Malnutrition leads to increased inflammation and expression of tuberculosis risk signatures in recently exposed household contacts of pulmonary tuberculosis

Abstract

Background: Most individuals exposed to Mycobacterium tuberculosis (Mtb) develop latent tuberculosis infection (LTBI) and remain at risk for progressing to active tuberculosis disease (TB). Malnutrition is an important risk factor driving progression from LTBI to TB. However, the performance of blood-based TB risk signatures in malnourished individuals with LTBI remains unexplored. The aim of this study was to determine if malnourished and control individuals had differences in gene expression, immune pathways and TB risk signatures.

Methods: We utilized data from 50 tuberculin skin test positive household contacts of persons with TB - 18 malnourished participants (body mass index [BMI] < 18.5 kg/m2) and 32 controls (individuals with BMI ≥ 18.5 kg/m2). Whole blood RNA-sequencing was conducted to identify differentially expressed genes (DEGs). Ingenuity Pathway Analysis was applied to the DEGs to identify top canonical pathways and gene regulators. Gene enrichment methods were then employed to score the performance of published gene signatures associated with progression from LTBI to TB.

Results: Malnourished individuals had increased activation of inflammatory pathways, including pathways involved in neutrophil activation, T-cell activation and proinflammatory IL-1 and IL-6 cytokine signaling. Consistent with known association of inflammatory pathway activation with progression to TB disease, we found significantly increased expression of the RISK4 (area under the curve [AUC] = 0.734) and PREDICT29 (AUC = 0.736) progression signatures in malnourished individuals.

Conclusion: Malnourished individuals display a peripheral immune response profile reflective of increased inflammation and a concomitant increased expression of risk signatures predicting progression to TB. With validation in prospective clinical cohorts, TB risk biomarkers have the potential to identify malnourished LTBI for targeted therapy.

Keywords: TB biomarkers; immunoregulation; inflammation; malnutrition; tuberculosis.

Figure 1

Differentially expressed genes separate individuals with LTBI who are malnourished from controls. Dimension reduction by PCA (A), tSNE (B, C), and UMAP (D) of RNA-sequencing data are plotted here, with the points in C colored by BMI. The top 500 DEGs (by least adjusted p-value) are depicted in the heatmap; columns are organized by BMI of individuals with LTBI from lowest to highest (E).

Figure 2

Increased inflammation and immune regulation pathways in malnourished individuals with latent TB infection. IPA of DEGs among malnourished individuals and control individuals showing top canonical pathways [p < 0.01; (A)], upstream regulators [p < 0.001; (B)], and causal regulators (p < 0.001; (C)). Pathways and regulators in blue represent upregulation and those in red represent downregulation in malnourished individuals.

Figure 3

Malnourished individuals with LTBI demonstrate a higher risk of TB progression than controls with LTBI. Accuracy of TB risk signatures in predicting differences between malnourished individuals and control groups as depicted by boxplots showing ssGSEA scores [RISK4, p=0.0003; PREDICT29, p = 0.0038; ACS COR, p = 0.076; and SWEENEY3, p = 0.10; (A)] and bootstrapped upper and lower AUC scores and means [RISK4, AUC = 0.73; PREDICT29, AUC = 0.74; ACS COR, AUC = 0.63; and SWEENEY3, AUC = 0.61; (B)]. * significant p value.