Davide Pisu, PhD

Biography

• Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of death from infectious diseases worldwide, claiming over 1.5 million lives annually. Despite significant advancements in our understanding of Mtb pathogenesis, crucial gaps remain in our knowledge of the factors that determine disease control in immune-competent individuals. The rise of drug-resistant Mtb strains and the limited efficacy of the Bacille Calmette-Guérin (BCG) vaccine highlight the urgent need for improved preventive and therapeutic strategies.
  
  
• Macrophages, as key players in the innate immune response, are the primary host cells that Mtb exploits to establish infection, replicate, and evade immune defenses. The interaction between Mtb and macrophages within the lung is complex and influences whether the infection is contained or progresses to active disease. Our lab is dedicated to dissecting these intricate host-pathogen dynamics, with a specific focus on identifying macrophage populations that differ in their susceptibility to Mtb and understanding how innate immune training or environmental factors modify their responses to infection.
  The overarching goal of our research is to understand the molecular and cellular mechanisms underlying macrophage heterogeneity and its impact on TB progression, leveraging this knowledge to improve treatment and vaccination strategies. Our approach integrates transcriptomics and proteomics studies to map gene and protein expression changes in macrophage subsets during Mtb infection, alongside CRISPR-based gene editing to investigate specific genes and pathways’ roles in Mtb infection, both in the host and Mtb. Functional assays and live sorting with fluorescent Mtb strains allows us to characterize infection dynamics in vivo, using both murine and non-human primate (NHP) models of tuberculosis. We also employ multi-modal omics techniques to simultaneously profile host and bacterial transcriptomes, providing insights into how diverse bacterial phenotypes interact with distinct macrophage populations.
  
  
• Our current research focuses on lung-resident alveolar macrophages (AMs), the initial immune cells infected by inhaled Mtb. While traditionally considered permissive to Mtb replication and spread, our recent studies using fluorescent Mtb fitness reporter strains and single-cell RNA sequencing (scRNA-seq) have revealed a more nuanced picture. We have identified multiple AM populations in the infected lung, differentiated by their origin and inflammatory potential. These include monocyte-derived and tissue-resident CD38+ pro-inflammatory AMs (moAMs and TR-AMs), which contain stressed bacteria and release high levels of nitric oxide (NO), and tissue-resident CD38- AMs, which lack NO expression and harbor replicating bacteria. Our findings suggest that CD38- AMs, with limited capacity to contain Mtb, are the predominant infected subset early in infection. Furthermore, intranasal BCG vaccination prior to Mtb exposure reduces the number of Mtb-infected host cells and increases the proportion of CD38+ AMs, indicating a protective role for this phenotype in mediating the initial immune response against Mtb. Our research further shows that, although CD38- and CD38+ AMs appear transcriptionally similar in naive mice, they exhibit distinct chromatin landscapes, suggesting that epigenetic constraints might be key to their divergent responses to Mtb infection. We are currently investigating the molecular basis of this differential responsiveness through several approaches:

1. Characterizing the Host Mechanisms Behind AM Diversity: We aim to identify the host genes and pathways that drive the differing responses between CD38+ and CD38- AMs during Mtb infection, uncovering the genetic and epigenetic factors responsible for these phenotypes.
2. Elucidating Mtb Survival Mechanisms Across AM Populations: We are exploring how Mtb adapts to and exploits different AM populations, identifying Mtb genes and pathways associated with CD38+ and CD38- AMs to understand the pathogen’s strategies for survival.
3. Increase Anti-TB Responses via Epigenetic Modulation: We are testing the potential of epigenetic compounds to modify AM populations in vivo, reshaping their chromatin landscape prior to infection to promote host-protective responses and favorably alter the initial course of infection.