Bridging genotype and phenotype through long-read, single-molecule multiomics | LC 25

Biography

Ruben Cools is a PhD student at the Integrative Cancer Genomics Lab (VIB–KU Leuven, Belgium), led by Prof. J. Demeulemeester. His research focuses on understanding the complex genomic variation that occurs during somatic evolution of rare tumours. His aim is to reconstruct the temporal order of these variations and evaluate their impact across different omic layers.

To do so, he is analysing different types of data modalities, including the host lab’s new long-read multiomics sequencing method.

Abstract

The rapid advancement of single-cell technologies has revolutionised our understanding of tumour heterogeneity and evolution. However, methods capable of accurately capturing genomic variation at the single-cell level while simultaneously providing insights into multiple omics layers remain limited. To address this gap, we developed a novel single-cell multiomics approach integrating the long-read capabilities of Oxford Nanopore sequencing with the high-throughput performance of the 10x Genomics Multiome Kit. To demonstrate its potential, we applied this approach to profile the evolution of paediatric B-cell acute lymphoblastic leukaemia (B-ALL) through chemotherapy and CAR-T therapy. Our method produces full-length barcoded cDNA for precise quantification of known genes, novel transcripts, and complex fusion events, alongside high-quality DNA libraries. These libraries can be computationally stratified into short fragments from highly accessible regions and long fragments, enabling simultaneous profiling of chromatin accessibility landscapes and genome-wide variant calling. By applying this approach, we revealed how clonal dynamics and phylogenies in B-ALL evolve over time, driven by somatic variants. Notably, we uncovered mechanisms of resistance to CD19-targeting CAR-T cells through the detection of novel CD19 isoforms, potentially arising from a mutation at the exon-intron junction. Additionally, we identified transcriptomic and chromatin accessibility shifts linked to immune evasion, offering critical insights into therapy resistance and relapse. In conclusion, our method delivers simultaneous genomic, epigenomic, and transcriptomic information across thousands of single cells using off-the-shelf kits and reagents, without additional lab equipment. This provides a powerful tool to dissect patterns of somatic evolution, bridging genomic variations to functional insights in unprecedented ways.