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A Whole-Genome Sequencing Study Implicates GRAMD1B in Multiple Sclerosis Susceptibility. Genes (Basel) 2022; 13:genes13122392. [PMID: 36553660 PMCID: PMC9777893 DOI: 10.3390/genes13122392] [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: 11/15/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
While the role of common genetic variants in multiple sclerosis (MS) has been elucidated in large genome-wide association studies, the contribution of rare variants to the disease remains unclear. Herein, a whole-genome sequencing study in four affected and four healthy relatives of a consanguineous Italian family identified a novel missense c.1801T > C (p.S601P) variant in the GRAMD1B gene that is shared within MS cases and resides under a linkage peak (LOD: 2.194). Sequencing GRAMD1B in 91 familial MS cases revealed two additional rare missense and two splice-site variants, two of which (rs755488531 and rs769527838) were not found in 1000 Italian healthy controls. Functional studies demonstrated that GRAMD1B, a gene with unknown function in the central nervous system (CNS), is expressed by several cell types, including astrocytes, microglia and neurons as well as by peripheral monocytes and macrophages. Notably, GRAMD1B was downregulated in vessel-associated astrocytes of active MS lesions in autopsied brains and by inflammatory stimuli in peripheral monocytes, suggesting a possible role in the modulation of inflammatory response and disease pathophysiology.
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Gómez-Pinedo U, Torre-Fuentes L, Matías-Guiu JA, Pytel V, Ojeda-Hernández DD, Selma-Calvo B, Montero-Escribano P, Vidorreta-Ballesteros L, Matías-Guiu J. Exonic variants of the P2RX7 gene in familial multiple sclerosis. Neurologia 2022:S2173-5808(22)00189-4. [PMID: 36470550 DOI: 10.1016/j.nrleng.2022.12.001] [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: 09/09/2022] [Accepted: 10/09/2022] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Several studies have analysed the presence of P2RX7 variants in patients with MS, reporting diverging results. METHODS Our study analyses P2RX7 variants detected through whole-exome sequencing (WES). RESULTS We analysed P2RX7, P2RX4, and CAMKK2 gene variants detected by whole-exome sequencing in all living members (n = 127) of 21 families including at least 2 individuals with multiple sclerosis. P2RX7 gene polymorphisms previously associated with autoimmune disease. Although no differences were observed between individuals with and without multiple sclerosis, we found greater polymorphism of gain-of-function variants of P2RX7 in families with individuals with multiple sclerosis than in the general population. Copresence of gain-of-function and loss-of-function variants was not observed to reduce the risk of presenting the disease. Three families displayed heterozygous gain-of-function SNPs in patients with multiple sclerosis but not in healthy individuals. We were unable to determine the impact of copresence of P2RX4 and CAMKK2 variants with P2RX7 variants, or the potential effect of the different haplotypes described in the gene. No clinical correlations with other autoimmune diseases were observed in our cohort. CONCLUSIONS Our results support the hypothesis that the disease is polygenic and point to a previously unknown mechanism of genetic predisposition to familial forms of multiple sclerosis. P2RX7 gene activity can be modified, which suggests the possibility of preventive pharmacological treatments for families including patients with familial multiple sclerosis.
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Affiliation(s)
- U Gómez-Pinedo
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain.
| | - L Torre-Fuentes
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - J A Matías-Guiu
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - V Pytel
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain; Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - D D Ojeda-Hernández
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - B Selma-Calvo
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - P Montero-Escribano
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - L Vidorreta-Ballesteros
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - J Matías-Guiu
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain; Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
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A comprehensive in silico analysis of multiple sclerosis related non-synonymous SNPs and their potential effects on protein structure and function. Mult Scler Relat Disord 2022; 68:104253. [PMID: 36544314 DOI: 10.1016/j.msard.2022.104253] [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: 09/04/2022] [Revised: 10/11/2022] [Accepted: 10/16/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND Multiple Sclerosis (MS) is an autoimmune and central nervous system disease characterized by an inflammatory demyelinating process in the brain. Although the exact cause of MS is still unclear, environmental, and genetic factors are known to play a role in the development of disease. New molecular markers must be identified to understand the mechanism of disease formation and progression. We investigated the effects of MS-related non-synonymous single-nucleotide polymorphisms (nsSNPs) on the structure and function of identified proteins in this study. METHODS Missense variations associated with MS were extracted from the NHGRI-EBI GWAS database. Functional and structural analysis of nsSNPs on mapped genes was performed using g:Profiler, Wikipathway, KEGG, Reactome and Gene ontology programs (p < 0.05 was accepted statistically significant). Amino acid sequence-based analysis was performed to identify deleterious variants by using PROVEAN and PredictSNP tools. Finally, protein structure analyzes were performed on deleterious protein variants by DynaMut, Mutabind2 and Missense3D servers to identify changes in protein stability and flexibility. RESULTS 10 target nsSNPs were identified. Among these rs34536443, rs10936599, rs2293152, rs11808092, rs1129183 were found deleterious according to amino acid sequence-based analysis. Furthermore, structure-based analyses show that TYK2 (P1104A), MYNN (H6Q), EVI5 (Q612H), and LZTFL1 (D246N) substitutions increase protein stability and decrease structure flexibility, whereas STAT3 (R426G) substitution decreases protein stability and increases structure flexibility. CONCLUSION We revealed that identified nsSNPs have potential effects on stability and flexibility of the target proteins. The prominent target genes are thought to have significant impacts on the pathogenesis of MS. Further in vitro and in vivo studies are required to validate our in silico results.
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Horjus J, van Mourik-Banda T, Heerings MAP, Hakobjan M, De Witte W, Heersema DJ, Jansen AJ, Strijbis EMM, de Jong BA, Slettenaar AEJ, Zeinstra EMPE, Hoogervorst ELJ, Franke B, Kruijer W, Jongen PJ, Visser LJ, Poelmans G. Whole Exome Sequencing in Multi-Incident Families Identifies Novel Candidate Genes for Multiple Sclerosis. Int J Mol Sci 2022; 23:ijms231911461. [PMID: 36232761 PMCID: PMC9570223 DOI: 10.3390/ijms231911461] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/22/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022] Open
Abstract
Multiple sclerosis (MS) is a degenerative disease of the central nervous system in which auto-immunity-induced demyelination occurs. MS is thought to be caused by a complex interplay of environmental and genetic risk factors. While most genetic studies have focused on identifying common genetic variants for MS through genome-wide association studies, the objective of the present study was to identify rare genetic variants contributing to MS susceptibility. We used whole exome sequencing (WES) followed by co-segregation analyses in nine multi-incident families with two to four affected individuals. WES was performed in 31 family members with and without MS. After applying a suite of selection criteria, co-segregation analyses for a number of rare variants selected from the WES results were performed, adding 24 family members. This approach resulted in 12 exonic rare variants that showed acceptable co-segregation with MS within the nine families, implicating the genes MBP, PLK1, MECP2, MTMR7, TOX3, CPT1A, SORCS1, TRIM66, ITPR3, TTC28, CACNA1F, and PRAM1. Of these, three genes (MBP, MECP2, and CPT1A) have been previously reported as carrying MS-related rare variants. Six additional genes (MTMR7, TOX3, SORCS1, ITPR3, TTC28, and PRAM1) have also been implicated in MS through common genetic variants. The proteins encoded by all twelve genes containing rare variants interact in a molecular framework that points to biological processes involved in (de-/re-)myelination and auto-immunity. Our approach provides clues to possible molecular mechanisms underlying MS that should be studied further in cellular and/or animal models.
