Spatial network mapping of pulmonary multidrug-resistant tuberculosis cavities using RNA sequencing

Keertan Dheda, Laura Lenders, Shashikant Srivastava, Gesham Magombedze, Helen Wainwright, Prithvi Raj, Stephen J. Bush, Gabriele Pollara, Rachelle Steyn, Malika Davids, Anil Pooran, Timothy Pennel, Anthony Linegar, Ruth McNerney, Loven Moodley, Jotam G. Pasipanodya, Carolin T. Turner, Mahdad Noursadeghi, Robin M. Warren, Edward WakelandTawanda Gumbo

Research output: Contribution to journalArticlepeer-review

19 Scopus citations


Rationale: There is poor understanding about protective immunity and the pathogenesis of cavitation in patients with tuberculosis. Objectives: To map pathophysiological pathways at anatomically distinct positions within the human tuberculosis cavity. Methods: Biopsies were obtained from eight predetermined locations within lung cavities of patients with multidrug-resistant tuberculosis undergoing therapeutic surgical resection (n = 14) and healthy lung tissue from control subjects without tuberculosis (n = 10). RNA sequencing, immunohistochemistry, and bacterial load determination were performed at each cavity position. Differentially expressed genes were normalized to control subjects without tuberculosis, and ontologically mapped to identify a spatially compartmentalized pathophysiological map of the cavity. In silico perturbation using a novel distance-dependent dynamical sink model was used to investigate interactions between immune networks and bacterial burden, and to integrate these identified pathways. Measurements and Main Results: The median (range) lung cavity volume on positron emission tomography/computed tomography scans was 50 cm3 (15–389 cm3). RNA sequence reads (31% splice variants) mapped to 19,049 annotated human genes. Multiple proinflammatory pathways were upregulated in the cavity wall, whereas a downregulation “sink” in the central caseum–fluid interface characterized 53% of pathways including neuroendocrine signaling, calcium signaling, triggering receptor expressed on myeloid cells-1, reactive oxygen and nitrogen species production, retinoic acid–mediated apoptosis, and RIG-I-like receptor signaling. The mathematical model demonstrated that neuroendocrine, protein kinase C-u, and triggering receptor expressed on myeloid cells-1 pathways, and macrophage and neutrophil numbers, had the highest correlation with bacterial burden (r . 0.6), whereas T-helper effector systems did not. Conclusions: These data provide novel insights into host immunity to Mycobacterium tuberculosis–related cavitation. The pathways defined may serve as useful targets for the design of host-directed therapies, and transmission prevention interventions.

Original languageEnglish (US)
Pages (from-to)370-380
Number of pages11
JournalAmerican journal of respiratory and critical care medicine
Issue number3
StatePublished - Aug 1 2019


  • In silico analysis
  • Pulmonary tuberculosis
  • TB cavitation
  • Transcriptomics

ASJC Scopus subject areas

  • Pulmonary and Respiratory Medicine
  • Critical Care and Intensive Care Medicine


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