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Pazhouhandeh M, Sahraian MA, Siadat SD, Fateh A, Vaziri F, Tabrizi F, Ajorloo F, Arshadi AK, Fatemi E, Piri Gavgani S, Mahboudi F, Rahimi Jamnani F. A systems medicine approach reveals disordered immune system and lipid metabolism in multiple sclerosis patients. Clin Exp Immunol 2018; 192:18-32. [PMID: 29194580 DOI: 10.1111/cei.13087] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 11/19/2017] [Accepted: 11/20/2017] [Indexed: 02/06/2023] Open
Abstract
Identification of autoimmune processes and introduction of new autoantigens involved in the pathogenesis of multiple sclerosis (MS) can be helpful in the design of new drugs to prevent unresponsiveness and side effects in patients. To find significant changes, we evaluated the autoantibody repertoires in newly diagnosed relapsing-remitting MS patients (NDP) and those receiving disease-modifying therapy (RP). Through a random peptide phage library, a panel of NDP- and RP-specific peptides was identified, producing two protein data sets visualized using Gephi, based on protein--protein interactions in the STRING database. The top modules of NDP and RP networks were assessed using Enrichr. Based on the findings, a set of proteins, including ATP binding cassette subfamily C member 1 (ABCC1), neurogenic locus notch homologue protein 1 (NOTCH1), hepatocyte growth factor receptor (MET), RAF proto-oncogene serine/threonine-protein kinase (RAF1) and proto-oncogene vav (VAV1) was found in NDP and was involved in over-represented terms correlated with cell-mediated immunity and cancer. In contrast, transcription factor RelB (RELB), histone acetyltransferase p300 (EP300), acetyl-CoA carboxylase 2 (ACACB), adiponectin (ADIPOQ) and phosphoenolpyruvate carboxykinase 2 mitochondrial (PCK2) had major contributions to viral infections and lipid metabolism as significant events in RP. According to these findings, further research is required to demonstrate the pathogenic roles of such proteins and autoantibodies targeting them in MS and to develop therapeutic agents which can ameliorate disease severity.
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Affiliation(s)
- M Pazhouhandeh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - M-A Sahraian
- MS Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - S D Siadat
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - A Fateh
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Vaziri
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Tabrizi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Ajorloo
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Biology, Faculty of Science, Islamic Azad University, East Tehran Branch, Tehran, Iran
| | - A K Arshadi
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - E Fatemi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - S Piri Gavgani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Mahboudi
- Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - F Rahimi Jamnani
- Human Antibody Lab, Innovation Center, Pasteur Institute of Iran, Tehran, Iran.,Department of Mycobacteriology and Pulmonary Research, Microbiology Research Center, Pasteur Institute of Iran, Tehran, Iran
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Genome-wide association study in a high-risk isolate for multiple sclerosis reveals associated variants in STAT3 gene. Am J Hum Genet 2010; 86:285-91. [PMID: 20159113 DOI: 10.1016/j.ajhg.2010.01.017] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 01/05/2010] [Accepted: 01/14/2010] [Indexed: 01/27/2023] Open
Abstract
Genetic risk for multiple sclerosis (MS) is thought to involve both common and rare risk alleles. Recent GWAS and subsequent meta-analysis have established the critical role of the HLA locus and identified new common variants associated to MS. These variants have small odds ratios (ORs) and explain only a fraction of the genetic risk. To expose potentially rare, high-impact alleles, we conducted a GWAS of 68 distantly related cases and 136 controls from a high-risk internal isolate of Finland with increased prevalence and familial occurrence of MS. The top 27 loci with p < 10(-4) were tested in 711 cases and 1029 controls from Finland, and the top two findings were validated in 3859 cases and 9110 controls from more heterogeneous populations. SNP (rs744166) within the STAT3 gene was associated to MS (p = 2.75 x 10(-10), OR 0.87, confidence interval 0.83-0.91). The protective haplotype for MS in STAT3 is a risk allele for Crohn disease, implying that STAT3 represents a shared risk locus for at least two autoimmune diseases. This study also demonstrates the potential of special isolated populations in search for variants contributing to complex traits.
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Kallio SP, Jakkula E, Purcell S, Suvela M, Koivisto K, Tienari PJ, Elovaara I, Pirttilä T, Reunanen M, Bronnikov D, Viander M, Meri S, Hillert J, Lundmark F, Harbo HF, Lorentzen AR, De Jager PL, Daly MJ, Hafler DA, Palotie A, Peltonen L, Saarela J. Use of a genetic isolate to identify rare disease variants: C7 on 5p associated with MS. Hum Mol Genet 2009; 18:1670-83. [PMID: 19221116 DOI: 10.1093/hmg/ddp073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Large case-control genome-wide association studies primarily expose common variants contributing to disease pathogenesis with modest effects. Thus, alternative strategies are needed to tackle rare, possibly more penetrant alleles. One strategy is to use special populations with a founder effect and isolation, resulting in allelic enrichment. For multiple sclerosis such a unique setting is reported in Southern Ostrobothnia in Finland, where the prevalence and familial occurrence of multiple sclerosis (MS) are exceptionally high. Here, we have studied one of the best replicated MS loci, 5p, and monitored for haplotypes shared among 72 regional MS cases, the majority of which are genealogically distantly related. The haplotype analysis over the 45 Mb region, covering the linkage peak identified in Finnish MS families, revealed only modest association at IL7R (P = 0.04), recently implicated in MS, whereas most significant association was found with one haplotype covering the C7-FLJ40243 locus (P = 0.0001), 5.1 Mb centromeric of IL7R. The finding was validated in an independent sample from the isolate and resulted in an odds ratio of 2.73 (P = 0.000003) in the combined data set. The identified relatively rare risk haplotype contains C7 (complement component 7), an important player of the innate immune system. Suggestive association with alleles of the region was seen also in more heterogeneous populations. Interestingly, also the complement activity correlated with the identified risk haplotype. These results suggest that the MS predisposing locus on 5p is more complex than assumed and exemplify power of population isolates in the identification of rare disease alleles.
