Abstract
Chromosome gains or losses often lead to copy number variations (CNV) and loss of heterozygosity (LOH). Both quantities are low in hematologic “liquid” cancers versus solid tumors in data of The Cancer Genome Atlas (TCGA) that also shows the fraction of a genome affected by LOH is ~ one-half of that with CNV. Suspension cultures of p53-null THP-1 leukemia-derived cells conform to these trends, despite novel evidence here of genetic heterogeneity and transiently elevated CNV after perturbation. Single-cell DNAseq indeed reveals at least 8 distinct THP-1 aneuploid clones with further intra-clonal variation, suggesting ongoing genetic evolution. Importantly, acute inhibition of the mitotic spindle assembly checkpoint (SAC) produces CNV levels that are typical of high-CNV solid tumors, with subsequent cell death and down-selection to novel CNV. Pan-cancer analyses show p53 inactivation associates with aneuploidy, but leukemias exhibit a weaker trend even though p53 inactivation correlates with poor survival. Overexpression of p53 in THP-1 does not rescue established aneuploidy or LOH but slightly increases cell death under oxidative or confinement stress, and triggers p21, a key p53 target, but without affecting net growth. Our results suggest that factors other than p53 exert stronger pressures against aneuploidy in liquid cancers, and identifying such CNV suppressors could be useful across liquid and solid tumor types.
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All data generated or analyzed during this study are included in this published article. All materials generated are available from the corresponding author on reasonable request.
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Acknowledgements
The authors acknowledge the following University of Pennsylvania core facilities: Cell Center Stockroom, the Penn Cytomics and Cell Sorting Resource Laboratory, and the Penn Genomic Analysis Core. We also acknowledge The Center for Applied Genomics Core in The Children’s Hospital of Philadelphia for SNPa's.
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This work was supported by funding from the National Institutes of Health/National Cancer Institute (U54 CA193417, U01 CA254886, P01 CA265794), NHLBI (R01 HL124106), NSF GRFP DGE-1845298 (BHH), National Science Foundation (MRSEC DMR-1720530 and DMR-1420530 and Grant Agreements CMMI 1548571 and 154857), Human Frontier Science Program Grant RGP00247/2017, and Pennsylvania Department of Health Grant HRFF 4100083101.
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Mai Wang performed experimental work, data analysis, figure construction, and contributed to conceptualization and design of the study. Steven Phan performed experimental work, analyzed data, and contributed to the figure construction. Brandon H. Hayes performed experimental work. Dennis E. Discher designed, conceptualized, and supervised the study. The manuscript was written by Mai Wang and Dennis E. Discher. All authors read and approved the final manuscript.
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Wang, M., Phan, S., Hayes, B. et al. Genetic heterogeneity in p53-null leukemia increases transiently with spindle assembly checkpoint inhibition and is not rescued by p53. Chromosoma 133, 77–92 (2024). https://doi.org/10.1007/s00412-023-00800-y
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DOI: https://doi.org/10.1007/s00412-023-00800-y