Deciphering heterogeneous tumour ecosystems with single-cell genomics.
The tumor microenvironment is a diverse collection of cell types, both cancerous and non-malignant, which interact to influence tumour biology and response to therapy. Traditional transcriptomic and genomic assays profile tumours as bulk samples, masking individual cell states and variability between them. In collaboration with the Princess Margaret Genomics Centre, we have implemented a suite single-cell genomics assays, notably droplet-based single-cell RNA-sequencing, to profile the tumour microenvironment at single cell resolution. Our lab aims to use these methods to provide novel insights into drug resistance, stem cell programs and tumour progression, as well as identify clinically relevant subsets of non-malignant cells to inform patient treatment.
Evaluation of methods to assign cell type labels to cell clusters from single-cell RNA-sequencing data.
Diaz-Mejia JJ, Meng EC, Pico AR, MacParland SA, Ketela T, Pugh TJ, Bader GD, Morris JH.
F1000Research. 2019. https://doi.org/10.12688/f1000research.18490.1. PMID: 31508207
CReSCENT: CanceR Single Cell ExpressioN Toolkit.
Mohanraj S, Díaz-Mejía JJ, Pham MD, Elrick H, Husić M, Rashid S, Luo P, Bal P, Lu K, Patel S, Mahalanabis A, Naidas A, Christensen E, Croucher D, Richards LM, Shooshtari P, Brudno M, Ramani AK, Pugh TJ.
Nucleic Acids Res. 2020 Jul 2;48(W1):W372-W379. PMID: 32479601