High prevalence of low-allele-fraction somatic mutations in STAT3 in peripheral blood CD8+ cells in multiple sclerosis patients and controls

• Published in: PloS one Vol. 17; no. 11; p. e0278245
• Main Authors: Valori, Miko, Lehikoinen, Joonas, Jansson, Lilja, Clancy, Jonna, Lundgren, Sofie A, Mustjoki, Satu, Tienari, Pentti
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28-11-2022; Public Library of Science (PLoS)
• Subjects: Alleles; Anemia; Antigens; Autoimmune Diseases; Biology and Life Sciences; Blood; Blood & organ donations; Cancer; CD8 antigen; CD8 lymphocytes; CD8-Positive T-Lymphocytes; Cloning; Diagnosis; Disease; Domains; Epstein-Barr virus; Exons; Genetic aspects; Health aspects; Health risk assessment; Humans; Immunoproliferative diseases; Leukocytes (neutrophilic); Lymphocytes; Magnetic resonance imaging; Medicine and Health Sciences; Multiple sclerosis; Multiple Sclerosis - genetics; Mutation; Outpatient care facilities; Peripheral blood; Phosphorylation; Prevalence; Research and Analysis Methods; Rheumatoid arthritis; Sequences; Stat3 protein; STAT3 Transcription Factor - genetics; Finland
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0278245

Somatic mutations have a central role in cancer, but there are also a few rare autoimmune diseases in which somatic mutations play a major role. We have recently shown that nonsynonymous somatic mutations with low allele fractions are preferentially detectable in CD8+ cells and that the STAT3 gene is a promising target for screening. Here, we analyzed somatic mutations in the STAT3 SH2 domain in peripheral blood CD8+ cells in a set of 94 multiple sclerosis (MS) patients and 99 matched controls. PCR amplicons targeting the exons 20 and 21 of STAT3 were prepared and sequenced using the Illumina MiSeq instrument with 2x300bp reads. We designed a novel variant calling method, optimized for large number of samples, high sequencing depth (>25,000x) and small target genomic area. Overall, we discovered 64 STAT3 somatic mutations in the 193 donors, of which 63 were non-synonymous and 77% have been previously reported in cancer or lymphoproliferative disease. The overall median variant allele fraction was 0.065% (range 0.007-1.2%), without significant difference between MS and controls (p = 0.82). There were 26 (28%) MS patients vs. 24 (24%) controls with mutations (p = 0.62). Two or more mutations were found in 9 MS patients vs. 2 controls (p = 0.03, pcorr = 0.12). Carriership of mutations associated with older age and lower neutrophil counts. These results demonstrate that STAT3 SH2 domain is a hotspot for somatic mutations in CD8+ cells with a prevalence of 26% among the participants. There were no significant differences in the mutation prevalences between MS patients and controls. Further research is needed to elucidate the role of antigenic stimuli in the expansion of the mutant clones. Furthermore, the high discovered prevalence of STAT3 somatic mutations makes it feasible to analyze these mutations directly in tissue-infiltrating CD8+ cells in autoimmune diseases.