Multiomics-driven discovery of predictive biomarkers and strategies to overcome resistance to SFK-YAP inhibition in cholangiocarcinoma

Kuipers, H.; Carlson, D. M.; Jessen, E.; Abeynayake, A. M.; Sample, J. W.; Mun, D.-G.; Tomlinson, J. L.; Abdelrahman, A. M.; Werneburg, N. W.; Li, B.; Ozmert, E. H.; Conboy, C. B.; Borad, M.; Truty, M. J.; Pandey, A.; Ilyas, S. I.; Gores, G. J.; Smoot, R. L.

doi:10.64898/2026.01.21.699926

bioRxiv · 10.64898/2026.01.21.699926

Multiomics-driven discovery of predictive biomarkers and strategies to overcome resistance to SFK-YAP inhibition in cholangiocarcinoma

Kuipers, H.·Carlson, D. M.·Jessen, E.·Abeynayake, A. M.·Sample, J. W.·Mun, D.-G.·Tomlinson, J. L.·Abdelrahman, A. M.·Werneburg, N. W.·Li, B.·Ozmert, E. H.·Conboy, C. B.·Borad, M.·Truty, M. J.·Pandey, A.·Ilyas, S. I.·Gores, G. J.·Smoot, R. L.

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Abstract

The limited efficacy of current therapies against cholangiocarcinoma (CCA) necessitates the development of novel treatment strategies. Src family kinases (SFKs) contribute significantly to tumor progression and resistance in CCA. Therefore, we investigated the novel, first-in-class SFK OFF inhibitor NXP900 in diverse preclinical CCA models, including those with acquired resistance. This study evaluated the therapeutic effects of NXP900 and detailed adaptive molecular responses to SFK inhibitor therapy. We also aimed to identify biomarkers predictive of drug sensitivity using integrated multiomic profiling and develop strategies to overcome resistance. NXP900 inhibited YAP activity through direct inhibition of tyrosine phosphorylation and indirect activation of the Hippo pathway via LATS. These effects were associated with decreased tumor cell viability in CCA cell lines and several in vivo models. Notably, IDH-mutant patient-derived xenograft CCA models were particularly sensitive to NXP900. NXP900 also synergized with gemcitabine/cisplatin chemotherapy, enhancing antitumor efficacy in both in vitro and in vivo models. Multiomic analyses combining transcriptomics, global proteomics, and phosphoproteomics identified molecular features associated with primary response and acquired resistance. IL13RA-AKT signaling was upregulated in resistant models; NXP900 sensitivity could be restored with AKT or IL13RA2 inhibition. Together, these findings demonstrate the therapeutic potential of NXP900 as a novel YAP inhibitor in CCA and support further investigation in a clinical trial. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/699926v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1cb9e6eorg.highwire.dtl.DTLVardef@10e50e2org.highwire.dtl.DTLVardef@e04dfaorg.highwire.dtl.DTLVardef@1f7334_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kuipers, H., Carlson, D. M., Jessen, E., Abeynayake, A. M., Sample, J. W., Mun, D.-G., Tomlinson, J. L., Abdelrahman, A. M., Werneburg, N. W., Li, B., Ozmert, E. H., Conboy, C. B., Borad, M., Truty, M. J., Pandey, A., Ilyas, S. I., Gores, G. J., Smoot, R. L.. 2026-01-23. Multiomics-driven discovery of predictive biomarkers and strategies to overcome resistance to SFK-YAP inhibition in cholangiocarcinoma. https://doi.org/10.64898/2026.01.21.699926

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