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Project

Somatic mosaicism in multiple sclerosis: Detection and insights into disease

Background: Multiple sclerosis (MS) is a complex disease, where both genetic and environmental factors contribute to disease susceptibility. Despite large‑scale efforts, the currently identified risk factors are insufficient to explain why some individuals develop MS and others do not. Somatic variants are variations in an individual’s genome acquired after the zygotic stadium. They are the result of multiple processes that interact in a complex manner.

Objective: We aim to determine whether somatic variation is a common source of genetic variation within and between individuals and whether somatic mosaicism contributes to susceptibility for immune‑mediated diseases, and in particular susceptibility for MS.

Methods: We developed a new pipeline for somatic variant calling in autoimmune disorders, focusing on somatic variants affecting few cells. We applied this pipeline on deep, targeted sequencing data from peripheral blood B and T lymphocytes of a heterogeneous group of persons with MS with a high MS genetic burden to identify variants with variant allele fractions (VAFs) ≥0.5%. Subsequently, we applied an updated pipeline to identify somatic variants with VAFs ≥1% across the whole exome in CD4+ and CD8+ T lymphocytes of 21 treatment‑naïve persons with MS with less than 5 years since disease onset and 16 healthy controls. We followed­‑up on a subset of variants, using, amongst others, single‑cell DNA sequencing and an in‑house‑developed targeted sequencing addition to a commercially available high‑throughput single‑cell transcriptomics method.

Results: In our proof‑of‑principle study, we identified 1‑9 somatic variants in T lymphocytes in 6 out of 10 persons with MS. Four persons additionally carried 1‑3 somatic variants in B lymphocytes. In the subsequent exome‑wide case‑control study, all subjects carried 1‑142 variants in CD4+ or CD8+ T lymphocytes. Variants were more common and more abundant in CD8+ T lymphocytes (0‑86 variants per subject) than in CD4+ T lymphocytes (0‑56 variants per subject), with a significant association with age in the CD8+ subset. Tested variants (N=5) affected memory subsets and most (15 out of 18, 83.3%) were stable over at least four years. Variants mostly do not co‑occur in the same cells, although exceptions exist (4 out of 15 variants in 1 out of 4 subjects co‑occurred with one other variant). Somatic mosaicism may affect cellular phenotype, as we associated the alternate allele of TREX1 p.L352V with increased PGM3 expression levels. Somatic mosaicism in peripheral blood T lymphocyte subsets is not specific to or enriched in MS. Recurrence of variants and regions within and across studies in known autoimmunity‑related genes suggests that a subset of variants may influence MS risk. We prioritize STAT3 and DNMT3A for large‑scale association studies using deep sequencing in large cohorts.

Conclusion: Our data emphasize that somatic mosaicism is common and a dynamic view of an individual’s genome should replace the traditional interpretation of a stable genome. Somatic mosaicism is not specific for or enriched in MS, but a subset of variants may influence disease susceptibility. Identifying this subset requires deep sequencing in large cohorts of persons with MS and control individuals.

Date:28 Aug 2017 →  17 Mar 2022
Keywords:Somatic mosaicism, Multiple sclerosis
Disciplines:Immunogenetics, Genetics not elsewhere classified
Project type:PhD project