1
|
Saferali A, Kim W, Xu Z, Chase RP, Cho MH, Laederach A, Castaldi PJ, Hersh CP. Colocalization analysis of 3' UTR alternative polyadenylation quantitative trait loci reveals novel mechanisms underlying associations with lung function. Hum Mol Genet 2024; 33:1164-1175. [PMID: 38569558 DOI: 10.1093/hmg/ddae055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 02/02/2024] [Indexed: 04/05/2024] Open
Abstract
While many disease-associated single nucleotide polymorphisms (SNPs) are expression quantitative trait loci (eQTLs), a large proportion of genome-wide association study (GWAS) variants are of unknown function. Alternative polyadenylation (APA) plays an important role in posttranscriptional regulation by allowing genes to shorten or extend 3' untranslated regions (UTRs). We hypothesized that genetic variants that affect APA in lung tissue may lend insight into the function of respiratory associated GWAS loci. We generated alternative polyadenylation (apa) QTLs using RNA sequencing and whole genome sequencing on 1241 subjects from the Lung Tissue Research Consortium (LTRC) as part of the NHLBI TOPMed project. We identified 56 179 APA sites corresponding to 13 582 unique genes after filtering out APA sites with low usage. We found that a total of 8831 APA sites were associated with at least one SNP with q-value < 0.05. The genomic distribution of lead APA SNPs indicated that the majority are intronic variants (33%), followed by downstream gene variants (26%), 3' UTR variants (17%), and upstream gene variants (within 1 kb region upstream of transcriptional start site, 10%). APA sites in 193 genes colocalized with GWAS data for at least one phenotype. Genes containing the top APA sites associated with GWAS variants include membrane associated ring-CH-type finger 2 (MARCHF2), nectin cell adhesion molecule 2 (NECTIN2), and butyrophilin subfamily 3 member A2 (BTN3A2). Overall, these findings suggest that APA may be an important mechanism for genetic variants in lung function and chronic obstructive pulmonary disease (COPD).
Collapse
Affiliation(s)
- Aabida Saferali
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, United States
| | - Wonji Kim
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, United States
| | - Zhonghui Xu
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, United States
| | - Robert P Chase
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, United States
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, United States
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, 75 Francis St, Boston, MA 02115, United States
| | - Alain Laederach
- Department of Biology, University of North Carolina at Chapel Hill, 120 South Road, Chapel Hill, NC 27599, United States
| | - Peter J Castaldi
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, United States
- Division of General Medicine and Primary Care, Brigham and Women's Hospital, 75 Francis Street, Boston, MA 02115, United States
| | - Craig P Hersh
- Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, MA 02115, United States
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, 75 Francis St, Boston, MA 02115, United States
| |
Collapse
|
2
|
