Candidate genes and sequence variants for susceptibility to mycobacterial infection identified by whole-exome sequencing

Alexander Varzari*, Igor V. Deyneko, Gitte Hoffmann Bruun, Maja Dembic, Winfried Hofmann, Victor M. Cebotari, Sergei S. Ginda, Brage S. Andresen, Thomas Illig

*Corresponding author for this work

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Abstract

Inborn errors of immunity are known to influence susceptibility to mycobacterial infections. The aim of this study was to characterize the genetic profile of nine patients with mycobacterial infections (eight with BCGitis and one with disseminated tuberculosis) from the Republic of Moldova using whole-exome sequencing. In total, 12 variants in eight genes known to be associated with Mendelian Susceptibility to Mycobacterial Disease (MSMD) were detected in six out of nine patients examined. In particular, a novel splice site mutation c.373–2A>C in STAT1 gene was found and functionally confirmed in a patient with disseminated tuberculosis. Trio analysis was possible for seven out of nine patients, and resulted in 23 candidate variants in 15 novel genes. Four of these genes - GBP2, HEATR3, PPP1R9B and KDM6A were further prioritized, considering their elevated expression in immune-related tissues. Compound heterozygosity was found in GBP2 in a single patient, comprising a maternally inherited missense variant c.412G>A/p.(Ala138Thr) predicted to be deleterious and a paternally inherited intronic mutation c.1149+14T>C. Functional studies demonstrated that the intronic mutation affects splicing and the level of transcript. Finally, we analyzed pathogenicity of variant combinations in gene pairs and identified five patients with putative oligogenic inheritance. In summary, our study expands the spectrum of genetic variation contributing to susceptibility to mycobacterial infections in children and provides insight into the complex/oligogenic disease-causing mode.

Original languageEnglish
Article number969895
JournalFrontiers in Genetics
Volume13
ISSN1664-8021
DOIs
Publication statusPublished - 20. Oct 2022

Keywords

  • BCG-itis
  • candidate genes approach
  • disseminated tuberculosis
  • oligogenic inheritance
  • pre-mRNA splicing
  • primary immunodeficiency (PID) disorders
  • trio analysis
  • whole-exome sequencing (WES)

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