PBRM1 loss is associated with increased sensitivity to MCL1 and CDK9 inhibition in clear cell renal cancer

MCL1 is a member of the BCL2 family of apoptosis regulators, which play a critical role in promoting cancer survival and drug resistance. We previously described PRT1419, a potent, MCL1 inhibitor with anti-tumor efficacy in various solid and hematologic malignancies. To identify novel biomarkers that predict sensitivity to MCL1 inhibition, we conducted a gene essentiality analysis using gene dependency data generated from CRISPR/Cas9 cell viability screens. We observed that clear cell renal cancer (ccRCC) cell lines with damaging PBRM1 mutations displayed a strong dependency on MCL1. PBRM1 (BAF180), is a chromatin-targeting subunit of mammalian pBAF complexes. PBRM1 is frequently altered in various cancers particularly ccRCC with ~40% of tumors harboring damaging PBRM1 alterations. We observed potent inhibition of tumor growth and induction of apoptosis by PRT1419 in various preclinical models of PBRM1-mutant ccRCC but not PBRM1-WT. Depletion of PBRM1 in PBRM1-WT ccRCC cell lines induced sensitivity to PRT1419. Mechanistically, PBRM1 depletion coincided with increased expression of pro-apoptotic factors, priming cells for caspase-mediated apoptosis following MCL1 inhibition. Increased MCL1 activity has been described as a resistance mechanism to Sunitinib and Everolimus, two approved agents for ccRCC. PRT1419 synergized with both agents to potently inhibit tumor growth in PBRM1-loss ccRCC. PRT2527, a potent CDK9 inhibitor which depletes MCL1, was similarly efficacious in monotherapy and in combination with Sunitinib in PBRM1-loss cells. Taken together, these findings suggest PBRM1 loss is associated with MCL1i sensitivity in ccRCC and provide rationale for the evaluation of PRT1419 and PRT2527 for the treatment for PBRM1-deficient ccRCC.

Abstract 1594: SMARCA2 (BRM) degraders promotes differentiation and inhibit proliferation in AML models

Dysregulated cellular differentiation is a major pathological feature of myeloid malignancies such as acute myeloid leukemia (AML). Targeting cellular differentiation programs has emerged as a novel therapeutic approach to treat patients with AML. Advantages of such differentiation therapy may include fewer systemic side-effects as well as opportunities to target leukemic stem cells (LSCs) and a broader range of clonal populations, likely resulting in lower frequencies of resistance and relapse in AML patients. The success of ATRA and decitabine in subsets of AML patients has proven that inducing differentiation can play a critical role in long-term durable responses. More agents targeting epigenetic regulators have been increasingly studied as differentiation inducers, including LSD1, DNMT1, Menin, and BET inhibitors. Recently, targeting SWI/SNF chromatin remodeling complexes has also been shown to regulate key leukemic gene expression signatures and induce AML differentiation. Small molecule inhibitors as well as gene knockdown for ATP-dependent SWI/SNF subunits SMARCA2 (BRM) and SMARCA4 (BRG1) are associated with re-direction of oncogenic transcriptional regulation to drive cellular differentiation and apoptosis in AML models. We have previously described the activity of highly potent, bispecific SMARCA2 degraders that efficiently promote SMARCA2 protein degradation in preclinical models. In the present study, we investigated the effects of our SMARCA2 selective degraders in AML models. Treatment with SMARCA2 degraders significantly inhibits AML cell line proliferation in vitro with IC50 ranging from 10 to 50 nM. In the SMARCA2 degrader treated cells, expression of PU.1 (SPI1), a key transcription factor in myeloid leukemias, was downregulated. In an in vivo OCI-AML3 xenograft model, treatment with a SMARCA2 selective degrader showed moderate tumor growth inhibition accompanied by robust increases in monocytic maturation markers CD11b and CD14. Further analyses of SMARCA2 degrader effects on global transcriptome and AML immunophenotypes as well as combination effects with other therapies are currently in progress. These findings highlight the potential of SMARCA2 degraders to target AML differentiation blocks and to improve the effectiveness of other therapeutic agents such as decitabine and venetoclax in AML patients.

