Abstract 101: Adaptive feedback reactivates MAPK signaling in KRAS-mutant cancers with inhibition of MEK, but not ERK

Activating mutations in the KRAS oncogene occur in about 40% of colorectal cancers (CRCs) and over 90% of pancreatic ductal adenocarcinomas (PDACs). Since development of small molecules capable of inhibiting KRAS directly has proven difficult, alternative strategies have instead focused on inhibiting downstream effector pathways, such as the MAPK pathway. However, inhibition of the MAPK pathway alone with MEK inhibitors, such as selumetinib and trametinib, produces only cytostatic effects and is insufficient to kill KRAS-mutant cancer cells.

We hypothesized that inhibition of an additional kinase during MEK inhibitor treatment could improve response. We performed a kinase-targeting shRNA screen to find kinases whose knockdown would cooperate with trametinib in KRAS-mutant CRC and PDAC cell lines. The kinases found in this screen represent potential therapeutic targets to inhibit in combination with MEK.

Interestingly, despite using a very high concentration of trametinib in the screen to enrich for hits outside of the MAPK pathway, the most highly ranked kinases in the screen were members of the MAPK pathway, including ARAF, BRAF, CRAF, and MEK1. This suggests that even at high concentration, trametinib produces suboptimal MAPK inhibition. Indeed, we found that while MEK inhibitors produce robust inhibition of MAPK signaling initially, pathway reactivation was observed by 48-96 hours despite regular replenishment of drug. This feedback reactivation was accompanied by marked increases in active CRAF and phosphorylated MEK. In fact, experimental approaches that artificially increased upstream signaling flux through the MAPK pathway led to a >10-fold reduction in the ability of MEK inhibitors to inhibit the MAPK pathway.

Remarkably, despite triggering the same degree of adaptive upstream MAPK signaling as seen with MEK inhibitor, we found that ERK inhibitors were able to maintain MAPK pathway suppression. Importantly, these differences in MAPK pathway suppression amount to differences in cell viability. Over four weeks, ERK inhibitor treatment reduces the outgrowth of KRAS-mutant cell lines compared to those treated with MEK inhibitors. Additionally, as these inhibitors are not used as monotherapies, replacement of trametinib with an ERK inhibitor in therapeutically relevant combination treatments improved cell responses over four weeks.

Despite the feedback reactivation of the MAPK pathway, we find that ERK inhibitors are less sensitive to this signaling than MEK inhibitors, and can effectively maintain suppression of MAPK signaling. The findings of our screen demonstrate that MAPK pathway targeting is key to successful treatment of KRAS-mutant cancers, and that ERK inhibition provides greater opportunity for inactivating MAPK. Further exploration into the mechanisms of pathway feedback will be necessary to developing valuable clinical combinations for KRAS-mutant cancers.

Citation Format: Leanne G. Ahronian, Sandra Misale, Jason T. Godfrey, Koki Nishimura, Lifeng Chen, Jeffrey A. Engelman, Ryan B. Corcoran. Adaptive feedback reactivates MAPK signaling in KRAS-mutant cancers with inhibition of MEK, but not ERK [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 101. doi:10.1158/1538-7445.AM2017-101

Molecular Landscape of Acquired Resistance to Targeted Therapy Combinations in BRAF-Mutant Colorectal Cancer

