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PBRM1 is an accessory subunit of the PBAF subclass of the SWI/SNF chromatin remodeler and the inactivation of PBRM1 is the second most frequent mutational event in kidney tumorigenesis. However, the impact of PBRM1 loss on chromatin remodeling, especially pertaining to kidney tumorigenesis, has not been examined previously. Here we show that in VHL-deficient ccRCC tumors, PBRM1 deficiency results in altered PBAF complexes that retain the association between SMARCA4 and ARID2 but disengage BRD7 from SMARCA4. The PBRM1-deficient PBAF complexes redistribute from promoter proximal regions to distal enhancer regions containing motifs of pro-tumorigenic factors including NF-κB. Subsequently, PBRM1-deficient cells display heightened NF-κB activity across multiple cell models. The ATPase function of SMARCA4 maintains chromatin occupancy of both pre-existing and newly acquired RELA specific to PBRM1 loss, and activates downstream target gene expression. Proteasome inhibitor bortezomib reverses NF-κB activation by reducing RELA occupancy and delays growth of PBRM1-deficient tumors. In conclusion, PBRM1 safeguards the chromatin by repressing aberrant liberation of pro-tumorigenic NF-κB target genes by residual PBRM1-deficient PBAF complexes. Citation Format: Xiaosai Yao, Jing Han Hong, Amrita Nargund, Michelle Shu Wen Ng, Hong Lee Heng, Zhimei Li, Peiyong Guan, Masahiro Sugiura, Pek Lim Chu, Loo Chien Wang, Xiaofen Ye, Robert Yauch, Kenneth Tou-En Chang, Radoslaw M. Sobota, Patrick Tan, Bin Tean Teh. PBRM1-deficient PBAF complexes target de novo genomic loci to activate NF-κB pathway in clear cell renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1494.

Colorectal cancer remains a major unmet medical need, prompting large-scale genomics efforts in the field to identify molecular drivers for which targeted therapies might be developed. We previously reported the identification of recurrent translocations in R-spondin genes present in a subset of colorectal tumours. Here we show that targeting RSPO3 in PTPRK-RSPO3-fusion-positive human tumour xenografts inhibits tumour growth and promotes differentiation. Notably, genes expressed in the stem-cell compartment of the intestine were among those most sensitive to anti-RSPO3 treatment. This observation, combined with functional assays, suggests that a stem-cell compartment drives PTPRK-RSPO3 colorectal tumour growth and indicates that the therapeutic targeting of stem-cell properties within tumours may be a clinically relevant approach for the treatment of colorectal tumours.

The mammalian SWI/SNF complex catalyzes the remodeling of chromatin through the helicase activity of two mutually-exclusive, paralogous subunits, BRG1 and BRM. BRG1 is frequently mutated in cancer and its inactivation results in a cellular dependence on BRM. Despite the attractiveness of BRM as a synthetic lethal therapeutic target, the selective inhibition of BRM represents a considerable challenge due to the high degree of homology between BRM and BRG1. Furthermore, published data indicate that achieving such selectivity is likely essential to afford an acceptable therapeutic index. We sought to mimic the synthetic lethality observed in BRG1-mutant cancers by identifying proteolysis-targeting chimera (PROTAC®) molecules capable of selectively degrading BRM via trimeric complex formation with the von Hippel-Lindau (VHL) E3 ligase. In this disclosure, we report our initial discovery of potent and selective chimeric BRM-degrader molecules which exhibit BRM DC50 values 25. Importantly, selective BRM degradation can be achieved in the absence of selective PROTAC® binding (BRG1/BRM Kd ratios Citation Format: Michael Berlin, Jennifer Cantley, Jing Wang, Mark Bookbinder, Gregory Cadelina, Emily Chan, Huifen Chen, Xin Chen, Kim Davenport, Tharu Fernando, Debbie Gordon, Brian Hamman, Roy Haskell, Alexey Ishchenko, Donald S. Kirkpatrick, Jonathan Maher, Mark Merchant, John Moffat, Alicia Morgan, An Nguyen, Jennifer Pizzano, Connor Quinn, Christopher M. Rose, Emma Rousseau, Vijay Sethuraman, Leanna Staben, Catherine Wilson, Xiaofen Ye, Fabio Broccatelli, Robert Yauch, Peter S. Dragovich. Selective, chemically-induced degradation of BRM (SMARCA2) enables in vivo efficacy in BRG1 (SMARCA4)-deficient xenograft tumor models [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5687.