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Affiliation(s)
- Julia Horjus
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Tineke van Mourik-Banda
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Marco A. P. Heerings
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Marina Hakobjan
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Ward De Witte
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Dorothea J. Heersema
- Department of Neurology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Anne J. Jansen
- Department of Neurology, Bravis Hospital, 4708 AE Bergen op Zoom, The Netherlands
| | - Eva M. M. Strijbis
- Department of Neurology, Amsterdam UMC, location VUmc, 1081 HV Amsterdam, The Netherlands
| | - Brigit A. de Jong
- Department of Neurology, MS Center Amsterdam, Amsterdam UMC, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | | | | | | | - Barbara Franke
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, 6525 GD Nijmegen, The Netherlands
- Department of Psychiatry, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Wiebe Kruijer
- Independent Life Science Consultant, 3831 CE Leusden, The Netherlands
| | - Peter J. Jongen
- MS4 Research Institute, 6522 KJ Nijmegen, The Netherlands
- Department of Community & Occupational Medicine, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Leo J. Visser
- Department of Neurology, St. Elisabeth-Tweesteden Hospital, 5022 GC Tilburg, The Netherlands
- Department of Care Ethics, University of Humanistic Studies, 3512 HD Utrecht, The Netherlands
| | - Geert Poelmans
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
- Correspondence:
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Zhou Y, Li X, Shen R, Wang X, Zhang F, Liu S, Li D, Liu J, Li P, Yan Y, Dong P, Zhang Z, Wu H, Zhuang L, Chowdhury R, Miller M, Issa M, Mao Y, Chen H, Feng J, Li J, Bai C, He F, Tao W. Novel Small Molecule Tyrosine Kinase 2 Pseudokinase Ligands Block Cytokine-Induced TYK2-Mediated Signaling Pathways. Front Immunol 2022; 13:884399. [PMID: 35693820 PMCID: PMC9186491 DOI: 10.3389/fimmu.2022.884399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/22/2022] [Indexed: 11/15/2022] Open
Abstract
A member of the Janus kinase (JAK) family, Tyrosine Kinase 2 (TYK2), is crucial in mediating various cytokine-signaling pathways such as interleukin-23 (IL23), interleukin-12 (IL12) and type I Interferons (IFN) which contribute to autoimmune disorders (e.g., psoriasis, lupus, and inflammatory bowel disease). Thus, TYK2 represents an attractive target to develop small-molecule therapeutics for the treatment of cytokine-driven inflammatory diseases. Selective inhibition of TYK2 over other JAK isoforms is critical to achieve a favorable therapeutic index in the development of TYK2 inhibitors. However, designing small molecule inhibitors to target the adenosine triphosphate (ATP) binding site of TYK2 kinase has been challenging due to the substantial structural homology of the JAK family catalytic domains. Here, we employed an approach to target the JAK homology 2 (JH2) pseudokinase regulatory domain of the TYK2 protein. We developed a series of small-molecule TYK2 pseudokinase ligands, which suppress the TYK2 catalytic activity through allosteric regulation. The TYK2 pseudokinase-binding small molecules in this study simultaneously achieve high affinity-binding for the TYK2 JH2 domain while also affording significantly reduced affinity for the TYK2 JAK homology 1 (JH1) kinase domain. These TYK2 JH2 selective molecules, although possessing little effect on suppressing the catalytic activity of the isolated TYK2 JH1 catalytic domain in the kinase assays, can still significantly block the TYK2-mediated receptor-stimulated pathways by binding to the TYK2 JH2 domain and allosterically regulating the TYK2 JH1 kinase. These compounds are potent towards human T-cell lines and primary immune cells as well as in human whole-blood specimens. Moreover, TYK2 JH2-binding ligands exhibit remarkable selectivity of TYK2 over JAK isoforms not only biochemically but also in a panel of receptor-stimulated JAK1/JAK2/JAK3-driven cellular functional assays. In addition, the TYK2 JH2-targeting ligands also demonstrate high selectivity in a multi-kinase screening panel. The data in the current study underscores that the TYK2 JH2 pseudokinase is a promising therapeutic target for achieving a high degree of biological selectivity. Meanwhile, targeting the JH2 domain represents an appealing strategy for the development of clinically well-tolerated TYK2 inhibitors that would have superior efficacy and a favorable safety profile compared to the existing Janus kinase inhibitors against autoimmune diseases.
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Affiliation(s)
- Yu Zhou
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
- *Correspondence: Yu Zhou, ; Xin Li,
| | - Xin Li
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
- *Correspondence: Yu Zhou, ; Xin Li,
| | - Ru Shen
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Xiangzhu Wang
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Fan Zhang
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Suxing Liu
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Di Li
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Jian Liu
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Puhui Li
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Yinfa Yan
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Ping Dong
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Zhigao Zhang
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Heping Wu
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Linghang Zhuang
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | | | - Matthew Miller
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Mena Issa
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Yuchang Mao
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Hongli Chen
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Jun Feng
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Jing Li
- R & D Center, Eternity Bioscience Inc., Cranbury, NJ, United States
| | - Chang Bai
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Feng He
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
| | - Weikang Tao
- R & D Center, Shanghai Hengrui Pharmaceutical Co. Ltd., Shanghai, China
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Hone L, Giovannoni G, Dobson R, Jacobs BM. Predicting Multiple Sclerosis: Challenges and Opportunities. Front Neurol 2022; 12:761973. [PMID: 35211072 PMCID: PMC8860835 DOI: 10.3389/fneur.2021.761973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Determining effective means of preventing Multiple Sclerosis (MS) relies on testing preventive strategies in trial populations. However, because of the low incidence of MS, demonstrating that a preventive measure has benefit requires either very large trial populations or an enriched population with a higher disease incidence. Risk scores which incorporate genetic and environmental data could be used, in principle, to identify high-risk individuals for enrolment in preventive trials. Here we discuss the concepts of developing predictive scores for identifying individuals at high risk of MS. We discuss the empirical efforts to do so using real cohorts, and some of the challenges-both theoretical and practical-limiting this work. We argue that such scores could offer a means of risk stratification for preventive trial design, but are unlikely to ever constitute a clinically-helpful approach to predicting MS for an individual.
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Affiliation(s)
- Luke Hone
- Preventive Neurology Unit, Wolfson Institute of Population Health, Barts and Queen Mary University of London, London, United Kingdom
| | - Gavin Giovannoni
- Preventive Neurology Unit, Wolfson Institute of Population Health, Barts and Queen Mary University of London, London, United Kingdom.,Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Ruth Dobson
- Preventive Neurology Unit, Wolfson Institute of Population Health, Barts and Queen Mary University of London, London, United Kingdom.,Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
| | - Benjamin Meir Jacobs
- Preventive Neurology Unit, Wolfson Institute of Population Health, Barts and Queen Mary University of London, London, United Kingdom.,Royal London Hospital, Barts Health NHS Trust, London, United Kingdom
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Borrelia burgdorferi is a poor inducer of interferon-gamma: amplification induced by interleukin-12. Infect Immun 2022; 90:e0055821. [PMID: 35130450 DOI: 10.1128/iai.00558-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Laboratory diagnosis of Lyme borreliosis (LB) is mainly based on serology, which has limitations, particularly in the early stages of the disease. In recent years there have been conflicting reports concerning a new diagnostic tool using the cytokine interferon-gamma (IFN-γ). Previous studies have generally found low concentrations of IFN-γ in early LB infection. The goal of this study is to investigate IFN-γ regulation during early LB and provide insights into the host response to B. burgdorferi. Methods We performed in vitro experiments with whole blood assays and peripheral blood mononuclear cells (PBMCs) of LB patients and healthy volunteers exposed to B. burgdorferi and evaluated the IFN-γ response using ELISA and related interindividual variation in IFN-γ production to the presence of single nucleotide polymorphisms. Results IFN-γ production of B. burgdorferi-exposed PBMCs and whole blood was amplified by the addition of IL-12 to the stimulation system. This effect was observed after 24 hours of B. burgdorferi stimulation in both healthy individuals and LB patients. The effect was highly variable between individuals, but was significantly higher in LB patients six weeks since the start of antibiotic treatment compared to healthy individuals. IL-12 p40 and IL-18 mRNA was upregulated upon exposure to B. burgdorferi, whereas IL-12 p35 and IFN-γ mRNA expression remained relatively unchanged. SNP Rs280520 in the downstream IL-12 pathway, Tyrosine Kinase 2, was associated with increased IFN-γ production. Conclusions This study shows that IL-12 evokes an IFN-γ response in B. burgdorferi exposed cells, and LB patients and healthy controls respond differently to this stimulation.
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Mascia E, Clarelli F, Zauli A, Guaschino C, Sorosina M, Barizzone N, Basagni C, Santoro S, Ferrè L, Bonfiglio S, Biancolini D, Pozzato M, Guerini FR, Protti A, Liguori M, Moiola L, Vecchio D, Bresolin N, Comi G, Filippi M, Esposito F, D'Alfonso S, Martinelli-Boneschi F. Burden of rare coding variants in an Italian cohort of familial multiple sclerosis. J Neuroimmunol 2022; 362:577760. [PMID: 34922125 DOI: 10.1016/j.jneuroim.2021.577760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/18/2021] [Accepted: 10/31/2021] [Indexed: 12/30/2022]
Abstract
BACKGROUND Multiple Sclerosis (MS) is a chronic inflammatory and neurodegenerative demyelinating disease of the central nervous system. It is a complex and heterogeneous disease caused by a combination of genetic and environmental factors, and it can cluster in families. OBJECTIVE to evaluate at gene-level the aggregate contribution of predicted damaging low-frequency and rare variants to MS risk in multiplex families. METHODS We performed whole exome sequencing (WES) in 28 multiplex MS families with at least 3 MS cases (81 affected and 42 unaffected relatives) and 38 unrelated healthy controls. A gene-based burden test was then performed, focusing on two sets of candidate genes: i) literature-driven selection and ii) data-driven selection. RESULTS We identified 11 genes enriched with predicted damaging low-frequency and rare variants in MS compared to healthy individuals. Among them, UBR2 and DST were the two genes with the strongest enrichment (p = 5 × 10-4 and 3 × 10-4, respectively); interestingly enough the association signal in UBR2 is driven by rs62414610, which was present in 25% of analysed families. CONCLUSION Despite limitations, this is one of the first studies evaluating the aggregate contribution of predicted damaging low-frequency and rare variants in MS families using WES data. A replication effort in independent cohorts is warranted to validate our findings and to evaluate the role of identified genes in MS pathogenesis.
