Identification of HLA-DQA1 as a Susceptibility Gene for Spinal Tuberculosis by Exome Sequencing

Med Sci Monit. 2018 May 24:24:3442-3449. doi: 10.12659/MSM.907864.


BACKGROUND Spinal tuberculosis (STB) is the main cause of bone and joint tuberculosis. This study aimed to screen and analyze the susceptibility genes for STB using whole-exome sequencing (WES). MATERIAL AND METHODS All exon regions of peripheral blood DNA from 6 STB patients were captured and sequenced using WES and the sequencing data were analyzed by modern bioinformatics methods to identify disease-causing mutations. Sanger sequencing was then used to validate the mutation sites in normal controls (207) and STB patients (193). The mRNA expression of the mutant gene and the serum levels of IL-6 and TNF-α were detected using qPCR or ELISA assay, respectively. RESULTS A nonsynonymous single-nucleotide polymorphism (SNP) in the gene HLA-DQA1 (rs796778515, c.592delCinsG, CAG to GAG, p.Q198E) was identified and further validated by Sanger sequencing. The percentage of the 3 genotypes C/C, C/G and G/G in STB patients and normal controls were 37.3%, 32.1%, and 30.6% and 47.8%, 33.8%, and 18.4%, respectively. Furthermore, the C>G mutation was significantly associated with the occurrence of STB. In addition, the levels of HLA-DQA1 mRNA were significantly lower in blood cells from STB patients compared with normal controls, while the serum levels of IL-6 and TNF-α were significantly higher. CONCLUSIONS The C>G mutation in the HLA-DQA1 gene was associated with the occurrence of STB. This variation may result in the decreased level of HLA-DQA1 mRNA and increased serum levels of IL-6 and TNF-α, which finally led the STB susceptibility.

MeSH terms

  • Aged
  • Alleles
  • Amino Acid Sequence
  • Base Sequence
  • Chemokines / metabolism
  • Exome / genetics*
  • Genetic Predisposition to Disease*
  • HLA-DQ alpha-Chains / blood
  • HLA-DQ alpha-Chains / chemistry
  • HLA-DQ alpha-Chains / genetics*
  • Humans
  • Inflammation Mediators / metabolism
  • Middle Aged
  • Polymorphism, Single Nucleotide / genetics
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Analysis, DNA*
  • Tuberculosis, Spinal / blood
  • Tuberculosis, Spinal / genetics*


  • Chemokines
  • HLA-DQ alpha-Chains
  • HLA-DQA1 antigen
  • Inflammation Mediators
  • RNA, Messenger