Host RNA biomarkers of tuberculosis disease and with people living with HIV

Tuberculosis remains a leading global health challenge, with early and accurate diagnosis critical for effective disease management. Transcriptomic studies have identified host blood RNA biomarkers as promising diagnostic tools, yet challenges remain in standardizing methodologies and ensuring diverse population representation. Tuberculosis in people living with HIV (PLHIV) presents unique immunological interactions that require further investigation. This master’s thesis project aimed to synthesize existing transcriptomic research on tuberculosis biomarkers through a scoping review and conduct a primary transcriptomic analysis to identify differentially expressed genes associated with tuberculosis in PLHIV. A PRISMA scoping review was conducted to evaluate published transcriptomic studies from 2000 to 2024, focusing on host blood biomarkers identified using microarray and RNA sequencing technologies. Furthermore, a primary transcriptomic analysis was performed using whole-blood and PBMC samples from 96 participants across four cohorts: tuberculosis in PLHIV (n=29), tuberculosis alone (n=31), HIV alone (n=23), and non-infected individuals (n=13). Differential gene expression analysis was conducted using DESeq2, with batch effects controlled using ComBat-Seq. Candidate biomarkers were identified by comparing differentially expressed genes with those frequently reported in the scoping review. The scoping review identified 60 tuberculosis gene signatures comprising 1,939 unique genes, with 15 genes appearing in at least 10 signatures. Microarray remained the dominant methodology; however, RNA sequencing datasets have increased in recent years. The primary study identified 10,308 differentially expressed genes, with six—GBP6, DHRS9, GBP5, CD274, FCGR1A, and ANKRD22—frequently appearing in tuberculosis gene signatures and showing significant upregulation in tuberculosis in PLHIV. These genes are linked to immune activation, inflammatory responses, and antigen processing, highlighting their potential as tuberculosis biomarkers. This master’s thesis project highlights the potential of transcriptomic biomarkers for tuberculosis diagnosis, particularly in PLHIV, while highlighting critical areas for future research. Expanding cohort recruitment in high tuberculosis burden countries such as India, Indonesia, China, the Philippines, Pakistan, Nigeria, Bangladesh, and the Democratic Republic of the Congo will be essential to enhance the generalizability of identified biomarkers. Additionally, considering tuberculosis as a disease spectrum—including incipient, minimal, and subclinical tuberculosis—will be crucial for refining diagnostic applications.