Low Vitamin-D Levels Combined with PKP3-SIGIRR-TMEM16J Host Variants Is Associated with Tuberculosis and Death in HIV-Infected and -Exposed Infants

PLoS One. 2016 Feb 12;11(2):e0148649. doi: 10.1371/journal.pone.0148649. eCollection 2016.


Background: This study examined the associations of 25-hydroxyvitamin D and specific host genetic variants that affect vitamin D levels or its effects on immune function, with the risk of TB or mortality in children.

Methods: A case-cohort sample of 466 South African infants enrolled in P1041 trial (NCT00080119) underwent 25-hydroxyvitamin D testing by chemiluminescent immunoassay. Single nucleotide polymorphisms (SNPs) that alter the effect of vitamin D [e.g. vitamin D receptor (VDR)], vitamin D levels [e.g. vitamin D binding protein (VDBP)], or toll like receptor (TLR) expression (SIGIRR including adjacent genes PKP3 and TMEM16J) were identified by real-time PCR. Outcomes were time to TB, and to the composite of TB or death by 192 weeks of follow-up. Effect modification between vitamin D status and SNPs for outcomes was assessed.

Findings: Median age at 25-hydroxyvitamin D determination was 8 months; 11% were breastfed, 51% were HIV-infected and 26% had low 25-hydroxyvitamin D (<32ng/mL). By 192 weeks, 138 incident TB cases (43 definite/probable, and 95 possible) and 26 deaths occurred. Adjusting for HIV status and potential confounders, low 25-hydroxyvitamin D was associated with any TB (adjusted hazard ratio [aHR] 1.76, 95% CI 1.01-3.05; p = 0.046) and any TB or death (aHR 1.76, 95% CI 1.03-3.00; p = 0.038). Children with low 25-hydroxyvitamin D and TMEM 16J rs7111432-AA or PKP3 rs10902158-GG were at increased risk for probable/definite TB or death (aHR 8.12 and 4.83, p<0.05) and any TB or death (aHR 4.78 and 3.26, p<0.005) respectively; SNPs in VDBP, VDR, and vitamin D precursor or hydroxylation genes were not. There was significant interaction between low 25-hydroxyvitamin D and, TMEM 16J rs7111432-AA (p = 0.04) and PKP3 rs10902158-GG (p = 0.02) SNPs.

Conclusions: Two novel SNPs, thought to be associated with innate immunity, in combination with low vitamin D levels were identified as increasing a young child's risk of developing TB disease or death. Identifying high-risk children and providing targeted interventions such as vitamin D supplementation may be beneficial.

Trial registration: ClinicalTrials.gov NCT00080119.

Publication types

  • Clinical Trial
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Anoctamins
  • Cohort Studies
  • Female
  • Follow-Up Studies
  • Gene Expression
  • Genetic Predisposition to Disease
  • HIV Infections / complications
  • HIV Infections / genetics*
  • HIV Infections / immunology
  • HIV Infections / mortality
  • Humans
  • Infant
  • Male
  • Membrane Proteins / genetics*
  • Membrane Proteins / immunology
  • Phospholipid Transfer Proteins
  • Plakophilins / genetics*
  • Plakophilins / immunology
  • Polymorphism, Single Nucleotide
  • Real-Time Polymerase Chain Reaction
  • Receptors, Calcitriol / genetics
  • Receptors, Calcitriol / immunology
  • Receptors, Interleukin-1 / genetics
  • Receptors, Interleukin-1 / immunology
  • Survival Analysis
  • Tuberculosis, Pulmonary / complications
  • Tuberculosis, Pulmonary / genetics*
  • Tuberculosis, Pulmonary / immunology
  • Tuberculosis, Pulmonary / mortality
  • Vitamin D / analogs & derivatives*
  • Vitamin D / blood
  • Vitamin D / immunology
  • Vitamin D Deficiency / complications
  • Vitamin D Deficiency / genetics*
  • Vitamin D Deficiency / immunology
  • Vitamin D Deficiency / mortality
  • Vitamin D-Binding Protein / genetics
  • Vitamin D-Binding Protein / immunology


  • ANO9 protein, human
  • Anoctamins
  • Membrane Proteins
  • PKP3 protein, human
  • Phospholipid Transfer Proteins
  • Plakophilins
  • Receptors, Calcitriol
  • Receptors, Interleukin-1
  • SIGIRR protein, human
  • VDR protein, human
  • Vitamin D-Binding Protein
  • Vitamin D
  • 25-hydroxyvitamin D

Associated data

  • ClinicalTrials.gov/NCT00080119