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Daei Sorkhabi A, Komijani E, Sarkesh A, Ghaderi Shadbad P, Aghebati-Maleki A, Aghebati-Maleki L. Advances in immune checkpoint-based immunotherapies for multiple sclerosis: rationale and practice. Cell Commun Signal 2023; 21:321. [PMID: 37946301 PMCID: PMC10634124 DOI: 10.1186/s12964-023-01289-9] [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: 05/11/2023] [Accepted: 08/19/2023] [Indexed: 11/12/2023] Open
Abstract
Beyond the encouraging results and broad clinical applicability of immune checkpoint (ICP) inhibitors in cancer therapy, ICP-based immunotherapies in the context of autoimmune disease, particularly multiple sclerosis (MS), have garnered considerable attention and hold great potential for developing effective therapeutic strategies. Given the well-established immunoregulatory role of ICPs in maintaining a balance between stimulatory and inhibitory signaling pathways to promote immune tolerance to self-antigens, a dysregulated expression pattern of ICPs has been observed in a significant proportion of patients with MS and its animal model called experimental autoimmune encephalomyelitis (EAE), which is associated with autoreactivity towards myelin and neurodegeneration. Consequently, there is a rationale for developing immunotherapeutic strategies to induce inhibitory ICPs while suppressing stimulatory ICPs, including engineering immune cells to overexpress ligands for inhibitory ICP receptors, such as program death-1 (PD-1), or designing fusion proteins, namely abatacept, to bind and inhibit the co-stimulatory pathways involved in overactivated T-cell mediated autoimmunity, and other strategies that will be discussed in-depth in the current review. Video Abstract.
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Affiliation(s)
- Amin Daei Sorkhabi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Erfan Komijani
- Department of Veterinary, Medicine, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Aila Sarkesh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pedram Ghaderi Shadbad
- Department of Veterinary, Medicine, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | - Ali Aghebati-Maleki
- Stem Cell Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Leili Aghebati-Maleki
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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2
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Lezhnyova V, Davidyuk Y, Mullakhmetova A, Markelova M, Zakharov A, Khaiboullina S, Martynova E. Analysis of herpesvirus infection and genome single nucleotide polymorphism risk factors in multiple sclerosis, Volga federal district, Russia. Front Immunol 2022; 13:1010605. [PMID: 36451826 PMCID: PMC9703080 DOI: 10.3389/fimmu.2022.1010605] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/03/2022] [Indexed: 09/29/2023] Open
Abstract
Multiple sclerosis (MS) is a heterogeneous disease where herpesvirus infection and genetic predisposition are identified as the most consistent risk factors. Serum and blood samples were collected from 151 MS and 70 controls and used to analyze circulating antibodies for, and DNA of, Epstein Barr virus (EBV), human cytomegalovirus (HCMV), human herpes virus 6 (HHV6), and varicella zoster virus (VZV). The frequency of selected single nucleotide polymorphisms (SNPs) in MS and controls were studied. Herpesvirus DNA in blood samples were analyzed using qPCR. Anti-herpesvirus antibodies were detected by ELISA. SNPs were analyzed by the allele-specific PCR. For statistical analysis, Fisher exact test, odds ratio and Kruskall-Wallis test were used; p<0.05 values were considered as significant. We have found an association between circulating anti-HHV6 antibodies and MS diagnosis. We also confirmed higher frequency of A and C alleles in rs2300747 and rs12044852 of CD58 gene and G allele in rs929230 of CD6 gene in MS as compared to controls. Fatigue symptom was linked to AC and AA genotype in rs12044852 of CD58 gene. An interesting observation was finding higher frequency of GG genotype in rs12722489 of IL2RA and T allele in rs1535045 of CD40 genes in patient having anti-HHV6 antibodies. A link was found between having anti-VZV antibodies in MS and CC genotype in rs1883832 of CD40 gene.
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Affiliation(s)
- Vera Lezhnyova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Yuriy Davidyuk
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Asia Mullakhmetova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Maria Markelova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Alexander Zakharov
- Department of Neurology and Neurosurgery, Samara State Medical University, Samara, Russia
| | - Svetlana Khaiboullina
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
| | - Ekaterina Martynova
- Institute of Fundamental Medicine and Biology, Kazan (Volga Region) Federal University, Kazan, Russia
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3
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Al-Eitan L, Al Qudah M, Al Qawasmeh M. Candidate gene association analysis of multiple sclerosis in the Jordanian Arab population: A case-control study. Gene 2020; 758:144959. [PMID: 32683075 DOI: 10.1016/j.gene.2020.144959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/12/2020] [Accepted: 07/13/2020] [Indexed: 01/21/2023]
Abstract
Multiple sclerosis (MS) is a clinically heterogeneous multifactorial disorder which is one of the most prevalent neurological disorders of females and young people. Both genetic and environmental factors are playing an important role in the pathophysiology of MS. The main objective of this study is to identify the relationship between numbers of genetic variants within different candidate genes (IL7R, LAG3, and CD40) and the risk of developing MS in the Jordanian Arab population. This case-control study consists of 218 MS patients chosen from neurology clinics at different hospitals in Jordan and ethnically matched 227 healthy controls. Genomic DNA was extracted from blood samples. Genotyping of the candidate gene polymorphisms was conducted using the Sequenom MassARRAY system. Statistical analysis was performed to identify the genetic association of the studied SNPs with MS. Twenty-one variants were studied, three of them were found to be associated with MS (rs6897932 (P-value = 0.01) and rs13188960 (P-value = 0.005) within IL7R gene and LAG3 rs2365095, (P-value = 0.03) within LAG3 gene). Moreover, no significant association was found between MS and the genetic polymorphisms of the CD40 gene. After correction for multiple comparisons, only rs13188960 SNP remained significantly with MS. This is the first study of the genetic association with MS in the Jordanian Arab population to provided evidence of the genetic association of IL7R (rs6897932, rs13188960) and LAG3 (rs2365095) gene polymorphisms with MS. These findings may contribute to our understanding of MS and optimize the therapy protocol for individuals.
