Identification of biomarkers for tuberculosis susceptibility via integrated analysis of gene expression and longitudinal clinical data

Qingyang Luo, Smriti Mehra, Nadia A. Golden, Deepak Kaushal, Michelle R. Lacey

Tuberculosis (TB) is an infectious disease caused by the bacteria Mycobacterium tuberculosis (Mtb) that affects millions of people worldwide. The majority of individuals who are exposed to Mtb develop latent infections, in which an immunological response to Mtb antigens is present but there is no clinical evidence of disease. Because currently available tests cannot differentiate latent individuals who are at low risk from those who are highly susceptible to developing active disease, there is considerable interest in the identification of diagnostic biomarkers that can predict reactivation of latent TB. We present results from our analysis of a controlled longitudinal experiment in which a group of rhesus macaques were exposed to a low dose of Mtb to study their progression to latent infection or active disease. Subsets of the animals were then euthanized at scheduled time points, and granulomas taken from their lungs were assayed for gene expression using microarrays. The clinical profiles associated with the animals following Mtb exposure revealed considerable variability, and we developed models for the disease trajectory for each subject using a Bayesian hierarchical B-spline approach. Disease severity estimates were derived from these fitted curves and included as covariates in linear models to identify genes significantly associated with disease progression. Our results demonstrate that the incorporation of clinical data increases the value of information extracted from the expression profiles and contributes to the identification of predictive biomarkers for TB susceptibility.