Citation Format: Anjana Agarwal, Olusola Peace Osinubi, Komali Vykuntam, Norman Fultang, Neha Bhagwat, Diane Heiser, Kris Vaddi, Koichi Ito, Peggy Scherle. SMARCA2 (BRM) degraders promotes differentiation and inhibit proliferation in AML models [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 1594.

Abstract 6147: MCL1 inhibitor PRT1419 demonstrates anti-tumor activity in PBRM1-altered clear cell renal cancer and synergizes with standard of care agents

Induced myeloid leukemia cell differentiation protein (MCL1) is a member of the B-cell lymphoma-2 (BCL2) family of apoptosis regulators, which plays a critical role in maintaining cellular homeostasis and promoting cancer cell survival. Increased expression of MCL1 in various cancers has been associated with poor prognosis and resistance to chemotherapeutic and targeted agents. We previously described PRT1419, a novel, potent, selective MCL1 inhibitor that demonstrates anti-tumor efficacy in various preclinical models of solid and hematologic malignancies. PRT1419 is currently under evaluation in Phase I clinical trials in patients with relapsed/refractory hematologic malignancies and advanced solid tumors. To identify novel biomarkers that might predict sensitivity to MCL1 inhibition, we conducted a gene essentiality analysis using publicly available human cancer cell line gene dependency data generated from genome-wide CRISPR/Cas9 cell viability screens. We observed that clear cell renal cancer (ccRCC) cell lines with deleterious alterations in PBRM1 (Polybromo 1) displayed a strong dependency on MCL1. PBRM1, also known as BAF180, is a chromatin-targeting subunit of mammalian pBAF (SWI/SNF-B) complexes. PBRM1 is frequently altered in various human cancers but it has a particularly high alteration rate in ccRCC with ~40% of tumors harboring damaging PBRM1 alterations. We had previously described alterations in other mammalian SWI/SNF factors as biomarkers of MCL1 inhibitor sensitivity.We observed potent inhibition of tumor growth as well as induction of apoptosis by PRT1419 in various preclinical models of PBRM1-mutant ccRCC but not in PBRM1-WT tumor models. Depletion of PBRM1 via RNAi in PBRM1-WT ccRCC induced sensitivity to PRT1419. Mechanistically, PBRM1 depletion coincided with increased expression of pro-apoptotic factors, priming PBRM1-loss cells for caspase-mediated cell death following MCL1 inhibition. Increased MCL1 activity has previously been described as a resistance mechanism to Sunitinib and Everolimus, two approved targeted agents for ccRCC. To investigate if MCL1 inhibition could potentiate the anti-tumor effects of these agents, we evaluated PRT1419 in combination with Sunitinib or Everolimus in PBRM1-loss ccRCC. PRT1419 synergized with both Sunitinib and Everolimus in inhibiting tumor growth in various models. Taken together, these findings suggest PBRM1 loss is associated with sensitivity to MCL1 inhibition in ccRCC and provide rationale for the evaluation of PRT1419 for the treatment for PBRM1-deficient ccRCC

Citation Format: Norman Fultang, Brian Vidal, Ashley M. Schwab, Alexander Grego, Diane Heiser, Kris Vaddi, Neha Bhagwat, Peggy Scherle. MCL1 inhibitor PRT1419 demonstrates anti-tumor activity in PBRM1-altered clear cell renal cancer and synergizes with standard of care agents. [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 6147.

Abstract 420: Combination of the MCL1 inhibitor PRT1419 and SMARCA2 degrader PRT3789 shows combinatorial benefit in SMARCA4 deleted lung cancer