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Affiliation(s)
- Laith Al-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan; Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan.
| | - Malak Al Qudah
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Majdi Al Qawasmeh
- Department of Neuroscience, Division of Neurology, Faculty of Medicine, Jordan University of Science and Technology, 22110, Jordan
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4
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Mohammadhosayni M, Khosrojerdi A, Lorian K, Aslani S, Imani D, Razi B, Babaie F, Torkamandi S. Matrix metalloproteinases (MMPs) family gene polymorphisms and the risk of multiple sclerosis: systematic review and meta-analysis. BMC Neurol 2020; 20:218. [PMID: 32471473 PMCID: PMC7257507 DOI: 10.1186/s12883-020-01804-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/24/2020] [Indexed: 01/11/2023] Open
Abstract
Background Several studies have reported the association between polymorphisms in Matrix metalloproteinases (MMPs) gene family and risk of Multiple sclerosis (MS). However, the results have been inconsistent and inconclusive. To resolve this issue, here we performed a systematic review and meta-analysis of the MMP-91562 C/T (rs3918242), MMP-3 (− 1612 5A/6A), and MMP-2 (− 1306 C/T) polymorphisms and susceptibility to MS. Methods We conducted a comprehensive systematic search in the major electronic database, including Scopus and PubMed to look up for relevant studies published before December 2019 that surveyed the association between the MMP-91562 C/T (rs3918242), MMP-3 (− 1612 5A/6A), and MMP-2 (− 1306 C/T) polymorphisms and susceptibility to MS. The level of association between the polymorphisms and susceptibility to MS in the polled analysis was determined by calculating the odds ratio (OR) and the corresponding 95% confidence interval (CI). Results We found 15 studies containing 2430 MS subjects and 2304 controls. A statistically significant association was observed in the all five comparisons of the MMP-91562 C/T polymorphism and MS risk as follows: dominant model (OR = 1.62, 95% CI = 1.03–2.53, P = 0.03), recessive model (OR = 2.69, 95% CI = 1.68–4.29, P < 0.001), allelic model (OR = 1.51, 95% CI = 1–2.28, P = 0.04), TT vs. CC model (OR = 3.20, 95% CI = 1.87–5.46, P < 0.001), and CT vs. CC model (OR = 1.53, 95% CI = 1.02–2.28, P = 0.04). Conclusions Our meta-analysis revealed significant association of MMP-9 (− 1562 C/T) Single-nucleotide polymorphism (SNP) with MS susceptibility that increased the disease risk.
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Affiliation(s)
| | - Arezou Khosrojerdi
- Department of Medical Immunology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Keivan Lorian
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Saeed Aslani
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Danyal Imani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Bahman Razi
- Department of Hematology and Blood Transfusion, School of Medicine, Tarbiat Modares University, Tehran, Iran
| | - Farhad Babaie
- Cellular and Molecular Research Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Shahram Torkamandi
- Department of Medical Genetics and Immunology, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran.
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Cacabelos R. Pharmacogenomics of drugs used to treat brain disorders. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020. [DOI: 10.1080/23808993.2020.1738217] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ramon Cacabelos
- International Center of Neuroscience and Genomic Medicine, EuroEspes Biomedical Research Center, Corunna, Spain
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6
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AL-Eitan L, Al Qudah M, Al Qawasmeh M. Association of Multiple Sclerosis Phenotypes with Single Nucleotide Polymorphisms of IL7R, LAG3, and CD40 Genes in a Jordanian Population: A Genotype-Phenotype Study. Biomolecules 2020; 10:biom10030356. [PMID: 32111053 PMCID: PMC7175123 DOI: 10.3390/biom10030356] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 02/17/2020] [Accepted: 02/20/2020] [Indexed: 01/01/2023] Open
Abstract
It is thought that genetic variations play a vital role in the Multiple Sclerosis (MS) etiology. However, the role of genetic factors that influence the clinical features of MS remains unclear. We investigated the correlation between 21 single nucleotide polymorphisms within three genes (IL7R, LAG3, and CD40) and MS clinical characteristics in the Jordanian population. Blood samples and clinical phenotypic data were collected from 218 Arab Jordanian MS patients, vitamin D was measured, genomic DNA was extracted, and genotyping of the candidate genes’ polymorphisms were analyzed using the Sequenom MassARRAY® system. The association of these single nucleotide polymorphisms (SNPs) with MS was performed using a Chi-square, Fisher exact test, and one-way ANOVA. We found a significant association between vitamin D deficiency and three SNPs of the IL7R gene, namely rs987107 (P-value = 0.047), rs3194051 (P-value = 0.03), and rs1494571 (P-value = 0.036), in addition to two SNPs of CD40, namely rs1883832 and rs6074022 (P-value = 0.049 for both). rs3194051 of the IL7R gene (P-value = 0.003) and rs1922452 of the LAG3 gene (P-value = 0.028) were strongly associated with comorbidity. The number of relapses before drug onset was found to be correlated with IL7R SNPs rs969128 (P-value = 0.04) and rs1494555 (P-value = 0.027), whereas the expanded disability status scale (EDSS) was associated with rs1494555 polymorphism of IL7R gene (P-value = 0.026). Current findings indicate important correlations between certain SNPs and the risk of various phenotypes of multiple sclerosis in the Jordanian community. Therefore, this will not only contribute to the understanding of MS, but will also assist with the development of personalized treatment procedures.