Subunits of the SWI/SNF chromatin remodeling complex are frequently mutated in human cancers leading to epigenetic dependencies that are therapeutically targetable. The dependency on the polycomb repressive complex (PRC2) and EZH2 represents one such vulnerability in tumors with mutations in the SWI/SNF complex subunit, SNF5; however, whether this vulnerability extends to other SWI/SNF subunit mutations is not well understood. Here we show that a subset of cancers harboring mutations in the SWI/SNF ATPase, SMARCA4, is sensitive to EZH2 inhibition. EZH2 inhibition results in a heterogenous phenotypic response characterized by senescence and/or apoptosis in different models, and also leads to tumor growth inhibition in vivo. Lower expression of the SMARCA2 paralog was associated with cellular sensitivity to EZH2 inhibition in SMARCA4 mutant cancer models, independent of tissue derivation. SMARCA2 is suppressed by PRC2 in sensitive models, and induced SMARCA2 expression can compensate for SMARCA4 and antagonize PRC2 targets. The induction of SMARCA2 in response to EZH2 inhibition is required for apoptosis, but not for growth arrest, through a mechanism involving the derepression of the lysomal protease cathepsin B. Expression of SMARCA2 also delineates EZH2 inhibitor sensitivity for other SWI/SNF complex subunit mutant tumors, including SNF5 and ARID1A mutant cancers. Our data support monitoring SMARCA2 expression as a predictive biomarker for EZH2-targeted therapies in the context of SWI/SNF mutant cancers.

Molecularly targeted drug therapies have revolutionized cancer treatment; however, resistance remains a major limitation to their overall efficacy. Epithelial-to-mesenchymal transition (EMT) has been linked to acquired resistance to tyrosine kinase inhibitors (TKI), independent of mutational resistance mechanisms. AXL is a receptor tyrosine kinase associated with EMT that has been implicated in drug resistance and has emerged as a candidate therapeutic target. Across 643 human cancer cell lines that were analyzed, elevated AXL was strongly associated with a mesenchymal phenotype, particularly in triple-negative breast cancer and non–small cell lung cancer. In an unbiased screen of small-molecule inhibitors of cancer-relevant processes, we discovered that AXL inhibition was specifically synergistic with antimitotic agents in killing cancer cells that had undergone EMT and demonstrated associated TKI resistance. However, we did not find that AXL inhibition alone could overcome acquired resistance to EGFR TKIs in the EMT setting, as previously reported. These findings reveal a novel cotreatment strategy for tumors displaying mesenchymal features that otherwise render them treatment refractory. Cancer Res; 74(20); 5878–90. ©2014 AACR.