Although recent clinical trials of BRAF inhibitor combinations have demonstrated improved efficacy in BRAF-mutant colorectal cancer, emergence of acquired resistance limits clinical benefit. Here, we undertook a comprehensive effort to define mechanisms underlying drug resistance with the goal of guiding development of therapeutic strategies to overcome this limitation. We generated a broad panel of BRAF-mutant resistant cell line models across seven different clinically relevant drug combinations. Combinatorial drug treatments were able to abrogate ERK1/2 phosphorylation in parental-sensitive cells, but not in their resistant counterparts, indicating that resistant cells escaped drug treatments through one or more mechanisms leading to biochemical reactivation of the MAPK signaling pathway. Genotyping of resistant cells identified gene amplification of EGFR, KRAS, and mutant BRAF, as well as acquired mutations in KRAS, EGFR, and MAP2K1 These mechanisms were clinically relevant, as we identified emergence of a KRAS G12C mutation and increase of mutant BRAF V600E allele frequency in the circulating tumor DNA of a patient at relapse from combined treatment with BRAF and MEK inhibitors. To identify therapeutic combinations capable of overcoming drug resistance, we performed a systematic assessment of candidate therapies across the panel of resistant cell lines. Independent of the molecular alteration acquired upon drug pressure, most resistant cells retained sensitivity to vertical MAPK pathway suppression when combinations of ERK, BRAF, and EGFR inhibitors were applied. These therapeutic combinations represent promising strategies for future clinical trials in BRAF-mutant colorectal cancer. Cancer Res; 76(15); 4504-15. ©2016 AACR.

Molecular Heterogeneity and Receptor Coamplification Drive Resistance to Targeted Therapy in MET-Amplified Esophagogastric Cancer

MET inhibition is effective in some patients with MET-amplified esophagogastric cancer (EGC), but understanding acquired and de novo resistance mechanisms will be critical to improving therapy. We identified KRAS mutation as a novel cause of acquired resistance in a patient after a 2-year response to a MET inhibitor. We also observed that 40% to 50% of patients with MET-amplified EGC harbor coamplification of HER2 and/or EGFR concurrently in the same tumor cells, which can drive de novo resistance. One patient with concurrent MET and HER2 amplification was refractory to HER2 blockade, but responded to combined MET/HER2 inhibition. We also found striking heterogeneity in MET amplification between distinct metastatic lesions and primary tumors in individual patients with EGC. In these patients, MET inhibition led to mixed responses and disease progression through outgrowth of non-MET-amplified clones, which could be monitored in circulating tumor DNA. Thus, receptor coamplification and molecular heterogeneity may be key drivers of clinical resistance in MET-amplified EGC.

SIGNIFICANCE

Coamplification of driver oncogenes occurs frequently in EGC and can drive therapeutic resistance, supporting a role for comprehensive molecular analysis prior to targeted therapy. EGCs can also exhibit extensive heterogeneity in gene amplification between distinct tumor lesions within the same patient, suggesting that molecular profiling of a single-lesion biopsy may be insufficient to guide targeted therapy selection.

Abstract LB-055: Clinical acquired resistance to RAF inhibitor combinations in BRAF-mutant colorectal cancer through MAPK pathway alterations

BRAF V600E mutations occur in ∼10% of colorectal cancer (CRC), and are associated with poor prognosis. RAF inhibition alone has not been an effective treatment in BRAF-mutant (BRAFm) CRC patients, with response rates of only 5%, due to persistence of MAPK signaling. Combined RAF/EGFR, RAF/MEK, or RAF/MEK/EGFR inhibitors have produced improved efficacy in BRAFm CRC patients, yet ultimately resistance develops after an initial treatment response. Understanding the mechanisms of clinical acquired resistance that arise to RAF inhibitor combinations in BRAFm CRC patients may lead to valuable opportunities to overcome resistance and prolong clinical response.

We sought to identify clinically relevant mechanisms of acquired resistance to RAF inhibitor combinations by obtaining tumor biopsies from BRAFm CRC patients upon disease progression, after initial response to RAF/EGFR or RAF/MEK inhibitor combinations. Matched pre-treatment, post-progression, and normal DNA were analyzed by whole exome sequencing (WES) and RNA-seq.