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Affiliation(s)
- Laith AL-Eitan
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan;
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
- Correspondence: ; Tel.: +962-2-720-1000 (ext. 23464); Fax: +962-2-720-1071
| | - Malak Al Qudah
- Department of Applied Biological Sciences, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Majdi Al Qawasmeh
- Department of Neuroscience, Division of Neurology, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan;
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7
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Tapia-Llanos R, Muñoz-Valle JF, Román-Fernández IV, Marín-Rosales M, Salazar-Camarena DC, Cruz A, Orozco-Barocio G, Guareña-Casillas JA, Oregon-Romero E, Palafox-Sánchez CA. Association of soluble CD40 levels with -1 C > T CD40 polymorphism and chronic kidney disease in systemic lupus erythematosus. Mol Genet Genomic Med 2019; 7:e1014. [PMID: 31642196 PMCID: PMC6900383 DOI: 10.1002/mgg3.1014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/25/2019] [Accepted: 10/07/2019] [Indexed: 12/17/2022] Open
Abstract
Background CD40 is a transmembrane protein mainly expressed on the antigen‐presenting cells surface. CD40 plays a crucial role in immunoglobulin class switching and antibodies production. Genetic polymorphisms in the CD40 gene have been associated with increased risk of systemic lupus erythematosus (SLE) in several populations. This study aimed to evaluate the association of CD40 polymorphisms (−1 C > T, rs1883832 and 6,048 G > T, rs4810485) with SLE susceptibility, as well as with mRNA expression and soluble CD40 (sCD40) levels. Methods The study included 293 patients with SLE and 294 control subjects (CS). Genotyping was performed by PCR‐RFLP method. CD40 mRNA expression was determined by quantitative real‐time PCR, and ELISA quantified sCD40 levels. Results The CD40 polymorphisms −1 C > T and 6,048 G > T were associated with SLE susceptibility. There was no difference between CD40 mRNA expression and CD40 polymorphisms. The sCD40 levels were lower in SLE patients with TT haplotype, whereas higher sCD40 levels were associated with damage and impaired renal function according to SLICC and KDIGO. The sCD40 levels were negatively correlated with eGFR. Conclusion The CD40 gene polymorphisms increase the risk of SLE in the western Mexican population. The sCD40 levels are associated with −1 C > T polymorphism and chronic kidney disease.
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Affiliation(s)
- Raziel Tapia-Llanos
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico.,Doctorado en Biología Molecular en Medicina, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - José F Muñoz-Valle
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Ilce V Román-Fernández
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Miguel Marín-Rosales
- Departamento de Reumatología, Hospital General de Occidente, Secretaría de Salud Jalisco, Guadalajara, Mexico
| | - Diana C Salazar-Camarena
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Alvaro Cruz
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Gerardo Orozco-Barocio
- Departamento de Reumatología, Hospital General de Occidente, Secretaría de Salud Jalisco, Guadalajara, Mexico
| | - Jorge A Guareña-Casillas
- Especialidad de Hemodinamia y Cardiología Intervencionista, Hospital Civil de Guadalajara Fray Antonio Alcalde, Universidad de Guadalajara, Guadalajara, Mexico
| | - Edith Oregon-Romero
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
| | - Claudia A Palafox-Sánchez
- Instituto de Investigación en Ciencias Biomédicas, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Mexico
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8
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Li H, Chen L, Ma X, Cui P, Lang W, Hao J. Shared Gene Expression Between Multiple Sclerosis and Ischemic Stroke. Front Genet 2019; 9:598. [PMID: 30809253 PMCID: PMC6379658 DOI: 10.3389/fgene.2018.00598] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/15/2018] [Indexed: 01/22/2023] Open
Abstract
Patients with multiple sclerosis (MS) appear to have an increased risk of ischemic stroke (IS). Although MS and IS have very different phenotypes, gene-based and pathway-based analyses of large-scale genome-wide association studies (GWAS) have increasingly enhanced our understanding of these two diseases. Whether there are common molecular mechanisms connecting MS and IS is still unclear. Here, we describe the outcome of gene-based test and pathway-based analysis of GWAS datasets that explored potential gene expression links between MS and IS. After identifying significant gene sets individually of MS and IS, we performed pathway-based analysis in four biological pathway databases (KEGG, PANTHER, REACTOME, and WikiPathways) and GO categories. We discovered that there were 9 shared pathways between MS and IS in KEGG, 2 in PANTHER, 14 in REACTOME, 1 in WikiPathways, and 194 in GO annotations (p < 0.05). These results provide an improved understanding about possible shared mechanisms and treatments strategies for MS and IS. They also provide some basis for further studies of how these two diseases are linked at the molecular level.
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Affiliation(s)
- He Li
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Lin Chen
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Xiaofeng Ma
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Pan Cui
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Wenjing Lang
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
| | - Junwei Hao
- Department of Neurology and Tianjin Neurological Institute, General Hospital, Tianjin Medical University, Tianjin, China.,Key Laboratory of Post-Neuroinjury Neuro-Repair and Regeneration in Central Nervous System, Tianjin Neurological Institute, Tianjin Medical University General Hospital, Ministry of Education and Tianjin City, Tianjin, China
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9
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Li G, Martínez-Bonet M, Wu D, Yang Y, Cui J, Nguyen HN, Cunin P, Levescot A, Bai M, Westra HJ, Okada Y, Brenner MB, Raychaudhuri S, Hendrickson EA, Maas RL, Nigrovic PA. High-throughput identification of noncoding functional SNPs via type IIS enzyme restriction. Nat Genet 2018; 50:1180-1188. [PMID: 30013183 PMCID: PMC6072570 DOI: 10.1038/s41588-018-0159-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Accepted: 05/04/2018] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies (GWAS) have identified many disease-associated noncoding variants, but cannot distinguish functional single-nucleotide polymorphisms (fSNPs) from others that reside incidentally within risk loci. To address this challenge, we developed an unbiased high-throughput screen that employs type IIS enzymatic restriction to identify fSNPs that allelically modulate the binding of regulatory proteins. We coupled this approach, termed SNP-seq, with flanking restriction enhanced pulldown (FREP) to identify regulation of CD40 by three disease-associated fSNPs via four regulatory proteins, RBPJ, RSRC2 and FUBP-1/TRAP150. Applying this approach across 27 loci associated with juvenile idiopathic arthritis, we identified 148 candidate fSNPs, including two that regulate STAT4 via the regulatory proteins SATB2 and H1.2. Together, these findings establish the utility of tandem SNP-seq/FREP to bridge the gap between GWAS and disease mechanism.
