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Briggs FBS, Sept C. Mining Complex Genetic Patterns Conferring Multiple Sclerosis Risk. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18052518. [PMID: 33802599 PMCID: PMC7967327 DOI: 10.3390/ijerph18052518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/23/2021] [Accepted: 03/02/2021] [Indexed: 01/21/2023]
Abstract
(1) Background: Complex genetic relationships, including gene-gene (G × G; epistasis), gene(n), and gene-environment (G × E) interactions, explain a substantial portion of the heritability in multiple sclerosis (MS). Machine learning and data mining methods are promising approaches for uncovering higher order genetic relationships, but their use in MS have been limited. (2) Methods: Association rule mining (ARM), a combinatorial rule-based machine learning algorithm, was applied to genetic data for non-Latinx MS cases (n = 207) and controls (n = 179). The objective was to identify patterns (rules) amongst the known MS risk variants, including HLA-DRB1*15:01 presence, HLA-A*02:01 absence, and 194 of the 200 common autosomal variants. Probabilistic measures (confidence and support) were used to mine rules. (3) Results: 114 rules met minimum requirements of 80% confidence and 5% support. The top ranking rule by confidence consisted of HLA-DRB1*15:01, SLC30A7-rs56678847 and AC093277.1-rs6880809; carriers of these variants had a significantly greater risk for MS (odds ratio = 20.2, 95% CI: 8.5, 37.5; p = 4 × 10−9). Several variants were shared across rules, the most common was INTS8-rs78727559, which was in 32.5% of rules. (4) Conclusions: In summary, we demonstrate evidence that specific combinations of MS risk variants disproportionately confer elevated risk by applying a robust analytical framework to a modestly sized study population.
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Affiliation(s)
- Farren B. S. Briggs
- Department of Population and Quantitative Health Sciences, School of Medicine, Case Western Reserve University, 2103 Cornell Rd, Cleveland, OH 44106, USA
- Correspondence: ; Tel.: +1-216-368-5636
| | - Corriene Sept
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA;
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Liu G, Zhang F, Hu Y, Jiang Y, Gong Z, Liu S, Chen X, Jiang Q, Hao J. Genetic Variants and Multiple Sclerosis Risk Gene SLC9A9 Expression in Distinct Human Brain Regions. Mol Neurobiol 2016; 54:6820-6826. [PMID: 27766536 DOI: 10.1007/s12035-016-0208-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 10/11/2016] [Indexed: 01/10/2023]
Abstract
A recent genome-wide association study reported a significant association between rs9828519 (G) and nonresponsiveness to interferon-beta (IFN-β) treatment and dysregulation of SLC9A9 expression in multiple sclerosis (MS) cases. We hypothesize that disease-relevant tissues are necessary to detect the effects of rs9828519-tagged SNPs on SLC9A9 expression. Here, we investigated whether SLC9A9 expression is regulated by rs9828519-tagged SNPs in human brain tissue. We used HaploReg to identify the proxy SNPs of the rs9828519 variant based on linkage disequilibrium information from the 1000 Genomes Project. We evaluated the potential association between these SNPs and SLC9A9 expression using multiple expression quantitative trait loci datasets including 10 brain regions of 134 individuals from Braineac, 2 brain regions of 773 samples from brain expression GWAS datasets, and 12 brain regions from the GTEx. We discovered differential SLC9A9 expression in different brain regions and identified 15 rs9828519-tagged SNPs that significantly regulated SLC9A9 expression only in occipital cortex, intralobular white matter, and substantia nigra. Our results advance the understanding of the involvement of SLC9A9 and rs9828519 mechanisms in MS.