Sahi N, Haider L, Chung K, Prados Carrasco F, Kanber B, Samson R, Thompson AJ, Gandini Wheeler-Kingshott CAM, Trip SA, Brownlee W, Ciccarelli O, Barkhof F, Tur C, Houlden H, Chard D. Genetic influences on disease course and severity, 30 years after a clinically isolated syndrome. Brain Commun 2023; 5:fcad255. [PMID: 37841069 PMCID: PMC10576246 DOI: 10.1093/braincomms/fcad255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/31/2023] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Multiple sclerosis risk has a well-established polygenic component, yet the genetic contribution to disease course and severity remains unclear and difficult to examine. Accurately measuring disease progression requires long-term study of clinical and radiological outcomes with sufficient follow-up duration to confidently confirm disability accrual and multiple sclerosis phenotypes. In this retrospective study, we explore genetic influences on long-term disease course and severity; in a unique cohort of clinically isolated syndrome patients with homogenous 30-year disease duration, deep clinical phenotyping and advanced MRI metrics. Sixty-one clinically isolated syndrome patients [41 female (67%): 20 male (33%)] underwent clinical and MRI assessment at baseline, 1-, 5-, 10-, 14-, 20- and 30-year follow-up (mean age ± standard deviation: 60.9 ± 6.5 years). After 30 years, 29 patients developed relapsing-remitting multiple sclerosis, 15 developed secondary progressive multiple sclerosis and 17 still had a clinically isolated syndrome. Twenty-seven genes were investigated for associations with clinical outcomes [including disease course and Expanded Disability Status Scale (EDSS)] and brain MRI (including white matter lesions, cortical lesions, and brain tissue volumes) at the 30-year follow-up. Genetic associations with changes in EDSS, relapses, white matter lesions and brain atrophy (third ventricular and medullary measurements) over 30 years were assessed using mixed-effects models. HLA-DRB1*1501-positive (n = 26) patients showed faster white matter lesion accrual [+1.96 lesions/year (0.64-3.29), P = 3.8 × 10-3], greater 30-year white matter lesion volumes [+11.60 ml, (5.49-18.29), P = 1.27 × 10-3] and higher annualized relapse rates [+0.06 relapses/year (0.005-0.11), P = 0.031] compared with HLA-DRB1*1501-negative patients (n = 35). PVRL2-positive patients (n = 41) had more cortical lesions (+0.83 [0.08-1.66], P = 0.042), faster EDSS worsening [+0.06 points/year (0.02-0.11), P = 0.010], greater 30-year EDSS [+1.72 (0.49-2.93), P = 0.013; multiple sclerosis cases: +2.60 (1.30-3.87), P = 2.02 × 10-3], and greater risk of secondary progressive multiple sclerosis [odds ratio (OR) = 12.25 (1.15-23.10), P = 0.031] than PVRL2-negative patients (n = 18). In contrast, IRX1-positive (n = 30) patients had preserved 30-year grey matter fraction [+0.76% (0.28-1.29), P = 8.4 × 10-3], lower risk of cortical lesions [OR = 0.22 (0.05-0.99), P = 0.049] and lower 30-year EDSS [-1.35 (-0.87,-3.44), P = 0.026; multiple sclerosis cases: -2.12 (-0.87, -3.44), P = 5.02 × 10-3] than IRX1-negative patients (n = 30). In multiple sclerosis cases, IRX1-positive patients also had slower EDSS worsening [-0.07 points/year (-0.01,-0.13), P = 0.015] and lower risk of secondary progressive multiple sclerosis [OR = 0.19 (0.04-0.92), P = 0.042]. These exploratory findings support diverse genetic influences on pathological mechanisms associated with multiple sclerosis disease course. HLA-DRB1*1501 influenced white matter inflammation and relapses, while IRX1 (protective) and PVRL2 (adverse) were associated with grey matter pathology (cortical lesions and atrophy), long-term disability worsening and the risk of developing secondary progressive multiple sclerosis.