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Affiliation(s)
- Gang Li
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Cardiology and The Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Marta Martínez-Bonet
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Di Wu
- Department of Periodontology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yu Yang
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Cardiology and The Aging Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jing Cui
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Hung N Nguyen
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Pierre Cunin
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anaïs Levescot
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Ming Bai
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Harm-Jan Westra
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Michael B Brenner
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Soumya Raychaudhuri
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- School of Biological Sciences, University of Manchester, Manchester, UK
| | - Eric A Hendrickson
- Biochemistry, Molecular Biology and Biophysics Department, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Richard L Maas
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Peter A Nigrovic
- Division of Rheumatology, Immunology and Allergy, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Division of Immunology, Boston Children's Hospital, Boston, MA, USA.
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10
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de J. Guerrero-García J, Rojas-Mayorquín AE, Valle Y, Padilla-Gutiérrez JR, Castañeda-Moreno VA, Mireles-Ramírez MA, Muñoz-Valle JF, Ortuño-Sahagún D. Decreased serum levels of sCD40L and IL-31 correlate in treated patients with Relapsing-Remitting Multiple Sclerosis. Immunobiology 2018; 223:135-141. [DOI: 10.1016/j.imbio.2017.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/09/2017] [Accepted: 10/03/2017] [Indexed: 01/21/2023]
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11
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Aarts SABM, Seijkens TTP, van Dorst KJF, Dijkstra CD, Kooij G, Lutgens E. The CD40-CD40L Dyad in Experimental Autoimmune Encephalomyelitis and Multiple Sclerosis. Front Immunol 2017; 8:1791. [PMID: 29312317 PMCID: PMC5732943 DOI: 10.3389/fimmu.2017.01791] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022] Open
Abstract
The CD40-CD40L dyad is an immune checkpoint regulator that promotes both innate and adaptive immune responses and has therefore an essential role in the development of inflammatory diseases, including multiple sclerosis (MS). In MS, CD40 and CD40L are expressed on immune cells present in blood and lymphoid organs, affected resident central nervous system (CNS) cells, and inflammatory cells that have infiltrated the CNS. CD40-CD40L interactions fuel the inflammatory response underlying MS, and both genetic deficiency and antibody-mediated inhibition of the CD40-CD40L dyad reduce disease severity in experimental autoimmune encephalomyelitis (EAE). Both proteins are therefore attractive therapeutic candidates to modulate aberrant inflammatory responses in MS. Here, we discuss the genetic, experimental and clinical studies on the role of CD40 and CD40L interactions in EAE and MS and we explore novel approaches to therapeutically target this dyad to combat neuroinflammatory diseases.
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Affiliation(s)
- Suzanne A. B. M. Aarts
- Department of Medical Biochemistry, Subdivision of Experimental Vascular Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Tom T. P. Seijkens
- Department of Medical Biochemistry, Subdivision of Experimental Vascular Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University (LMU), Munich, Germany
| | | | - Christine D. Dijkstra
- Department of Molecular Cell Biology and Immunology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Gijs Kooij
- Department of Molecular Cell Biology and Immunology, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, Netherlands
| | - Esther Lutgens
- Department of Medical Biochemistry, Subdivision of Experimental Vascular Biology, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Institute for Cardiovascular Prevention (IPEK), Ludwig Maximilians University (LMU), Munich, Germany
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12
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A comprehensive analysis of the association of common variants of ABCG2 with gout. Sci Rep 2017; 7:9988. [PMID: 28855613 PMCID: PMC5577061 DOI: 10.1038/s41598-017-10196-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 08/04/2017] [Indexed: 12/27/2022] Open
Abstract
The objective of the present study was to determine whether there was an association between single nucleotide polymorphisms (SNPs) in ABCG2 and gout. We recruited 333 participants including 210 patients with gout and 123 controls and genotyped 45 SNPs in both cohorts. We found that 24 SNPs in ABCG2 are susceptibility loci associated with gout. Haplotype analysis revealed five blocks across the ABCG2 locus were associated with an increased risk of gout with odds ratios (ORs) from 2.59–3.17 (all P < 0.0001). A novel finding in the present study was the identification of rs3114018 in block 3 and its association with increased gout risk. We found that the rs2231142T allele in block 2 and the rs3114018C-rs3109823T (C-T) risk haplotype in block 3 conferred the greatest evidence of association to gout risk (P = 1.19 × 10−12 and P = 9.20 × 10−11, respectively). Our study provides an improved understanding of ABCG2 variations in patients with gout and, as shown by haplotype analysis, that ABCG2 may have a role in gout susceptibility.