A synthetic lethality caused by EZH2 inhibition in the context of SNF5 mutations is supported by both preclinical and recent clinical data, however the extent of the synthetic lethal relationship in the context of other SWI/SNF subunit mutations is not well understood. We determined that a subset of SMARCA4 mutant cancer models are sensitive to EZH2 inhibition. EZH2 inhibition resulted in a heterogenous phenotypic response characterized by senescence and/or apoptosis amongst models, and further lead to tumor growth inhibition in vivo. The differential sensitivity to EZH2 inhibition was not caused by a differential pharmacodynamic effect of the drug, nor differences in basal histone methylation or PRC2 subunit levels. However, expression of the SWI/SNF subunit, SMARCA2, delineated sensitivity amongst SMARCA4 mutant models tested. Expression of SMARCA2 further delineated sensitivity amongst other SWI/SNF mutant models tested, including SNF5 and ARID1A mutants. We determined that SMARCA2 is under PRC2 mediated suppression and the derepression of SMARCA2 was necessary for apoptosis, but not senescence, in response to EZH2 inhibition. SMARCA2 has been shown to be concurrently lost in a high percentage of SNF5 mutant malignant rhabdoid tumors and SMARCA4 mutant SCCOHT tumors, however we determined that ≈15% of SMARCA4 mutant NSCLCs concurrently lose SMARCA2. Our data supports monitoring SMARCA2 expression as a predictive biomarker for EZH2-targeted therapies that are currently being developed in the context of SWI/SNF mutant cancers. Citation Format: Thomas Januario, Xiaofen Ye, Russell Bainer, Bruno Alicke, Margaret Solon, Benjamin Haley, Zora Modrusan, Stephen Gould, Hartmut Koeppen, Robert L. Yauch. PRC2 mediated repression of SMARCA2 predicts for EZH2 inhibitor activity in tumors with SWI/SNF mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2790. doi:10.1158/1538-7445.AM2017-2790

Axl is expressed in various types of cancer and is involved in multiple processes of tumorigenesis, including promoting tumor cell growth, migration, invasion, metastasis as well as angiogenesis. To evaluate further the mechanisms involved in the expression/activation of Axl in various aspects of tumorigenesis, especially its roles in modulating tumor stromal functions, we have developed a phage-derived mAb (YW327.6S2) that recognizes both human and murine Axl. YW327.6S2 binds to both human and murine Axl with high affinity. It blocks the ligand Gas6 binding to the receptor, downregulates receptor expression, inhibits receptor activation and downstream signaling. In A549 non-small-cell lung cancer (NSCLC) and MDA-MB-231 breast cancer models, YW327.6S2 attenuates xenograft tumor growth and potentiates the effect of anti-VEGF treatment. In NSCLC models, YW327.6S2 also enhances the effect of erlotinib and chemotherapy in reducing tumor growth. Furthermore, YW327.6S2 reduces the metastasis of MDA-MB-231 breast cancer cells to distant organs. YW327.6S2 induces tumor cell apoptosis in NSCLC, reduces tumor-associated vascular density and inhibits the secretion of inflammatory cytokines and chemokines from tumor-associated macrophages in the breast cancer model. In conclusion, anti-Axl mAb can enhance the therapeutic efficacy of anti-VEGF, EGFR small-molecule inhibitors as well as chemotherapy. Axl mAb affects not only tumor cells but also tumor stroma through its modulation of tumor-associated vasculature and immune cell functions.

Molecularly-targeted drug therapies have revolutionized cancer treatment, however, resistance remains a major limitation to their overall efficacy. Epithelial to mesenchymal transition (EMT) has been linked to acquired resistance to tyrosine kinase inhibitors (TKIs), independent of mutational resistance mechanisms. AXL is a receptor tyrosine kinase (RTK) associated with EMT that has been implicated in drug resistance, and has emerged as a candidate therapeutic target. Across 643 human cancer cell lines that were analyzed, we found that elevated AXL was strongly associated with a mesenchymal phenotype, particularly in triple negative breast cancer and non-small cell lung cancer. Here we experimentally established a model system to induced EMT by exposure to TGF-β and we observed that the resulting TGF-β-induced mesenchymal cells exhibit substantially increased AXL expression, become relatively drug-resistant to their appropriate TKI and cross-resistant to a variety of anti-cancer agents. We tested the ability of AXL inhibition to restore erlotinib sensitivity, in both a TGF-β-induced resistance model and in two different models of acquired resistance to erlotinib. Here, our observations do not support the previously reported role for AXL inhibition in overcoming acquired resistance to TKIs in the EMT context. However, in an unbiased screen of small molecule inhibitors of cancer-relevant processes, we discovered that AXL inhibition was specifically synergistic with anti-mitotic agents in killing cancer cells that had undergone EMT and demonstrated associated TKI resistance. Inhibition of AXL in combination with anti-mitotic agents enhances death in mitosis by promoting cells to enter mitosis through the down-regulation of CDK1, resulting in G2M cell cycle arrest. In summary, our findings highlight the utility of combination drug screening to reveal novel potentially useful anti-cancer drug combinations to improve clinical responses. While we did not identify a functional role for AXL in the context of acquired resistance to TKI therapies, we did observe that AXL inhibition may be an effective therapy in the context of mesenchymal tumors, specifically when used in combination with anti-mitotic agents. These findings reveal a novel therapeutic strategy for tumors displaying mesenchymal features that otherwise render them treatment-refractory. Citation Format: Catherine Wilson, Thinh Pham, Xiaofen Ye, Eva Lin, Sara Chan, Erin McNamara, Richard M. Neve, Lisa Belmont, Hartmut Koeppen, Robert L. Yauch, Avi Ashkenazi, Jeff Settleman. AXL tyrosine kinase inhibition selectively sensitizes mesenchymal cancer cells to antimitotic agents. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 693. doi:10.1158/1538-7445.AM2014-693