In one BRAFm CRC patient with prolonged stable disease on a RAF/EGFR combination, WES identified KRAS amplification in a progressing lesion. FISH confirmed the presence of KRAS amplification in the post-progression biopsy, and RNA-seq revealed KRAS transcript overexpression. Interestingly, in resistant clones generated from BRAFm CRC cell lines selected with either RAF/EGFR or RAF/MEK inhibitors, KRAS exon 2 mutations were identified. Either KRAS amplification or KRAS mutation led to sustained MAPK pathway activity and cross-resistance to either RAF/EGFR or RAF/MEK inhibitor combinations.

In a second patient with a minor response to a RAF/EGFR inhibitor combination, BRAF amplification was identified in a progressing lesion, which was confirmed by FISH and was not present in a pre-treatment biopsy of the same lesion. BRAF amplification led to cross-resistance to the BRAF/MEK inhibitor combination.

In a third patient with a minor response to a RAF/MEK inhibitor combination, WES identified the presence of an ARAF Q489L mutation and a MEK1 F53L mutation in a single progressing lesion, suggesting possible intra-lesional heterogeneity of acquired resistance mechanisms. However, utilizing a cell line derived from the patient's post-progression biopsy, we found that 30 out of 30 single-cell clones harbored both the ARAF and MEK1 mutations, and that MEK1 F53L seemed to function as the primary driver of acquired resistance in these resistant cells. MEK1 F53L expression markedly abrogated the ability of RAF/MEK and RAF/EGFR inhibitor combinations to suppress MAPK signaling.

Despite developing resistance to upstream MAPK pathway inhibitors, we found that each of the acquired resistance mechanisms we detected remained sensitive to ERK inhibition, which could effectively suppress MAPK signaling. Our findings demonstrate the central importance of MAPK pathway activity in BRAFm CRC, and highlight the critical need for MAPK pathway inhibition in the prevention of disease progression. Additionally, our work indicates ERK inhibitors may be valuable additions to future therapeutic combinations for BRAFm CRC patients. Further efforts to understand acquired resistance mechanisms will be vital to developing novel therapeutic strategies to overcome resistance and extend clinical benefit in this lethal CRC subtype.

Citation Format: Leanne G. Ahronian, Erin M. Sennott, Eliezer M. Van Allen, Nikhil Wagle, Eunice L. Kwak, Jason E. Faris, Jason T. Godfrey, Koki Nishimura, Kerry D. Lynch, Craig H. Mermel, Elizabeth L. Lockerman, Anuj Kalsy, Joseph M. Gurski, Samira Bahl, Kristin Anderka, Lisa M. Green, Niall J. Lennon, Tiffany G. Huynh, Mari Mino-Kenudson, Gad Getz, Dora Dias-Santagata, A. John Iafrate, Jeffrey A. Engelman, Levi A. Garraway, Ryan B. Corcoran. Clinical acquired resistance to RAF inhibitor combinations in BRAF-mutant colorectal cancer through MAPK pathway alterations. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-055. doi:10.1158/1538-7445.AM2015-LB-055

Clinical Acquired Resistance to RAF Inhibitor Combinations in BRAF-Mutant Colorectal Cancer through MAPK Pathway Alterations

BRAF mutations occur in approximately 10% of colorectal cancers. Although RAF inhibitor monotherapy is highly effective in BRAF-mutant melanoma, response rates in BRAF-mutant colorectal cancer are poor. Recent clinical trials of combined RAF/EGFR or RAF/MEK inhibition have produced improved efficacy, but patients ultimately develop resistance. To identify molecular alterations driving clinical acquired resistance, we performed whole-exome sequencing on paired pretreatment and postprogression tumor biopsies from patients with BRAF-mutant colorectal cancer treated with RAF inhibitor combinations. We identified alterations in MAPK pathway genes in resistant tumors not present in matched pretreatment tumors, including KRAS amplification, BRAF amplification, and a MEK1 mutation. These alterations conferred resistance to RAF/EGFR or RAF/MEK combinations through sustained MAPK pathway activity, but an ERK inhibitor could suppress MAPK activity and overcome resistance. Identification of MAPK pathway reactivating alterations upon clinical acquired resistance underscores the MAPK pathway as a critical target in BRAF-mutant colorectal cancer and suggests therapeutic options to overcome resistance.

