Genetic control of early mycobacterium tuberculosis inflammatory responses

The National Institute of Allergy and Infectious Diseases awarded $447,960 to Michigan State University (Henry Ford Health+Michigan State University Health Sciences) on February 13, 2026, under the Allergy and Infectious Diseases Research program (CFDA 93.855, R21AI197453) to investigate genetic control of early Mycobacterium tuberculosis inflammatory responses.

The award funds creation and validation of an indexed library of fetal liver-derived alveolar-like macrophages (FLAMs) derived from the Collaborative Cross mouse panel—a mammalian genetics resource comprising over 70 mosaic strains created by intercrossing eight genetically distinct founder strains. The work tests the hypothesis that heterogeneous MTB-AM interactions contribute to distinct trajectories of tuberculosis disease. Aim 1 establishes and validates the CC-FLAM library by barcoding FLAMs across Collaborative Cross strains to enable tracking of genotype-specific responses during infection. Aim 2 employs single-cell RNA sequencing and quantitative trait locus mapping to define transcriptional networks and genetic loci associated with inflammatory cytokine production, comparing findings with published disease-outcome QTLs to identify mechanistic drivers of alveolar macrophage heterogeneity linked to TB progression.

Work is performed in East Lansing, Michigan, with performance period through January 31, 2028. The University of Massachusetts Medical School (Sassetti lab) received a sub-award (R21AI197453-RC118986UMass, June 19, 2026) to confirm cellular library composition and genotype categorization integrity and to perform single-cell RNA sequencing and associated analysis.

Abstract

The inflammatory disease tuberculosis (TB) remains a major cause of mortality worldwide. The long treatment times required for drug therapy highlight the urgent need for new approaches to protect against TB disease. Complicating treatment efforts is the heterogeneity of disease states observed in humans. To address these knowledge gaps, we are using the collaborative cross (CC) a mammalian genetics resource that comprises of over 70 mosaic strains of mice, created by intercrossing 8 genetically distinct founder strains. Using the CC, we are identifying unique models of distinct TB disease states. However, cell-type complexity in animals complicates our understanding of the underlying mechanisms. In particular, a critical knowledge GAP exists in our understanding of how early infection events drive distinct TB disease trajectories. These early host-MTB interactions are almost exclusively with airway resident alveolar macrophages (AMS) that are functionally distinct from myeloid-derived macrophages but challenging to study. To overcome this experimental limitation, we developed fetal liver-derived alveolar-like macrophages (flams), a genetically tractable EX vivo am model that mimics lung am function. This proposal will create an indexed library of flams derived from the CC panel to test they hypothesis that heterogeneous MTB-am interactions contribute to distinct trajectories of TB disease. In aim 1 we will create and validate the CC-flam library by barcoding flams across CC strains, enabling tracking of genotype-specific responses during infection. In aim 2 we will employ single-cell RNA sequencing and quantitative trait locus (QTL) mapping to define transcriptional networks and genetic loci associated with inflammatory cytokine production, comparing these findings with published disease-outcome qtls. The work will identify mechanistic drivers of am heterogeneity linked to TB progression, offering insights into patient risk of disease. By integrating genetic heterogeneity with EX vivo and in vivo models, this exploratory study lays the groundwork for developing therapies targeting early host-pathogen interactions while developing an innovative CC-flam platform that will be broadly useful to dissect pulmonary inflammation in other respiratory diseases.