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Affiliation(s)
- E Mascia
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - F Clarelli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - A Zauli
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - C Guaschino
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Department of Neurology, Sant'Antonio Abate Hospital, Gallarate, Italy
| | - M Sorosina
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - N Barizzone
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), UPO, University of Eastern Piedmont, A. Avogadro, 28100 Novara, Italy
| | - C Basagni
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), UPO, University of Eastern Piedmont, A. Avogadro, 28100 Novara, Italy
| | - S Santoro
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - L Ferrè
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - S Bonfiglio
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - D Biancolini
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - M Pozzato
- Neurology Unit and MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy
| | - F R Guerini
- IRCCS Fondazione Don Carlo Gnocchi, ONLUS, Milan, Italy
| | - A Protti
- Ospedale Niguarda, Department of Neurology, Milan, Italy
| | - M Liguori
- National Research Council, Institute of Biomedical Technologies, Bari Unit, 70126 Bari, Italy
| | - L Moiola
- Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - D Vecchio
- SCDU Neurology, AOU Maggiore della Carità, 28100 Novara, Italy
| | - N Bresolin
- Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy
| | - G Comi
- Institute of Experimental Neurology, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - M Filippi
- Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy; Neuroimaging Research Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy; Neurophysiology Unit, IRCCS San Raffaele Scientific Institute, San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - F Esposito
- Laboratory of Human Genetics of Neurological Disorders, Institute of Experimental Neurology (INSPE), Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Neurology Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 48, 20132 Milan, Italy
| | - S D'Alfonso
- Department of Health Sciences, Center on Autoimmune and Allergic Diseases (CAAD), UPO, University of Eastern Piedmont, A. Avogadro, 28100 Novara, Italy
| | - F Martinelli-Boneschi
- Neurology Unit and MS Centre, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Via Francesco Sforza 35, 20122 Milan, Italy; Department of Pathophysiology and Transplantation (DEPT), Dino Ferrari Centre, Neuroscience Section, University of Milan, Via Francesco Sforza 35, 20122 Milan, Italy.
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Hromadová D, Elewaut D, Inman RD, Strobl B, Gracey E. From Science to Success? Targeting Tyrosine Kinase 2 in Spondyloarthritis and Related Chronic Inflammatory Diseases. Front Genet 2021; 12:685280. [PMID: 34290741 PMCID: PMC8287328 DOI: 10.3389/fgene.2021.685280] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/02/2021] [Indexed: 12/16/2022] Open
Abstract
Spondyloarthritis (SpA) is a family of inflammatory arthritic diseases, which includes the prototypes of psoriatic arthritis and ankylosing spondylitis. SpA is commonly associated with systemic inflammatory diseases, such as psoriasis and inflammatory bowel disease. Immunological studies, murine models and the genetics of SpA all indicate a pathogenic role for the IL-23/IL-17 axis. Therapeutics targeting the IL-23/IL-17 pathway are successful at providing symptomatic relief, but may not provide complete protection against progression of arthritis. Thus there is still tremendous interest in the discovery of novel therapeutic targets for SpA. Tyrosine kinase 2 (TYK2) is a member of the Janus kinases, which mediate intracellular signaling of cytokines via signal transducer and activator of transcription (STAT) activation. TYK2 plays a crucial role in mediating IL-23 receptor signaling and STAT3 activation. A plethora of natural mutations in and around TYK2 have provided a wealth of data to associate this kinase with autoimmune/autoinflammatory diseases in humans. Induced and natural mutations in murine Tyk2 largely support human data; however, key inter-species differences exist, which means extrapolation of data from murine models to humans needs to be done with caution. Despite these reservations, novel selective TYK2 inhibitors are now proving successful in advanced clinical trials of inflammatory diseases. In this review, we will discuss TYK2 from basic biology to therapeutic targeting, with an emphasis on studies in SpA. Seminal studies uncovering the basic science of TYK2 have provided sound foundations for targeting it in SpA and related inflammatory diseases. TYK2 inhibitors may well be the next blockbuster therapeutic for SpA.
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Affiliation(s)
- Dominika Hromadová
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Dirk Elewaut
- Molecular Immunology and Inflammation Unit, VIB Centre for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
| | - Robert D. Inman
- Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada
- Departments of Medicine and Immunology, University of Toronto, Toronto, ON, Canada
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Eric Gracey
- Molecular Immunology and Inflammation Unit, VIB Centre for Inflammation Research, Ghent University, Ghent, Belgium
- Department of Rheumatology, Ghent University Hospital, Ghent, Belgium
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10
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Peng Y, Chen B, Sheng X, Qian Y. Polymorphisms in IRF5 and TYK2 Genes Are Associated with Rheumatoid Arthritis in a Chinese Han Population. Med Sci Monit 2021; 27:e928455. [PMID: 33583939 PMCID: PMC7893827 DOI: 10.12659/msm.928455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/30/2020] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND The IRF5 and TYK2 gene polymorphisms are associated with autoimmune diseases. However, the relationship between the IRF5 and TYK2 gene polymorphisms and RA risk in the Chinese Han population was inconsistent. MATERIAL AND METHODS A total of 578 RA patients (case group) and 578 healthy controls (control group) were assessed in a case-control study. Genotyping of IRF5 (Exon 6 insertion/deletion (in/de), rs2004640, rs2070197, rs10954213) and TYK2 (rs280500, rs280519, rs280521, rs8108236, rs12720253) was performed by direct sequencing method. Data analysis was performed by SHEsis. RESULTS The rs2004640T allele (P=0.0003) and the dominant (P=0.001) and recessive (P=0.01) models of rs2004640 were associated with RA risk after stringent Bonferroni correction (0.05/4). The IRF5 exon 6 (in), rs2070197 and rs10954213 were not associated with RA (P>0.05). Two haplotypes of IRF5 (DTAT and DTGG) were associated with RA susceptibility (P<0.05). In addition, the frequencies of TYK2 rs280500A, rs280521A, and rs8108236A were significantly higher in the RA group compared with the control group (P<0.05). TYK2 rs280500, rs280521, and rs8108236 were associated with RA susceptibility in the dominant model, but the same was not observed for rs280519 and rs12720253 (P<0.05). Furthermore, 3 risk haplotypes (AAAGT, AGGAT, and GAAAT) and a protective haplotype (GAGGT) of TYK2 gene were associated with RA susceptibility (P<0.05). CONCLUSIONS Our results suggest that IRF5 rs2004640, TYK2 rs280500, rs280521, rs8108236, and haplotypes IRF5 (DTAT and DTGG) and TYK2 (AAAGT, AGGAT, GAAAT, and GAGGT) are susceptible factors for RA in a Chinese Han population.
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11
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Gatta V, Mengod G, Reale M, Tata AM. Possible Correlation between Cholinergic System Alterations and Neuro/Inflammation in Multiple Sclerosis. Biomedicines 2020; 8:E153. [PMID: 32521719 PMCID: PMC7345633 DOI: 10.3390/biomedicines8060153] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/05/2020] [Accepted: 06/06/2020] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is an autoimmune and demyelinating disease of the central nervous system. Although the etiology of MS is still unknown, both genetic and environmental factors contribute to the pathogenesis of the disease. Acetylcholine participates in the modulation of central and peripheral inflammation. The cells of the immune system, as well as microglia, astrocytes and oligodendrocytes express cholinergic markers and receptors of muscarinic and nicotinic type. The role played by acetylcholine in MS has been recently investigated. In the present review, we summarize the evidence indicating the cholinergic dysfunction in serum and cerebrospinal fluid of relapsing-remitting (RR)-MS patients and in the brains of the MS animal model experimental autoimmune encephalomyelitis (EAE). The correlation between the increased activity of the cholinergic hydrolyzing enzymes acetylcholinesterase and butyrylcholinesterase, the reduced levels of acetylcholine and the increase of pro-inflammatory cytokines production were recently described in immune cells of MS patients. Moreover, the genetic polymorphisms for both hydrolyzing enzymes and the possible correlation with the altered levels of their enzymatic activity have been also reported. Finally, the changes in cholinergic markers expression in the central nervous system of EAE mice in peak and chronic phases suggest the involvement of the acetylcholine also in neuro-inflammatory processes.
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Affiliation(s)
- Valentina Gatta
- Department of Psychological, Health and Territorial Sciences, School of Medicine and Health Sciences, “G. d’Annunzio” University, 66100 Chieti, Italy;
| | | | - Marcella Reale
- Department of Medical, Oral and Biotechnological Science, University “G. d’Annunzio” Chieti-Pescara, 66100 Chieti, Italy;
| | - Ada Maria Tata
- Department of Biology and Biotechnologies C. Darwin, “Sapienza” University of Rome, 00185 Rome, Italy
- Research Center of Neurobiology Daniel Bovet, “Sapienza” University of Rome, 00185 Rome, Italy
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12
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Shademan B, Biray Avci C, Nikanfar M, Nourazarian A. Application of Next-Generation Sequencing in Neurodegenerative Diseases: Opportunities and Challenges. Neuromolecular Med 2020; 23:225-235. [PMID: 32399804 DOI: 10.1007/s12017-020-08601-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 05/01/2020] [Indexed: 12/28/2022]
Abstract
Genetic factors (gene mutations) lead to various rare and prevalent neurological diseases. Identification of underlying mutations in neurodegenerative diseases is of paramount importance due to the heterogeneous nature of the genome and different clinical manifestations. An early and accurate molecular diagnosis are cardinal for neurodegenerative patients to undergo proper therapeutic regimens. The next-generation sequencing (NGS) method examines up to millions of sequences at a time. As a result, the rare molecular diagnoses, previously presented with "unknown causes", are now possible in a short time. This method generates a large amount of data that can be utilized in patient management. Since each person has a unique genome, the NGS has transformed diagnostic and therapeutic strategies into sequencing and individual genomic mapping. However, this method has disadvantages like other diagnostic methods. Therefore, in this review, we aimed to briefly summarize the NGS method and correlated studies to unravel the genetic causes of neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, epilepsy, and MS. Finally, we discuss the NGS challenges and opportunities in neurodegenerative diseases.