SIGNIFICANCE

RAF inhibitor combinations represent promising approaches in clinical development for BRAF-mutant colorectal cancer. Initial characterization of clinical acquired resistance mechanisms to these regimens identified several MAPK pathway alterations driving resistance by reactivating MAPK signaling, highlighting the critical dependence of BRAF-mutant colorectal cancers on MAPK signaling and offering potential strategies to overcome resistance.

TORC1 suppression predicts responsiveness to RAF and MEK inhibition in BRAF-mutant melanoma

RAF and MEK (mitogen-activated or extracellular signal-regulated protein kinase kinase) inhibitors are effective in treating patients with BRAF-mutant melanoma. However, most responses are partial and short-lived, and many patients fail to respond at all. We found that suppression of TORC1 activity in response to RAF or MEK inhibitors, as measured by decreased phosphorylation of ribosomal protein S6 (P-S6), effectively predicted induction of cell death by the inhibitor in BRAF-mutant melanoma cell lines. In resistant melanomas, TORC1 activity was maintained after treatment with RAF or MEK inhibitors, in some cases despite robust suppression of mitogen-activated protein kinase (MAPK) signaling. In in vivo mouse models, suppression of TORC1 after MAPK inhibition was necessary for induction of apoptosis and tumor response. Finally, in paired biopsies obtained from patients with BRAF-mutant melanoma before treatment and after initiation of RAF inhibitor therapy, P-S6 suppression predicted significantly improved progression-free survival. Such a change in P-S6 could be readily monitored in real time by serial fine-needle aspiration biopsies, making quantitation of P-S6 a valuable biomarker to guide treatment in BRAF-mutant melanoma.

Inhibition of KRAS-driven tumorigenicity by interruption of an autocrine cytokine circuit

Although the roles of mitogen-activated protein kinase (MAPK) and phosphoinositide 3-kinase (PI3K) signaling in KRAS-driven tumorigenesis are well established, KRAS activates additional pathways required for tumor maintenance, the inhibition of which are likely to be necessary for effective KRAS-directed therapy. Here, we show that the IκB kinase (IKK)-related kinases Tank-binding kinase-1 (TBK1) and IKKε promote KRAS-driven tumorigenesis by regulating autocrine CCL5 and interleukin (IL)-6 and identify CYT387 as a potent JAK/TBK1/IKKε inhibitor. CYT387 treatment ablates RAS-associated cytokine signaling and impairs Kras-driven murine lung cancer growth. Combined CYT387 treatment and MAPK pathway inhibition induces regression of aggressive murine lung adenocarcinomas driven by Kras mutation and p53 loss. These observations reveal that TBK1/IKKε promote tumor survival by activating CCL5 and IL-6 and identify concurrent inhibition of TBK1/IKKε, Janus-activated kinase (JAK), and MEK signaling as an effective approach to inhibit the actions of oncogenic KRAS.

Abstract C137: Rapid assessment of TORC1 suppression as a functional biomarker predicting responsiveness to RAF and MEK inhibitors in BRAF-mutant melanoma patients

