Eleni Mimitou, PhD
Associate Director, Single Cell Technologies,
Immunai

Talk: Highly multimodal measurements of single cells

High-throughput single-cell RNA sequencing (scRNA-seq) has rapidly progressed from a tremendous technical achievement to a standard tool for phenotypic interpretation of complex biological systems. We have previously described Cellular Indexing of Transcriptomes and Epitopes by sequencing (CITE-seq), Cell Hashing for sample multiplexing and Expanded CRISPR-compatible CITE-seq (ECCITE-seq), to layer detection of surface protein and sgRNA abundance on scRNA-seq platforms.

Now, we extend our multimodal approaches to simultaneously profile accessible chromatin and protein levels with ASAP-seq (ATAC with Select Antigen Profiling by sequencing). Our approach pairs sparse scATAC-seq data with robust detection of cell surface and intracellular protein markers and uses a novel bridging approach that repurposes antibody:oligo conjugates designed for existing technologies.

Finally, we describe DOGMA-seq, a novel adaptation of our existing CITE-seq method for measuring gene activity across the central dogma of gene regulation. We demonstrate the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA, and surface proteins during native hematopoietic differentiation, peripheral blood mononuclear cell stimulation, and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.

Rachel Thijssen, PhD
Postdoctoral Fellow,
Walter and Eliza Hall Institute of Medical Research

Talk: Unexpected and complex tumour heterogeneity revealed by a novel multi-omics approach

Drug resistance continues to be the principal limiting factor to achieving cures in patients with cancers. While introduction of novel targeted inhibitors has markedly altered the therapeutic options for treating patients with blood cancers, relapses due to acquired resistance after initial response remain a major problem. Although DNA bulk sequencing can provide clues to the resistance mechanisms such as gene amplification or mutation, it cannot accurately measure tumour heterogeneity, distinguish in which cells mutation and/or gene amplification occur, or definitively elucidate what is happening in the cells not harbouring these alterations.

To delineate drug resistance, we applied a novel single-cell omics approach on samples from patients with progressive leukaemia who failed therapy with a targeted agent. Here we show that multiple mechanisms often operate even within a patient to confer resistance. Combining short-read with full-length targeted and whole transcriptome sequencing identified mutations and alternative transcripts in specific sub-clones of the tumour at relapsed disease. Thus, our single-cell integration of short-read and full-length transcriptome provides novel insights into how complex tumour heterogeneity evolves upon acquisition of drug resistance.