Histone H3K14 hypoacetylation and H3K27 hypermethylation along with HDAC1 up-regulation and KDM6B down-regulation are associated with active pulmonary tuberculosis disease

Abstract

The aim of this study is to determine the roles of global histone acetylation (Ac)/methylation (me), their modifying enzymes, and gene-specific histone enrichment in active pulmonary tuberculosis (TB) disease. Global histone H3K27me3, H3K27me2, H3K9me3, H3K9Ac, and H3K14Ac expressions, and their modifying enzyme expressions, including KDM1A, KDM6B, EZH2, HDAC1, and HDAC2, were assessed in blood leukocytes from 81 patients with active pulmonary TB disease and 44 matched healthy subjects (HS). TLR2, TNF-α, IFN-γ, and IL12B-specific histone enrichment of peripheral blood mononuclear cells was measured by chromatin immunoprecipitation method. We found that Global H3K14Ac was decreased and H3K27me2 was increased in TB patients as compared with that in HS. TB patients with low H3K14Ac had lower one-year survival. Global H3K27me3 was increased in TB patients with high bacterial burden, or systemic symptoms as compared with that in those without the attribute or HS. HDAC1 gene/protein expressions were increased in TB patients as compared with that in HS, whereas KDM6B gene/protein expressions were decreased. Global H3K27me2, HDAC1 and KDM6B protein expressions were all reversed to normal after 6-month anti-TB treatment. TNF-α/IL12B promoter-specific H3K14Ac and TNF-α/IL12B/IFN-γ promoter-specific H3K27me2 enrichment were all decreased in 10 TB patients as compared with that in 10 HS. Among them, IL12B-specific H3K27me2 enrichment was reversed to normal after treatment, while the other 4 remained depressed. In conclusions, H3K14 hypoacetylation and H3K27 hypermethylation play a role in the development of active pulmonary TB disease or its clinical phenotypes, probably through up-regulation of HDAC1 and down-regulation of KDM6B, respectively.

Keywords: HDAC1; KDM6B; Pulmonary tuberculosis; histone H3K14 acetylation; histone H3K27 methylation; interleukin 12B.

Figure 1

Global H3K14Ac, H3K27me2, and H3K27me3 expressions of blood leukocytes in patients with active pulmonary TB disease and healthy subjects (HS). The error bars show 95% confidence interval (CI) and mean. Compared with HS, (A) global H3K14Ac was significantly decreased, and (B) global H3K27me2 was increased in TB patients. (C) TB patients with a low H3K14Ac expression had lower one-year survival than those with a high value (P = 0.008, by Log-Rank test). TB patients with (D) high bacterial burden (sputum AFB 2+ to 4+) or (E) systemic symptoms (BWL or fever) had significantly increased H3K27me3 expression than those without this phenotype or HS. (F) Global H3K14Ac expression was negatively correlated with H3K27me3 expression (r = 0.433, P < 0.001). Both (G) global H3K27me3/H3K14Ac and (H) H3K27me2/H3K14Ac expression ratios were significantly increased in TB patients as compared with that in HS.

Figure 2

HDAC1 and KDM6B gene/protein expressions of blood leukocytes in patients with active pulmonary TB disease and HS. The error bars show 95% CI and mean. (A) HDAC1 gene expression levels were significantly increased, and (B) KDM6B gene expression levels were decreased in TB patients as compared with that in HS. (C) HDAC1 protein expression levels were significantly increased, and (D) KDM6B protein expression levels were decreased in TB patients as compared with that in HS. (E) HDAC1/KDM6B protein expression ratio was significantly increased in TB patients as compared with that in HS. (F) The corresponding ROC curves showed that the diagnostic performance was well captured by HDAC1/KDM6B protein expression ratio (AUC = 0.879±0.025, 95% CI 0.831-0.928, P < 0.001).

Figure 3

Changes in global H3K27me2, HDAC1 protein, KDM6B protein expressions, and gene-specific H3K14Ac/H3K27me2 enrichment in pulmonary TB patients before and after 6-month anti-TB treatment. The error bars show 95% CI and mean. Both (A) global H3K27me2 and (B) H3K27me2/H3K14Ac expression ratio showed significant reduction after therapy. (C) HDAC1 protein expression showed significant reduction, (D) KDM6B protein expression showed significant elevation, and (E) HDAC1/KDM6B protein expression ratio showed significant reduction after therapy. (F) TNF-α promoter-specific and (G) IL12B promoter-specific H3K14AC enrichment were both decreased in active TB patients, and remained depressed after anti-TB treatment. (H) TNF-α promoter-specific, (I) IL12B promoter-specific, and (J) IFN-γ promoter-specific H3K27me2 enrichment were all decreased in active TB patients, and the second marker was reversed to normal after anti-TB treatment. The box plots show 25th, 50th, 75th percentiles, maximal, and minimal. *P < 0.05 for comparison between TB patients and healthy subjects (HS). **P < 0.01 for comparison between TB patients and HS. #P < 0.05 for comparisons between TB patients before and after anti-TB treatment.