The clinical development of selective RAF and MEK inhibitors has transformed the treatment of the ∼50% of melanoma patients whose tumors harbor BRAF mutations. However, a substantial percentage of these patients fail to respond to therapy, and most responses are partial and short-lived. Although multiple mechanisms of resistance have been identified in BRAF-mutant melanoma, no clinically useful biomarkers have been established to predict which patients are most likely to demonstrate sensitivity or resistance to RAF or MEK inhibitors. We found that suppression of TORC1 activity in response to RAF or MEK inhibitors, as measured by decreased phosphorylation of ribosomal protein-S6 (P-S6), was a functional biomarker that effectively predicted sensitivity in BRAF-mutant melanoma cell lines in vitro and in mouse tumor xenografts. In sensitive melanomas, TORC1 and P-S6 were suppressed in response to RAF or MEK inhibitors, but in resistant melanomas, TORC1 activity was maintained, in some cases despite robust suppression of MAPK signaling by these inhibitors. In mouse models, suppression of TORC1 after MAPK inhibition was necessary for induction of apoptosis and tumor response in vivo. Notably, in paired biopsies obtained from patients with BRAF-mutant melanoma before treatment and after initiation of RAF inhibitor therapy, P-S6 suppression was associated with significantly improved progression-free survival [HR 0.19, 95% CI 0.01-0.84, p=0.03]. Finally, we found that changes in P-S6 in patients’ tumor cells could be readily monitored in real-time by multiplexed, quantitative immunofluorescence microscopy of serial fine-needle aspiration biopsies obtained from patients before and during the first 2 weeks of RAF inhibitor therapy. This approach provides a minimally-invasive means of rapidly monitoring the efficacy of treatment, before changes in tumor volume are apparent by traditional radiographic imaging. Together, these results establish suppression of P-S6 after initiation of RAF inhibitor therapy as a robust potential functional biomarker to guide the treatment of patients with BRAF-mutant melanoma, and present a powerful methodology for monitoring changes in potentially any signaling pathway in response to targeted therapies in patients.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C137.

Citation Format: Ryan B. Corcoran, S. Michael Rothenberg, Aaron N. Hata, Anthony C. Faber, Adriano Piris, Rosalynn M. Nazarian, Ronald D. Brown, Jason T. Godfrey, Daniel Winokur, John Walsh, Mari Mino-Kenudson, Shyamala Maheswaran, Jeffrey Settleman, Jennifer A. Wargo, Keith T. Flaherty, Daniel A. Haber, Jeffrey A. Engelman. Rapid assessment of TORC1 suppression as a functional biomarker predicting responsiveness to RAF and MEK inhibitors in BRAF-mutant melanoma patients. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr C137.

Abstract PR09: Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS-mutant cancer models

Although KRAS is the most commonly mutated oncogene in human cancer, KRAS has proven difficult to target pharmacologically, and no effective therapies exist for KRAS-mutant cancers. Recently, there has been evidence that targeted therapy combinations inhibiting multiple downstream effectors of KRAS may be a promising approach for KRAS-mutant cancers. We developed a pooled shRNA-drug screen strategy to identify genes that, when inhibited, cooperate with MEK inhibitors to kill KRAS-mutant cancer cells. The anti-apoptotic BH3 family gene BCL-XL emerged as a top hit through this approach. ABT-263 (navitoclax), a chemical inhibitor that blocks the ability of BCL-XL to bind and inhibit pro-apoptotic proteins, in combination with a MEK inhibitor led to dramatic apoptosis in the vast majority of KRAS-mutant cell lines tested from different tissue types. Mechanistic studies revealed that MEK inhibition led to marked induction of the pro-apoptotic protein BIM in KRAS-mutant cancer cells, but that BIM remained bound and inhibited by BCL-XL. Pharmacologic inhibition of BCL-XL with ABT-263 disrupted this inhibitory complex, allowing BIM to trigger apoptosis. Epithelial differentiation and E-cadherin expression correlated with increased sensitivity to this inhibitor combination across a panel of 30 KRAS-mutant cell lines, while epithelial-to-mesenchymal transition (EMT) correlated with resistance. This combination also caused marked in vivo tumor regressions in three independent KRAS-mutant xenografts and in established lung tumors in two genetically-engineered KRAS-driven lung cancer mouse models. These data support combined BCL-XL/MEK inhibition as a promising therapeutic approach for evaluation in future clinical trials for patients with KRAS-mutant cancers.

This abstract is also presented as Poster B19.