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Affiliation(s)
- Behrouz Shademan
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey
| | - Cigir Biray Avci
- Department of Medical Biology, Medical Faculty, Ege University, 35100, Bornova, Izmir, Turkey.
| | - Masoud Nikanfar
- Department of Neurology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Nourazarian
- Department of Biochemistry and Clinical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Golgasht St., 51666-16471, Tabriz, Iran. .,Neurosciences Research Center (NSRC), Tabriz University of Medical Sciences, Tabriz, Iran.
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Ziliotto N, Marchetti G, Scapoli C, Bovolenta M, Meneghetti S, Benazzo A, Lunghi B, Balestra D, Laino LA, Bozzini N, Guidi I, Salvi F, Straudi S, Gemmati D, Menegatti E, Zamboni P, Bernardi F. C6orf10 Low-Frequency and Rare Variants in Italian Multiple Sclerosis Patients. Front Genet 2019; 10:573. [PMID: 31297130 PMCID: PMC6607989 DOI: 10.3389/fgene.2019.00573] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 05/31/2019] [Indexed: 12/14/2022] Open
Abstract
In light of the complex nature of multiple sclerosis (MS) and the recently estimated contribution of low-frequency variants into disease, decoding its genetic risk components requires novel variant prioritization strategies. We selected, by reviewing MS Genome Wide Association Studies (GWAS), 107 candidate loci marked by intragenic single nucleotide polymorphisms (SNPs) with a remarkable association (p-value ≤ 5 × 10-6). A whole exome sequencing (WES)-based pilot study of SNPs with minor allele frequency (MAF) ≤ 0.04, conducted in three Italian families, revealed 15 exonic low-frequency SNPs with affected parent-child transmission. These variants were detected in 65/120 Italian unrelated MS patients, also in combination (22 patients). Compared with databases (controls gnomAD, dbSNP150, ExAC, Tuscany-1000 Genome), the allelic frequencies of C6orf10 rs16870005 and IL2RA rs12722600 were significantly higher (i.e., controls gnomAD, p = 9.89 × 10-7 and p < 1 × 10-20). TET2 rs61744960 and TRAF3 rs138943371 frequencies were also significantly higher, except in Tuscany-1000 Genome. Interestingly, the association of C6orf10 rs16870005 (Ala431Thr) with MS did not depend on its linkage disequilibrium with the HLA-DRB1 locus. Sequencing in the MS cohort of the C6orf10 3′ region revealed 14 rare mutations (10 not previously reported). Four variants were null, and significantly more frequent than in the databases. Further, the C6orf10 rare variants were observed in combinations, both intra-locus and with other low-frequency SNPs. The C6orf10 Ser389Xfr was found homozygous in a patient with early onset of the MS. Taking into account the potentially functional impact of the identified exonic variants, their expression in combination at the protein level could provide functional insights in the heterogeneous pathogenetic mechanisms contributing to MS.
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Affiliation(s)
- Nicole Ziliotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giovanna Marchetti
- Department of Biomedical and Specialty Surgical Sciences, University of Ferrara, Ferrara, Italy
| | - Chiara Scapoli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Matteo Bovolenta
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Silvia Meneghetti
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Andrea Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Barbara Lunghi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Dario Balestra
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Lorenza Anna Laino
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Nicolò Bozzini
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Irene Guidi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Fabrizio Salvi
- IRCCS Institute of Neurological Sciences, Hospital Bellaria, Bologna, Italy
| | - Sofia Straudi
- Department of Neurosciences and Rehabilitation, S. Anna University Hospital, Ferrara, Italy
| | - Donato Gemmati
- Department of Biomedical & Specialty Surgical Sciences and Centre Haemostasis & Thrombosis, Section of Medical Biochemistry, Molecular Biology & Genetics, University of Ferrara, Ferrara, Italy
| | - Erica Menegatti
- Department of Morphology, Surgery and Experimental Medicine, Vascular Diseases Center, University of Ferrara, Ferrara, Italy
| | - Paolo Zamboni
- Department of Morphology, Surgery and Experimental Medicine, Vascular Diseases Center, University of Ferrara, Ferrara, Italy
| | - Francesco Bernardi
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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Vidmar L, Maver A, Drulović J, Sepčić J, Novaković I, Ristič S, Šega S, Peterlin B. Multiple Sclerosis patients carry an increased burden of exceedingly rare genetic variants in the inflammasome regulatory genes. Sci Rep 2019; 9:9171. [PMID: 31235738 PMCID: PMC6591387 DOI: 10.1038/s41598-019-45598-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 06/03/2019] [Indexed: 12/17/2022] Open
Abstract
The role of rare genetic variation and the innate immune system in the etiology of multiple sclerosis (MS) is being increasingly recognized. Recently, we described several rare variants in the NLRP1 gene, presumably conveying an increased risk for familial MS. In the present study we aimed to assess rare genetic variation in the inflammasome regulatory network. We performed whole exome sequencing of 319 probands, comprising patients with familial MS, sporadic MS and control subjects. 62 genes involved in the NLRP1/NLRP3 inflammasome regulation were screened for potentially pathogenic rare genetic variation. Aggregate mutational burden was analyzed, considering the variants' predicted pathogenicity and frequency in the general population. We demonstrate an increased (p = 0.00004) variant burden among MS patients which was most pronounced for the exceedingly rare variants with high predicted pathogenicity. These variants were found in inflammasome genes (NLRP1/3, CASP1), genes mediating inflammasome inactivation via auto and mitophagy (RIPK2, MEFV), and genes involved in response to infection with DNA viruses (POLR3A, DHX58, IFIH1) and to type-1 interferons (TYK2, PTPRC). In conclusion, we present new evidence supporting the importance of rare genetic variation in the inflammasome signaling pathway and its regulation via autophagy and interferon-β to the etiology of MS.
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Affiliation(s)
- Lovro Vidmar
- Clinical Institute of Medical Genetics, Slajmerjeva 3, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Ales Maver
- Clinical Institute of Medical Genetics, Slajmerjeva 3, University Medical Centre Ljubljana, Ljubljana, Slovenia
| | - Jelena Drulović
- Clinic of Neurology, CCS, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Juraj Sepčić
- Postgraduate Study, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Ivana Novaković
- Faculty of Medicine, University of Belgrade, Institute of Human Genetics, 26 Visegradska, Belgrade, Serbia
| | - Smiljana Ristič
- Department of Biology and Medical Genetics, School of Medicine, University of Rijeka, Rijeka, Croatia
| | - Saša Šega
- Division of Neurology, University Medical Centre Ljubljana, Zaloška 2, 1000, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Medical Genetics, Slajmerjeva 3, University Medical Centre Ljubljana, Ljubljana, Slovenia.
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15
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Hammarén HM, Virtanen AT, Raivola J, Silvennoinen O. The regulation of JAKs in cytokine signaling and its breakdown in disease. Cytokine 2019; 118:48-63. [DOI: 10.1016/j.cyto.2018.03.041] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 03/29/2018] [Accepted: 03/30/2018] [Indexed: 01/12/2023]
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Pytel V, Matías-Guiu JA, Torre-Fuentes L, Montero-Escribano P, Maietta P, Botet J, Álvarez S, Gómez-Pinedo U, Matías-Guiu J. Exonic variants of genes related to the vitamin D signaling pathway in the families of familial multiple sclerosis using whole-exome next generation sequencing. Brain Behav 2019; 9:e01272. [PMID: 30900415 PMCID: PMC6456803 DOI: 10.1002/brb3.1272] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/27/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Vitamin D (VD) deficiency has been associated with multiple sclerosis (MS) and other autoimmune diseases (AIDs). However, the effect of the genetics of VD on the risk of MS is subject to debate. This study focuses on genes linked to the VD signaling pathway in families with MS. The evaluation of gene variants in all the members of families could contribute to an additional knowledge on the information obtained from case-control studies that use nonrelated healthy people. MATERIAL AND METHODS We studied 94 individuals from 15 families including at least two patients with MS. We performed whole-exome next generation sequencing on all individuals and analyzed variants of the DHCR7, CYP2R1, CYP3A4, CYP27A1, GC, CYP27B1, LRP2, CUBN, DAB2, FCGR, RXR, VDR, CYP24A1, and PDIA3 genes. We also studied PTH, FGF23, METTL1, METTL21B, and the role of the linkage disequilibrium block on the long arm of chromosome 12, through analysis of the CDK4, TSFM, AGAP2, and AVIL genes. We compared patients with MS, other AIDs and unaffected members from different family types. RESULTS The study described the variants in the VD signaling pathway that appear in families with at least two patients with MS. Some infrequent variants were detected in these families, but no significant difference was observed between patients with MS and/or other AIDs and unaffected family members in the frequency of these variants. Variants previously associated with MS in the literature were not observed in these families or were distributed similarly in patients and unaffected family members. CONCLUSION The study of genes involved in the VD signaling pathway in families that include more than one patient with MS did not identify any variants that could explain the presence of the disease, suggesting that VD metabolism could probably play a role in MS more as an environmental factor rather than as a genetic factor. Our study also supports the analysis of cases and unaffected individuals within families in order to determine the influence of genetic factors.
