Multi-omics analysis of TNBC organoids identifies phosphorylation of the membrane trafficking machinery as a key event associated with FER-mediated invasion

Elshout, C.; Mota, G.; Cunha, J.; Largher, S.; Alcaraz, P. S.; Silva, A.; Cavadas, B.; Haughton, P. D.; Nguyen, T.; Es, R. M. v.; Monteiro, B. S.; Araujo, A. R.; Marques, A.; Pinto, M. T.; Peixoto, M.; Kempen, S. v.; Graaf, K. v. d.; Fortier, A.-M.; Park, M.; Khalil, A. A.; Fernandes, R.; Vos, H. R.; Derksen, P. W. B.; Janody, F.; Tavares, S.

doi:10.64898/2025.12.18.695070

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bioRxiv · 10.64898/2025.12.18.695070

Multi-omics analysis of TNBC organoids identifies phosphorylation of the membrane trafficking machinery as a key event associated with FER-mediated invasion

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Abstract

Triple Negative Breast Cancer (TNBC) is characterised by unfavourable outcome due to the combination of its metastatic propensity, chemo-refractory behaviour and the lack of effective targeted interventions. Expression of the feline sarcoma-related (FER) kinase constitutes an independent prognostic factor that correlates with poor patient survival. FER promotes invasive behaviour in TNBC cells by regulating endosomal sorting and recycling (ESR) of adhesion proteins. Yet, the ESR machinery supporting invasion in TNBC, particularly within 3D environments, remains poorly understood. Here, we used FER-expressing TNBC patient-derived xenograft organoids (PDXOs) and MDA-MB-231 cells to identify the membrane trafficking machinery promoting invasion. Using a combination of proteomics, phospho-proteomics, and single cell RNA-sequencing, we show that the invasion of FER-expressing PDXO cells in collagen-I is mainly associated with the differential phosphorylation of membrane trafficking regulators, including SEC16A and a marked increase in Rab4-positive tubules. SEC16A depletion impairs cell invasion and reduces the number of focal adhesions and Rab4-positive tubules. Importantly, FER regulates SEC16A levels and localization, specifically in TNBC. Altogether, we identified SEC16A as a key player in FER-driven TNBC invasion, highlighting the membrane trafficking machinery as a promising target for the development of new therapeutic strategies.

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Elshout, C., Mota, G., Cunha, J., Largher, S., Alcaraz, P. S., Silva, A., Cavadas, B., Haughton, P. D., Nguyen, T., Es, R. M. v., Monteiro, B. S., Araujo, A. R., Marques, A., Pinto, M. T., Peixoto, M., Kempen, S. v., Graaf, K. v. d., Fortier, A.-M., Park, M., Khalil, A. A., Fernandes, R., Vos, H. R., Derksen, P. W. B., Janody, F., Tavares, S.. 2025-12-21. Multi-omics analysis of TNBC organoids identifies phosphorylation of the membrane trafficking machinery as a key event associated with FER-mediated invasion. https://doi.org/10.64898/2025.12.18.695070

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