Collapse
Affiliation(s)
- Nitin Sahi
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Lukas Haider
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- Department of Biomedical Imaging and Image Guided Therapy, Medical University Vienna, 1090 Vienna, Austria
| | - Karen Chung
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Ferran Prados Carrasco
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, UK
- Universitat Oberta de Catalunya, 08018 Barcelona, Spain
| | - Baris Kanber
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, UK
- Department of Clinical and Experimental Epilepsy, University College London, London WC1N 3BG, UK
| | - Rebecca Samson
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Alan J Thompson
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Claudia A M Gandini Wheeler-Kingshott
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- Department of Brain and Behavioural Sciences, University of Pavia, 27100 Pavia, Italy
- Brain MRI 3T Research Centre, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - S Anand Trip
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
| | - Wallace Brownlee
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- National Institute for Health and Care Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London W1T 7DN, UK
| | - Olga Ciccarelli
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- National Institute for Health and Care Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London W1T 7DN, UK
| | - Frederik Barkhof
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- Centre for Medical Image Computing (CMIC), Department of Medical Physics and Biomedical Engineering, University College London, London WC1E 6BT, UK
- National Institute for Health and Care Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London W1T 7DN, UK
- Department of Radiology and Nuclear Medicine, VU University Medical Centre, 1081 HV Amsterdam, The Netherlands
| | - Carmen Tur
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- MS Centre of Catalonia (Cemcat), Vall d'Hebron Institute of Research, Vall d'Hebron Barcelona Hospital Campus, 08035 Barcelona, Spain
| | - Henry Houlden
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen’s Square House, Queen’s Square, London, WC1N 3BG, UK
| | - Declan Chard
- NMR Research Unit, Queen Square Multiple Sclerosis Centre, University College London Queen Square Institute of Neurology, London WC1N 3BG, UK
- National Institute for Health and Care Research (NIHR) University College London Hospitals (UCLH) Biomedical Research Centre, London W1T 7DN, UK
| |
Collapse
|
3
|
Abstract
Nectins are immunoglobulin-like cell adhesion molecules constituting a family with four members, nectin-1, nectin-2, nectin-3, and nectin-4. In the brain, nectin-2 as well as nectin-1 and nectin-3 are expressed whereas nectin-4 is hardly expressed. In the nervous system, physiological functions of nectin-1 and nectin-3, such as synapse formation, mossy fiber trajectory regulation, interneurite affinity, contextual fear memory formation, and stress-related mental disorders, have been revealed. Nectin-2 is ubiquitously expressed in non-neuronal tissues and various nectin-2 functions in non-nervous systems have been extensively investigated, but nectin-2 functions in the brain have not been revealed until recently. Recent findings have revealed that nectin-2 is expressed in the specific areas of the brain and plays important roles, such as homeostasis of astrocytes and neurons and the formation of synapses. Moreover, a single nucleotide polymorphism in the human NECTIN2 gene is associated with Alzheimer's disease. We here summarize recent progress in our understanding of nectin-2 functions in the brain.
Collapse
|
4
|
Miyata M, Mandai K, Maruo T, Sato J, Shiotani H, Kaito A, Itoh Y, Wang S, Fujiwara T, Mizoguchi A, Takai Y, Rikitake Y. Localization of nectin-2δ at perivascular astrocytic endfoot processes and degeneration of astrocytes and neurons in nectin-2 knockout mouse brain. Brain Res 2016; 1649:90-101. [PMID: 27545667 DOI: 10.1016/j.brainres.2016.08.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Revised: 08/09/2016] [Accepted: 08/18/2016] [Indexed: 10/21/2022]
Abstract
Nectins are Ca2+-independent immunoglobulin-like cell-cell adhesion molecules. In the nervous system, among four members (nectin-1, -2, -3, and -4), nectin-1 and -3 are asymmetrically localized at puncta adherentia junctions formed between the mossy fiber terminals and the dendrites of CA3 pyramidal neurons in the mouse hippocampus and heterophilic trans-interactions between nectin-1 and nectin-3 are involved in the selective interaction of axons and dendrites of cultured neurons. By contrast, nectin-2, which has two splicing variants, nectin-2α and -2δ, has not been well characterized in the brain. We showed here that nectin-2α was expressed in both cultured mouse neurons and astrocytes whereas nectin-2δ was selectively expressed in the astrocytes. Nectin-2δ was localized at the adhesion sites between adjacent cultured astrocytes, but in the brain it was localized on the plasma membranes of astrocytic perivascular endfoot processes facing the basement membrane of blood vessels. Genetic ablation of nectin-2 caused degeneration of astrocytic perivascular endfoot processes and neurons in the cerebral cortex. These results uncovered for the first time the localization and critical functions of nectin-2 in the brain.