Citation Format: Ryan B. Corcoran, Katherine A. Cheng, Aaron N. Hata, Anthony C. Faber, Hiromichi Ebi, Erin M. Coffee, Patricia Greninger, Ronald D. Brown, Jason T. Godfrey, Travis J. Cohoon, Youngchul Song, Eugene Lifshits, Toshi Shioda, Dora Dias-Santagata, Anurag Singh, Jeffrey Settleman, Cyril H. Benes, Mari Mino-Kenudson, Kwok-Kin Wong, Jeffrey A. Engelman. Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS-mutant cancer models. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Synthetic Lethal Approaches to Cancer Vulnerabilities; May 17-20, 2013; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(5 Suppl):Abstract nr PR09.

Abstract 4568: Rapid assessment of TORC1 suppression predicts responsiveness to RAF and MEK inhibition in BRAF mutant melanoma

The clinical development and potent efficacy of selective RAF and MEK inhibitors has transformed the treatment of the ∼50% of melanoma patients whose tumors harbor BRAF mutations. However, a substantial percentage of these patients fail to respond to therapy, and all who respond eventually develop resistance. We found that suppression of TORC1 activity, as measured by decreases in ribosomal protein S6 phosphorylation (P-S6) in response to RAF or MEK inhibitors, was a highly effective predictor of sensitivity in BRAF mutant melanoma cell lines in vitro and in mouse xenografts. TORC1 and P-S6 were suppressed in response to RAF or MEK inhibitors in sensitive but not resistant melanoma cells, despite robust suppression of the MAPK pathway by these inhibitors. Notably, suppression of P-S6 levels, as assessed by immunohistochemistry in paired biopsies obtained from BRAF mutant melanoma patients before and during treatment, was associated with significantly improved progression-free survival. Finally, we show that changes in P-S6 levels specifically in tumor cells can be readily monitored by multiplexed, quantitative immunofluorescence microscopy of fine needle aspiration biopsies obtained from patients before and during the first two weeks of BRAF inhibitor therapy. This provides a minimally invasive means for monitoring the efficacy of treatment in real time, before changes in tumor volume are apparent on traditional radiographs. Together, these results establish changes in P-S6 levels with therapy as a robust biomarker to guide the treatment of patients with BRAF mutant melanoma, and present a powerful methodology for monitoring changes in potentially any signaling pathway in response to therapy in patients.

Citation Format: Ryan B. Corcoran, Stephen M. Rothenberg, Aaron N. Hata, Anthony C. Faber, Daniel Winokur, Adriano Piris, Rosalynn M. Nazarian, Ronald D. Brown, Jason T. Godfrey, Mari Mino-Kenudson, Jeffrey Settleman, Jennifer A. Wargo, Keith T. Flaherty, Daniel A. Haber, Jeffrey A. Engelman. Rapid assessment of TORC1 suppression predicts responsiveness to RAF and MEK inhibition in BRAF mutant melanoma. [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 4568. doi:10.1158/1538-7445.AM2013-4568

Synthetic lethal interaction of combined BCL-XL and MEK inhibition promotes tumor regressions in KRAS mutant cancer models

KRAS is the most commonly mutated oncogene, yet no effective targeted therapies exist for KRAS mutant cancers. We developed a pooled shRNA-drug screen strategy to identify genes that, when inhibited, cooperate with MEK inhibitors to effectively treat KRAS mutant cancer cells. The anti-apoptotic BH3 family gene BCL-XL emerged as a top hit through this approach. ABT-263 (navitoclax), a chemical inhibitor that blocks the ability of BCL-XL to bind and inhibit pro-apoptotic proteins, in combination with a MEK inhibitor led to dramatic apoptosis in many KRAS mutant cell lines from different tissue types. This combination caused marked in vivo tumor regressions in KRAS mutant xenografts and in a genetically engineered KRAS-driven lung cancer mouse model, supporting combined BCL-XL/MEK inhibition as a potential therapeutic approach for KRAS mutant cancers.