Selection of pre-leukemic hematopoietic stem cells driven by distinct extracellular matrix molecules

Jassinskaja, M.; Bode, D.; Gonka, M.; Roumeliotis, T. I.; Hogg, A. J.; Rubio Lara, J. A.; Bennett, E.; Milek, J.; Theeuwes, B.; Vijayabaskar, M. S.; Cabrera Cosme, L.; Che, J. L. C.; MacDonald, S.; Ahmed, S.; Hall, B. A.; Vasey, G.; Kooi, H.; Belmonte, M.; Shepherd, M. S.; Brackenbury, W. J.; Kucinski, I.; Yamazaki, S.; Holding, A. N.; Cull, A. H.; Wilson, N. K.; Gottgens, B.; Chaudhary, J. S.; Kent, D. G.

doi:10.1101/2025.01.20.633881

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bioRxiv · 10.1101/2025.01.20.633881

Selection of pre-leukemic hematopoietic stem cells driven by distinct extracellular matrix molecules

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Abstract

Despite rapid advances in mapping genetic drivers and gene expression changes in hematopoietic stem cells (HSCs), there is a relative paucity of studies at the protein level. Here, we perform a deep, multi-omic characterization (epigenome, transcriptome and proteome) of HSCs carrying a loss-of-function mutation in Tet2, a key driver of increased self-renewal in blood cancers. Using state-of-the-art, multiplexed, low-input mass spectrometry (MS)-based proteomics, we profile wildtype (WT) and TET2-deficient (Tet2-/-) HSCs and show that the proteome captures previously unrecognized molecular processes which define the pre-leukemic HSC molecular landscape. Specifically, we obtain more accurate stratification of WT and Tet2-/- HSCs than transcriptomic approaches and identify extracellular matrix (ECM) molecules as novel points of dysregulation upon TET2 loss. HSC expansion assays using ECM-functionalized hydrogels confirm a selective effect on the expansion of Tet2-mutant HSCs. Taken together, our study represents a comprehensive molecular characterization of Tet2-mutant HSCs and identifies a previously unanticipated role of ECM molecules in regulating self-renewal of disease-driving HSCs.

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Jassinskaja, M., Bode, D., Gonka, M., Roumeliotis, T. I., Hogg, A. J., Rubio Lara, J. A., Bennett, E., Milek, J., Theeuwes, B., Vijayabaskar, M. S., Cabrera Cosme, L., Che, J. L. C., MacDonald, S., Ahmed, S., Hall, B. A., Vasey, G., Kooi, H., Belmonte, M., Shepherd, M. S., Brackenbury, W. J., Kucinski, I., Yamazaki, S., Holding, A. N., Cull, A. H., Wilson, N. K., Gottgens, B., Chaudhary, J. S., Kent, D. G.. 2025-01-22. Selection of pre-leukemic hematopoietic stem cells driven by distinct extracellular matrix molecules. https://doi.org/10.1101/2025.01.20.633881

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