SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy

Bhuyan, G. S.; Yan, F.; Nguyen, M. N. T.; Zou, X.; Gullapalli, V.; Vaughan, L.; Stonehouse, O.; Hampton, H. R.; Shen, S.; Truong, P.; Dissanayake, R.; Ghodousi, E. S.; Joshi, S.; Koch, F. C.; Chung, H. M.; Zanini, F.; Vafaee, F.; Huang, Y.; Thoms, J. A. I.; Faridani, O.; Jolly, C. J.; Pimanda, J. E.

doi:10.64898/2026.04.26.720516

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bioRxiv · 10.64898/2026.04.26.720516

SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy

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Abstract

5-azacytidine improves haematopoiesis and delays leukaemic progression in myelodysplastic neoplasms, but responses vary and are complicated by clonal mosaicism and heterogenous demethylation. Using a novel single-cell pipeline ("SCIMETAR-seq"), we found 5-azacytidine induced clonally distinct differentiation responses, with nuclear DNA demethylation occurring primarily in cycling progenitors. Despite the absence of significant nuclear DNA demethylation, quiescent stem cells underwent transcriptional remodelling in vivo, accompanied by 5-azacytidine-induced C*G-to-G*C mutations in mitochondria.

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Bhuyan, G. S., Yan, F., Nguyen, M. N. T., Zou, X., Gullapalli, V., Vaughan, L., Stonehouse, O., Hampton, H. R., Shen, S., Truong, P., Dissanayake, R., Ghodousi, E. S., Joshi, S., Koch, F. C., Chung, H. M., Zanini, F., Vafaee, F., Huang, Y., Thoms, J. A. I., Faridani, O., Jolly, C. J., Pimanda, J. E.. 2026-04-28. SCIMETAR-seq tracks immunophenotype, demethylation, mutations, and transcriptomes in single cells undergoing HMA therapy. https://doi.org/10.64898/2026.04.26.720516

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