Author ORCID Identifier

https://orcid.org/0000-0002-2050-2628

Date of Award

Spring 6-15-2025

Document Type

Thesis (Ph.D.)

Department or Program

Microbiology and Immunology

First Advisor

Claudia V. Jakubzick

Abstract

Macrophages are critical custodians of the lung, orchestrating immune surveillance, maintaining tissue homeostasis, and coordinating both innate and adaptive responses. This dissertation examines their heterogeneity and specialized functions, focusing on IMs, which reside in the lung interstitium, and AMs, which occupy the airspace. Through comprehensive single-cell transcriptomic profiling of murine and human samples, we identify multiple IM and AM subsets defined by distinct chemokine, cytokine, receptor, and innate immune gene signatures. These subsets display clear divisions of labor, contributing to immune cell recruitment, tertiary lymphoid structure formation, and alveolar homeostasis.

In IMs, coordinated chemokine programs not only recruit inflammatory cells but also shape the architecture of tertiary lymphoid tissues, as shown by the depletion of specific IM subsets leading to reduced lymphoid organization. Further analyses reveal unique cytokine networks, innate immune pathways, and tissue-specific migratory cues, underscoring the complexity and adaptability of IMs. For AMs, single-cell RNA sequencing of bronchoalveolar lavage samples from healthy individuals and those with cystic fibrosis (CF) indicates the presence of multiple functionally specialized AM families, each harboring subclusters with distinct interferon, chemokine, lipid metabolism, and growth factor gene profiles. Notably, these subsets persist in relatively stable proportions under steady-state conditions but can shift in response to inflammatory challenges such as CF or viral infections like COVID-19.

The translational impact of these findings is underscored by studies in mild and severe CF, where persistent AM activation contributes to ongoing lung inflammation—even in the era of highly effective modulator therapies. Characterizing the crosstalk between macrophages and other immune cell types in CF provides insights into potential therapeutic targets aimed at mitigating chronic inflammation and improving disease outcomes. Finally, analyses in mouse models highlight both evolutionary conservation and divergence in AM subsets between species, revealing a shared “division of labor” that governs lung immunity and homeostasis and laying the groundwork for future translational studies

Collectively, these studies redefine our understanding of lung macrophage complexity, establishing a framework for how IM and AM heterogeneity underpins immune regulation, tissue maintenance, and disease pathogenesis. By illuminating the intricate interplay among macrophage subsets across health and disease states, this work opens new avenues for targeted interventions in pulmonary inflammation and other macrophage-involving pathologies.

Original Citation

Li, X. and Jakubzick, C.V., 2025. The Heterogeneity, Parallels, and Divergence of Alveolar Macrophages in Humans and Mice. American Journal of Respiratory Cell and Molecular Biology, 72(3), pp.335-337.

Li, X., Mara, A.B., Musial, S.C., Kolling, F.W., Gibbings, S.L., Gerebtsov, N. and Jakubzick, C.V., 2024. Coordinated chemokine expression defines macrophage subsets across tissues. Nature immunology, 25(6), pp.1110-1122.

Li, X., Kolling, F.W., Aridgides, D., Mellinger, D., Ashare, A. and Jakubzick, C.V., 2022. ScRNA-seq expression of IFI27 and APOC2 identifies four alveolar macrophage superclusters in healthy BALF. Life science alliance.

Download

Share

COinS