Combinatorial drug treatment has been used as a strategy to overcome resistant clones, but it is challenging to find suitable combinations. Non-small cell lung cancer (NSCLC) cell lines are great models for a combinatorial drug screen as they possess multiple forms of resistant clones. The development of Chromium Next GEM Single Cell 3’ HT enables one-million-cell experiments across 192 independent conditions, all in one microfluidic chip, streamlining the drug screening process and empowering researchers to address the most complex biological questions.
An aggregation of all the treatment and time point conditions showed that H1975 cells, bearing an EGFR mutation, are more responsive to combinatorial drug treatment than that of A549 cells, bearing a KRAS mutation. The cell cycle and DNA repair pathways were down-regulated as early as 4h and continued until 24h. The combinatorial treatment primarily impacts cell cycle checkpoint and DNA double-strand break repair gene networks. The impact of single treatment conditions is significantly less, suggesting that synergistic regulation of multiple pathways determines the effect on the gene network.
Next, primary tumor cells from seven NSCLC patients were profiled with single cell transcriptomics and cell surface protein markers, which enables better cell type detection and annotation. The scale of the Single Cell HT assay provides an opportunity for identifying rare tumor types, which is key to understanding evolution of drug resistance and metastasis clones. This study sheds light on therapeutic discovery of actionable targets. We found the common signaling pathways shared by the primary NSCLC cells and A549, indicating A549 is a great model to perform large-scale screening for the KRAS-mutated type of NSCLC.
Overall, this study highlights the scalability of single cell approaches using Chromium Single Cell HT platform along with the applicability of multiomic technologies on the platform to enable high resolution study of biology.