FLT3 stop mutation increases FLT3 ligand level and risk of autoimmune thyroid disease

Nature. 2020 Aug;584(7822):619-623. doi: 10.1038/s41586-020-2436-0. Epub 2020 Jun 24.

Abstract

Autoimmune thyroid disease is the most common autoimmune disease and is highly heritable1. Here, by using a genome-wide association study of 30,234 cases and 725,172 controls from Iceland and the UK Biobank, we find 99 sequence variants at 93 loci, of which 84 variants are previously unreported2-7. A low-frequency (1.36%) intronic variant in FLT3 (rs76428106-C) has the largest effect on risk of autoimmune thyroid disease (odds ratio (OR) = 1.46, P = 2.37 × 10-24). rs76428106-C is also associated with systemic lupus erythematosus (OR = 1.90, P = 6.46 × 10-4), rheumatoid factor and/or anti-CCP-positive rheumatoid arthritis (OR = 1.41, P = 4.31 × 10-4) and coeliac disease (OR = 1.62, P = 1.20 × 10-4). FLT3 encodes fms-related tyrosine kinase 3, a receptor that regulates haematopoietic progenitor and dendritic cells. RNA sequencing revealed that rs76428106-C generates a cryptic splice site, which introduces a stop codon in 30% of transcripts that are predicted to encode a truncated protein, which lacks its tyrosine kinase domains. Each copy of rs76428106-C doubles the plasma levels of the FTL3 ligand. Activating somatic mutations in FLT3 are associated with acute myeloid leukaemia8 with a poor prognosis and rs76428106-C also predisposes individuals to acute myeloid leukaemia (OR = 1.90, P = 5.40 × 10-3). Thus, a predicted loss-of-function germline mutation in FLT3 causes a reduction in full-length FLT3, with a compensatory increase in the levels of its ligand and an increased disease risk, similar to that of a gain-of-function mutation.

Publication types

  • Meta-Analysis
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Autoimmune Diseases / genetics
  • Codon, Nonsense / genetics*
  • Databases, Factual
  • Genetic Predisposition to Disease / genetics*
  • Genome-Wide Association Study
  • Germ-Line Mutation
  • Humans
  • Iceland
  • Introns / genetics
  • Leukemia, Myeloid, Acute
  • Ligands*
  • Loss of Function Mutation
  • Mutation*
  • RNA Splice Sites / genetics
  • Thyroiditis, Autoimmune / genetics*
  • United Kingdom
  • fms-Like Tyrosine Kinase 3 / genetics*
  • fms-Like Tyrosine Kinase 3 / metabolism*

Substances

  • Codon, Nonsense
  • Ligands
  • RNA Splice Sites
  • FLT3 protein, human
  • fms-Like Tyrosine Kinase 3