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Affiliation(s)
- Vanesa Pytel
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain.,Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Jordi A Matías-Guiu
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Laura Torre-Fuentes
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Paloma Montero-Escribano
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | | | | | | | - Ulises Gómez-Pinedo
- Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
| | - Jorge Matías-Guiu
- Department of Neurology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain.,Laboratory of Neurobiology, Institute of Neurosciences, IdISSC, Hospital Clínico San Carlos, Universidad Complutense de Madrid, Madrid, Spain
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Mescheriakova JY, Verkerk AJ, Amin N, Uitterlinden AG, van Duijn CM, Hintzen RQ. Linkage analysis and whole exome sequencing identify a novel candidate gene in a Dutch multiple sclerosis family. Mult Scler 2018; 25:909-917. [PMID: 29873607 PMCID: PMC6545620 DOI: 10.1177/1352458518777202] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
BACKGROUND Multiple sclerosis (MS) is a complex disease resulting from the joint effect of many genes. It has been speculated that rare variants might explain part of the missing heritability of MS. OBJECTIVE To identify rare coding genetic variants by analyzing a large MS pedigree with 11 affected individuals in several generations. METHODS Genome-wide linkage screen and whole exome sequencing (WES) were performed to identify novel coding variants in the shared region(s) and in the known 110 MS risk loci. The candidate variants were then assessed in 591 MS patients and 3169 controls. RESULTS Suggestive evidence for linkage was obtained to 7q11.22-q11.23. In WES data, a rare missense variant p.R183C in FKBP6 was identified that segregated with the disease in this family. The minor allele frequency was higher in an independent cohort of MS patients than in healthy controls (1.27% vs 0.95%), but not significant (odds ratio (OR) = 1.33 (95% confidence interval (CI): 0.8-2.4), p = 0.31). CONCLUSION The rare missense variant in FKBP6 was identified in a large Dutch MS family segregating with the disease. This association to MS was not found in an independent MS cohort. Overall, genome-wide studies in larger cohorts are needed to adequately investigate the role of rare variants in MS risk.
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Affiliation(s)
- Julia Y Mescheriakova
- Department of Neurology, MS Center ErasMS, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Centre, Rotterdam, the Netherlands
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Rogier Q Hintzen
- Department of Neurology, MS Center ErasMS, Erasmus Medical Centre, Rotterdam, The Netherlands
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18
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Mosca L, Mantero V, Penco S, La Mantia L, De Benedetti S, Marazzi MR, Spreafico C, Erminio C, Grassi L, Lando G, Zagaria M, Agostoni E, Protti A. HLA-DRB1*15 association with multiple sclerosis is confirmed in a multigenerational Italian family. FUNCTIONAL NEUROLOGY 2018; 32:83-88. [PMID: 28676141 DOI: 10.11138/fneur/2017.32.2.083] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Environmental and genetic factors seem to play a pathogenetic role in multiple sclerosis (MS). The genetic component is partly suggested by familial aggregation of cases; however, MS families with affected subjects over different generations have rarely been described. The aim of this study was to report clinical and genetic features of a multigenerational MS family and to perform a review of the literature on this topic. We describe a multigenerational Italian family with six individuals affected by MS, showing different clinical and neuroradiological findings. HLA-DRB1* typing revealed the presence of the DRB1*15:01 allele in all the MS cases and in 4/5 non-affected subjects. Reports on six multigenerational MS families have previously been published, giving similar results. The HLA-DRB1*15:01 allele was confirmed to be linked to MS disease in this family; moreover, its presence in non-affected subjects suggests the involvement of other susceptibility factors in the development and expression of the disease, in accordance with the complex disease model now attributed to MS.
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Zaplakhova OV, Timasheva YR, Bakhtiyarova KZ, Tuktarova IA, Mustafina OE. [Clinical and molecular genetic analysis of a case of familial multiple sclerosis in the Republic of Bashkortostan]. Zh Nevrol Psikhiatr Im S S Korsakova 2017; 117:31-41. [PMID: 28617359 DOI: 10.17116/jnevro20171172231-41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
AIM To investigate clinical manifestations of multiple sclerosis (MS) and the genetic makeup of six affected members of one family. MATERIAL AND METHODS Six members of the family of Russian ethnic origin were examined. Pedigree analysis and genotyping of polymorphic markers of candidate genes for multiple sclerosis were performed. RESULTS AND CONCLUSION The accumulation of alleles that were associated with autoimmune diseases according to the results of genome-wide association studies (rs1109670*C, rs3129934*T, rs9523762*G, rs1570538*T) was found in the family. The results confirm the contribution of several genetic variants to familial forms of MS.
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Affiliation(s)
- O V Zaplakhova
- Institute of Biochemistry and Genetics Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia; Bashkir State Medical University, Ufa, Russia
| | - Ya R Timasheva
- Institute of Biochemistry and Genetics Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | | | - I A Tuktarova
- Institute of Biochemistry and Genetics Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
| | - O E Mustafina
- Institute of Biochemistry and Genetics Ufa Scientific Centre of Russian Academy of Sciences, Ufa, Russia
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Abstract
The genetic etiology and the contribution of rare genetic variation in multiple sclerosis (MS) has not yet been elucidated. Although familial forms of MS have been described, no convincing rare and penetrant variants have been reported to date. We aimed to characterize the contribution of rare genetic variation in familial and sporadic MS and have identified a family with two sibs affected by concomitant MS and malignant melanoma (MM). We performed whole exome sequencing in this primary family and 38 multiplex MS families and 44 sporadic MS cases and performed transcriptional and immunologic assessment of the identified variants. We identified a potentially causative homozygous missense variant in NLRP1 gene (Gly587Ser) in the primary family. Further possibly pathogenic NLRP1 variants were identified in the expanded cohort of patients. Stimulation of peripheral blood mononuclear cells from MS patients with putatively pathogenic NLRP1 variants showed an increase in IL-1B gene expression and active cytokine IL-1β production, as well as global activation of NLRP1-driven immunologic pathways. We report a novel familial association of MS and MM, and propose a possible underlying genetic basis in NLRP1 gene. Furthermore, we provide initial evidence of the broader implications of NLRP1-related pathway dysfunction in MS.
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21
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Nozuma S, Matsuura E, Kodama D, Tashiro Y, Matsuzaki T, Kubota R, Izumo S, Takashima H. Effects of host restriction factors and the HTLV-1 subtype on susceptibility to HTLV-1-associated myelopathy/tropical spastic paraparesis. Retrovirology 2017; 14:26. [PMID: 28420387 PMCID: PMC5395872 DOI: 10.1186/s12977-017-0350-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 04/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although human T-lymphotropic virus type 1 (HTLV-1) infection is a prerequisite for the development of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), specific provirus mutations in HAM/TSP have not yet been reported. In this study, we examined whether HAM/TSP patients had the disease-specific genomic variants of HTLV-1 by analyzing entire sequences of HTLV-1 proviruses in these patients, including familial cases. In addition, we investigated the genetic variants of host restriction factors conferring antiretroviral activity to determine which mutations may be related to resistance or susceptibility to HAM/TSP. RESULTS The subjects included 30 patients with familial HAM/TSP (f-HAM/TSP), 92 patients with sporadic HAM/TSP (s-HAM/TSP), and 89 asymptomatic HTLV-1 carriers (ACs). In all 211 samples, 37 samples (18%) were classified into transcontinental subtype and 174 samples (82%) were classified as Japanese subtype. Among three groups, the percentage of transcontinental subtype in f-HAM/TSP, s-HAM/TSP and ACs was 33, 23 and 7%, respectively. The frequency of transcontinental subtype was significantly higher in both f-HAM/TSP (p < 0.001) and s-HAM/TSP (p < 0.001) than in ACs. Fifty mutations in HTLV-1 sequences were significantly more frequent in HAM/TSP patients than in ACs, however, they were common only in transcontinental subtype. Among these mutations, ten common mutations causing amino acid changes in the HTLV-1 sequences were specific to the transcontinental subtype. We examined host restriction factors, and detected a rare variant in TRIM5α in HAM/TSP patients. The patients with TRIM5α 136Q showed lower proviral loads (PVLs) than those with 136R (354 vs. 654 copies/104 PBMC, p = 0.003). The patients with the 304L variant of TRIM5α had significantly higher PVLs than those with 304H (1669 vs. 595 copies/104 PBMC, p = 0.025). We could not find any HAM/TSP-specific mutations of host restriction factors. CONCLUSIONS Transcontinental subtype is susceptible to HAM/TSP, especially in familial cases. Ten common mutations causing amino acid changes in the HTLV-1 gene were specific to the transcontinental subtype. TRIM5α polymorphisms were associated with PVLs, indicating that TRIM5α could be implicated in HTLV-1 replication.
