TDP1 splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition

Abstract:: HAP1, is a near-haploid human cell line commonly used for its ease of genome editing due to its hemizygous nature. Its unusual hypersensitivity to camptothecin, an antineoplastic drug that stabilizes abortive topoisomerase I cleavage complexes (TOP1ccs), was intriguing. We show here that deficiency of TDP1, a key phosphodiesterase involved in resolving abortive TOP1ccs, is the key driving factor for the observed HAP1 phenotype. Whole exome sequencing and subsequent restoration of TDP1 protein via endogenous genome editing indicated that TDP1 deficiency in HAP1 is attributed to a splice variant (TDP1 c.660-1G>A) that causes exon skipping and TDP1 loss of function. The lack of TDP1 in HAP1 cells should be carefully considered when studying topoisomerase-associated DNA damage repair (DDR) and potentially extrapolating results to other cells. Finally, we also report the generation of HAP1 clones (HAP1-BE3 A2G) with restored TDP1 expression and function, which may be useful in further studies to probe cellular phenotypes relating to TOP1cc repair.

Authors:: CG Goh, A Bader, T-A Tran, R Belotserkovskaya, G D'Alessandro, S Jackson

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