002687. [PMID: 36597991 PMCID: PMC9723951 DOI: 10.1136/rmdopen-2022-002687] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Affiliation(s)
- Gaetane Nocturne
- Department of Rheumatology, Université Paris-Saclay, INSERM UMR1184 : Center for immunology of viral infections and autoimmune diseases, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin-Bicêtre, France
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Saclay, INSERM UMR1184 : Center for immunology of viral infections and autoimmune diseases, Assistance Publique-Hôpitaux de Paris (AP-HP), Hôpital Bicêtre, Le Kremlin-Bicêtre, France
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34
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She J, Du M, Xu Z, Jin Y, Li Y, Zhang D, Tao C, Chen J, Wang J, Yang E. The landscape of hervRNAs transcribed from human endogenous retroviruses across human body sites. Genome Biol 2022; 23:231. [PMID: 36329469 PMCID: PMC9632151 DOI: 10.1186/s13059-022-02804-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Human endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most have lost their transcriptional abilities under physiological conditions. However, mounting evidence shows that several expressed HERVs do exert biological functions. Here, we systematically characterize physiologically expressed HERVs and examine whether they may give insight into the molecular fundamentals of human development and disease. RESULTS We systematically identify 13,889 expressed HERVs across normal body sites and demonstrate that they are expressed in body site-specific patterns and also by sex, ethnicity, and age. Analyzing cis-ERV-related quantitative trait loci, we find that 5435 hervRNAs are regulated by genetic variants. Combining this with a genome-wide association study, we elucidate that the dysregulation of expressed HERVs might be associated with various complex diseases, particularly neurodegenerative and psychiatric diseases. We further find that physiologically activated hervRNAs are associated with histone modifications rather than DNA demethylation. CONCLUSIONS Our results present a locus-specific landscape of physiologically expressed hervRNAs, which represent a hidden layer of genetic architecture in development and disease.
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Affiliation(s)
- Jianqi She
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Minghao Du
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zhanzhan Xu
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yueqi Jin
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yu Li
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Daoning Zhang
- Peking University First Hospital, Beijing, 100034, China
| | - Changyu Tao
- Department of Human Anatomy, Histology & Embryology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Jian Chen
- Chinese Institute for Brain Research, Beijing, 102206, China
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Ence Yang
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, NHC Key Laboratory of Medical Immunology (Peking University), Beijing, 100191, China.
- Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
- Chinese Institute for Brain Research, Beijing, 102206, China.
- Taizhou Medical New & Hi-tech Industrial Development Zone, Jiangsu, 225326, China.
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A Systems Biology Approach on the Regulatory Footprint of Human Endogenous Retroviruses (HERVs). Diseases 2022; 10:diseases10040098. [PMID: 36412592 PMCID: PMC9680359 DOI: 10.3390/diseases10040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/22/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Human endogenous retroviruses (HERVs) are a family of endogenous retroviruses that comprise the ~8.93% of the human genome sequence, with a high proportion being human specific. The recent expansion of repeated HERV sequences has offered a framework for genetic and epigenetic innovation. In the current report, a systematic approach is implemented to catalogue regulatory elements within HERVs, as a roadmap to potential functions of HERV sequences in gene networks. ENCODE Project has offered a wealth of epigenetic data based on omics technologies. I analyzed the presence of HERV sequences on consensus cis-regulatory elements (cCREs) from ENCODE data. On the one side, HERVs are in 1 out of 9 cCREs (>100.000 cCREs in total), dispersed within the genome and present in cis-regulatory regions of ~81% of human genes, as calculated following gene enrichment analysis. On the other side, promoter-associated HERV cCREs are present adjacent to (in a 200 bp window) the transcription start sites of 256 human genes. Regulatory network production, followed by centrality analysis led to the discovery of 90 core genes containing HERV-associated promoters. Pathway analysis on the core network genes and their immediate neighbors revealed a regulatory footprint that, among others, is associated with inflammation, chemokine signaling and response to viral infection. Collectively, these results support the concept that the expansion of regulatory sequences derived from HERVs is critical for epigenetic innovation that may have wired together genes into novel transcriptional networks with critical roles in cellular physiology and pathology.
