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Wieland L, Schwarz T, Engel K, Volkmer I, Krüger A, Tarabuko A, Junghans J, Kornhuber ME, Hoffmann F, Staege MS, Emmer A. Epstein-Barr Virus-Induced Genes and Endogenous Retroviruses in Immortalized B Cells from Patients with Multiple Sclerosis. Cells 2022; 11:cells11223619. [PMID: 36429047 PMCID: PMC9688211 DOI: 10.3390/cells11223619] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/28/2022] [Accepted: 11/06/2022] [Indexed: 11/18/2022] Open
Abstract
The immune pathogenesis of multiple sclerosis (MS) is thought to be triggered by environmental factors in individuals with an unfavorable genetic predisposition. Epstein-Barr virus (EBV) infection is a major risk factor for subsequent development of MS. Human endogenous retroviruses (HERVs) can be activated by EBV, and might be a missing link between an initial EBV infection and the later onset of MS. In this study, we investigated differential gene expression patterns in EBV-immortalized lymphoblastoid B cell lines (LCL) from MS-affected individuals (MSLCL) and controls by using RNAseq and qRT-PCR. RNAseq data from LCL mapped to the human genome and a virtual virus metagenome were used to identify possible biomarkers for MS or disease-relevant risk factors, e.g., the relapse rate. We observed that lytic EBNA-1 transcripts seemed to be negatively correlated with age leading to an increased expression in LCL from younger PBMC donors. Further, HERV-K (HML-2) GAG was increased upon EBV-triggered immortalization. Besides the well-known transactivation of HERV-K18, our results suggest that another six HERV loci are up-regulated upon stimulation with EBV. We identified differentially expressed genes in MSLCL, e.g., several HERV-K loci, ERVMER61-1 and ERV3-1, as well as genes associated with relapses. In summary, EBV induces genes and HERV in LCL that might be suitable as biomarkers for MS or the relapse risk.
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Affiliation(s)
- Lisa Wieland
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Tommy Schwarz
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Kristina Engel
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Ines Volkmer
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Anna Krüger
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Alexander Tarabuko
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Jutta Junghans
- Department of Neurology, Martha-Maria Hospital Halle-Dölau, 06120 Halle (Saale), Germany
| | - Malte E. Kornhuber
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
| | - Frank Hoffmann
- Department of Neurology, Martha-Maria Hospital Halle-Dölau, 06120 Halle (Saale), Germany
| | - Martin S. Staege
- Department of Surgical and Conservative Pediatrics and Adolescent Medicine, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
- Correspondence: ; Tel.: +49-34-5557-7280
| | - Alexander Emmer
- Department of Neurology, Medical Faculty, Martin Luther University Halle-Wittenberg, 06120 Halle (Saale), Germany
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Wang Q, Chang W, Yang X, Cheng Y, Zhao X, Zhou L, Li J, Li J, Zhang K. Levels of miR-31 and its target genes in dermal mesenchymal cells of patients with psoriasis. Int J Dermatol 2018; 58:198-204. [PMID: 30198149 DOI: 10.1111/ijd.14197] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 06/27/2018] [Accepted: 08/01/2018] [Indexed: 12/13/2022]
Abstract
BACKGROUND Psoriasis is characterized by chronic inflammatory dermatosis, and the pathogenesis of psoriasis is associated with mesenchymal stem cells (MSCs) and deregulation of the expression of miR-31. This study aimed to clarify the function of miR-31 in dermal MSCs (DMSCs) in the pathogenesis of psoriasis. METHODS The expression of miR-31 was assayed by a microarray and that of target genes of miR-31 was tested by quantitative PCR. RESULTS The expression of miR-31 in the psoriasis group was 0.2677 folds that of the control group. The expression of EMP1 and EIG121L genes, whose products are located on the cell membrane, in the psoriasis group was 4.095579 and 5.367017 folds that in the control group, respectively. The expression of GRB10, PTPN14, QKI, RNF144B, and TACC2 genes, whose products are located in the cytoplasm, in the psoriasis group was 1.440428, 1.198335, 1.737285, 7.379546, and 1.531947 folds that of the control. The expression of PRELP, whose products are secreted in the extracellular space, in the psoriasis group was 1.351684 folds that of the control. The expression of RBMS1, KHDRBS3, and SATB2, whose products play a role in the nucleus, in the psoriasis group was 2.237199, 1.277159, and 1.005742 folds that of the control, respectively. CONCLUSIONS Our results suggest that the low expression of miR-31 in DMSCs in patients with psoriasis causes an increase in the expression of some of its target genes, which in turn facilitates T lymphocyte activation by inhibiting the proliferation of DMSCs and therefore participates in the pathogenesis of psoriasis.