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Affiliation(s)
- Guiyou Liu
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.,School of Life Science and Technology, Harbin Institute of Technology, Room 415, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Fang Zhang
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Yang Hu
- School of Life Science and Technology, Harbin Institute of Technology, Room 415, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China
| | - Yongshuai Jiang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhongying Gong
- Department of Neurology, Tianjin First Central Hospital, Tianjin, China
| | - Shoufeng Liu
- Department of Neurology, Tianjin HuanHu Hospital, Tianjin, China
| | - Xiuju Chen
- Department of Neurology, Tianjin NanKai Hospital, Tianjin, China
| | - Qinghua Jiang
- School of Life Science and Technology, Harbin Institute of Technology, Room 415, Building 2E, Science Park, Yikuang Street, Nangang District, Harbin, 150080, China.
| | - Junwei Hao
- Department of Neurology and Tianjin Neurological Institute, Tianjin Medical University General Hospital, Tianjin, 300052, China.
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3
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Creanza TM, Liguori M, Liuni S, Nuzziello N, Ancona N. Meta-Analysis of Differential Connectivity in Gene Co-Expression Networks in Multiple Sclerosis. Int J Mol Sci 2016; 17:E936. [PMID: 27314336 PMCID: PMC4926469 DOI: 10.3390/ijms17060936] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/09/2016] [Accepted: 05/24/2016] [Indexed: 12/20/2022] Open
Abstract
Differential gene expression analyses to investigate multiple sclerosis (MS) molecular pathogenesis cannot detect genes harboring genetic and/or epigenetic modifications that change the gene functions without affecting their expression. Differential co-expression network approaches may capture changes in functional interactions resulting from these alterations. We re-analyzed 595 mRNA arrays from publicly available datasets by studying changes in gene co-expression networks in MS and in response to interferon (IFN)-β treatment. Interestingly, MS networks show a reduced connectivity relative to the healthy condition, and the treatment activates the transcription of genes and increases their connectivity in MS patients. Importantly, the analysis of changes in gene connectivity in MS patients provides new evidence of association for genes already implicated in MS by single-nucleotide polymorphism studies and that do not show differential expression. This is the case of amiloride-sensitive cation channel 1 neuronal (ACCN1) that shows a reduced number of interacting partners in MS networks, and it is known for its role in synaptic transmission and central nervous system (CNS) development. Furthermore, our study confirms a deregulation of the vitamin D system: among the transcription factors that potentially regulate the deregulated genes, we find TCF3 and SP1 that are both involved in vitamin D3-induced p27Kip1 expression. Unveiling differential network properties allows us to gain systems-level insights into disease mechanisms and may suggest putative targets for the treatment.
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Affiliation(s)
- Teresa Maria Creanza
- Institute of Intelligent Systems for Automation, National Research Council of Italy, 70126 Bari, Italy.
- Center for Complex Systems in Molecular Biology and Medicine, University of Turin, 10123 Turin, Italy.
| | - Maria Liguori
- Institute of Biomedical Technologies, National Research Council of Italy, 70126 Bari, Italy.
| | - Sabino Liuni
- Institute of Biomedical Technologies, National Research Council of Italy, 70126 Bari, Italy.
| | - Nicoletta Nuzziello
- Institute of Biomedical Technologies, National Research Council of Italy, 70126 Bari, Italy.
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari, 70126 Bari, Italy.
| | - Nicola Ancona
- Institute of Intelligent Systems for Automation, National Research Council of Italy, 70126 Bari, Italy.