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Association between CD40 rs1883832 and immune-related diseases susceptibility: A meta-analysis. Oncotarget 2017; 8:102235-102243. [PMID: 29254239 PMCID: PMC5731949 DOI: 10.18632/oncotarget.18704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/17/2017] [Indexed: 12/31/2022] Open
Abstract
Background/objective It has been reported that CD40 rs1883832 might be associated with immune-related diseases susceptibility. Owing to mixed and inconclusive results, we conducted a meta-analysis of case–control studies to summarize and clarify this association. Methods/main results A systematic search of studies on the association between CD40 rs1883832 and immune-related diseases susceptibility was conducted in databases. Odds ratios and 95% confidence intervals were used to pool the effect size. 40 articles were included in our meta-analysis. Conclusions CD40 rs1883832 is associated with decreased risk of Graves’ disease, especially in Asian; CD40 rs1883832 is associated with increased risk of multiple sclerosis; CD40 -1C>T (rs1883832) is not associated with the susceptibility of Hashimoto's thyroiditis, systemic sclerosis or Asthma; there is insufficient data to fully confirm the association between CD40 rs1883832 and systemic lupus erythematosus (SLE), rheumatoid arthritis (RA), Behçet's disease (BD), myasthenia gravis (MG), Crohn's disease (CD), ulcerative colitis (UC), Sarcoidosis, Fuch uveitis syndrome (FUS), Vogt-Koyanagi-Harada syndrome (VKH), Kawasaki disease (KD), giant cell arteritis (GCA) or Immune thrombocytopenia (ITP).
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14
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Deng ZH, Sun MH, Li YS, Luo W, Zhang FJ, Tian J, Wu P, Xiao WF. Single nucleotide polymorphisms in the CD40 gene associate with the disease susceptibility and severity in knee osteoarthritis in the Chinese Han population: a case-control study. BMC Musculoskelet Disord 2017; 18:115. [PMID: 28320398 PMCID: PMC5360092 DOI: 10.1186/s12891-017-1466-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/18/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND This study explored the association between single nucleotide polymorphisms (SNPs) in the CD40 gene, rs4810485 G > T and rs1883832 C > T, as well as disease susceptibility and severity in knee osteoarthritis (KOA) in the Chinese Han population. METHOD Peripheral venous blood was collected from 133 KOA patients (KOA group) and 143 healthy people (control group) from December 2012 to November 2013. The patients in the KOA group were classified into mild, moderate and severe groups according to disease severity. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to test the genotypes of all subjects. Binary logistic regression analyses were performed to analyze the risk factors for KOA. RESULTS The KOA group was significantly different from the control group in living environment (P < 0.05). The KOA group had a lower frequency of TT genotype and T allele distribution of rs4810485 G > T compared with the control group, and rs4810485 G > T TT genotype and T allele may associate with low incidence of KOA (all P < 0.05). Besides, T allele and mutant homozygous TT genotype of rs1883832 C > T increased the susceptibility to KOA. Genotype and allele distribution of rs4810485 G > T and rs1883832 C > T were significantly different among the mild, moderate and severe groups (P < 0.05). There were more patients with rs4810485 G > T GG genotype and rs1883832 C > T TT genotype in the severe group than other genotypes of these two SNPs. According to binary logistic regression analysis, rs4810485 G > T TT genotype could alleviate disease severity in KOA, rs1883832 C > T TT genotype increase the severity of KOA and living environment is an important external factor that affects KOA severity. CONCLUSIONS These data provide evidences that rs4810485 G > T and rs1883832 C > T in the CD40 gene may be associated with disease susceptibility and severity in KOA.
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Affiliation(s)
- Zhen-Han Deng
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ming-Hua Sun
- Department of Orthopaedics, Affiliated Hospital, Logistics University of Chinese People's Armed Police Forces, Tianjin, 300162, China
| | - Yu-Sheng Li
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Wei Luo
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Fang-Jie Zhang
- Department of Emergency Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Jian Tian
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China
| | - Ping Wu
- Department of Emergency Medicine, Xiangya Hospital, Central South University, Changsha, 410008, China.
| | - Wen-Feng Xiao
- Department of Orthopaedics, Xiangya Hospital, Central South University, Changsha, 410008, China.
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15
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Chen D, Ireland SJ, Remington G, Alvarez E, Racke MK, Greenberg B, Frohman EM, Monson NL. CD40-Mediated NF-κB Activation in B Cells Is Increased in Multiple Sclerosis and Modulated by Therapeutics. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2016; 197:4257-4265. [PMID: 27798157 PMCID: PMC5312703 DOI: 10.4049/jimmunol.1600782] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022]
Abstract
CD40 interacts with CD40L and plays an essential role in immune regulation and homeostasis. Recent research findings, however, support a pathogenic role of CD40 in a number of autoimmune diseases. We previously showed that memory B cells from relapsing-remitting multiple sclerosis (RRMS) patients exhibited enhanced proliferation with CD40 stimulation compared with healthy donors. In this study, we used a multiparameter phosflow approach to analyze the phosphorylation status of NF-κB and three major MAPKs (P38, ERK, and JNK), the essential components of signaling pathways downstream of CD40 engagement in B cells from MS patients. We found that memory and naive B cells from RRMS and secondary progressive MS patients exhibited a significantly elevated level of phosphorylated NF-κB (p-P65) following CD40 stimulation compared with healthy donor controls. Combination therapy with IFN-β-1a (Avonex) and mycophenolate mofetil (Cellcept) modulated the hyperphosphorylation of P65 in B cells of RRMS patients at levels similar to healthy donor controls. Lower disease activity after the combination therapy correlated with the reduced phosphorylation of P65 following CD40 stimulation in treated patients. Additionally, glatiramer acetate treatment also significantly reduced CD40-mediated P65 phosphorylation in RRMS patients, suggesting that reducing CD40-mediated p-P65 induction may be a general mechanism by which some current therapies modulate MS disease.
