Deciphering Features of Protective or Maladaptive Cellular Immunity in the Airways Following Primary and Repeated Pathogen Exposure

The human respiratory tract is constantly subject to environmental stressors and perturbations that cause deviations from homeostatic conditions. The airway’s cellular constituents – epithelial, stromal, and immune cells – maintain local and global homeostasis by facilitating gas exchange and providing a barrier against noxious environmental agents (e.g., xenobiotics, allergens, toxins, and microbes). Infection with viral, microbial, and eukaryotic pathogens can disrupt airway homeostasis, leading to local and systemic inflammation, which can either contribute to the clearance or persistence of the pathogen. Prior antigenic exposure - prophylactically or from a previous infection - can promote transient and long-lived changes in cellular epigenetics, gene expression networks, and cell type composition that may contribute to protective (or maladaptive) immunity; however, we lack a complete understanding of the pathogen and cellular determinants that modulate immunity upon reinfection. In this thesis, we employed single-cell RNA-seq (scRNA-seq), computational methods, and microbial assays to discover the host and pathogen determinants governing airway homeostasis during primary infection and reinfection at barrier sites where the infection begins and may persist: the nasopharynx, airways, and lung parenchyma. First, we leveraged scRNA-seq to identify the cellular and molecular features of mild, moderate, and severe COVID-19, revealing that persons with severe COVID-19 have blunted anti-viral immunity in the nasopharynx. We further extended these findings by profiling nasopharyngeal swabs from vaccinated and unvaccinated individuals across three waves of SARS-CoV-2 variants, revealing shifts in viral tropism and that intramuscular COVID-19 vaccines promote the recruitment of putative antigen presenting macrophages to the nasal mucosa. Next, we used rhesus macaques to interrogate temporal host-pathogen interactions during SARS-CoV-2 infection and reinfection in the lower respiratory tract. This work identified innate training-like gene programs among myeloid populations that provided enhanced protection against SARS-CoV-2 reinfection. Finally, we used cynomolgus macaques as a model to study Mtb infection and reinfection, demonstrating that CD4+ T cells are required to restrict bacterial growth and induce protective immunomodulatory gene programming and cell-cell interaction networks in pulmonary granulomas formed following Mtb reinfection. These findings extend beyond long-held paradigms of protective TB immunity, revealing that CD4+ T cells regulate pro- and anti-inflammatory granuloma equilibria. Collectively, the work presented in this thesis highlights the utility of single-cell genomics for studying respiratory infection- and immuno-biology and provides a framework for contextualizing pathogen-induced deviations from biological homeostasis in the airways, which has implications for the development of prophylactics and therapeutics.

Name thesis:degree_name

Doctoral

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Biology

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2025

Author dc:creator

• Bromley, Joshua David

Advisor dc:contributor.advisor

• Shalek, Alex K.

Statement dc:rights

• In Copyright - Educational Use Permitted
• Copyright retained by author(s)

Licence dc:rights.uri

• https://rightsstatements.org/page/InC-EDU/1.0/

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/163530

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/163530