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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: 13] [Impact Index Per Article: 6.5] [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.
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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.
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Patoori S, Barnada SM, Large C, Murray JI, Trizzino M. Young transposable elements rewired gene regulatory networks in human and chimpanzee hippocampal intermediate progenitors. Development 2022; 149:276504. [PMID: 36052683 PMCID: PMC9641669 DOI: 10.1242/dev.200413] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 08/21/2022] [Indexed: 01/19/2023]
Abstract
The hippocampus is associated with essential brain functions, such as learning and memory. Human hippocampal volume is significantly greater than expected compared with that of non-human apes, suggesting a recent expansion. Intermediate progenitors, which are able to undergo multiple rounds of proliferative division before a final neurogenic division, may have played a role in evolutionary hippocampal expansion. To investigate the evolution of gene regulatory networks underpinning hippocampal neurogenesis in apes, we leveraged the differentiation of human and chimpanzee induced pluripotent stem cells into TBR2 (or EOMES)-positive hippocampal intermediate progenitor cells (hpIPCs). We found that the gene networks active in hpIPCs are significantly different between humans and chimpanzees, with ∼2500 genes being differentially expressed. We demonstrate that species-specific transposon-derived enhancers contribute to these transcriptomic differences. Young transposons, predominantly endogenous retroviruses and SINE-Vntr-Alus (SVAs), were co-opted as enhancers in a species-specific manner. Human-specific SVAs provided substrates for thousands of novel TBR2-binding sites, and CRISPR-mediated repression of these SVAs attenuated the expression of ∼25% of the genes that are upregulated in human intermediate progenitors relative to the same cell population in the chimpanzee.
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Affiliation(s)
- Sruti Patoori
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Samantha M. Barnada
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Christopher Large
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John I. Murray
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Marco Trizzino
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA,Author for correspondence ()
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38
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Zhou JG, Zeng Y, Wang H, Jin SH, Wang YJ, He S, Frey B, Fietkau R, Hecht M, Ma H, Zhang W, Gaipl US. Identification of an endogenous retroviral signature to predict anti-PD1 response in advanced clear cell renal cell carcinoma: an integrated analysis of three clinical trials. Ther Adv Med Oncol 2022; 14:17588359221126154. [PMID: 37614979 PMCID: PMC10442641 DOI: 10.1177/17588359221126154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/26/2022] [Indexed: 08/25/2023] Open
Abstract
Background Endogenous retrovirus (ERV) elements are genomic footprints of ancestral retroviral infections within the human genome. Previous studies have demonstrated that dysregulated ERV transcription level is associated with immune cell infiltration in cancers, but the association between ERV expression and programmed cell death protein 1 (PD-1) blockade response is currently unraveled for solid cancers, such as advanced clear cell renal cell carcinoma (ccRCC). Methods ERV mRNA profiles were obtained from three clinical trials of ccRCC where the patients were treated with anti-PD-1 (CM-009, CM-010, CM-025, and TCGA-KIRC data). Patients treated with nivolumab were divided into training and test cohort, while the TCGA-KIRC cohort was used as an external validation. Univariate Cox regression analysis and least absolute shrinkage and selection operator regression were used to establish the signature. Immune cell infiltration analysis and gene set enrichment analysis were performed to explore potential biological mechanisms. Results An ERV signature was established based on nine ERV expression patterns. In the training cohort, the median overall survival in the low- and high-risk group was 45.2 and 19.6 months [hazard ratio (HR) = 0.49, 0.32-0.75, p < 0.001], respectively. The results were confirmed in the test (HR = 0.41, 0.20-0.83, p = 0.013), and in the TCGA-KIRC cohort (HR = 0.55, 0.34-0.90, p = 0.017). Moreover, in the CM-025 cohort, the low-risk group that received nivolumab had a more favorable survival compared with those that received the mTOR inhibitor everolimus, while no significant differences were observed in the high-risk group. CD8+ T cells were enriched in the low-risk group, while immune suppressive pathways were suppressed. Conclusion The newly identified ERV signature is not only a prognostic, but also a predictive biomarker for advanced ccRCC patients who received anti-PD-1 therapy, which can guide personalized treatment in cancer patients in the future.