Collapse
Affiliation(s)
- Muneaki Miyata
- Division of Signal Transduction, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan
| | - Kenji Mandai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan; CREST, Japan Science and Technology Agency, Kobe, Japan
| | - Tomohiko Maruo
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan; CREST, Japan Science and Technology Agency, Kobe, Japan
| | - Junya Sato
- Division of Cardiovascular Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan
| | - Hajime Shiotani
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan; Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Aika Kaito
- CREST, Japan Science and Technology Agency, Kobe, Japan; Department of Neural Regeneration and Cell Communication, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yu Itoh
- CREST, Japan Science and Technology Agency, Kobe, Japan; Department of Neural Regeneration and Cell Communication, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Shujie Wang
- CREST, Japan Science and Technology Agency, Kobe, Japan; Department of Neural Regeneration and Cell Communication, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Takeshi Fujiwara
- CREST, Japan Science and Technology Agency, Kobe, Japan; Department of Neural Regeneration and Cell Communication, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Akira Mizoguchi
- CREST, Japan Science and Technology Agency, Kobe, Japan; Department of Neural Regeneration and Cell Communication, Mie University Graduate School of Medicine, Tsu 514-8507, Japan
| | - Yoshimi Takai
- Division of Pathogenetic Signaling, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0047, Japan; CREST, Japan Science and Technology Agency, Kobe, Japan.
| | - Yoshiyuki Rikitake
- Division of Signal Transduction, Department of Biochemistry and Molecular Biology, Kobe University Graduate School of Medicine, Kobe 650-0017, Japan; CREST, Japan Science and Technology Agency, Kobe, Japan; Department of Medical Pharmaceutics, Kobe Pharmaceutical University, Kobe 658-8558, Japan.
| |
Collapse
|
5
|
Novaes E Brito RR, Xander P, Pérez EC, Maricato JT, Laurindo MF, De Lorenzo BHP, Pellegrino R, Bernardo V, Lopes JD, Mariano M. Gene expression in B-1 cells from lupus-prone mice. Immunol Invest 2014; 43:675-92. [PMID: 24950194 DOI: 10.3109/08820139.2014.915413] [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: 11/13/2022]
Abstract
New Zealand Black X New Zealand White F1 [(NZB/NZW)F1] mice develop an autoimmune condition with similarities to human systemic lupus erythematosus (SLE). In this study, we demonstrate that B-1 cells, which have previously been reported to be involved in several autoimmune diseases, have altered gene expression in these mice. RNA was extracted from purified B-1 cells of disease-free C57BL/6 mice and lupus-prone (NZB/NZW)F1 mice. Gene expression was analysed using DNA microarray techniques and validated by real time reverse transcriptase polymerase chain reaction (RT-PCR). In (NZB/NZW)F1 mice, some genes had altered expression patterns compared to disease-free controls. Specifically, the upregulation of Ifitm1, Pvrl2 and Ifi202b and downregulation of Trp53bp1 mRNA were observed in (NZB/NZW)F1 mice. These genes are known to be associated with autoimmune diseases. This pattern of gene expression in B-1 cells could understanding of the pathogenesis of SLE. Thus, it is reasonable to hypothesise that the altered gene expression observed in B-1 cells in our experimental model is important for SLE prognosis and therapy, and these implications are discussed herein.
Collapse
Affiliation(s)
- Ronni Rômulo Novaes E Brito
- Disciplina de Imunologia, Departamento de Microbiologia, Imunologia e Parasitologia Universidade Federal de São Paulo , Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Members 6B and 14 of the TNF receptor superfamily in multiple sclerosis predisposition. Genes Immun 2010; 12:145-8. [PMID: 20962851 DOI: 10.1038/gene.2010.42] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
TNFRSF6B and TNFRSF14 genes were recently associated with Crohn's disease and rheumatoid arthritis. TNFRSF14 is known as herpes virus entry mediator (HVEM), and herpes viruses have been involved in the aetiology of multiple sclerosis (MS). MS patients present human herpes virus 6 (HHV6) in active plaques and increased antibody responses to HHV6. We aimed to ascertain the role of these genes in MS susceptibility and to investigate the relationship of the gene encoding the widely expressed HVEM receptor with the active replication of HHV6 found in some MS patients. Genotyping of 1370 Spanish MS patients and 1715 ethnically matched controls was performed. HHV6A DNA levels (surrogate of active viral replication) were analysed in serum of MS patients during a 2-year follow-up. Both polymorphisms were associated with MS predisposition, with stronger effect in patients with HHV6 active replication-TNFRSF6B-rs4809330(*)A: P=0.028, OR=1.13; TNFRSF14-rs6684865(*)A: overall P=0.0008, OR=1.2; and HHV6-positive patients vs controls: P=0.017, OR=1.69.