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Affiliation(s)
- Satoshi Nozuma
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Eiji Matsuura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan.
| | - Daisuke Kodama
- Division of Molecular Pathology, Center for Chronic Viral Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Yuichi Tashiro
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Toshio Matsuzaki
- Division of Molecular Pathology, Center for Chronic Viral Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Ryuji Kubota
- Division of Molecular Pathology, Center for Chronic Viral Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Shuji Izumo
- Division of Molecular Pathology, Center for Chronic Viral Diseases, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima, 890-8520, Japan
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Majoros A, Platanitis E, Kernbauer-Hölzl E, Rosebrock F, Müller M, Decker T. Canonical and Non-Canonical Aspects of JAK-STAT Signaling: Lessons from Interferons for Cytokine Responses. Front Immunol 2017; 8:29. [PMID: 28184222 PMCID: PMC5266721 DOI: 10.3389/fimmu.2017.00029] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 01/09/2017] [Indexed: 01/07/2023] Open
Abstract
Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signal transduction mediates cytokine responses. Canonical signaling is based on STAT tyrosine phosphorylation by activated JAKs. Downstream of interferon (IFN) receptors, activated JAKs cause the formation of the transcription factors IFN-stimulated gene factor 3 (ISGF3), a heterotrimer of STAT1, STAT2 and interferon regulatory factor 9 (IRF9) subunits, and gamma interferon-activated factor (GAF), a STAT1 homodimer. In recent years, several deviations from this paradigm were reported. These include kinase-independent JAK functions as well as extra- and intranuclear activities of U-STATs without phosphotyrosines. Additionally, transcriptional control by STAT complexes resembling neither GAF nor ISGF3 contributes to transcriptome changes in IFN-treated cells. Our review summarizes the contribution of non-canonical JAK-STAT signaling to the innate antimicrobial immunity imparted by IFN. Moreover, we touch upon functions of IFN pathway proteins beyond the IFN response. These include metabolic functions of IRF9 as well as the regulation of natural killer cell activity by kinase-dead TYK2 and different phosphorylation isoforms of STAT1.
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Affiliation(s)
- Andrea Majoros
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Ekaterini Platanitis
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Elisabeth Kernbauer-Hölzl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Felix Rosebrock
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Decker
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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Leitner NR, Witalisz-Siepracka A, Strobl B, Müller M. Tyrosine kinase 2 - Surveillant of tumours and bona fide oncogene. Cytokine 2015; 89:209-218. [PMID: 26631911 DOI: 10.1016/j.cyto.2015.10.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 10/29/2015] [Indexed: 12/16/2022]
Abstract
Tyrosine kinase 2 (TYK2) is a member of the Janus kinase (JAK) family, which transduces cytokine and growth factor signalling. Analysis of TYK2 loss-of-function revealed its important role in immunity to infection, (auto-) immunity and (auto-) inflammation. TYK2-deficient patients unravelled high similarity between mice and men with respect to cellular signalling functions and basic immunology. Genome-wide association studies link TYK2 to several autoimmune and inflammatory diseases as well as carcinogenesis. Due to its cytokine signalling functions TYK2 was found to be essential in tumour surveillance. Lately TYK2 activating mutants and fusion proteins were detected in patients diagnosed with leukaemic diseases suggesting that TYK2 is a potent oncogene. Here we review the cell intrinsic and extrinsic functions of TYK2 in the characteristics preventing and enabling carcinogenesis. In addition we describe an unexpected function of kinase-inactive TYK2 in tumour rejection.
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Affiliation(s)
- Nicole R Leitner
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Agnieszka Witalisz-Siepracka
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Birgit Strobl
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria
| | - Mathias Müller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Veterinärplatz 1, 1210 Vienna, Austria.
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Ma Y, Shi N, Li M, Chen F, Niu H. Applications of Next-generation Sequencing in Systemic Autoimmune Diseases. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:242-9. [PMID: 26432094 PMCID: PMC4610970 DOI: 10.1016/j.gpb.2015.09.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 09/04/2015] [Accepted: 09/14/2015] [Indexed: 12/14/2022]
Abstract
Systemic autoimmune diseases are a group of heterogeneous disorders caused by both genetic and environmental factors. Although numerous causal genes have been identified by genome-wide association studies (GWAS), these susceptibility genes are correlated to a relatively low disease risk, indicating that environmental factors also play an important role in the pathogenesis of disease. The intestinal microbiome, as the main symbiotic ecosystem between the host and host-associated microorganisms, has been demonstrated to regulate the development of the body’s immune system and is likely related to genetic mutations in systemic autoimmune diseases. Next-generation sequencing (NGS) technology, with high-throughput capacity and accuracy, provides a powerful tool to discover genomic mutations, abnormal transcription and intestinal microbiome identification for autoimmune diseases. In this review, we briefly outlined the applications of NGS in systemic autoimmune diseases. This review may provide a reference for future studies in the pathogenesis of systemic autoimmune diseases.
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Affiliation(s)
- Yiyangzi Ma
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical Collage, Beijing 100021, China
| | - Na Shi
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical Collage, Beijing 100021, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical Collage, Beijing 100730, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Haitao Niu
- Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical Collage, Beijing 100021, China.
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Moran CJ, Klein C, Muise AM, Snapper SB. Very early-onset inflammatory bowel disease: gaining insight through focused discovery. Inflamm Bowel Dis 2015; 21:1166-75. [PMID: 25895007 PMCID: PMC6165626 DOI: 10.1097/mib.0000000000000329] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The pathogenesis of pediatric inflammatory bowel disease (IBD) is only partially understood. Strong evidence implicates a strong genetic component including high monozygotic twin concordance and familial disease phenotype concordance rates. Genome-wide association studies have identified associations between >160 genetic loci and the risk for developing IBD. The roles of implicated genes are largely immune-mediated, although other functions include cellular migration, oxidative stress, and carbohydrate metabolism. Additionally, growing literature describes monogenic causes of IBD that frequently present as infantile or very early-onset IBD. The interplay between IBD risk single nucleotide polymorphisms and rare genetic variants has yet to be determined. Studying patients with very early-onset IBD may elicit genetic factors that could be applied to broader populations of IBD. This review describes what is known about the genetic causes of very early-onset IBD and genetic strategies that may unravel more of the genetic causes of IBD.
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Affiliation(s)
- Christopher J. Moran
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, MassGeneral Hospital for Children, Boston, Massachusetts
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Christoph Klein
- Dr von Hauner Children’s Hospital, Ludwig Maximilians University, Munich, Germany
| | - Aleixo M. Muise
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, Hospital for Sick Children, Toronto, ON, Canada
- SickKids Inflammatory Bowel Disease Center and Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, ON, Canada
| | - Scott B. Snapper
- Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Department of Medicine, Children’s Hospital Boston, Boston, Massachusetts
- Division of Gastroenterology and Hepatology, Brigham & Women’s Hospital, Boston, Massachusetts
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
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Hayes CE, Hubler SL, Moore JR, Barta LE, Praska CE, Nashold FE. Vitamin D Actions on CD4(+) T Cells in Autoimmune Disease. Front Immunol 2015; 6:100. [PMID: 25852682 PMCID: PMC4364365 DOI: 10.3389/fimmu.2015.00100] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 02/23/2015] [Indexed: 12/11/2022] Open
Abstract
This review summarizes and integrates research on vitamin D and CD4+ T-lymphocyte biology to develop new mechanistic insights into the molecular etiology of autoimmune disease. A deep understanding of molecular mechanisms relevant to gene–environment interactions is needed to deliver etiology-based autoimmune disease prevention and treatment strategies. Evidence linking sunlight, vitamin D, and the risk of multiple sclerosis and type 1 diabetes is summarized to develop the thesis that vitamin D is the environmental factor that most strongly influences autoimmune disease development. Evidence for CD4+ T-cell involvement in autoimmune disease pathogenesis and for paracrine calcitriol signaling to CD4+ T lymphocytes is summarized to support the thesis that calcitriol is sunlight’s main protective signal transducer in autoimmune disease risk. Animal modeling and human mechanistic data are summarized to support the view that vitamin D probably influences thymic negative selection, effector Th1 and Th17 pathogenesis and responsiveness to extrinsic cell death signals, FoxP3+CD4+ T-regulatory cell and CD4+ T-regulatory cell type 1 (Tr1) cell functions, and a Th1–Tr1 switch. The proposed Th1–Tr1 switch appears to bridge two stable, self-reinforcing immune states, pro- and anti-inflammatory, each with a characteristic gene regulatory network. The bi-stable switch would enable T cells to integrate signals from pathogens, hormones, cell–cell interactions, and soluble mediators and respond in a biologically appropriate manner. Finally, unanswered questions and potentially informative future research directions are highlighted to speed delivery of etiology-based strategies to reduce autoimmune disease.
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Affiliation(s)
- Colleen Elizabeth Hayes
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Shane L Hubler
- Department of Statistics, College of Letters and Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Jerott R Moore
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Lauren E Barta
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Corinne E Praska
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
| | - Faye E Nashold
- Department of Biochemistry, College of Agricultural and Life Sciences, University of Wisconsin-Madison , Madison, WI , USA
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Jiang T, Tan MS, Tan L, Yu JT. Application of next-generation sequencing technologies in Neurology. ANNALS OF TRANSLATIONAL MEDICINE 2015; 2:125. [PMID: 25568878 DOI: 10.3978/j.issn.2305-5839.2014.11.11] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/20/2013] [Accepted: 03/01/2013] [Indexed: 12/11/2022]
Abstract
Genetic risk factors that underlie many rare and common neurological diseases remain poorly understood because of the multi-factorial and heterogeneous nature of these disorders. Although genome-wide association studies (GWAS) have successfully uncovered numerous susceptibility genes for these diseases, odds ratios associated with risk alleles are generally low and account for only a small proportion of estimated heritability. These results implicated that there are rare (present in <5% of the population) but not causative variants exist in the pathogenesis of these diseases, which usually have large effect size and cannot be captured by GWAS. With the decreasing cost of next-generation sequencing (NGS) technologies, whole-genome sequencing (WGS) and whole-exome sequencing (WES) have enabled the rapid identification of rare variants with large effect size, which made huge progress in understanding the basis of many Mendelian neurological conditions as well as complex neurological diseases. In this article, recent NGS-based studies that aimed to investigate genetic causes for neurological diseases, including Alzheimer's disease, Parkinson's disease, epilepsy, multiple sclerosis, stroke, amyotrophic lateral sclerosis and spinocerebellar ataxias, have been reviewed. In addition, we also discuss the future directions of NGS applications in this article.