MCL1 is a member of the anti-apoptotic BCL2 family of proteins and plays a critical role in maintaining cellular homeostasis and promoting cell survival. MCL1 amplifications occur frequently in multiple tumor types. It has also been implicated in mediating resistance to chemotherapeutic agents and targeted therapies. We have previously described a novel, potent and orally bioavailable MCL1 inhibitor, PRT1419, that demonstrates anti-tumor efficacy in various preclinical models of cancer and is currently under evaluation in a Phase I clinical trial in patients with relapsed/refractory hematologic malignancies and advanced solid tumors. In an effort to identify novel biomarkers that might predict sensitivity to MCL1 inhibition, we conducted a gene dependency analysis using publicly available human cancer cell line data generated from genome-wide CRISPR/Cas9-mediated cell viability screens. We observed that mutations in the SWI/SNF complex, particularly in lung and ovarian cancer cell lines, conferred a strong functional dependency on MCL1. The mammalian SWI/SNF complex functions as a tumor suppressor in a number of cancers and regulates gene expression via chromatin-remodeling. It is comprised of multiple subunits, including one of two catalytic ATPases (SMARCA2 or SMARAC4), DNA-binding proteins ARID1A, ARID1B and ARID2, and other chromatin-binding subunits. Gene mutations in members of this complex occur in >20% of human cancers, and therapeutic agents targeting its function are under active clinical investigation. We and others have shown potent synthetic lethality with the use of SMARCA2 targeted protein degraders in SMARCA4 deleted lung cancer models. A previously published genome-wide CRISPR screen in SMARCA4-mut lung cancer cell lines demonstrated that loss of MCL1 could sensitize these cells to SMARCA2 degradation. Therefore, we evaluated PRT1419 in combination with a novel and selective SMARCA2 degrader, PRT3789, in SMARCA4 deleted lung cancer models. We observed a potent synergistic interaction in SMARCA4 deleted cell lines in vitro, whereas no additive benefit was seen in SMARCA4 WT lines. Further, combining PRT1419 and PRT3789 in vivo in cell line-derived xenograft models resulted in significant tumor growth inhibition, including tumor regressions. Additionally, we profiled PRT1419 ex vivo in a panel of lung cancer PDX models and observed significant, dose-dependent effects on cell viability in SMARCA4 deleted models with low SMARCA2 expression. In a broader lung cancer cell line viability screen conducted with PRT1419, we observed that the presence of multiple, co-occurring alterations in SWI/SNF family members such as SMARCA4, ARID1A/B mutations and loss of SMARCA2 protein were associated with sensitivity to PRT1419. Based on these findings, preclinical evaluation of PRT1419 in other tumor types with recurrent SWI/SNF mutations is ongoing.

Citation Format: Norman Fultang, Neha Bhagwat, Diane Heiser, Alexander Grego, Michael Hulse, Venkat Thodima, Koichi Ito, Kris Vaddi, Bruce Ruggeri, Peggy Scherle. Combination of the MCL1 inhibitor PRT1419 and SMARCA2 degrader PRT3789 shows combinatorial benefit in SMARCA4 deleted lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 420.

c-Rel-dependent monocytes are potent immune suppressor cells in cancer

Myeloid-derived suppressor cells (MDSCs) are a heterogeneous population of leukocytes that are important for tumorigenesis and tumor immunotherapy. They comprise up to 10% of leukocytes in the blood of tumor patients and their depletion may be required for successful tumor immunotherapy. However, the identity of MDSCs remains obscure, primarily due to their heterogeneity and lack of a known lineage-specific transcription factor specifying their differentiation. Using single-cell transcriptomics and gene knockout approaches, we now describe a subset of murine and human myeloid suppressor cells, named rel-dependent monocytes (rMos), which are programmed by the transcription factor c-Rel of the NF-κB family. Unlike MDSCs described previously, the c-Rel-dependent monocytes expressed a high amount of the proinflammatory cytokine IL-1β together with a low level of suppressive molecule arginase 1. Both in vitro and in tumor-bearing mice, these c-Rel⁺ IL-1β^hi Arg1^- monocytes promoted tumor growth by potently suppressing T cell function and showed a strong migratory phenotype, all of which were impaired by c-Rel deficiency or inhibition. Mechanistic studies revealed that c-Rel controlled the expression of monocyte signature genes through a unique transcriptional complex called the c-Rel enhanceosome, and IL-1β-CCL2 crosstalk between tumor cells and the rel-dependent monocytes maintained the suppressive tumor microenvironment. Thus, c-Rel specifies the development of a suppressive monocyte population and could be selectively targeted for treating cancer.