Collapse
|
7
|
Kerstens HH, Kollers S, Kommadath A, Del Rosario M, Dibbits B, Kinders SM, Crooijmans RP, Groenen MA. Mining for single nucleotide polymorphisms in pig genome sequence data. BMC Genomics 2009; 10:4. [PMID: 19126189 PMCID: PMC2637895 DOI: 10.1186/1471-2164-10-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2008] [Accepted: 01/06/2009] [Indexed: 11/30/2022] Open
Abstract
Background Single nucleotide polymorphisms (SNPs) are ideal genetic markers due to their high abundance and the highly automated way in which SNPs are detected and SNP assays are performed. The number of SNPs identified in the pig thus far is still limited. Results A total of 4.8 million whole genome shotgun sequences obtained from the NCBI trace-repository with center name "SDJVP", and project name "Sino-Danish Pig Genome Project" were analysed for the presence of SNPs. Available BAC and BAC-end sequences and their naming and mapping information, all obtained from SangerInstitute FTP site, served as a rough assembly of a reference genome. In 1.2 Gb of pig genome sequence, we identified 98,151 SNPs in which one of the sequences in the alignment represented the polymorphism and 6,374 SNPs in which two sequences represent an identical polymorphism. To benchmark the SNP identification method, 163 SNPs, in which the polymorphism was represented twice in the sequence alignment, were selected and tested on a panel of three purebred boar lines and wild boar. Of these 163 in silico identified SNPs, 134 were shown to be polymorphic in our animal panel. Conclusion This SNP identification method, which mines for SNPs in publicly available porcine shotgun sequences repositories, provides thousands of high quality SNPs. Benchmarking in an animal panel showed that more than 80% of the predicted SNPs represented true genetic variation.
Collapse
Affiliation(s)
- Hindrik Hd Kerstens
- Animal Breeding and Genetics Group, Wageningen University, Wageningen, the Netherlands.
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Ramagopalan SV, Deluca GC, Degenhardt A, Ebers GC. The genetics of clinical outcome in multiple sclerosis. J Neuroimmunol 2008; 201-202:183-99. [PMID: 18632165 DOI: 10.1016/j.jneuroim.2008.02.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2008] [Revised: 02/11/2008] [Accepted: 02/11/2008] [Indexed: 11/18/2022]
Abstract
Multiple sclerosis (MS) is a common inflammatory disease of the central nervous system (CNS), the clinical course of which varies considerably between patients. Genetic complexity and interactions with as yet unknown environmental factors have hindered researchers from fully elucidating the aetiology of the disease. In addition to influencing disease susceptibility, epidemiological evidence suggests that genetic factors may affect phenotypic expression of the disease. Genes that affect clinical outcome may be more effective therapeutic targets than those which determine susceptibility. We present in this review a comprehensive survey of the genes (both MHC- and non-MHC-related) that have been investigated for their role in disease outcome in MS. Recent studies implicating the role of the genotype and epistatic interactions in the MHC in determining outcome are highlighted.