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Affiliation(s)
- Teng Jiang
- 1 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 2 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Meng-Shan Tan
- 1 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 2 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Lan Tan
- 1 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 2 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
| | - Jin-Tai Yu
- 1 Department of Neurology, Qingdao Municipal Hospital, Nanjing Medical University, Qingdao 266071, China ; 2 College of Medicine and Pharmaceutics, Ocean University of China, Qingdao 266071, China ; 3 Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266071, China
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Reinhold WC, Varma S, Rajapakse VN, Luna A, Sousa FG, Kohn KW, Pommier YG. Using drug response data to identify molecular effectors, and molecular "omic" data to identify candidate drugs in cancer. Hum Genet 2015; 134:3-11. [PMID: 25213708 PMCID: PMC4282979 DOI: 10.1007/s00439-014-1482-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 08/19/2014] [Indexed: 12/31/2022]
Abstract
The current convergence of molecular and pharmacological data provides unprecedented opportunities to gain insights into the relationships between the two types of data. Multiple forms of large-scale molecular data, including but not limited to gene and microRNA transcript expression, DNA somatic and germline variations from next-generation DNA and RNA sequencing, and DNA copy number from array comparative genomic hybridization are all potentially informative when one attempts to recognize the panoply of potentially influential events both for cancer progression and therapeutic outcome. Concurrently, there has also been a substantial expansion of the pharmacological data being accrued in a systematic fashion. For cancer cell lines, the National Cancer Institute cell line panel (NCI-60), the Cancer Cell Line Encyclopedia (CCLE), and the collaborative Genomics of Drug Sensitivity in Cancer (GDSC) databases all provide subsets of these forms of data. For the patient-derived data, The Cancer Genome Atlas (TCGA) provides analogous forms of genomic information along with treatment histories. Integration of these data in turn relies on the fields of statistics and statistical learning. Multiple algorithmic approaches may be chosen, depending on the data being considered, and the nature of the question being asked. Combining these algorithms with prior biological knowledge, the results of molecular biological studies, and the consideration of genes as pathways or functional groups provides both the challenge and the potential of the field. The ultimate goal is to provide a paradigm shift in the way that drugs are selected to provide a more targeted and efficacious outcome for the patient.
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Affiliation(s)
- William C Reinhold
- Developmental Therapeutic Branch, Center for Cancer Research, NCI, NIH, 9000 Rockville Pike, Building 37, room 5041, Bethesda, MD, 20892, USA,
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NCI-60 whole exome sequencing and pharmacological CellMiner analyses. PLoS One 2014; 9:e101670. [PMID: 25032700 PMCID: PMC4102467 DOI: 10.1371/journal.pone.0101670] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 06/05/2014] [Indexed: 01/01/2023] Open
Abstract
Exome sequencing provides unprecedented insights into cancer biology and pharmacological response. Here we assess these two parameters for the NCI-60, which is among the richest genomic and pharmacological publicly available cancer cell line databases. Homozygous genetic variants that putatively affect protein function were identified in 1,199 genes (approximately 6% of all genes). Variants that are either enriched or depleted compared to non-cancerous genomes, and thus may be influential in cancer progression and differential drug response were identified for 2,546 genes. Potential gene knockouts are made available. Assessment of cell line response to 19,940 compounds, including 110 FDA-approved drugs, reveals ≈80-fold range in resistance versus sensitivity response across cell lines. 103,422 gene variants were significantly correlated with at least one compound (at p<0.0002). These include genes of known pharmacological importance such as IGF1R, BRAF, RAD52, MTOR, STAT2 and TSC2 as well as a large number of candidate genes such as NOM1, TLL2, and XDH. We introduce two new web-based CellMiner applications that enable exploration of variant-to-compound relationships for a broad range of researchers, especially those without bioinformatics support. The first tool, “Genetic variant versus drug visualization”, provides a visualization of significant correlations between drug activity-gene variant combinations. Examples are given for the known vemurafenib-BRAF, and novel ifosfamide-RAD52 pairings. The second, “Genetic variant summation” allows an assessment of cumulative genetic variations for up to 150 combined genes together; and is designed to identify the variant burden for molecular pathways or functional grouping of genes. An example of its use is provided for the EGFR-ERBB2 pathway gene variant data and the identification of correlated EGFR, ERBB2, MTOR, BRAF, MEK and ERK inhibitors. The new tools are implemented as an updated web-based CellMiner version, for which the present publication serves as a compendium.
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Abstract
Genome-wide association studies have revolutionised the genetic analysis of multiple sclerosis. Through international collaborative efforts involving tens of thousands of cases and controls, more than 100 associated common variants have now been identified. These variants consistently implicate genes associated with immunological processes, overwhelmingly lie in regulatory rather than coding regions, and are frequently associated with other autoimmune diseases. The functional implications of these associated variants are mostly unknown; however, early work has shown that several variants have effects on splicing that result in meaningful changes in the balance between different isoforms in relevant tissues. Including the well established risk attributable to variants in genes encoding human leucocyte antigens, only about a quarter of reported heritability can now be accounted for, suggesting that a substantial potential for further discovery remains.
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Affiliation(s)
- Stephen Sawcer
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK.
| | - Robin J M Franklin
- Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK; Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Maria Ban
- Department of Clinical Neurosciences, Cambridge Biomedical Campus, University of Cambridge, Cambridge, UK
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Abstract
The study of rare variants in monogenic forms of autoimmune disease has offered insight into the aetiology of more complex pathologies. Research in complex autoimmune disease initially focused on sequencing candidate genes, with some early successes, notably in uncovering low-frequency variation associated with Type 1 diabetes mellitus. However, other early examples have proved difficult to replicate, and a recent study across six autoimmune diseases, re-sequencing 25 autoimmune disease-associated genes in large sample sizes, failed to find any associated rare variants. The study of rare and low-frequency variation in autoimmune diseases has been made accessible by the inclusion of such variants on custom genotyping arrays (e.g. Immunochip and Exome arrays). Whole-exome sequencing approaches are now also being utilised to uncover the contribution of rare coding variants to disease susceptibility, severity and treatment response. Other sequencing strategies are starting to uncover the role of regulatory rare variation.
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Liang Y, Zhu Y, Xia Y, Peng H, Yang XK, Liu YY, Xu WD, Pan HF, Ye DQ. Therapeutic potential of tyrosine kinase 2 in autoimmunity. Expert Opin Ther Targets 2014; 18:571-80. [PMID: 24654603 DOI: 10.1517/14728222.2014.892925] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
INTRODUCTION Tyrosine kinase 2 (Tyk2) is a Janus kinase family member that is crucial for signaling transduction in response to a wide variety of cytokines, including type I IFNs, IL-6, IL-10, IL-12 and IL-23. An appropriate expression of Tyk2-mediated signaling might be essential for maintaining normal immune responses. AREAS COVERED This review summarizes that Tyk2 is essential for the differentiation and function of a wide variety of immune cells, including natural killer cells, B cells, as well as T helper cells. In addition, Tyk2-mediated signaling promoted the production of autoimmune-associated components, which is implicated in the pathogenesis of autoimmune diseases, such as rheumatoid arthritis, systemic lupus erythematosus, multiple sclerosis. Aberrant expression of Tyk2 was observed in many autoimmune conditions. EXPERT OPINION Until recently, no patent filings had claimed selective inhibitors of Tyk2. Both CP-690,500 and CMP6 failed to be used in clinical treatment due to the difficulties of finding suitable selective leads or due to detrimental toxicities. Although the result of Cmpd1 is promising, it remains to be seen how specific the Tyk2 inhibitor is and how they are working. Currently, structure-based drug design (SBDD) technology has provided us with a quite useful window for SBDD of Tyk2 inhibitors.
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Affiliation(s)
- Yan Liang
- Anhui Medical University, School of Public Health, Department of Epidemiology and Biostatistics , 81 Meishan Road, Hefei, Anhui, 230032 , PR China +86 551 65167726 ; +86 551 65161171 ;
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Pulit SL, Leusink M, Menelaou A, de Bakker PIW. Association claims in the sequencing era. Genes (Basel) 2014; 5:196-213. [PMID: 24705293 PMCID: PMC3978519 DOI: 10.3390/genes5010196] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/24/2014] [Accepted: 02/24/2014] [Indexed: 12/13/2022] Open
Abstract
Since the completion of the Human Genome Project, the field of human genetics has been in great flux, largely due to technological advances in studying DNA sequence variation. Although community-wide adoption of statistical standards was key to the success of genome-wide association studies, similar standards have not yet been globally applied to the processing and interpretation of sequencing data. It has proven particularly challenging to pinpoint unequivocally disease variants in sequencing studies of polygenic traits. Here, we comment on a number of factors that may contribute to irreproducible claims of association in scientific literature and discuss possible steps that we can take towards cultural change.