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Affiliation(s)
- Jian-Guo Zhou
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, GermanyDepartment of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Yu Zeng
- Department of Neurosurgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haitao Wang
- Thoracic Surgery Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Su-Han Jin
- Department of Orthodontic, School of Stomatology, Zunyi Medical University, Zunyi, China
| | - Yun-Jia Wang
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Sisi He
- Department of Oncology, The second affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Benjamin Frey
- Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, GermanyDepartment of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Rainer Fietkau
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Markus Hecht
- Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Hu Ma
- Director of Department of Oncology, Vice President of the second affiliated Hospital of Zunyi Medical University, Intersection of Xinlong And Xinpu Avenue, Zunyi, 563000, China
| | - Wenchuan Zhang
- Director of Department of Neurosurgery, Department of Neurosurgery, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, 639 Zhizaoju Road, Shanghai, 200011, China
| | - Udo S. Gaipl
- Head of Translational Radiobiology, Department of Radiation Oncology, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Universitätsstraße 27, Erlangen, 91054, Germany.Department of Radiation Oncology, Universitätsklinikum Erlangen, Erlangen, Germany. Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
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39
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Sorek M, Meshorer E, Schlesinger S. Impaired activation of transposable elements in SARS-CoV-2 infection. EMBO Rep 2022; 23:e55101. [PMID: 35972201 PMCID: PMC9442302 DOI: 10.15252/embr.202255101] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 12/14/2022] Open
Abstract
Emerging evidence shows that transposable elements (TEs) are induced in response to viral infections. This TE induction is suggested to trigger a robust and durable interferon response, providing a host defense mechanism. Here, we analyze TE expression changes in response to SARS-CoV-2 infection in different human cellular models. Unlike other viruses, SARS-CoV-2 infection does not lead to global upregulation of TEs in primary cells. We report a correlation between TEs activation and induction of interferon-related genes, suggesting that failure to activate TEs may account for the weak interferon response. Moreover, we identify two variables that explain most of the observed diverseness in immune responses: basal expression levels of TEs in the pre-infected cells and the viral load. Finally, analyzing the SARS-CoV-2 interactome and the epigenetic landscape around the TEs activated following infection, we identify SARS-CoV-2 interacting proteins, which may regulate chromatin structure and TE transcription. This work provides a possible functional explanation for SARS-CoV-2 success in its fight against the host immune system and suggests that TEs could serve as potential drug targets for COVID-19.
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Affiliation(s)
- Matan Sorek
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Animal Sciences, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Eran Meshorer
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Sharon Schlesinger
- Department of Animal Sciences, Faculty of Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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40
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Li Q, Gloudemans MJ, Geisinger JM, Fan B, Aguet F, Sun T, Ramaswami G, Li YI, Ma JB, Pritchard JK, Montgomery SB, Li JB. RNA editing underlies genetic risk of common inflammatory diseases. Nature 2022; 608:569-577. [PMID: 35922514 PMCID: PMC9790998 DOI: 10.1038/s41586-022-05052-x] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/29/2022] [Indexed: 12/12/2022]
Abstract
A major challenge in human genetics is to identify the molecular mechanisms of trait-associated and disease-associated variants. To achieve this, quantitative trait locus (QTL) mapping of genetic variants with intermediate molecular phenotypes such as gene expression and splicing have been widely adopted1,2. However, despite successes, the molecular basis for a considerable fraction of trait-associated and disease-associated variants remains unclear3,4. Here we show that ADAR-mediated adenosine-to-inosine RNA editing, a post-transcriptional event vital for suppressing cellular double-stranded RNA (dsRNA)-mediated innate immune interferon responses5-11, is an important potential mechanism underlying genetic variants associated with common inflammatory diseases. We identified and characterized 30,319 cis-RNA editing QTLs (edQTLs) across 49 human tissues. These edQTLs were significantly enriched in genome-wide association study signals for autoimmune and immune-mediated diseases. Colocalization analysis of edQTLs with disease risk loci further pinpointed key, putatively immunogenic dsRNAs formed by expected inverted repeat Alu elements as well as unexpected, highly over-represented cis-natural antisense transcripts. Furthermore, inflammatory disease risk variants, in aggregate, were associated with reduced editing of nearby dsRNAs and induced interferon responses in inflammatory diseases. This unique directional effect agrees with the established mechanism that lack of RNA editing by ADAR1 leads to the specific activation of the dsRNA sensor MDA5 and subsequent interferon responses and inflammation7-9. Our findings implicate cellular dsRNA editing and sensing as a previously underappreciated mechanism of common inflammatory diseases.
