UBC Faculty Research and Publications

Predicting heterogeneity in clone-specific therapeutic vulnerabilities using single-cell transcriptomic signatures Suphavilai, Chayaporn; Chia, Shumei; Sharma, Ankur; Tu, Lorna; Da Silva, Rafael P.; Mongia, Aanchal; DasGupta, Ramanuj; Nagarajan, Niranjan


While understanding molecular heterogeneity across patients underpins precision oncology, there is increasing appreciation for taking intra-tumor heterogeneity into account. Based on large-scale analysis of cancer omics datasets, we highlight the importance of intra-tumor transcriptomic heterogeneity (ITTH) for predicting clinical outcomes. Leveraging single-cell RNA-seq (scRNA-seq) with a recommender system (CaDRReS-Sc), we show that heterogeneous gene-expression signatures can predict drug response with high accuracy (80%). Using patient-proximal cell lines, we established the validity of CaDRReS-Sc’s monotherapy (Pearson r>0.6) and combinatorial predictions targeting clone-specific vulnerabilities (>10% improvement). Applying CaDRReS-Sc to rapidly expanding scRNA-seq compendiums can serve as in silico screen to accelerate drug-repurposing studies. Availability: https://github.com/CSB5/CaDRReS-Sc .

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