Mycobacterium tuberculosis host-pathogen interface


We are interested in the interface between intracellular bacterial pathogens and the hosts they infect.  In particular, we study the notorious human pathogen, Mycbacterium tuberculosis, which remains a major global health threat.  M. tuberculosis has evolved a variety of specific adaptations to not only survive but also replicate within the harsh environment inside a macrophage.  We want to understand the mechanisms by which M. tuberculosis is able to modulate the innate immune response to establish an infection as well as how the host detects and responds to M. tuberculosis.

How is Mtb sensed within a macrophage?

Cytosolic DNA is an important "danger signal" that alerts macrophages and other host cells that they are infected by a intracellular pathogen. We are primarily focused on two major outcomes of cytosolic DNA sensing during M. tuberculosis infection: targeting of Mtb to autolysosomes by ubiquitin-dependent selective autophagy and activation of a type I IFN cytokine program. Interestingly, activation of these two pathways lead to opposite infection outcomes, with autophagy being required to control M. tuberculosis infection and type I IFNs exacerbating M. tuberculosis pathogenesis. Ultimately, by identifying the players involved in each of these pathways, we hope to one day develop host-directed therapeutics that can polarize DNA sensing outcomes in favor of the host. 

To interrogate the biology occurring between M. tuberculosis and its host, we use a number of techniques, including immunofluorescence microscopy, cell culture infection, protein biochemistry, genetic manipulation of host cells (shRNA knockdown and CRISPR/Cas9 knockout), and in vivo infection using mutant mouse strains. We perform experiments using wild-type M. tuberculosis in biosafety level 3 containment facilities. 

the role of the spliceosome in Shaping innate immune outcomes


Despite the substantial impact pre-mRNA splicing has on gene expression outcomes, little is known about how the spliceosome itself is modified and regulated during cellular reprogramming. Innate immune cells like macrophages reprogram gene expression when they sense a “danger signal,” such as a pathogen, organelle damage, or chemical signal, to combat the detected threat. While changes that occur transcriptionally during macrophage activation are well characterized, almost nothing is known about how pre-mRNA splicing is regulated following immune stimuli. The long-term goal of the Patrick lab is to uncover how macrophage activation modifies the spliceosome and to connect these changes with innate immune gene expression outcomes. The spliceosome is a complex and dynamic macromolecular machine. Its ability to recognize introns and catalyze their removal relies on numerous RNA binding proteins that recognize specific sequences in exons and introns to “read” the splicing code. We predict that during macrophage activation, post-translational modification of splicing factors directs assembly of a specialized spliceosome characterized by a distinct cohort of protein-protein interactions that promotes the innate immune gene expression program. To elucidate the nature of this "immunospliceosome", my lab combines high-throughput approaches, including affinity purification-mass spectrometry, phosphoproteomics, RNA-seq, and RNA CLIP-seq with targeted genetic and biochemical experiments. Our hope is that our research will fill key gaps in our knowledge of how splicing is regulated following macrophage activation and further our understanding of how the spliceosome reads and interprets the splicing code not only during innate immune activation but also during other cellular reprogramming, including differentiation, stress, starvation, and carcinogenesis.