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Affiliation(s)
- Ding Chen
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Sara J Ireland
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Gina Remington
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Enrique Alvarez
- Department of Neurology, University of Colorado, Aurora, CO 80045
| | - Michael K Racke
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH 43210; and
| | - Benjamin Greenberg
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Elliot M Frohman
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Nancy L Monson
- Department of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX 75390;
- Department of Immunology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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16
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Lill CM, Luessi F, Alcina A, Sokolova EA, Ugidos N, de la Hera B, Guillot-Noël L, Malhotra S, Reinthaler E, Schjeide BMM, Mescheriakova JY, Mashychev A, Wohlers I, Akkad DA, Aktas O, Alloza I, Antigüedad A, Arroyo R, Astobiza I, Blaschke P, Boyko AN, Buttmann M, Chan A, Dörner T, Epplen JT, Favorova OO, Fedetz M, Fernández O, García-Martínez A, Gerdes LA, Graetz C, Hartung HP, Hoffjan S, Izquierdo G, Korobko DS, Kroner A, Kubisch C, Kümpfel T, Leyva L, Lohse P, Malkova NA, Montalban X, Popova EV, Rieckmann P, Rozhdestvenskii AS, Schmied C, Smagina IV, Tsareva EY, Winkelmann A, Zettl UK, Binder H, Cournu-Rebeix I, Hintzen R, Zimprich A, Comabella M, Fontaine B, Urcelay E, Vandenbroeck K, Filipenko M, Matesanz F, Zipp F, Bertram L. Genome-wide significant association with seven novel multiple sclerosis risk loci. J Med Genet 2015; 52:848-55. [DOI: 10.1136/jmedgenet-2015-103442] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/17/2015] [Indexed: 11/04/2022]
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17
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Cassiano GC, Santos EJM, Maia MHT, Furini ADC, Storti-Melo LM, Tomaz FMB, Trindade PCA, Capobianco MP, Amador MAT, Viana GMR, Póvoa MM, Santos SEB, Machado RLD. Impact of population admixture on the distribution of immune response co-stimulatory genes polymorphisms in a Brazilian population. Hum Immunol 2015; 76:836-42. [PMID: 26429313 DOI: 10.1016/j.humimm.2015.09.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 09/08/2014] [Accepted: 09/27/2015] [Indexed: 12/21/2022]
Abstract
Co-stimulatory molecules are essential in the orchestration of immune response and polymorphisms in their genes are associated with various diseases. However, in the case of variable allele frequencies among continental populations, this variation can lead to biases in genetic studies conducted in admixed populations such as those from Brazil. The aim of this study was to evaluate the influence of genomic ancestry on distributions of co-stimulatory genes polymorphisms in an admixed Brazilian population. A total of 273 individuals from the north of Brazil participated in this study. Nine single nucleotide polymorphisms in 7 genes (CD28, CTLA4, ICOS, CD86, CD40, CD40L and BLYS) were determined by polymerase chain reaction-restriction fragment length polymorphism. We also investigated 48 insertion/deletion ancestry markers to characterize individual African, European and Amerindian ancestry proportions in the samples. The analysis showed that the main contribution was European (43.9%) but also a significant contribution of African (31.6%) and Amerindian (24.5%) ancestry. ICOS, CD40L and CD86 polymorphisms were associated with genomic ancestry. However there were no significant differences in the proportions of ancestry for the other SNPs and haplotypes studied. Our findings reinforce the need to apply AIMs in genetic association studies involving these polymorphisms in the Brazilian population.
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Affiliation(s)
- Gustavo Capatti Cassiano
- Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, São José do Rio Preto, Brazil; Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil.
| | | | | | - Adriana da Cruz Furini
- Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil
| | | | - Franciele Maira Batista Tomaz
- Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil
| | | | - Marcela Petrolini Capobianco
- Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, São José do Rio Preto, Brazil; Faculdade de Medicina de São José do Rio Preto, Centro de Investigação de Microrganismos, São José do Rio Preto, Brazil
| | | | - Giselle Maria Rachid Viana
- Laboratório de Pesquisas Básicas em Malária, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ananindeua, Brazil
| | - Marinete Marins Póvoa
- Laboratório de Pesquisas Básicas em Malária, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ananindeua, Brazil
| | | | - Ricardo Luiz Dantas Machado
- Universidade Estadual Paulista, Instituto de Biociências, Letras e Ciências Exatas, São José do Rio Preto, Brazil; Laboratório de Pesquisas Básicas em Malária, Instituto Evandro Chagas, Secretaria de Vigilância em Saúde, Ananindeua, Brazil
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18
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The MS Risk Allele of CD40 Is Associated with Reduced Cell-Membrane Bound Expression in Antigen Presenting Cells: Implications for Gene Function. PLoS One 2015; 10:e0127080. [PMID: 26068105 PMCID: PMC4465929 DOI: 10.1371/journal.pone.0127080] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 04/10/2015] [Indexed: 12/31/2022] Open
Abstract
Human genetic and animal studies have implicated the costimulatory molecule CD40 in the development of multiple sclerosis (MS). We investigated the cell specific gene and protein expression variation controlled by the CD40 genetic variant(s) associated with MS, i.e. the T-allele at rs1883832. Previously we had shown that the risk allele is expressed at a lower level in whole blood, especially in people with MS. Here, we have defined the immune cell subsets responsible for genotype and disease effects on CD40 expression at the mRNA and protein level. In cell subsets in which CD40 is most highly expressed, B lymphocytes and dendritic cells, the MS-associated risk variant is associated with reduced CD40 cell-surface protein expression. In monocytes and dendritic cells, the risk allele additionally reduces the ratio of expression of full-length versus truncated CD40 mRNA, the latter encoding secreted CD40. We additionally show that MS patients, regardless of genotype, express significantly lower levels of CD40 cell-surface protein compared to unaffected controls in B lymphocytes. Thus, both genotype-dependent and independent down-regulation of cell-surface CD40 is a feature of MS. Lower expression of a co-stimulator of T cell activation, CD40, is therefore associated with increased MS risk despite the same CD40 variant being associated with reduced risk of other inflammatory autoimmune diseases. Our results highlight the complexity and likely individuality of autoimmune pathogenesis, and could be consistent with antiviral and/or immunoregulatory functions of CD40 playing an important role in protection from MS.