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Affiliation(s)
- Qin Li
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Michael J. Gloudemans
- Department of Pathology, Stanford University, Stanford, CA, USA.,Biomedical Informatics Training Program, Stanford University, Stanford, CA, USA
| | | | - Boming Fan
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | | | - Tao Sun
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Gokul Ramaswami
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Yang I. Li
- Department of Genetics, Stanford University, Stanford, CA, USA.,Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Jin-Biao Ma
- State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jonathan K. Pritchard
- Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, Stanford, CA, USA.,Department of Pathology, Stanford University, Stanford, CA, USA.,These authors contributed equally: Stephen B. Montgomery, Jin Billy Li
| | - Jin Billy Li
- Department of Genetics, Stanford University, Stanford, CA, USA.
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Kwon J, Choi H, Han C. A Dual Role of DDX3X in dsRNA-Derived Innate Immune Signaling. Front Mol Biosci 2022; 9:912727. [PMID: 35874614 PMCID: PMC9299366 DOI: 10.3389/fmolb.2022.912727] [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: 04/04/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
DEAD-Box Helicase 3 X-Linked (DDX3X) is essential for RNA metabolism and participates in various cellular processes involving RNA. DDX3X has been implicated in cancer growth and metastasis. DDX3X is involved in antiviral responses for viral RNAs and contributes to pro- or anti-microbial responses. A better understanding of how human cells regulate innate immune response against the viral “non-self” double-stranded RNAs (dsRNAs) and endogenous viral-like “self” dsRNAs is critical to understanding innate immune sensing, anti-microbial immunity, inflammation, immune cell homeostasis, and developing novel therapeutics for infectious, immune-mediated diseases, and cancer. DDX3X has known for activating the viral dsRNA-sensing pathway and innate immunity. However, accumulating research reveals a more complex role of DDX3X in regulating dsRNA-mediated signaling in cells. Here, we discuss the role of DDX3X in viral dsRNA- or endogenous dsRNA-mediated immune signaling pathways.
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Affiliation(s)
- Juntae Kwon
- Department of Oncology, Georgetown University School of Medicine, Washington, DC, United States
| | - Hyeongjwa Choi
- Department of Biomedical Science and Technology, Konkuk University, Seoul, South Korea
| | - Cecil Han
- Department of Oncology, Georgetown University School of Medicine, Washington, DC, United States.,Lombardi Comprehensive Cancer Center, Washington, DC, United States
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Ansaloni F, Gualandi N, Esposito M, Gustincich S, Sanges R. TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized fragments. Bioinformatics 2022; 38:4430-4433. [PMID: 35876845 PMCID: PMC9477521 DOI: 10.1093/bioinformatics/btac526] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
SUMMARY Transposable elements (TEs) play key roles in crucial biological pathways. Therefore, several tools enabling the quantification of their expression were recently developed. However, many of the existing tools lack the capability to distinguish between the transcription of autonomously expressed TEs and TE fragments embedded in canonical coding/non-coding non-TE transcripts. Consequently, an apparent change in the expression of a given TE may simply reflect the variation in the expression of the transcripts containing TE-derived sequences. To overcome this issue, we have developed TEspeX, a pipeline for the quantification of TE expression at the consensus level. TEspeX uses Illumina RNA-seq short reads to quantify TE expression avoiding counting reads deriving from inactive TE fragments embedded in canonical transcripts. AVAILABILITY AND IMPLEMENTATION The tool is implemented in python3, distributed under the GNU General Public License (GPL) and available on Github at https://github.com/fansalon/TEspeX (Zenodo URL: https://doi.org/10.5281/zenodo.6800331). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Federico Ansaloni
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy,Central RNA Laboratory, Istituto Italiano di Tecnologia, Genova 16163, Italy
| | - Nicolò Gualandi
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | - Mauro Esposito
- Area of Neuroscience, Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste 34136, Italy
| | | | - Remo Sanges
- To whom correspondence should be addressed. or