Collapse
|
9
|
Oksenberg JR, Baranzini SE, Sawcer S, Hauser SL. The genetics of multiple sclerosis: SNPs to pathways to pathogenesis. Nat Rev Genet 2008; 9:516-26. [PMID: 18542080 DOI: 10.1038/nrg2395] [Citation(s) in RCA: 257] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multiple sclerosis (MS) is an autoimmune demyelinating disease and a common cause of neurological disability in young adults. The modest heritability of MS reflects complex genetic effects and multifaceted gene-environment interactions. The human leukocyte antigen (HLA) region is the strongest susceptibility locus for MS, but a genome-wide association study recently identified new susceptibility genes. Progress in high-throughput genotyping and sequencing technologies and a better understanding of the structural organization of the human genome, together with powerful brain-imaging techniques that refine the phenotype, suggest that the tools could finally exist to identify the full set of genes influencing the pathogenesis of MS.
Collapse
Affiliation(s)
- Jorge R Oksenberg
- Department of Neurology, School of Medicine, University of California at San Francisco, 513 Parnassus Avenue, San Francisco, California 94143-0435, USA.
| | | | | | | |
Collapse
|
10
|
Skogsberg J, Lundström J, Kovacs A, Nilsson R, Noori P, Maleki S, Köhler M, Hamsten A, Tegnér J, Björkegren J. Transcriptional profiling uncovers a network of cholesterol-responsive atherosclerosis target genes. PLoS Genet 2008; 4:e1000036. [PMID: 18369455 PMCID: PMC2265530 DOI: 10.1371/journal.pgen.1000036] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Accepted: 02/13/2008] [Indexed: 11/18/2022] Open
Abstract
Despite the well-documented effects of plasma lipid lowering regimes halting atherosclerosis lesion development and reducing morbidity and mortality of coronary artery disease and stroke, the transcriptional response in the atherosclerotic lesion mediating these beneficial effects has not yet been carefully investigated. We performed transcriptional profiling at 10-week intervals in atherosclerosis-prone mice with human-like hypercholesterolemia and a genetic switch to lower plasma lipoproteins (Ldlr−/−Apo100/100Mttpflox/flox Mx1-Cre). Atherosclerotic lesions progressed slowly at first, then expanded rapidly, and plateaued after advanced lesions formed. Analysis of lesion expression profiles indicated that accumulation of lipid-poor macrophages reached a point that led to the rapid expansion phase with accelerated foam-cell formation and inflammation, an interpretation supported by lesion histology. Genetic lowering of plasma cholesterol (e.g., lipoproteins) at this point all together prevented the formation of advanced plaques and parallel transcriptional profiling of the atherosclerotic arterial wall identified 37 cholesterol-responsive genes mediating this effect. Validation by siRNA-inhibition in macrophages incubated with acetylated-LDL revealed a network of eight cholesterol-responsive atherosclerosis genes regulating cholesterol-ester accumulation. Taken together, we have identified a network of atherosclerosis genes that in response to plasma cholesterol-lowering prevents the formation of advanced plaques. This network should be of interest for the development of novel atherosclerosis therapies. Atherosclerosis is present in the major arteries of all adults. In industrial societies, atherosclerosis progression in ∼50% of adults leads to clinical manifestations such as stroke and myocardial infarction, and eventually death. Lowering circulating LDL-cholesterol levels can slow atherosclerosis progression and even cause regression. Yet, little is known about the genes in the atherosclerotic arterial wall that mediate those effects. To identify such genes, we studied genetically modified mice in which high levels of human-like LDL-cholesterol cause rapid progression of atherosclerosis; the mice also had a genetic “switch” to lower LDL-cholesterol. Lowering LDL-cholesterol at a critical point before advanced plaques developed stopped lesion progression. Analysis of gene expression in response to the lowering of plasma LDL-cholesterol revealed 37 lesion genes as possible mediators of this effect. We validated some of these genes in macrophages using siRNA incubated with acetylated-LDL to mimic foam cells, which are central to atherosclerosis progression. “Reverse engineering” of whole-genome expression data from these experiments revealed a regulatory gene network of cholesterol-responsive atherosclerosis genes that control foam cell formation. This network and the individual genes within it merit further attention as targets for drugs to prevent the transformation of early harmless lesions into advanced, clinically significant plaques.