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19
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Mesbah-Uddin M, Elango R, Banaganapalli B, Shaik NA, Al-Abbasi FA. In-silico analysis of inflammatory bowel disease (IBD) GWAS loci to novel connections. PLoS One 2015; 10:e0119420. [PMID: 25786114 PMCID: PMC4364731 DOI: 10.1371/journal.pone.0119420] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 01/13/2015] [Indexed: 12/19/2022] Open
Abstract
Genome-wide association studies (GWASs) for many complex diseases, including inflammatory bowel disease (IBD), produced hundreds of disease-associated loci—the majority of which are noncoding. The number of GWAS loci is increasing very rapidly, but the process of translating single nucleotide polymorphisms (SNPs) from these loci to genomic medicine is lagging. In this study, we investigated 4,734 variants from 152 IBD associated GWAS loci (IBD associated 152 lead noncoding SNPs identified from pooled GWAS results + 4,582 variants in strong linkage-disequilibrium (LD) (r2 ≥0.8) for EUR population of 1K Genomes Project) using four publicly available bioinformatics tools, e.g. dbPSHP, CADD, GWAVA, and RegulomeDB, to annotate and prioritize putative regulatory variants. Of the 152 lead noncoding SNPs, around 11% are under strong negative selection (GERP++ RS ≥2); and ~30% are under balancing selection (Tajima’s D score >2) in CEU population (1K Genomes Project)—though these regions are positively selected (GERP++ RS <0) in mammalian evolution. The analysis of 4,734 variants using three integrative annotation tools produced 929 putative functional SNPs, of which 18 SNPs (from 15 GWAS loci) are in concordance with all three classifiers. These prioritized noncoding SNPs may contribute to IBD pathogenesis by dysregulating the expression of nearby genes. This study showed the usefulness of integrative annotation for prioritizing fewer functional variants from a large number of GWAS markers.
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Affiliation(s)
- Md. Mesbah-Uddin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (MMU); (FAA)
| | - Ramu Elango
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Babajan Banaganapalli
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Noor Ahmad Shaik
- Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Genetic Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- * E-mail: (MMU); (FAA)
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20
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Bashinskaya VV, Kulakova OG, Kiselev IS, Baulina NM, Favorov AV, Boyko AN, Tsareva EY, Favorova OO. GWAS-identified multiple sclerosis risk loci involved in immune response: validation in Russians. J Neuroimmunol 2015; 282:85-91. [PMID: 25903733 DOI: 10.1016/j.jneuroim.2015.03.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/15/2015] [Accepted: 03/16/2015] [Indexed: 01/01/2023]
Abstract
Multiple sclerosis (MS) is a chronic neuro-inflammatory disease of complex etiology. The results of GWAS, a high-throughput method to discover genetic architecture of MS, require replication in independent ethnic groups. We performed a replication study of nine GWAS-identified SNPs in immune response in Russians. Associations of CLEC16A and IL2RA with MS were validated. Besides, we observed the associations of CLEC16A and IRF8 in women, and IL7RA and CD58 in men. With multi-locus association analysis two protective biallelic combinations: (TNFRSF1A*T+CLEC16A*A) and (TNFRSF1A*T+IRF8*A) were identified in women. Associations of CLEC16A*G/G and both biallelic combinations in women with MS survived the permutation test.
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Affiliation(s)
- V V Bashinskaya
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia.
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia
| | - I S Kiselev
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia
| | - N M Baulina
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia
| | - A V Favorov
- Johns Hopkins School of Medicine, 550 North Broadway, Baltimore, MD 21205, USA; Vavilov Institute of General Genetics, Russian Academy of Sciences, Gubkina str. 3, 119333 Moscow, Russia
| | - A N Boyko
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia
| | - E Yu Tsareva
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Ostrovitianov str. 1, 117997 Moscow, Russia; Russian Cardiology Scientific and Production Center, 3-d Cherepkovskaya str, 15A, Moscow 121552 Russia
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21
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MS risk allele rs1883832T is associated with decreased mRNA expression of CD40. J Mol Neurosci 2015; 56:540-5. [PMID: 25600834 DOI: 10.1007/s12031-015-0490-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 01/05/2015] [Indexed: 12/25/2022]
Abstract
CD40-CD40L interactions mediate T-dependent B cell response and efficient T cell priming. Therefore, genes encoding these molecules are attractive candidates for studies on autoimmune diseases, such as multiple sclerosis (MS), in which activated T and B cells are involved. Thus, we analyzed CD40 and CD40L mRNA expression in whole blood samples from MS patients and controls. Additionally, we examined the effect of three SNPs of CD40 (rs1883832C>T, rs11569343C>G, and rs752118C>T) and two SNPs of CD40L (rs3092923T>C and rs3092952A>G) on their mRNA expression. Our results showed that the rs1883832C>T SNP affects CD40 gene expression. Our analysis revealed that individuals possessing CT and TT genotypes (predisposing to MS) had decreased level of CD40 mRNA in comparison to those with CC. Moreover, we demonstrated the potential role of impaired CD40-CD40L interaction in developing of multiple sclerosis.
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22
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Thude H, Kramer K, Koch M, Peine S, Sterneck M, Nashan B. Lack of association between CD40 polymorphisms and acute rejection in German liver transplant recipients. Hum Immunol 2014; 75:1123-7. [PMID: 25305459 DOI: 10.1016/j.humimm.2014.09.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 09/27/2014] [Accepted: 09/27/2014] [Indexed: 01/15/2023]
Abstract
CD40 and its ligand, CD154, are major costimulatory molecules whose interactions are important in alloreactive transplant rejection. The aim of this study was to examine the association of CD40 polymorphisms with the susceptibility to acute rejection episodes in liver transplantation. In total, 112 liver transplant recipients with biopsy proven acute rejections (BPAR), 97 without BPAR (WBPAR), and 112 healthy control individuals were enrolled in the study. Two single nucleotide polymorphisms (SNPs) of CD40 gene (rs1883832 and rs4810485) were genotyped by polymerase chain reaction-allele specific restriction enzyme analysis (PCR-ASRA). Both SNPs has been tested for a recessive and a dominant model. No significant differences were found in the genotype and allele frequencies of the SNPs rs1883832 and rs4810485 between BPAR liver recipients and WBPAR recipients. Our results do not suggest an important role of tested CD40 SNPs in the susceptibility to acute liver transplant rejection in a Caucasian population.
