Integrated in silico and in vitro approaches identify SNX.2112 as a drug vulnerability in t(7;12) AML stem-like cells

Ciciro, Y.; Ragusa, D.; Johnson, E. M.; Johns, A.; Kanannejad, S.; Gurung, R.; Oporto Espuelas, M.; Suen, C.-W.; Torregrosa-Cortes, G.; Giustacchini, A.; Tosi, S.; Pina, C.

doi:10.1101/2025.09.06.674620

bioRxiv · 10.1101/2025.09.06.674620

Integrated in silico and in vitro approaches identify SNX.2112 as a drug vulnerability in t(7;12) AML stem-like cells

Ciciro, Y.·Ragusa, D.·Johnson, E. M.·Johns, A.·Kanannejad, S.·Gurung, R.·Oporto Espuelas, M.·Suen, C.-W.·Torregrosa-Cortes, G.·Giustacchini, A.·Tosi, S.·Pina, C.

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Abstract

The t(7;12) translocation is a chromosomal rearrangement characteristic of infant Acute Myeloid Leukemia (AML). It arises in utero and results in ectopic overexpression of homeobox gene MNX1. Using a 3-dimensional (3D) model of blood development, we recently showed that t(7;12)-AML originates at the endothelial-to-hematopoietic transition, explaining its characteristic gene expression signature. Herein, we employ that signature to interrogate the transcriptional profiles of hundreds of human cell lines against the GDSC database of drug sensitivities to identify candidate drugs against t(7;12)-AML. We employ a cell line in which we engineered t(7;12) and systematically test the candidate drugs by cell surface phenotype and clonogenic assays. Importantly, we identify HSP90 inhibitor SNX.2112 as a potential therapeutic agent against t(7;12)-AML. SNX.2112 selectively eliminates colony-initiating leukemia progenitors in vitro and decreases MNX1 expression, effects recapitulated by other HSP90 inhibitors. SNX.2112 acts at least partly through destabilisation of STAT5 signalling. Critically, SNX.2112-differential signatures uniquely map to progenitors with hemato-endothelial characteristics in t(7;12)-AML patient blasts, suggesting targeting of leukemia-initiating cells. Combinatorial treatment with chemotherapeutic agents indicates synergy, suggesting SNX.2112 potential as a targeted and cytotoxicity-sparing therapeutic approach. Overall, we successfully use an integrated computational and multi-model experimental approach to identify a drug vulnerability of t(7;12)-AML. Key pointsO_LIClassifier-based in silico drug screening identifies vulnerabilities of t(7;12)-infant leukemia C_LIO_LI2D and 3D models of t(7;12)-leukemia match HSP90 inhibition cellular and molecular responses to candidate leukemia stem cells in t(7;12) patient analysis. C_LI

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Ciciro, Y., Ragusa, D., Johnson, E. M., Johns, A., Kanannejad, S., Gurung, R., Oporto Espuelas, M., Suen, C.-W., Torregrosa-Cortes, G., Giustacchini, A., Tosi, S., Pina, C.. 2025-09-11. Integrated in silico and in vitro approaches identify SNX.2112 as a drug vulnerability in t(7;12) AML stem-like cells. https://doi.org/10.1101/2025.09.06.674620

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