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Zhang M, Zheng S, Liang JQ. Transcriptional and reverse transcriptional regulation of host genes by human endogenous retroviruses in cancers. Front Microbiol 2022; 13:946296. [PMID: 35928153 PMCID: PMC9343867 DOI: 10.3389/fmicb.2022.946296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/29/2022] [Indexed: 11/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) originated from ancient retroviral infections of germline cells millions of years ago and have evolved as part of the host genome. HERVs not only retain the capacity as retroelements but also regulate host genes. The expansion of HERVs involves transcription by RNA polymerase II, reverse transcription, and re-integration into the host genome. Fast progress in deep sequencing and functional analysis has revealed the importance of domesticated copies of HERVs, including their regulatory sequences, transcripts, and proteins in normal cells. However, evidence also suggests the involvement of HERVs in the development and progression of many types of cancer. Here we summarize the current state of knowledge about the expression of HERVs, transcriptional regulation of host genes by HERVs, and the functions of HERVs in reverse transcription and gene editing with their reverse transcriptase.
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Affiliation(s)
- Mengwen Zhang
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Ministry of Education Key Laboratory of Cancer Prevention and Intervention, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
| | - Shu Zheng
- The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
- Ministry of Education Key Laboratory of Cancer Prevention and Intervention, Second Affiliated Hospital, Cancer Institute, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Shu Zheng,
| | - Jessie Qiaoyi Liang
- Department of Medicine and Therapeutics, Faculty of Medicine, Center for Gut Microbiota Research, Li Ka Shing Institute of Health Sciences, Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Jessie Qiaoyi Liang,
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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.
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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.
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Shen Z, Fang M, Sun W, Tang M, Liu N, Zhu L, Liu Q, Li B, Sun R, Shi Y, Guo C, Lin J, Qu K. A transcriptome atlas and interactive analysis platform for autoimmune disease. Database (Oxford) 2022; 2022:6618550. [PMID: 35758882 PMCID: PMC9235372 DOI: 10.1093/database/baac050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/18/2022] [Accepted: 06/09/2022] [Indexed: 11/12/2022]
Abstract
With the rapid development of next-generation sequencing technology, many laboratories have produced a large amount of single-cell transcriptome data of blood and tissue samples from patients with autoimmune diseases, which enables in-depth studies of the relationship between gene transcription and autoimmune diseases. However, there is still a lack of a database that integrates the large amount of autoimmune disease transcriptome sequencing data and conducts effective analysis. In this study, we developed a user-friendly web database tool, Interactive Analysis and Atlas for Autoimmune disease (IAAA), which integrates bulk RNA-seq data of 929 samples of 10 autoimmune diseases and single-cell RNA-seq data of 783 203 cells in 96 samples of 6 autoimmune diseases. IAAA also provides customizable analysis modules, including gene expression, difference, correlation, similar gene detection and cell–cell interaction, and can display results in three formats (plot, table and pdf) through custom parameters. IAAA provides valuable data resources for researchers studying autoimmune diseases and helps users deeply explore the potential value of the current transcriptome data. IAAA is available. Database URL: http://galaxy.ustc.edu.cn/IAAA
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Affiliation(s)
- Zhuoqiao Shen
- School of Data Sciences, University of Science and Technology of China, No. 443, Huangshan Road, Shushan District, Hefei, Anhui 230027, China.,Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China.,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Wangjiang West Road, Shushan District, Hefei, Anhui 230088, China
| | - Minghao Fang
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Wujianan Sun
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China.,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Wangjiang West Road, Shushan District, Hefei, Anhui 230088, China.,CAS Center for Excellence in Molecular Cell Sciences, the CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, No. 373 Huangshan Road, Shushan District, Hefei, Anhui 230027, China
| | - Meifang Tang
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Nianping Liu
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Lin Zhu
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Qian Liu
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Bin Li