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Affiliation(s)
- Hansjörg Thude
- University Medical Center Hamburg-Eppendorf, Department of Hepatobiliary and Transplant Surgery, Martinistraße 52, 20246 Hamburg, Germany
| | - Kathrin Kramer
- University Medical Center Hamburg-Eppendorf, Department of Hepatobiliary and Transplant Surgery, Martinistraße 52, 20246 Hamburg, Germany
| | - Martina Koch
- University Medical Center Hamburg-Eppendorf, Department of Hepatobiliary and Transplant Surgery, Martinistraße 52, 20246 Hamburg, Germany
| | - Sven Peine
- University Medical Center Hamburg-Eppendorf, Institute for Transfusion Medicine, Martinistraße 52, 20246 Hamburg, Germany
| | - Martina Sterneck
- University Medical Center Hamburg-Eppendorf, Department of Medicine, Martinistraße 52, 20246 Hamburg, Germany
| | - Björn Nashan
- University Medical Center Hamburg-Eppendorf, Department of Hepatobiliary and Transplant Surgery, Martinistraße 52, 20246 Hamburg, Germany
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Investigation of gene-gene interactions between CD40 and CD40L in Polish multiple sclerosis patients. Hum Immunol 2014; 75:796-801. [PMID: 24912008 DOI: 10.1016/j.humimm.2014.05.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 03/11/2014] [Accepted: 05/29/2014] [Indexed: 12/11/2022]
Abstract
CD40-CD40L interaction is necessary for the activation of both humoral and cellular immune response and has been suggested to play a role in the pathogenesis of multiple sclerosis (MS). Therefore, we analyzed the combined influence of the CD40 and CD40L variants on MS susceptibility and progression on well-defined Polish population. Our investigation revealed that CT individuals in rs1883832 locus of CD40 possessed almost 1.5-fold higher risk for MS than CC individuals (OR = 1.44; 95%CI = 1.03-2.1; p = 0.032), while this risk for TT individuals was almost 2.5-fold higher (OR = 2.36; 95%CI = 1.19-4.78; p = 0.014). Moreover, for the first time, we observed the association of CD40 gene with MS development and progression. We observed that for the rs1883832CC individuals the age at diagnosis was on average 2 years lower than for the rs1883832CT and rs1883832TT individuals (CI95% = -3.69-(-0.29); p = 0.023). Additionally, we detected that individuals with TT and CT genotypes showed lower risk of developing secondary progressive course in comparison to those with CC genotype. For rs1883832TT individuals this risk was 4-fold lower (HR = 0.24; CI95% = 0.10-0.53; p = 0.00062). Despite the fact that CD40-CD40L pathway plays a key role in development of autoimmune diseases, we were not able to detect gene-gene interactions between CD40 and CD40L polymorphisms associated with multiple sclerosis.
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Lomakin YA, Zakharova MY, Belogurov AA, Bykova NA, Dronina MA, Tupikin AE, Knorre VD, Boyko AN, Favorov AV, Kabilov MR, Ponomarenko NA, Gabibov AG. Polyreactive monoclonal autoantibodies in multiple sclerosis: functional selection from phage display library and characterization by deep sequencing analysis. Acta Naturae 2013; 5:94-104. [PMID: 24455188 PMCID: PMC3890994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multiple Sclerosis (MS) is a chronic inflammatory demyelinating disease of the central nervous system that primarily affects young and middle-aged people. It is widely accepted that B lymphocyte activation is required for MS progression. Despite the fact that the exact triggering mechanisms of MS remain enigmatic, one may suggest that MS can be induced by viral or bacterial infection in combination with specific genetic and environmental factors. Using deep sequencing and functional selection methodologies we characterized clones of poly- and cross-reactive antibodies that are capable of simultaneous recognition of viral proteins and autoantigens. The latter, in turn, possibly may trigger MS progression through molecular mimicry. It was identified that two cross-reactive antigens are probably recognized by light or heavy chains individually. According to the high structural homology between selected autoantibodies and a number of various antiviral IgGs, we suggest that a wide range of pathogens, instead of a single virus, be regarded as possible triggers of MS.
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Affiliation(s)
- Y. A. Lomakin
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - M. Yu. Zakharova
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - A. A. Belogurov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia,Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - N. A. Bykova
- Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, 127994, Moscow, Russia,Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - M. A. Dronina
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - A. E. Tupikin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia,Genomics Core Facility, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - V. D. Knorre
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - A. N. Boyko
- Moscow Multiple Sclerosis Center at the City Hospital #11, 127018, Moscow, Russia,Pirogov Russian National Research Medical University, Department of Fundamental and Clinical Neurology and Neurosurgery, 117997, Moscow, Russia
| | - A. V. Favorov
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119991, Moscow, Russia,Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, 21218, Baltimore, Maryland, USA,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika, 117545, Moscow, Russia
| | - M. R. Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia,Genomics Core Facility, Siberian Branch, Russian Academy of Sciences, 630090, Novosibirsk, Russia
| | - N. A. Ponomarenko
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia
| | - A. G. Gabibov
- Shemyakin–Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997, Moscow, Russia,Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia,Faculty of Chemistry, Lomonosov Moscow State University, 119991, Moscow, Russia
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