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Wiens, Matthew

University of British Columbia

Epithelioid Sarcoma (ES) is a rare and aggressive cancer with a poor prognosis. Most ES tumors are characterized by homozygous loss of expression of SMARCB1, a tumor suppressor involved in a wide variety of cell-cycle pathways and altered in many cancers. Our lab has developed a mouse model of Smarcb1-loss-induced tumors which resemble human ES. This model may act as a platform for interrogating epithelioid sarcomagenesis and testing potential therapies. Variant calling is increasingly being applied to various single-cell modalities to resolve genetic signatures of intercellular heterogeneity. Various variant calling approaches, notably calling on the pooled reads or on individual cells, are being applied in Chromium single-cell libraries. However, the viability of these approaches is not yet established. We apply matched WGS as ground truth to benchmark a variety of bulk and individual-cell variant calling approaches on Chromium scRNA-seq and scATAC-seq libraries from tumor samples. We find that calling on pooled reads almost always outperforms calling at the single-cell level for detecting ground-truth variants. We find many novel variants are called in scRNA-seq which appear to be due to modality-specific artifacts. However, many of these variants match existing RNA-editing event databases and may have utility in further studies. Following previous studies, we investigate variants unique to individual-cell-calling approaches as possible rare somatic mutations and, through characterization of wild type samples, find that most candidates are likely artifactual/noise. Using single-cell and WGS libraries, we review the biological similarity of the mouse model to human ES and characterize multiple dysregulated pathways possibly underpinning tumor development. We find that the tumors exhibit characteristic transcriptomic markers of human ES. Investigation of pathways known to be affected by Smarcb1-loss finds that the Retinoblastoma/E2F, Hedgehog, and Wnt pathways are active at different levels in each sample. Genomic profiling reveals a tumor mutational burden similar to human ES, as well as sub-clonal chromosomal deletion events. Overall, we benchmark variant calling in Chromium single-cell methodologies and give recommendations to maximize performance, while in parallel establishing the equivalence of our model to human ES and identify promising pathways meriting further investigation in follow-up studies.

Text

2024-06-30

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/82082

Biomedical Engineering

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/