Understanding host-pathogen interactions through development of new co-transcriptomic single cell RNA sequencing technologies

Aim

 To establish a co-transcriptomic single cell RNA sequencing pipeline for simultaneously interrogating host and pathogen gene expression profiles, so that this technology can be used to advance and expedite infection and immunity research programs across UQ. 

Brief project outline

Infectious diseases represent a very significant global challenge, particularly in the context of widespread antibiotic resistance. New approaches to tackle antibiotic-resistant bacterial infections are urgently needed. Applying single cell RNA sequencing (scRNAseq) to map both host and pathogen transcriptomic responses at a single cell level could teach us about individual innate defence mechanisms and how pathogens combat each type of mechanism. The major outcomes from this proposed project would be an innovative technological platform for the very significant UQ infection & immunity research community, thus enabling internationally competitive genomic- and transcriptomic-related infectious diseases research at UQ. 

Genomics-based innovative aspect of proposal

While many, many published studies have performed scRNAseq to examine host responses to pathogen challenge, very few studies have performed co-transcriptomics to map both host and pathogen responses at the single cell level. Exciting opportunities exist to develop new and improved methodologies around host-pathogen co-transcriptomics through GIH (e.g. methods that will increase throughput, reduce rRNA contamination and enrich bacterial transcripts, which is currently a major impediment). 

Broad applicability of the technique

Infectious disease research is a major focus of UQ, as exemplified by the success of the Australian Infectious Disease Research Centre, which has now been expanded in collaboration with QIMRB to encompass more than 100 different research groups. We will store all data and methods on the UQ RDM, present the outcomes of our work in seminar forums at the IMB, SCMB and elsewhere at UQ, and share our detailed methods/protocols with other UQ researchers. We will also aim to publish the methodology, so that the approaches and methods used would be widely available to the international research community.