Abstract 2261: A multimodal single-cell workflow to interrogate cellular responses to cancer therapy

Abstract Understanding the genomic landscape of cancer in single cells can be valuable for the characterization of molecular events that drive evolution of tumorigenesis and fostering progress in identifying druggable regimens for patient treatment scenarios. We report a new approach to measure multiple modalities simultaneously from up to 10,000 individual cells using microfluidics paired with next generation sequencing. Our procedure determines targeted protein levels, mRNA transcript levels and somatic gDNA sequence variations including copy number variants. This approach can resolve over 20 proteins, 100s of targeted transcripts and DNA amplicons. We employ oligo-conjugated antibody panels to probe cell surface markers and targeted RNA and DNA amplification to resolve gene expression levels and genomic variants. Cell suspensions are first stained with the antibody panel then loaded onto the Mission Bio Tapestri for generation of a droplet. This droplet biochemistry allows for concurrent cell lysis and release of gDNA/mRNA. A second droplet formation event brings together a barcoded bead and multiplex PCR amplification reagents. After amplification, the combined libraries are sequenced yielding a multimodal readout. We applied this technique to several dynamic immunology and oncology in vitro models. As fusion gene detection has long been a focus of cancer research, we demonstrate this multi-modal workflow on cell lines containing variants of BCR-ABL transcripts with high sensitivities and specificities. We further explored the relationship between genotype-to-phenotype in imatinib impact on retinoblastoma and BCR-ABL driven leukemic cells. Our pilot studies demonstrate the utility of multimodal resolution in further illuminating cellular states and biological responses in cancer cells. Citation Format: Dalia Dhingra, Aik Ooi, Alex Li, Adam Sciambi, Shu Wang, Saurabh Gulati, David Ruff. A multimodal single-cell workflow to interrogate cellular responses to cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2261.