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Ruoming Sun
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Yu Shi
- School of Medicine, China Pharmaceutical University, No. 639, Longmian Avenue, Jiangning District, Nanjing, Jiangsu 211198, China
| | - Chuang Guo
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China
| | - Jun Lin
- Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China.,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Wangjiang West Road, Shushan District, Hefei, Anhui 230088, China
| | - Kun Qu
- School of Data Sciences, University of Science and Technology of China, No. 443, Huangshan Road, Shushan District, Hefei, Anhui 230027, China.,Department of Oncology, The First Affiliated Hospital of USTC, Department of Basic Medicine, Division of Life Sciences and Medicine, University of Science and Technology of China, No. 17, Lujiang Road, Luyang District, Hefei, Anhui 230021, China.,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Wangjiang West Road, Shushan District, Hefei, Anhui 230088, China.,CAS Center for Excellence in Molecular Cell Sciences, the CAS Key Laboratory of Innate Immunity and Chronic Disease, University of Science and Technology of China, No. 373 Huangshan Road, Shushan District, Hefei, Anhui 230027, China
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Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data. BIOLOGY 2022; 11:biology11060826. [PMID: 35741347 PMCID: PMC9220773 DOI: 10.3390/biology11060826] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 02/08/2023]
Abstract
Simple Summary Transposable elements (TEs) are repetitive sequences comprising more than one third of the human genome with the original ability to change their location within the genome. Owing to their repetitive nature, the quantification of TEs results often challenging. RNA-seq is a useful tool for genome-wide TEs quantification, nevertheless it also presents technical issues, including low reads mappability and erroneous quantification derived from the transcription of TEs fragments embedded in canonical transcripts. Fragments derived from TEs are found within the introns of most genes, which led to the hypothesis that intron retention (IR) can affect the unbiased quantification of TEs expression. Performing meta-analysis of public RNA-seq datasets, here we observe that IR can indeed impact the quantification of TEs by increasing the number of reads mapped on intronic TE copies. Our work highlights a correlation between IR and TEs expression measurement by RNA-seq that should be taken into account to achieve reliable TEs quantification, especially in samples characterized by extensive IR, because differential IR might be confused with differential TEs expression. Abstract Transposable elements (TEs), also known as “jumping genes”, are repetitive sequences with the capability of changing their location within the genome. They are key players in many different biological processes in health and disease. Therefore, a reliable quantification of their expression as transcriptional units is crucial to distinguish between their independent expression and the transcription of their sequences as part of canonical transcripts. TEs quantification faces difficulties of different types, the most important one being low reads mappability due to their repetitive nature preventing an unambiguous mapping of reads originating from their sequences. A large fraction of TEs fragments localizes within introns, which led to the hypothesis that intron retention (IR) can be an additional source of bias, potentially affecting accurate TEs quantification. IR occurs when introns, normally removed from the mature transcript by the splicing machinery, are maintained in mature transcripts. IR is a widespread mechanism affecting many different genes with cell type-specific patterns. We hypothesized that, in an RNA-seq experiment, reads derived from retained introns can introduce a bias in the detection of overlapping, independent TEs RNA expression. In this study we performed meta-analysis using public RNA-seq data from lymphoblastoid cell lines and show that IR can impact TEs quantification using established tools with default parameters. Reads mapped on intronic TEs were indeed associated to the expression of TEs and influence their correct quantification as independent transcriptional units. We confirmed these results using additional independent datasets, demonstrating that this bias does not appear in samples where IR is not present and that differential TEs expression does not impact on IR quantification. We concluded that IR causes the over-quantification of intronic TEs and differential IR might be confused with differential TEs expression. Our results should be taken into account for a correct quantification of TEs expression from RNA-seq data, especially in samples in which IR is abundant.
