Aziz Alafage, Director of Molecular R&D at Broad Clinical Labs, presents their ambitious deployment of Roche's new SVX platform across two key genomic areas: high-scale multiomic drug response profiling using multiplex PRISM cell lines and ultra-high throughput single-cell RNA isoform sequencing.
The single-cell project, focusing on KRAS-mutated cancers, involved treating PRISM cell line pools with RAS inhibitors and performing multiomic single-cell profiling (RNA and protein) followed by survival assays. The SPX platform generated an impressive 80 billion reads, yielding high-quality data that allowed linking survival outcomes to early drug responses and identifying mutation enrichments correlated with drug sensitivity or resistance. Notably, capturing both RNA and protein expression proved crucial due to their sometimes discordant correlation, especially for post-translationally regulated transcription factors.
The RNA isoform sequencing efforts demonstrated the SVX's capability to resolve canonical cell types and biomarker genes. Analysis of read length distribution (peaking 500-800 bp) showed high confidence in spanning multiple splice junctions and resolving full-length isoforms, even identifying a novel, unannotated isoform. The presentation concludes by highlighting the transformative potential of these approaches for systematic identification and targeting of drug resistance mechanisms.
Summarizing the Broad Clinical Labs' Genomics Work with Roche's SVX Platform
0:00 Introduction: Aziz Alafage from Broad Clinical Labs introduces the deployment of Roche's new SVX platform for cutting-edge genomics.
0:39 Research Focus Areas: Two main areas are being explored: high-scale multiomic drug response profiling with multiplex PRISM cell lines and ultra-high throughput single-cell RNA isoform sequencing.
1:08 KRAS Drug Resistance: The single-cell project focuses on KRAS, a cancer driver, and understanding therapeutic evasion and drug resistance to small molecule inhibitors.
1:51 Experimental Setup: PRISM cell line pools (500 unique co-cultured lines) were treated with RAS inhibitors (BA 2865, RMC 6236) and controls. Single-cell profiling was performed at 3 and 6 hours, with survival assays at 5 days.
2:34 Multiomic Data Capture: Experiments captured PRISM barcodes for cell line identification, protein expression (320+ targets) using the Protein-Tex discovery panel, and whole transcriptome RNA using the 10x Flex platform.
3:14 SPX Sequencing Power: Sequencing on the SPX platform yielded 80 billion reads for the experiment, leading to "phenomenal" data quality with no obvious batch effects.
4:30 Impressive Protein Data: Protein expression data alone could resolve many cell lines, with a median of 300 proteins detected per cell.
4:57 Value of Dual Modalities: Capturing both RNA and protein is crucial because their expression can be poorly correlated, especially for post-translationally regulated transcription factors.
7:07 Survival Outcomes & Mutation Enrichment: Analysis of 5-day survival data revealed cell lines resistant or sensitive to drugs. Unique mutation enrichments were found in different response classes (e.g., KRAS in sensitive, BRAF in resistant), consistent with literature.
8:57 Paradigm Shift in Drug Development: This high-yield approach aims to systematically identify, validate, and target mechanisms of drug resistance, marking a paradigm shift for drug development.
10:49 RNA Isoform Sequencing: The SVX platform's read length distribution (mostly 500-800 bp) enabled high confidence in resolving full-length isoforms by spanning multiple splice junctions.
11:28 Novel Isoform Discovery: The team identified a previously unannotated isoform for the CD1C gene, highlighting the platform's capability for novel discovery.
11:52 Acknowledgments: The intensive single-cell experiment was a success due to collaborative efforts with Roche, utilizing "transformational technology."