ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas

Denu, R. A.; Singh, A. K.; Jiang, Y.; Zheng, Z.; Ingram, D. R.; Wani, K. M.; Lazcano, R.; Ginn, M. P.; Anand, K.; Singh, B. K.; Ballard, J. C.; Kochat, V.; Chatterjee, B.; Padron, W.; Landers, S. M.; Bhalla, A.; Multani, A.; Dharmaiah, S.; Malgulwar, P. B.; Cai, Y.; Lin, H.; Huse, J. T.; Ying, H. T.; Keung, E. Z.; Wang, W.-L.; Conley, A. P.; Patel, S.; Somaiah, N.; Farooqi, A.; Lazar, A. J.; Nassif Haddad, E. F.; Torres, K. E.; Rai, K.

doi:10.1101/2025.11.23.689992

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bioRxiv · 10.1101/2025.11.23.689992

ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas

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Abstract

ATRX is one of the most frequently altered genes in sarcoma and encodes an ATP-dependent chromatin remodeler implicated in maintaining heterochromatin. However, ATRX alterations have not been leveraged for sarcoma treatment. We observed loss of ATRX protein in 14% of soft tissue leiomyosarcoma (STLMS, n =127), 53% of uterine leiomyosarcoma (ULMS, n = 95), 37% of undifferentiated pleomorphic sarcoma (UPS, n = 82), and 8% of dedifferentiated liposarcoma (DDLPS, n = 84). ATRX loss was associated with significantly worse outcomes in ULMS, UPS, and DDLPS. ATRX knockout in sarcoma cells increased proliferation in cooperation with TP53 deletion. ATRX knockout led to chromatin de-repression and enrichment of PRDM4 and NFIX transcription factor (TF) motifs. PRDM4 and NFIX knockdown in ATRX-mutant sarcoma lines resulted in reduced proliferation and invasion suggesting epistatic relationship. Consistent with the known functional relationship between PRMD4 and YAP1, we observed that ATRX/TP53 KO cells were more sensitive to the TEAD inhibitor VT103 compared to TP53 KO and ATRX WT controls. Overall, our results identify ATRX loss as a prognostic factor of worse outcomes, implicate the ATRX-PRDM4-YAP1 axis as a novel underlying mechanism, and suggest use of TEAD inhibition as a potential therapeutic strategy for ATRX-deficient sarcomas. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=45 SRC="FIGDIR/small/689992v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@a759ecorg.highwire.dtl.DTLVardef@100c580org.highwire.dtl.DTLVardef@1a675c9org.highwire.dtl.DTLVardef@17f1f91_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Denu, R. A., Singh, A. K., Jiang, Y., Zheng, Z., Ingram, D. R., Wani, K. M., Lazcano, R., Ginn, M. P., Anand, K., Singh, B. K., Ballard, J. C., Kochat, V., Chatterjee, B., Padron, W., Landers, S. M., Bhalla, A., Multani, A., Dharmaiah, S., Malgulwar, P. B., Cai, Y., Lin, H., Huse, J. T., Ying, H. T., Keung, E. Z., Wang, W.-L., Conley, A. P., Patel, S., Somaiah, N., Farooqi, A., Lazar, A. J., Nassif Haddad, E. F., Torres, K. E., Rai, K.. 2025-11-26. ATRX Loss Predicts Poor Outcomes and Reveals a Therapeutic Vulnerability to TEAD Inhibition in Soft Tissue Sarcomas. https://doi.org/10.1101/2025.11.23.689992

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