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Taura M, Frank JA, Takahashi T, Kong Y, Kudo E, Song E, Tokuyama M, Iwasaki A. APOBEC3A regulates transcription from interferon-stimulated response elements. Proc Natl Acad Sci U S A 2022; 119:e2011665119. [PMID: 35549556 PMCID: PMC9171812 DOI: 10.1073/pnas.2011665119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 04/11/2022] [Indexed: 01/04/2023] Open
Abstract
APOBEC3A (A3A) is a cytidine deaminase that inactivates a variety of viruses through introduction of lethal mutations to the viral genome. Additionally, A3A can suppress HIV-1 transcription in a deaminase-independent manner by binding to the long terminal repeat of proviral HIV-1. However, it is unknown whether A3A targets additional host genomic loci for repression. In this study, we found that A3A suppresses gene expression by binding TTTC doublets that are in close proximity to each other. However, one TTTC motif is sufficient for A3A binding. Because TTTC doublets are present in interferon (IFN)-stimulated response elements (ISRE), we hypothesized that A3A may impact IFN-stimulated gene (ISG) expression. After scanning the human genome for TTTC doublet occurrences, we discovered that these motifs are enriched in the proximal promoters of genes associated with antiviral responses and type I IFN (IFN-I) signaling. As a proof of principle, we examined whether A3A can impact ISG15 expression. We found that A3A binding to the ISRE inhibits phosphorylated STAT-1 binding and suppresses ISG15 induction in response to IFN-I treatment. Consistent with these data, our RNA-sequencing analyses indicate that A3A loss results in increased IFN-I–dependent induction of several ISGs. This study revealed that A3A plays an unexpected role in ISG regulation and suggests that A3A contributes to a negative feedback loop during IFN signaling.
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Affiliation(s)
- Manabu Taura
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- Laboratory of Bioresponse Regulation, Graduate School of Pharmaceutical Sciences, Osaka University, 565-0871 Suita, Japan
| | - John A. Frank
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Takehiro Takahashi
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Yong Kong
- Department of Molecular Biophysics and Biochemistry, W. M. Keck Foundation Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06520
| | - Eriko Kudo
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Eric Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Maria Tokuyama
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
- HHMI, Chevy Chase, MD 20815
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Chen J, Zhang P, Chen H, Wang X, He X, Zhong J, Zheng H, Li X, Jakovlić I, Zhang Y, Chen Y, Shen B, Deng C, Wu Y. Whole-genome sequencing identifies rare missense variants of WNT16 and ERVW-1 causing the systemic lupus erythematosus. Genomics 2022; 114:110332. [PMID: 35283196 DOI: 10.1016/j.ygeno.2022.110332] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/27/2022] [Accepted: 03/06/2022] [Indexed: 01/14/2023]
Abstract
Systemic lupus erythematosus (SLE, OMIM 152700) is a rare autoimmune disease with high heritability that affects ~0.1% of the population. Previous studies have revealed several common variants with small effects in European and East Asian SLE patients. However, there is still no rare variant study on Chinese SLE patients using the whole-genome sequencing technology (WGS). Here, we designed a family based WGS study to identify novel rare variants with large effects. Based on large-scale allele frequency data from the gnomAD database, we identified rare protein-coding gene variants with disruptive and sequence-altering impacts in SLE patients. We found that the burden of rare variants was significantly higher than that of common variants in patients, suggesting a larger effect of rare variants on the SLE pathogenesis. We identified the pathogenic risk of rare missense variants with significant odds ratios (p < 0.05) in two genes, including WNT16 (NC_000007.14:g.121329757G > C, NP_057171.2:p.(Ala86Pro) and 7 g.121329760G > C, NP_057171.2:p.(Ala87Pro)), which explains five out of seven patients covering all three families but are absent from all controls, and ERVW-1 (NC_000007.14:g.92469882A > G, NP_001124397.1:p.(Leu167Pro), rs74545114; NC_000007.14:g.92469907G > A, NP_001124397.1:p.(Arg159Cys), rs201142302; NC_000007.14:g.92469919G > A, NP_001124397.1:p.(His155Tyr), rs199552228), which explains the other two patients. None of these variants were identified in any of the controls. These associations are supported by known gene expression studies in SLE patients based on literature review. We further tested the wild and mutant types using the luciferase assays and qPCR in cells. We found that WNT16 can activate the canonical Wnt/β-catenin pathway while the mutant cannot. Additionally, the wild ERVW-1 expression can be significantly up-regulated by cAMP while the mutant cannot. Our study provides the first direct genetic and in vitro evidence for the pathogenic risk of mutant WNT16 and ERVW-1, which may facilitate the design of precision therapy for SLE.
