This presentation by Aziz Alafage of Broad Clinical Labs details two ambitious projects leveraging Roche's new SPX sequencing platform. The primary focus is a large-scale, multiomic study aimed at understanding drug resistance mechanisms to KRAS inhibitors in cancer. Using a pool of 500 multiplexed PRISM cancer cell lines, the team simultaneously profiled single-cell RNA expression, protein expression for over 320 targets, and cell line identity. The experiment, which generated 80 billion reads, successfully linked drug sensitivity and resistance profiles to specific genetic mutations (e.g., KRAS and BRAF), highlighting the power of capturing both RNA and protein data, which are not always correlated. The second, smaller project demonstrates the SPX platform's capability for single-cell RNA isoform sequencing. By analyzing full-length cDNA, the team showed that the platform's longer read lengths (500-800 bp) significantly improve the ability to resolve full splice variants and even identify novel, unannotated isoforms.
Leveraging the SPX Platform for Drug Discovery and Isoform Sequencing
00:00:26 Project Goals: The presentation outlines two key projects utilizing Roche's new SPX platform: 1) a high-scale multiomic study of drug response in cancer cell lines, and 2) an evaluation of the platform for single-cell RNA isoform sequencing.
00:01:51 Multiomic Drug Response Study: To understand resistance to KRAS inhibitors, researchers treated a pool of 500 unique, co-cultured PRISM cancer cell lines with two different inhibitors. They then performed single-cell analysis at 3 and 6 hours, plus a 5-day survival assay.
00:03:14 Simultaneous Data Capture: The experiment captured three data types from each cell: its unique PRISM barcode (to identify the cell line), its full transcriptome (RNA), and the expression of over 320 proteins.
00:03:55 Massive Scale and High-Quality Data: The sequencing run on the SPX platform produced 80 billion reads. The resulting data was of "phenomenal" quality, with high gene detection per cell and no detectable batch effects.
00:05:35 The Power of Multiomics: The study underscores the importance of measuring both RNA and protein. While some genes show high correlation, others (like transcription factors) do not, meaning RNA is not always a reliable proxy for protein-level activity.
00:07:57 Linking Genetics to Drug Resistance: The 5-day survival data allowed researchers to classify cell lines into four categories (e.g., sensitive to both drugs, resistant to both). These classifications correlated strongly with known genetic mutations; for example, cell lines with BRAF mutations were resistant, as expected.
00:10:05 RNA Isoform Sequencing: The second project used the SPX platform to sequence full-length cDNA libraries to assess its ability to identify different RNA isoforms from single cells.
00:10:51 Longer Reads Improve Isoform Resolution: The platform generated a high proportion of reads between 500-800 bp. Analysis showed a sharp increase in the ability to identify "full splice match" isoforms with these longer reads compared to shorter ones.
00:11:52 Discovery of Novel Isoforms: The longer read lengths were able to span multiple exons, allowing researchers to not only resolve known isoforms but also discover new, previously unannotated splice variants.
00:12:34 Key Takeaway: The speaker concludes that the Roche SPX platform is a "transformational technology" that enables a "paradigm shift" for complex applications like drug discovery and advanced RNA biology.