All-trans retinoic acid recalibrates macrophage transcriptional responses to drug-resistant Mycobacterium tuberculosis through strain-specific immunometabolic reprogramming

Roshan Singh, M.; Kumar, R.; Anand, S.; Pahuja, I.; Hussain, A.; kumar, R.; Singh, A.; Dwivedi, V. P.; Kumar, M.; Ojesina, A. I.; Singh, I. K.

doi:10.64898/2026.04.01.715810

bioRxiv · 10.64898/2026.04.01.715810

All-trans retinoic acid recalibrates macrophage transcriptional responses to drug-resistant Mycobacterium tuberculosis through strain-specific immunometabolic reprogramming

Roshan Singh, M.·Kumar, R.·Anand, S.·Pahuja, I.·Hussain, A.·kumar, R.·Singh, A.·Dwivedi, V. P.·Kumar, M.·Ojesina, A. I.·Singh, I. K.

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Abstract

Tuberculosis (TB) caused by Mycobacterium tuberculosis (M.tb) remains the leading infectious cause of death worldwide, with multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains presenting an escalating therapeutic crisis. All-trans retinoic acid (ATRA), an active vitamin A metabolite with established immunomodulatory properties, has emerged as a candidate host-directed therapy, yet its genome-wide transcriptional effects on macrophage across strains of differing drug-resistance profiles remain uncharacterized. We performed RNA sequencing of murine peritoneal macrophages infected with drug-susceptible H37Rv, MDR-2261, or XDR-MCY M.tb strains, with and without ATRA treatment, validated by RT-PCR and flow cytometry. All three strains activated a conserved pro-inflammatory program dominated by Nos2, Il1b, and Acod1 induction with progressive suppression of host translational and mitochondrial machinery. XDR-MCY uniquely induced Ifnb1/IFN-{beta}, suppressed Prdx1 and Gpx4, the latter shared with MDR-2261 and showed selective downregulation of MHC-II processing genes, suggesting a multilayered immune evasion strategy. ATRA activated canonical retinoid signaling across all infection states and consistently induced Arg1-mediated resolution signaling, with Nos2 suppression observed in H37Rv- and MDR-infected macrophages. ATRA selectively restored Epas1/HIF-2 in H37Rv- and MDR-infected macrophages without disrupting the HIF-1-driven antimicrobial program or itaconate biosynthesis. ATRA responsiveness progressively attenuated with drug resistance, with XDR-MCY-infected macrophages largely refractory to transcriptional reprogramming. These findings provide a transcriptional rationale for evaluating ATRA as a host-directed adjunct in drug-resistant TB and identify Gpx4 suppression in drug-resistant strains and XDR-specific Ifnb1 induction as vulnerabilities necessitating further investigation.

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Roshan Singh, M., Kumar, R., Anand, S., Pahuja, I., Hussain, A., kumar, R., Singh, A., Dwivedi, V. P., Kumar, M., Ojesina, A. I., Singh, I. K.. 2026-04-02. All-trans retinoic acid recalibrates macrophage transcriptional responses to drug-resistant Mycobacterium tuberculosis through strain-specific immunometabolic reprogramming. https://doi.org/10.64898/2026.04.01.715810

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