Differentially expressed transcript isoforms associate with resistance to tuberculin skin test and interferon gamma release assay conversion

• Published in: PloS one Vol. 18; no. 4; p. e0284498
• Main Authors: Simmons, Jason D., Segnitz, R. Max, Dill-McFarland, Kimberly A., Stein, Catherine M., Peterson, Glenna J., Mayanja-Kizza, Harriet, Boom, W. Henry, Hawn, Thomas R.
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 14.04.2023; Public Library of Science (PLoS)
• Subjects: Acquired immune deficiency syndrome; AIDS; Analysis; Asymptomatic; BCG; BCG vaccines; Biological response modifiers; Biology and Life Sciences; Conversion; Diagnosis; Drug resistance in microorganisms; Experiments; Gene expression; Gene sequencing; Genes; Genetic aspects; Genetic transcription; Genomes; Genotype & phenotype; Health aspects; HIV; Human immunodeficiency virus; Humans; Immune response; Infection; Infections; Interferon; Interferon gamma; Interferon-gamma Release Tests - methods; Isoforms; Isolation media; Latent Infection; Latent Tuberculosis - complications; Latent Tuberculosis - diagnosis; Latent Tuberculosis - genetics; Medicine and Health Sciences; Monocytes; Mycobacterium tuberculosis; Pathogens; Phenotype; Phenotypes; Proteins; Research and analysis methods; Review boards; RNA; RNA sequencing; Skin; Skin resistance; Skin tests; Tuberculin; Tuberculin Test - methods; Tuberculosis; γ-Interferon; Uganda
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0284498

A mechanistic understanding of uncommon immune outcomes such as resistance to infection has led to the development of novel therapies. Using gene level analytic methods, we previously found distinct monocyte transcriptional responses associated with resistance to Mycobacterium tuberculosis (Mtb) infection defined as persistently negative tuberculin skin test (TST) and interferon gamma release assay (IGRA) reactivity among highly exposed contacts (RSTR phenotype). Using transcript isoform analyses, we aimed to identify novel RSTR-associated genes hypothesizing that previous gene-level differential expression analysis obscures isoform-specific differences that contribute to phenotype. Monocytes from 49 RSTR versus 52 subjects with latent Mtb infection (LTBI) were infected with M. tuberculosis (H37Rv) or left unstimulated (media) prior to RNA isolation and sequencing. RSTR-associated gene expression was then identified using differential transcript isoform analysis. We identified 81 differentially expressed transcripts (DETs) in 70 genes (FDR <0.05) comparing RSTR and LTBI phenotypes with the majority (n = 79 DETs) identified under Mtb-stimulated conditions. Seventeen of these genes were previously identified with gene-level bulk RNAseq analyses including genes in the IFNγ response that had increased expression among LTBI subjects, findings consistent with a clinical phenotype based on IGRA reactivity. Among the subset of 23 genes with positive differential expression among Mtb-infected RSTR monocytes, 13 were not previously identified. These novel DET genes included PDE4A and ZEB2, which each had multiple DETs with higher expression among RSTR subjects, and ACSL4 and GAPDH that each had a single transcript isoform associated with RSTR. Transcript isoform-specific analyses identify transcriptional associations, such as those associated with resistance to TST/IGRA conversion, that are obscured when using gene-level approaches. These findings should be validated with additional RSTR cohorts and whether the newly identified candidate resistance genes directly influence the monocyte Mtb response requires functional study.