Ailesel multipl skleroz'da bağlantı analizi ve genom çapı ilişkilendirme çalışması

Multiple Sclerosis (MS) is an immune-mediated, neuroinflammatory and neurodegenerative disorder affecting the central nervous system (CNS), and characterised by multifocal lesions in white and grey matter with demyelination, axonal transection, neuronal degeneration, gliosis, and perivenular inflammatory cell infiltrates. MS is a complex disease, which develops in genetically susceptible individuals under specific environmental influences. Early observations from classical genetic studies have shown that MS has a genetic background with a broad range of heritability estimates (25%-76%) reported by different studies. Early linkage analyses revealed a strong association of HLA-DRB1 locus of the class II human leukocyte antigen (HLA) region with MS. Subsequent linkage and candidate-gene based analyses have identified different HLA allele associations and a non-HLA association, interleukin 7 receptor alpha (IL7RA) gene. Further chip-based genome wide association studies (GWAS) have identified a total of 110 non-HLA associations, most of which are related to immune pathways, supporting the immune basis of MS. However, current knowledge on MS genetics can explain only about 27% of the predicted MS heritability, leaving much to be explored. We have previously conducted a proteome study in our MS cohort that have been collected in Istanbul University, Cerrahpaşa Faculty of Medical, Neurology Department since 2007. The proteome study identified pathological pathways in MS including renin-angiotensin, aldestorene-regulated sodium reabsorption, complement-coagulation and notch signalling patways with potential biomarkers. In the current study, to our knowledge for the first time, we wanted to correlate genomic data from familial MS pedigrees and unrelated patient/control groups with the proteome data. To this end, first we conducted a linkage analysis in MS patients and their affected and unaffected relatives. 10 multiplex MS families with 35 individuals were included in the analysis and SNP genotyping on the Illumina CytoSNP 300K array was performed for genomes of each individual. NPL scores were calculated for each of 3118 informative SNP markers spaced at an average of 1 cM intervals using SimWalk multipoint NPL analysis. Fine mapping of regions showing NPL scores higher than 1.7 was performed for each SNP markers spaced at every 0.2 cM, revealing that the most promising loci for linkage were mapped to 13q13.3 and 21q22.2, with NPL scores of 1.82 and 1.85, respectively. From the resulted loci, Interferon (Alpha, Beta, and Omega) Receptor 1 (IFNAR1) 18417, Interferon (Alpha, Beta, and Omega) Receptor 2 IFNAR2 11876 polymorphisms, and Mab-21- Like 1 (MAB21L1) CAG repeat number were selected as candidate genes for further analyses. Selected regions were amplified by polymerase chain reaction (PCR) and genotyped in 27 unrelated patients with MS and 10 healthy controls of Turkish origin. Statistical analyses were performed to calculate genotype and allele frequencies, revealing a significant association of IFNAR2 11876 GG genotype with increased risk of MS (P = 0.027, OR 3.64 [95% CI 1.09 – 12.1]). We further conducted a GWAS comprising of 11 unrelated MS cases that had been included in the proteomic analyses and in the linkage study, and 60 healthy controls of Turkish origin, revealing 14 SNPs with significant association (P < 10-4), and 106 SNPs showing suggestive association with MS (P < 10-3). Subsequently, chromosomal regions from the linkage analysis and SNPs from the GWAS were analysed in order to observe a correlation with the previous proteomic findings. One gene with significant (INS-IGF2, P = 4.39E-07), and eight genes with suggestive associations (PRKCE, MAPK9, RBPJL, ADAMTSL1, NR6A1, NOTCH2, IL1R1, NTN1) from the GWAS were found to involve in pathways those shown to be affected in MS subtypes, and there were three genes common between the GWAS and linkage results (CLDN14, RUNX1, LINC00598). When individual proteome data of each patient involved in the genetic analyses was observed, a total of 20 proteins having altered expression level in one or more patients were also found to have significant or suggestive association in the GWAS. Among them, CNTN5 had the only significantly associated SNP markers (P = 4.71E-05 and P = 7.79E-05). Using a multi-disciplinary approach that combined genetic, proteomic, and bioinformatic analyses, we identified several candidate genes, whose possible roles will be explored in our further studies.