­The mammalian immu­ne system is composed of complex networks of functionally diverse cell types, signaling pathways, regulatory circuits, and molecular mechanisms. Effective host defense depends on coordinated interactions of these numerous components. Recent technological advances have enabled the study of these complex molecular and cellular systems at unprecedented throughput and resolution.

Our laboratory is focused on developing and applying high throughput sequencing (HTS) and related high dimensional techniques to gain new understandings of immune function in viral infection. Many current projects utilize custom implementations of high throughput single cell RNA-Seq methodologies.

Functional immune profiling by high throughput sequencing at single cell resolution

During a systemic viral infection, the innate immune response is mediated by a diverse collection of different cell types and mechanisms. Furthermore, the adaptive immune system employs an immense amount of molecular diversity in T cell receptors and immunoglobulins to recognize and respond to different antigenic targets. As such, the high throughput analysis of innate and adaptive immunity presents distinct challenges and requires specialized techniques. Combining molecular biology, microfluidics and bioinformatics, our laboratory is developing novel methodologies for comprehensive HTS immune profiling at single cell resolution. We are using these approaches to explore immune function in a variety of different contexts, with a focus on viral infection.

Immune function during Hepatitis C virus infection: a transcriptomics approach

Hepatitis C virus (HCV) infection is a leading cause of liver disease morbidity and mortality worldwide. Within weeks of HCV exposure, some individuals eliminate the virus, while most transition to a decades-long chronic infection; the underlying immune mechanisms responsible for these different outcomes are incompletely understood. Our laboratory uses RNA-seq to gain new insights into how the human immune system functions during HCV infection. In collaboration with our colleagues at Université de Montréal (led by Dr. Naglaa Shoukry), we are characterizing the immune response to acute HCV infection in a unique set of clinical samples. Our analysis is focused on understanding the innate antiviral mechanisms and immune cell dynamics active shortly after initial infection. Complementary projects exploring the effects of chronic HCV infection on immune function are also ongoing.

RNA-Seq analysis strategies for diverse aspects of host-virus interactions

Viral infections and corresponding host responses can result in profound transcriptional changes. These may include not only differences in gene expression programs, but also RNA nucleotide modifications and/or alterations in splicing patterns. RNA-Seq and related methodologies offer powerful tools to investigate these changes and their functional impact at a transcriptome-wide scale. However, studying these molecular processes often requires non-standard analysis strategies. Our laboratory develops and applies tailored RNA-Seq workflows to diverse projects exploring the interaction of host cells and viral pathogens. Recent examples include defining the “editome” of the ADAR1 RNA editing enzyme and its impact on the innate antiviral response, and quantifying transcript splice intermediates in virus-susceptible humans with a genetic deficiency in RNA processing.