Deconstructing Cell Intrinsic Immunity and Host-Pathogen Interactions Using Single-Cell Genomics

Abstract

The outcome of infection by a virus or microorganism is determined by a complex set of interactions between host tissues and the virulence mechanisms of the invading agent. Among directly infected and bystander cells, the concerted efforts of immune and stromal cellular communities can neutralize and clear the pathogen with minimal inflammatory damage, or can be circumvented by the pathogen, leading to excessive immunopathology without effective neutralization. At barrier tissues and within their draining lymphoid organs, diverse cell types, microenvironments, commensal organisms, and pathogens create an immensely complicated network of intracellular and intercellular interactions. To understand the basic biology of infectious diseases and to design effective therapeutics, we must chart the critical “nodes” within these host-pathogen networks that lead to emergent properties and outcomes. Methods in single-cell genomics have transformed our ability to comprehensively map host cell types and their behavior during health and disease. Emerging technical and computational approaches expand our toolbox from solely mapping host transcription to the inclusion of data on gene regulatory elements, genomic material from co-resident microbes, cell and tissue developmental dynamics, and the complex cellular communities underlying tissue structure. In the work presented here, we develop and apply new approaches in single-cell genomics to offer deeper understanding into fundamental organismal biology and immunology. First, we detail our work to understand how seemingly disparate organ systems – the sensory arm of the peripheral nervous system and the immune system within lymphoid tissues – together orchestrate the host response to barrier tissue injury. Here, we describe a previously-unappreciated neuro-immune circuit which can respond to pathogenic insult and be manipulated by neuro-tropic viruses (Chapter 2). Next, we map the putative cellular tropism of SARS-CoV-2, the virus that causes COVID-19, and discover mechanisms of viral exploitation and evasion of conserved host defenses (Chapters 3-4). Further, we develop molecular and computational techniques to directly tie intracellular pathogen life cycles across diverse viruses and microbes to host cell biology on an individual cell level (Chapter 4). Finally, using engineered fluorescent small molecules, we advance our capacity to specifically tag and manipulate cells within 2D and 3D systems by their morphology, molecular phenotype, and microenvironment (Chapter 5). Collectively, this work advances the molecular and computational approaches for interrogating host-pathogen interactions underlying major human infectious diseases, with a focus on enabling a deep understanding of pathogen biology, the scope and variance in human disease pathophysiology, and the complex dynamics of host mucosal and systemic immunity. We propose that systems for rapid and comprehensive characterization of emerging infectious agents are critical tools in the efforts to curb current disease outbreaks, and will likely prove instrumental in addressing future pandemic diseases.