Regulation of cancer stem cells in triple negative breast cancer

Triple Negative Breast Cancer (TNBC) is the most lethal subtype of breast cancer. Despite the successes of emerging targeted therapies, relapse, recurrence, and therapy failure rates in TNBC significantly outpace other subtypes of breast cancer. Mounting evidence suggests accumulation of therapy resistant Cancer Stem Cell (CSC) populations within TNBCs contributes to poor clinical outcomes. These CSCs are enriched in TNBC compared to non-TNBC breast cancers. The mechanisms underlying CSC accumulation have been well-characterized and discussed in other reviews. In this review, we focus on TNBC-specific mechanisms that allow the expansion and activity of self-renewing CSCs. We highlight cellular signaling pathways and transcription factors, specifically enriched in TNBC over non-TNBC breast cancer, contributing to stemness. We also analyze publicly available single-cell RNA-seq data from basal breast cancer tumors to highlight the potential of emerging bioinformatic approaches in identifying novel drivers of stemness in TNBC and other cancers.

Abstract LBA007: Discovery and characterization of oncogenic KRAS:RAF1 conformational modulators with in vitro and in vivo MAPK inhibition

Oncogenic mutations in the RAS family are the most frequently occurring among human cancers. The recent development of KRAS-targeted covalent inhibitors display efficacy in KRAS-mutant tumors; however, this approach is limited to KRASG12C mutant cancers. Here, we describe a novel drug discovery program to target the full-scope of mutant RAS-driven cancers through allosteric inhibition of the oncogenic KRAS-RAF1 signaling complex. To identify novel allosteric inhibitors, we developed a second harmonic generation (SHG) assay to detect conformational changes in the KRAS-RAF1 membrane-bound complex. Fully processed farnesylated and methylated KRAS4b-G12D protein (KRASG12D-FMe) was complexed with the RAF1 N-terminal RAS-binding domain (RBD) and cysteine rich domain (CRD) and immobilized on a phosphatidylserine-enriched bilayer. The RAF1RBD-CRD protein was rendered SHG-active by chemical conjugation and tethered to the bilayer by KRASG12D-FMe, thus replicating the physiological complex orientation. Ligands that disrupted or altered the orientation of the complex relative to the surface were identified from a curated diversity library of 60,000 chemical compounds based on % SHG signal change relative to baseline. Validated hit compounds were selected for SAR characterization and development wherein newly synthesized molecules were assayed by SHG and inhibition of cellular ERK phosphorylation by HTRF. Quanta (QTX) molecules were confirmed to rapidly inhibit ERK phosphorylation across multiple RAS-mutant cell lines by Western blot. Biochemical cellular target engagement studies reveal inhibition of RAF1:BRAF dimerization downstream of allosteric modulation of the KRAS:RAF1 signaling complex. Mass spectrometry with a photoactive derivative identified modified residues clustered along the KRAS:RAF1 interface, thus providing structural evidence for this unique mechanism of action. In addition to MAPK inhibition, we observe inhibition of cellular proliferation across mutant RAS cell lines. Cellular growth assays in the presence of QTX molecules combined with the SHP-2 inhibitor, RMC4550, displayed synergistic growth inhibition, providing a rationale combination therapy. Moreover, RAS-mutant cell-line derived xenograft tumors treated with QTX inhibitors elicited significant tumor growth inhibition and dose-dependent reductions in the pharmacodynamic MAPK targets, P-ERK and DUSP6, which is consistent with anti-tumor activity. This research illustrates a promising approach towards the development of mutant RAS-targeted inhibitors with a unique mechanism of action and target engagement.

Citation Format: Elizabeth Donohue Vo, Juan Luengo, Hong Lin, Jerry Chen, Ben Reid, Brooke McDonough, Norman Fultang, Jillian Silva, Cameron Pitt. Discovery and characterization of oncogenic KRAS:RAF1 conformational modulators with in vitro and in vivo MAPK inhibition [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr LBA007.