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Affiliation(s)
- Suvi P Kallio
- Finnish Institute for Molecular Medicine, Biomedicum, Helsinki, Finland
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Li KC, Palotie A, Yuan S, Bronnikov D, Chen D, Wei X, Choi OW, Saarela J, Peltonen L. Finding disease candidate genes by liquid association. Genome Biol 2008; 8:R205. [PMID: 17915034 PMCID: PMC2246280 DOI: 10.1186/gb-2007-8-10-r205] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2007] [Revised: 08/23/2007] [Accepted: 10/04/2007] [Indexed: 01/29/2023] Open
Abstract
A novel approach to finding candidate genes by using gene-expression data has been developed and used to identify a multiple sclerosis susceptibility candidate genes. A novel approach to finding candidate genes by using gene expression data through liquid association is developed and used to identify multiple sclerosis susceptibility candidate genes.
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Affiliation(s)
- Ker-Chau Li
- Department of Statistics, UCLA, 8125 Math Sciences Bldg, Los Angeles, California 90095-1554, USA
- Institute of Statistical Science, Academia Sinica, Academia Road, Nankang, Taipei 115, Taiwan
| | - Aarno Palotie
- The Finnish Genome Center and Department of Clinical Chemistry, University of Helsinki, Haartmaninkatu, 00290 Helsinki, Finland
- The Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
- Department of Pathology and Laboratory Medicine, Gonda Researach Center, UCLA, Los Angeles, California 90095-1766, USA
- Department of Human Genetics, UCLA, 695 Charles E. Young Drive South, Los Angeles, California 90095-1766, USA
| | - Shinsheng Yuan
- Institute of Statistical Science, Academia Sinica, Academia Road, Nankang, Taipei 115, Taiwan
| | - Denis Bronnikov
- The Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
- National Public Health Institute, Helsinki, Finland, Biomedicum Helsinki, Haartmaninkatu, 00290 Helsinki, Finland
| | - Daniel Chen
- The Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Xuelian Wei
- Department of Statistics, UCLA, 8125 Math Sciences Bldg, Los Angeles, California 90095-1554, USA
| | - Oi-Wa Choi
- The Broad Institute of Harvard and MIT, Cambridge Center, Cambridge, Massachusetts 02142, USA
| | - Janna Saarela
- National Public Health Institute, Helsinki, Finland, Biomedicum Helsinki, Haartmaninkatu, 00290 Helsinki, Finland
| | - Leena Peltonen
- National Public Health Institute, Helsinki, Finland, Biomedicum Helsinki, Haartmaninkatu, 00290 Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Biomedicum Helsinki, Haartmaninkatu, 00290 Helsinki, Finland
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Mononen N, Seppälä EH, Duggal P, Autio V, Ikonen T, Ellonen P, Saharinen J, Saarela J, Vihinen M, Tammela TLJ, Kallioniemi O, Bailey-Wilson JE, Schleutker J. Profiling Genetic Variation along the Androgen Biosynthesis and Metabolism Pathways Implicates Several Single Nucleotide Polymorphisms and Their Combinations as Prostate Cancer Risk Factors. Cancer Res 2006; 66:743-7. [PMID: 16424004 DOI: 10.1158/0008-5472.can-05-1723] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Several candidate genes along androgen pathway have been suggested to affect prostate cancer risk but no single gene seems to be overwhelmingly important for a large fraction of the patients. In this study, we first screened for variants in candidate genes and then chose to explore the association between 18 variants and prostate cancer risk by genotyping DNA samples from unselected (n = 847) and familial (n = 121) prostate cancer patients and population controls (n = 923). We identified a novel single nucleotide polymorphism (SNP) in the CYP19A1 gene, T201M, with a mild significant association with prostate cancer [odds ratio (OR), 2.04; 95% confidence interval (95% CI), 1.03-4.03; P = 0.04]. Stratified analysis revealed that this risk was most apparent in patients with organ-confined (T(1)-T(2)) and low-grade (WHO grade 1) tumors (OR, 5.42; 95% CI, 2.33-12.6; P < 0.0001). In contrast, CYP17A1 -34T>C alteration was associated with moderate to poorly differentiated (WHO grade 2-3) organ-confined disease (OR, 1.42; 95% CI, 1.09-1.83; P = 0.007). We also tested a multigenic model of prostate cancer risk by calculating the joint effect of CYP19A1 T201M with five other common SNPs. Individuals carrying both the CYP19A1 and KLK3 -252A>G variant alleles had a significantly increased risk for prostate cancer (OR, 2.87; 95% CI, 1.10-7.49; P = 0.03). In conclusion, our results suggest that several SNPs along the androgen pathway, especially in CYP19A1 and CYP17A1, may influence prostate cancer development and progression. These genes may have different contributions to distinct clinical subsets as well as combinatorial effects in others illustrating that profiling and joint analysis of several genes along each pathway may be needed to understand genetic contributions to prostate cancer etiology.
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Affiliation(s)
- Nina Mononen
- Laboratory of Cancer Genetics, Institute of Medical Technology, University of Tampere and Tampere University Hospital, Tampere FIN-33014, Finland
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