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Affiliation(s)
- Qiang Wang
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Wenjuan Chang
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Xiaohong Yang
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Yueai Cheng
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Xincheng Zhao
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Ling Zhou
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Juan Li
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Junqin Li
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
| | - Kaiming Zhang
- Shanxi Key Laboratory of stem cell for Immunological Dermatosis, Institute of Dermatology, Taiyuan City Centre Hospital, Taiyuan, Shanxi Province, China
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Tan Q, Ku W, Zhang C, Heyilimu P, Tian Y, Ke Y, Lu Z. Mutation analysis of the EBV-lymphoblastoid cell line cautions their use as antigen-presenting cells. Immunol Cell Biol 2018; 96:204-211. [PMID: 29363169 DOI: 10.1111/imcb.1030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/10/2017] [Accepted: 11/10/2017] [Indexed: 12/13/2022]
Abstract
Lymphoblastoid cell lines (LCLs) have been widely used as professional antigen-presenting cells (APCs). However, neoantigen-loaded LCLs could induce nonspecific T-cell response, which could be due to expression of both Epstein-Barr virus (EBV) antigens and nonsynonymous mutations arising in LCLs. Since the number of passages could influence mutational characteristics of LCLs, and moreover extensive proliferation of LCLs in vitro is necessary to activate T cells for immunotherapy, we comprehensively profiled mutational characteristics by comparing eight sets of B cells and matched high-passage LCLs using whole-exome sequencing in order to assess the effect of nonsynonymous mutations arising in LCLs on nonspecific T-cell response. We found 315 nongermline mutations (approximately 40mut/subject) randomly distributed across all chromosomes including 18 mutations in immunoglobulin V and J genes in eight LCLs, of which 137 candidate neoantigens (approximately 17mut/subject) were identified. The underlying mutational processes linked to EBV-transformed LCLs could be attributed to activation induced cytidine deaminase gene expression which contributes to cytosine mutation clusters in LCLs through cytosine deamination. Pathways significantly enriched by nonsilent mutations of each LCL were totally different among all LCLs. In conclusion, high-passage LCLs may not be suitable to serve as APCs due to random nonsilent mutations, particularly for presentation of neoantigens of low immunogenicity, although further experimental proofs are needed.
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Affiliation(s)
- Qin Tan
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Wenjing Ku
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Chaoting Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Palashati Heyilimu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
| | - Yuan Tian
- Department of Radiation Oncology, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong, China
| | - Yang Ke
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Laboratory of Genetics, Peking University Cancer Hospital & Institute, Beijing, China
| | - Zheming Lu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Biochemistry and Molecular Biology, Peking University Cancer Hospital & Institute, Beijing, China
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Tschochner M, Leary S, Cooper D, Strautins K, Chopra A, Clark H, Choo L, Dunn D, James I, Carroll WM, Kermode AG, Nolan D. Identifying Patient-Specific Epstein-Barr Nuclear Antigen-1 Genetic Variation and Potential Autoreactive Targets Relevant to Multiple Sclerosis Pathogenesis. PLoS One 2016; 11:e0147567. [PMID: 26849221 PMCID: PMC4744032 DOI: 10.1371/journal.pone.0147567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 01/05/2016] [Indexed: 12/15/2022] Open
Abstract
Background Epstein-Barr virus (EBV) infection represents a major environmental risk factor for multiple sclerosis (MS), with evidence of selective expansion of Epstein-Barr Nuclear Antigen-1 (EBNA1)-specific CD4+ T cells that cross-recognize MS-associated myelin antigens in MS patients. HLA-DRB1*15-restricted antigen presentation also appears to determine susceptibility given its role as a dominant risk allele. In this study, we have utilised standard and next-generation sequencing techniques to investigate EBNA-1 sequence variation and its relationship to HLA-DR15 binding affinity, as well as examining potential cross-reactive immune targets within the central nervous system proteome. Methods Sanger sequencing was performed on DNA isolated from peripheral blood samples from 73 Western Australian MS cases, without requirement for primary culture, with additional FLX 454 Roche sequencing in 23 samples to identify low-frequency variants. Patient-derived viral sequences were used to predict HLA-DRB1*1501 epitopes (NetMHCII, NetMHCIIpan) and candidates were evaluated for cross recognition with human brain proteins. Results EBNA-1 sequence variation was limited, with no evidence of multiple viral strains and only low levels of variation identified by FLX technology (8.3% nucleotide positions at a 1% cut-off). In silico epitope mapping revealed two known HLA-DRB1*1501-restricted epitopes (‘AEG’: aa 481–496 and ‘MVF’: aa 562–577), and two putative epitopes between positions 502–543. We identified potential cross-reactive targets involving a number of major myelin antigens including experimentally confirmed HLA-DRB1*15-restricted epitopes as well as novel candidate antigens within myelin and paranodal assembly proteins that may be relevant to MS pathogenesis. Conclusions This study demonstrates the feasibility of obtaining autologous EBNA-1 sequences directly from buffy coat samples, and confirms divergence of these sequences from standard laboratory strains. This approach has identified a number of immunogenic regions of EBNA-1 as well as known and novel targets for autoreactive HLA-DRB1*15-restricted T cells within the central nervous system that could arise as a result of cross-reactivity with EBNA-1-specific immune responses.
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Affiliation(s)
- Monika Tschochner
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- * E-mail:
| | - Shay Leary
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Don Cooper
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Kaija Strautins
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Abha Chopra
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Hayley Clark
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Linda Choo
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - David Dunn
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - Ian James
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
| | - William M. Carroll
- Department of Neurology, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Centre for Neuromuscular and Neurological Disorders, Australian Neuromuscular Research Institute, Nedlands, Western Australia, Australia
| | - Allan G. Kermode
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Department of Neurology, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
- Centre for Neuromuscular and Neurological Disorders, Australian Neuromuscular Research Institute, Nedlands, Western Australia, Australia
| | - David Nolan
- Institute for Immunology & Infectious Diseases, Murdoch University, Perth, Western Australia, Australia
- Department of Clinical Immunology, Royal Perth Hospital, Perth, Western Australia, Australia
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