SummaryInduction of procoagulant factors in malignant cells is considered to be the major cause of coagulation disorders in cancer. Thrombomodulin (TM), a negative regulator of coagulation was also found to be expressed in cancer cells. We report here evidence for another anticoagulant, the endothelial cell protein C receptor (EPCR), in cancer cells. EPCR was detected in several cell lines derived from various types of cancer. Significant levels of protein C (PC) activation were detected only with cell lines expressed both EPCR and TM. Anti-EPCR monoclonal antibodies (mAbs) specifically inhibited the activation. Thus, EPCR function appears to be important for PC activation by cancer cells. In addition, we detected EPCR expression in tumor cells from breast cancer patients, with an extremely high frequency. EPCR function may contribute to progression or pathogenesis of some types of cancer, and may explain the complexity of coagulopathy in cancer patients.

Treatment of NSCLC patients harboring activating EGFR mutations with EGFR TKIs results in anti-tumor responses to therapy, however patients ultimately progress on therapy due to the acquisition of drug resistance. Known mechanisms of resistance include secondary mutations in the EGFR gene (EGFRT790M) or MET gene amplification, however the underlying mechanism of resistance remains to be elucidated in ∼40-45% of cases. Previous studies provide evidence for an epithelial-to-mesenchymal transition (EMT) in a subset of cases that is not associated with the known mechanisms of resistance. In this study, we identify 2 models of acquired resistance to erlotinib that are associated with an EMT phenotype and a dependence on autocrine FGF-FGFR signaling for resistance. Evidence for FGFR pathway activation in the erlotinib-resistant cell population included an increase in FGF2, FGFR1 and phospho-FRS2. Inhibition of FGFR signaling using a small molecule kinase inhibitor or FGFR1-Fc neutralization of FGFR1 ligands re-sensitized resistant cells to erlotinib. Re-sensitization was accompanied by an inhibition of downstream signaling. In contrast, inhibition of AXL, a kinase that has recently been identified as an EMT-associated driver of erlotinib resistance in some pre-clinical models, failed to re-sensitize erlotinib-resistant cells. Our findings are consistent with autocrine FGFR pathway activation, as FGF ligand neutralization in the absence of an exogenous source of ligand can re-sensitize cells to erlotinib. Finally, FGFR pathway inhibition suppressed the development of resistance to erlotinib in sensitive parental cells. These data indicate that FGFR activation could potentially serve as a mechanism of acquired resistance to erlotinib in cases associated with an EMT and suggest that combined inhibition of EGFR and FGFR signaling could be beneficial in treating such cases. Citation Format: Xiaofen Ye, Peng Yue, Rajesh Patel, Zora Modrusan, Jeff Settleman, Avi Ashkenazi, Robert L. Yauch. Activation of FGFR signaling as a mechanism of acquired resistance to erlotinib in EGFR-mutant lung cancer associated with an EMT. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4463. doi:10.1158/1538-7445.AM2013-4463