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Affiliation(s)
- Sara L Pulit
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
| | - Maarten Leusink
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
| | - Androniki Menelaou
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
| | - Paul I W de Bakker
- Department of Medical Genetics, Institute for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands.
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Dobson R, Ramagopalan SV, Giovannoni G. Genome-wide association studies: will we ever predict susceptibility to multiple sclerosis through genetics? Expert Rev Neurother 2014; 13:235-7. [DOI: 10.1586/ern.13.13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Abstract
Familial aggregation and the studies of twins indicate that heredity contributes to multiple sclerosis (MS) risk. Immunologic studies of leukocyte antigens subsequently followed by gene-mapping techniques identified the primary MS susceptibility locus to be within the major histocompatibility complex (MHC). The primary risk allele is HLA-DRB1*15, although other alleles of this gene also influence MS susceptibility. Other genes within the MHC also contribute to MS susceptibility. Genome-wide association studies have identified over 50 additional common variants of genes across the genome. Estimates suggest that there may be as many as 200 genes involved in MS susceptibility. In addition to these common polymorphisms, studies have identified several rare risk alleles in some families. Interestingly, the majority of the genes identified have known immunologic functions and many contribute to the risk of inheriting other autoimmune diseases. Genetic variants in the vitamin D metabolic pathway have also been identified. That vitamin D contributes to MS susceptibility as both an environmental as well as genetic risk factor underscores the importance of this metabolic pathway in disease pathogenesis. Current efforts are focused on understanding how the myriad of genetic risk alleles interact within networks to influence MS risk at family level as well as within populations.
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Affiliation(s)
- Bruce A C Cree
- Department of Neurology, University of California, San Francisco, USA.
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37
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One calcitriol dose transiently increases Helios+FoxP3+ T cells and ameliorates autoimmune demyelinating disease. J Neuroimmunol 2013; 263:64-74. [DOI: 10.1016/j.jneuroim.2013.07.016] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 01/10/2023]
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38
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Handel AE, Disanto G, Ramagopalan SV. Next-generation sequencing in understanding complex neurological disease. Expert Rev Neurother 2013; 13:215-27. [PMID: 23368808 DOI: 10.1586/ern.12.165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Next-generation sequencing techniques have made vast quantities of data on human genomes and transcriptomes available to researchers. Huge progress has been made towards understanding the basis of many Mendelian neurological conditions, but progress has been considerably slower in complex neurological diseases (multiple sclerosis, migraine, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and so on). The authors review current next-generation sequencing methodologies and present selected studies illustrating how these have been used to cast light on the genetic etiology of complex neurological diseases with specific focus on multiple sclerosis. The authors highlight particular pitfalls in next-generation sequencing experiments and speculate on both clinical and research applications of these sequencing platforms for complex neurological disorders in the future.
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Affiliation(s)
- Adam E Handel
- Department of Physiology, Anatomy and Genetics, University of Oxford, UK
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Muñoz-Culla M, Irizar H, Otaegui D. The genetics of multiple sclerosis: review of current and emerging candidates. Appl Clin Genet 2013; 6:63-73. [PMID: 24019748 PMCID: PMC3760455 DOI: 10.2147/tacg.s29107] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Multiple sclerosis (MS) is a complex disease in which environmental, genetic, and epigenetic factors determine the risk of developing the disease. The human leukocyte antigen region is the strongest susceptibility locus linked to MS, but it does not explain the whole heritability of the disease. To find other non-human leukocyte antigen loci associated with the disease, high-throughput genotyping, sequencing, and gene-expression studies have been performed, producing a valuable quantity of information. An overview of the genomic and expression studies is provided in this review, as well as microRNA-expression studies, highlighting the importance of combining all the layers of information in order to elucidate the causes or pathological mechanisms occurring in the disease. Genetics in MS is a promising field that is presumably going to be very productive in the next decade understanding the cross talk between all the factors contributing to the development of MS.
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Affiliation(s)
- Maider Muñoz-Culla
- Multiple Sclerosis Unit, Instituto Biodonostia, San Sebastián, Spain
- Red Española de Esclerosis Múltiple (REEM), Barcelona, Spain
| | - Haritz Irizar
- Multiple Sclerosis Unit, Instituto Biodonostia, San Sebastián, Spain
- Red Española de Esclerosis Múltiple (REEM), Barcelona, Spain
| | - David Otaegui
- Multiple Sclerosis Unit, Instituto Biodonostia, San Sebastián, Spain
- Red Española de Esclerosis Múltiple (REEM), Barcelona, Spain
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Qiu W, Pham K, James I, Nolan D, Castley A, Christiansen FT, Czarniak P, Luo Y, Wu J, Garlepp M, Wilton S, Carroll WM, Mastaglia FL, Kermode AG. The influence of non-HLA gene polymorphisms and interactions on disease risk in a Western Australian multiple sclerosis cohort. J Neuroimmunol 2013; 261:92-7. [PMID: 23726763 DOI: 10.1016/j.jneuroim.2013.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 03/17/2013] [Accepted: 04/30/2013] [Indexed: 01/01/2023]
Abstract
Non-Human Leukocyte Antigen (HLA) genes have concomitant, although modest, effects on multiple sclerosis (MS) susceptibility; however findings have varied in different populations. Here we present the results of an association study of 16 single nucleotide polymorphisms (SNPs) in 10 non-HLA genes (IL7R, IL2RA, CLEC-16A, TYK2, CD58, IRF5, STAT3, CTLA-4, APOE, ICAM-1) in a Western Australian cohort of 350 MS patients and 498 population control subjects. Our results indicate that in this population, SNPs in IL7R, TYK2, IRF5 and APOE have modifying effects on MS susceptibility. We also found evidence of interactive protective effects between polymorphisms in the IL7R/CD58, CLEC-16A/CTLA-4, and TYK2/IRF5 genes, which in some instances are restricted within HLA- or gender-defined groups.
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Affiliation(s)
- Wei Qiu
- Department of Neurology, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
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Li Z, Gakovic M, Ragimbeau J, Eloranta ML, Rönnblom L, Michel F, Pellegrini S. Two rare disease-associated Tyk2 variants are catalytically impaired but signaling competent. THE JOURNAL OF IMMUNOLOGY 2013; 190:2335-44. [PMID: 23359498 DOI: 10.4049/jimmunol.1203118] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Tyk2 belongs to the Janus protein tyrosine kinase family and is involved in signaling of immunoregulatory cytokines (type I and III IFNs, IL-6, IL-10, and IL-12 families) via its interaction with shared receptor subunits. Depending on the receptor complex, Tyk2 is coactivated with either Jak1 or Jak2, but a detailed molecular characterization of the interplay between the two enzymes is missing. In human populations, the Tyk2 gene presents high levels of genetic diversity with >100 nonsynonymous variants being detected. In this study, we characterized two rare Tyk2 variants, I684S and P1104A, which have been associated with susceptibility to autoimmune disease. Specifically, we measured their in vitro catalytic activity and their ability to mediate Stat activation in fibroblasts and genotyped B cell lines. Both variants were found to be catalytically impaired but rescued signaling in response to IFN-α/β, IL-6, and IL-10. These data, coupled with functional study of an engineered Jak1 P1084A, support a model of nonhierarchical activation of Janus kinases in which one catalytically competent Jak is sufficient for signaling provided that its partner behaves as proper scaffold, even if inactive. Through the analysis of IFN-α and IFN-γ signaling in cells with different Jak1 P1084A levels, we also illustrate a context in which a hypomorphic Jak can hamper signaling in a cytokine-specific manner. Given the multitude of Tyk2-activating cytokines, the cell context-dependent requirement for Tyk2 and the catalytic defect of the two disease-associated variants studied in this paper, we predict that these alleles are functionally significant in complex immune disorders.
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Affiliation(s)
- Zhi Li
- Unit of Cytokine Signaling, Institut Pasteur, Paris 75724, France
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42
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Estimating the proportion of variation in susceptibility to multiple sclerosis captured by common SNPs. Sci Rep 2012; 2:770. [PMID: 23105968 PMCID: PMC3480808 DOI: 10.1038/srep00770] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Accepted: 09/06/2012] [Indexed: 01/21/2023] Open
Abstract
Multiple sclerosis (MS) is a complex disease with underlying genetic and environmental factors. Although the contribution of alleles within the major histocompatibility complex (MHC) are known to exert strong effects on MS risk, much remains to be learned about the contributions of loci with more modest effects identified by genome-wide association studies (GWASs), as well as loci that remain undiscovered. We use a recently developed method to estimate the proportion of variance in disease liability explained by 475,806 single nucleotide polymorphisms (SNPs) genotyped in 1,854 MS cases and 5,164 controls. We reveal that ~30% of MS genetic liability is explained by SNPs in this dataset, the majority of which is accounted for by common variants. These results suggest that the unaccounted for proportion could be explained by variants that are in imperfect linkage disequilibrium with common GWAS SNPs, highlighting the potential importance of rare variants in the susceptibility to MS.
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