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4
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Keshari PK, Harbo HF, Myhr KM, Aarseth JH, Bos SD, Berge T. Allelic imbalance of multiple sclerosis susceptibility genes IKZF3 and IQGAP1 in human peripheral blood. BMC Genet 2016; 17:59. [PMID: 27080863 PMCID: PMC4832550 DOI: 10.1186/s12863-016-0367-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 04/07/2016] [Indexed: 01/09/2023] Open
Abstract
Background Multiple sclerosis is a chronic inflammatory, demyelinating disease of the central nervous system. Recent genome-wide studies have revealed more than 110 single nucleotide polymorphisms as associated with susceptibility to multiple sclerosis, but their functional contribution to disease development is mostly unknown. Results Consistent allelic imbalance was observed for rs907091 in IKZF3 and rs11609 in IQGAP1, which are in strong linkage disequilibrium with the multiple sclerosis associated single nucleotide polymorphisms rs12946510 and rs8042861, respectively. Using multiple sclerosis patients and healthy controls heterozygous for rs907091 and rs11609, we showed that the multiple sclerosis risk alleles at IKZF3 and IQGAP1 are expressed at higher levels as compared to the protective allele. Furthermore, individuals homozygous for the multiple sclerosis risk allele at IQGAP1 had a significantly higher total expression of IQGAP1 compared to individuals homozygous for the protective allele. Conclusions Our data indicate a possible regulatory role for the multiple sclerosis-associated IKZF3 and IQGAP1 variants. We suggest that such cis-acting mechanisms may contribute to the multiple sclerosis association of single nucleotide polymorphisms at IKZF3 and IQGAP1. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0367-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pankaj K Keshari
- Department of Neurology, Oslo University Hospital, Oslo, Norway. .,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Hanne F Harbo
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Kjell-Morten Myhr
- Norwegian Multiple Sclerosis Registry and Biobank, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Jan H Aarseth
- Norwegian Multiple Sclerosis Registry and Biobank, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,KG Jebsen Centre for MS-research, Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Steffan D Bos
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tone Berge
- Department of Neurology, Oslo University Hospital, Oslo, Norway
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Fernández-Menéndez S, Fernández-Morán M, Fernández-Vega I, Pérez-Álvarez A, Villafani-Echazú J. Epstein-Barr virus and multiple sclerosis. From evidence to therapeutic strategies. J Neurol Sci 2016; 361:213-9. [PMID: 26810546 DOI: 10.1016/j.jns.2016.01.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/21/2015] [Accepted: 01/05/2016] [Indexed: 10/22/2022]
Abstract
Multiple sclerosis is caused by a complex interaction between genetic predisposition and environmental factors. Epstein-Barr virus (EBV) is an environmental risk factor that is strongly related to multiple sclerosis (MS), since EBV seropositivity is linked to a significant risk of developing MS. EBV may be involved in the pathogenesis of the disease and it is possibly a prerequisite for the development of MS. EBV infection persists in B-cells during the lifetime of the host and can modulate their function. In addition, MS patients might have a deficient capacity to eliminate latent EBV infection in the central nervous system and this would promote the accumulation of infected B cells. Several mechanisms of pathogenesis, including a direct and indirect function of infected B cells, have been postulated in inflammation and neurodegeneration. A relationship between EBV and human endogenous retroviruses in the pathogenesis of MS has also been reported. If EBV is important in the pathogenesis of MS, different therapeutic strategies seem possible for MS treatment.
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Affiliation(s)
| | - Marta Fernández-Morán
- Department of Neuropaediatrics, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Iván Fernández-Vega
- Pathology department (Neuropathology division), Hospital Universitario Araba, Álava, Spain
| | - Angel Pérez-Álvarez
- Department of Neurology, Hospital Universitario Central de Asturias, Oviedo, Spain
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Briggs FB, Green MC, Ritterman Weintraub ML. Role of socioeconomic position in multiple sclerosis etiology. Neurodegener Dis Manag 2015; 5:333-43. [DOI: 10.2217/nmt.15.22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Multiple sclerosis (MS) is a debilitating autoimmune disease with a prominent inflammatory component. There have been strides identifying genetic and environmental MS risk factors, though much of the disease risk remains unknown. Recent large observational studies suggest adverse socioeconomic position increases the risk for MS, however the mediating biological processes are not understood. We hypothesize a prominent role for stress response, both the autonomic nervous system and the hypothalamic–pituitary–adrenal axis, which become maladaptive under frequent or chronic stimulation resulting in a proinflammatory phenotype. Thus, adverse SEP and chronic stress may predispose individuals for MS.
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Affiliation(s)
- Farren B Briggs
- Department of Epidemiology & Biostatistics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4945, USA
| | - Matthew C Green
- Department of Public Health, Touro University California, CA 94592, USA
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