Collapse
Affiliation(s)
- Josefin Skogsberg
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jesper Lundström
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Alexander Kovacs
- Atherosclerosis Research Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Roland Nilsson
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
- Division of Computational Biology, Department of Physics, Linköpings Institute for Technology, Linköping University, Linköping, Sweden
| | - Peri Noori
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Shohreh Maleki
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Marina Köhler
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Anders Hamsten
- Atherosclerosis Research Unit, Center for Molecular Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
| | - Jesper Tegnér
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
- Division of Computational Biology, Department of Physics, Linköpings Institute for Technology, Linköping University, Linköping, Sweden
| | - Johan Björkegren
- The Computational Medicine Group, Karolinska Institutet, Karolinska University Hospital Solna, Stockholm, Sweden
- * E-mail:
| |
Collapse
|
11
|
Gregory SG, Schmidt S, Seth P, Oksenberg JR, Hart J, Prokop A, Caillier SJ, Ban M, Goris A, Barcellos LF, Lincoln R, McCauley JL, Sawcer SJ, Compston DAS, Dubois B, Hauser SL, Garcia-Blanco MA, Pericak-Vance MA, Haines JL. Interleukin 7 receptor alpha chain (IL7R) shows allelic and functional association with multiple sclerosis. Nat Genet 2007; 39:1083-91. [PMID: 17660817 DOI: 10.1038/ng2103] [Citation(s) in RCA: 462] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2007] [Accepted: 06/18/2007] [Indexed: 01/22/2023]
Abstract
Multiple sclerosis is a demyelinating neurodegenerative disease with a strong genetic component. Previous genetic risk studies have failed to identify consistently linked regions or genes outside of the major histocompatibility complex on chromosome 6p. We describe allelic association of a polymorphism in the gene encoding the interleukin 7 receptor alpha chain (IL7R) as a significant risk factor for multiple sclerosis in four independent family-based or case-control data sets (overall P = 2.9 x 10(-7)). Further, the likely causal SNP, rs6897932, located within the alternatively spliced exon 6 of IL7R, has a functional effect on gene expression. The SNP influences the amount of soluble and membrane-bound isoforms of the protein by putatively disrupting an exonic splicing silencer.
Collapse
Affiliation(s)
- Simon G Gregory
- Center for Human Genetics, Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina 27710, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
12
|
Ramagopalan SV, Deluca GC, Morrison KM, Herrera BM, Dyment DA, Orton S, Bihoreau MT, Degenhardt A, Pugliatti M, Sadovnick AD, Sotgiu S, Ebers GC. No effect of APOE and PVRL2 on the clinical outcome of multiple sclerosis. J Neuroimmunol 2007; 186:156-60. [PMID: 17376543 DOI: 10.1016/j.jneuroim.2007.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 02/13/2007] [Accepted: 02/16/2007] [Indexed: 11/23/2022]
Abstract
Multiple sclerosis (MS) is a common inflammatory disease of the central nervous system unsurpassed for its variability in disease outcome. Apolipoprotein E (APOE) is involved in neuronal remodelling and several studies have attempted to examine the effect of APOE on MS disease severity, but its function in modifying the course of MS is controversial. It has been suggested recently that PVRL2, not APOE, is the locus on chromosome 19 which influences clinical outcome of MS. A cohort of sporadic MS cases, taken from opposite extremes of the putative distribution of long-term outcome using the most stringent clinical criteria to date, was used to determine the role of APOE and PVRL2 on MS disease severity. The MS cases selected represent the prognostic best 5% (benign MS) and worst 5% (malignant MS) of cases in terms of clinical outcome assessed by the EDSS. Genotyping the two sets of MS patients (112 benign and 51 malignant) and a replication cohort from Sardinia provided no evidence to suggest that APOE or PVRL2 have any outcome modifying activity. We conclude that APOE and PVRL2 have little or no effect on the clinical outcome of MS.
Collapse
|