Black, G. S. | Search bioRxiv

bioRxiv2026

A multimodal precision oncology platform integrating genomics,single-cell transcriptomics, and functional drug screening expandstherapeutic options in pediatric brain tumors

Precision oncology for pediatric brain tumors mainly relies on clinically validated, targetable genomic alterations, which are often sparse, yield few matched therapies, and do not guide chemotherapy selection. We developed a tiered framework in which deep whole-genome sequencing and single-cell RNA sequencing extend targeted-therapy selection, with ex vivo functional drug screening supporting selection of both targeted therapies and chemotherapies. We applied it to 17 children with malignant CNS tumors. The approach expanded recommendations beyond genomics: functional screening provided every patient with at least one high-confidence targeted-therapy or chemotherapy nomination, while single-cell RNA sequencing identified an average of 37 druggable gene targets per patient, producing a fourfold increase in high-confidence targeted-therapy recommendations. In an exploratory analysis, functional classifications were directionally consistent with outcomes in 8 of 10 evaluable cases, although combination treatments and radiation precluded causal attribution. Single-cell profiling also identified subclone-specific vulnerabilities, supporting prospective evaluation of the platform's feasibility and predictive utility.

cancer biology↗

bioRxiv2024

Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotype and phenotype in chronic lymphocytic leukemia

Brutons tyrosine kinase (BTK) inhibitors are effective for the treatment of chronic lymphocytic leukemia (CLL) due to BTKs role in B cell survival and proliferation. Treatment resistance is most commonly caused by the emergence of the hallmark BTKC481S mutation that inhibits drug binding. In this study, we aimed to investigate whether the presence of additional CLL driver mutations in cancer subclones harboring a BTKC481S mutation accelerates subclone expansion. In addition, we sought to determine whether BTK-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we employ our recently published method (Qiao et al. 2024) that combines bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for the presence or absence of subclone-defining mutations. While the most common approach for scRNA-seq includes short-read sequencing, transcript coverage is limited due to the vast majority of the reads being concentrated at the priming end of the transcript. Here, we utilized MAS-seq, a long-read scRNAseq technology, to substantially increase transcript coverage across the entire length of the transcripts and expand the set of informative mutations to link cells to cancer subclones in six CLL patients who acquired BTKC481S mutations during BTK inhibitor treatment. We found that BTK-mutated subclones often acquire additional mutations in CLL driver genes, leading to faster subclone proliferation. When examining subclone-specific gene expression, we found that in one patient, BTK-mutated subclones are transcriptionally distinct from the rest of the malignant B cell population with an overexpression of CLL-relevant genes.

genomics↗