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Affiliation(s)
- Jianhai Chen
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China; Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ping Zhang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Haidi Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuefei He
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jie Zhong
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - HuaPing Zheng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoyu Li
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | | | - Yong Zhang
- Key Laboratory of Transplant Engineering and Immunology, Ministry of Health, Institutes for Systems Genetics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, China
| | - Younan Chen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Cheng Deng
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yongkang Wu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
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Transgenerational Transcriptomic and DNA Methylome Profiling of Mouse Fetal Testicular Germline and Somatic Cells after Exposure of Pregnant Mothers to Tributyltin, a Potent Obesogen. Metabolites 2022; 12:metabo12020095. [PMID: 35208169 PMCID: PMC8874857 DOI: 10.3390/metabo12020095] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/03/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
Obesogens such as tributyltin (TBT) are xenobiotic compounds that promote obesity, in part by distorting the normal balance of lipid metabolism. The obesogenic effects of TBT can be observed in directly exposed (F1 and F2 generations) and also subsequent generations (F3 and beyond) that were never exposed. To address the effects of TBT exposure on germ cells, we exposed pregnant transgenic OG2 mouse dams (F0), which specifically express EGFP in germline cells, to an environmentally relevant dose of TBT or DMSO throughout gestation through drinking water. When fed with a high-fat diet, F3 male offspring of TBT-exposed F0 dams (TBT-F3) accumulated much more body fat than did DMSO-F3 males. TBT-F3 males also lost more body fluid and lean compositions than did DMSO-F3 males. Expression of genes involved in transcriptional regulation or mesenchymal differentiation was up-regulated in somatic cells of TBT-F1 (but not TBT-F3) E18.5 fetal testes, and promoter-associated CpG islands were hyper-methylated in TBT-F1 somatic cells. Global mRNA expression of protein-coding genes in F1 or F3 fetal testicular cells was unaffected by F0 exposure to TBT; however, expression of a subset of endogenous retroviruses was significantly affected in F1 and F3. We infer that TBT may directly target testicular somatic cells in F1 testes to irreversibly affect epigenetic suppression of endogenous retroviruses in both germline and somatic cells.
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Buttler CA, Chuong EB. Emerging roles for endogenous retroviruses in immune epigenetic regulation. Immunol Rev 2022; 305:165-178. [PMID: 34816452 PMCID: PMC8766910 DOI: 10.1111/imr.13042] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/21/2021] [Accepted: 11/12/2021] [Indexed: 01/03/2023]
Abstract
In recent years, there has been significant progress toward understanding the transcriptional networks underlying mammalian immune responses, fueled by advances in regulatory genomic technologies. Epigenomic studies profiling immune cells have generated detailed genome-wide maps of regulatory elements that will be key to deciphering the regulatory networks underlying cellular immune responses and autoimmune disorders. Unbiased analyses of these genomic maps have uncovered endogenous retroviruses as an unexpected ally in the regulation of human immune systems. Despite their parasitic origins, studies are finding an increasing number of examples of retroviral sequences having been co-opted for beneficial immune function and regulation by the host cell. Here, we review how endogenous retroviruses have given rise to numerous regulatory elements that shape the epigenetic landscape of host immune responses. We will discuss the implications of these elements on the function, dysfunction, and evolution of innate immunity.
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