Myeloid-Derived Suppressor Cell Differentiation in Cancer: Transcriptional Regulators and Enhanceosome-Mediated Mechanisms

Myeloid-derived Suppressor Cells (MDSCs) are a sub-population of leukocytes that are important for carcinogenesis and cancer immunotherapy. During carcinogenesis or severe infections, inflammatory mediators induce MDSCs via aberrant differentiation of myeloid precursors. Although several transcription factors, including C/EBPβ, STAT3, c-Rel, STAT5, and IRF8, have been reported to regulate MDSC differentiation, none of them are specifically expressed in MDSCs. How these lineage-non-specific transcription factors specify MDSC differentiation in a lineage-specific manner is unclear. The recent discovery of the c-Rel−C/EBPβ enhanceosome in MDSCs may help explain these context-dependent roles. In this review, we examine several transcriptional regulators of MDSC differentiation, and discuss the concept of non-modular regulation of MDSC signature gene expression by transcription factors such as c-Rel and C/EBPß.

ROR1 regulates chemoresistance in Breast Cancer via modulation of drug efflux pump ABCB1

Chemoresistance is one of the leading causes of mortality in breast cancer (BC). Understanding the molecules regulating chemoresistance is critical in order to combat chemoresistant BC. Drug efflux pump ABCB1 is overexpressed in chemoresistant neoplasms where it effluxes various chemotherapeutic agents from cells. Because it is expressed in normal and cancerous cells alike, attempts at targeting ABCB1 directly have failed due to low specificity and disruption of normal tissue. A proposed method to inhibit ABCB1 is to target its cancer-specific, upstream regulators, mitigating damage to normal tissue. Few such cancer-specific upstream regulators have been described. Here we characterize ROR1 as an upstream regulator of ABCB1. ROR1 is highly expressed during development but not expressed in normal adult tissue. It is however highly expressed in several cancers. ROR1 is overexpressed in chemoresistant BC where it correlates with poor therapy response and tumor recurrence. Our data suggests, ROR1 inhibition sensitizes BC cells to chemo drugs. We also show ROR1 regulates ABCB1 stability and transcription via MAPK/ERK and p53. Validating our overall findings, inhibition of ROR1 directly correlated with decreased efflux of chemo-drugs from cells. Overall, our results highlight ROR1’s potential as a therapeutic target for multidrug resistant malignancies.

Strictinin, a novel ROR1-inhibitor, represses triple negative breast cancer survival and migration via modulation of PI3K/AKT/GSK3ß activity

Triple Negative Breast Cancer (TNBC), the most aggressive subtype of breast cancer, is characterized by the absence of hormone receptors usually targeted by hormone therapies like Tamoxifen. Because therapy success and survival rates for TNBC lag far behind other breast cancer subtypes, there is significant interest in developing novel anti-TNBC agents that can target TNBC specifically, with minimal effects on non-malignant tissue. To this aim, our study describes the anti-TNBC effect of strictinin, an ellagitanin previously isolated from Myrothamnus flabellifolius. Using various in silico and molecular techniques, we characterized the mechanism of action of strictinin in TNBC. Our results suggest strictinin interacts strongly with Receptor Tyrosine Kinase Orphan like 1 (ROR1). ROR1 is an oncofetal receptor highly expressed during development but not in normal adult tissue. It is highly expressed in several human malignancies however, owing to its numerous pro-tumor functions. Via its interaction and inhibition of ROR1, strictinin reduced AKT phosphorylation on ser-473, inhibiting downstream phosphorylation and inhibition of GSK3β. The reduction in AKT phosphorylation also correlated with decreased cell survival and activation of the caspase-mediated intrinsic apoptotic cascade. Strictinin treatment also repressed cell migration and invasion in a beta-catenin independent manner, presumably via the reactivated GSK3ß’s repressing effect on microtubule polymerization and focal adhesion turnover. This could be of potential therapeutic interest considering heightened interest in ROR1 and other receptor tyrosine kinases as targets for development of anti-cancer agents. Further studies are needed to validate these findings in other ROR1-expressing malignancies but also in more systemic models of TNBC. Our findings do however underline the potential of strictinin and other ROR1-targeting agents as therapeutic tools to reduce TNBC proliferation, survival and motility.

Abstract P5-07-13: MicroRNA-mediated restoration of tamoxifen sensitivity in triple negative breast cancer through modulation of estrogen receptor alpha/beta ratio using Myrothamnus flabellifolius

Triple negative breast cancer (TNBC) represents approximately 20% of all breast cancer cases worldwide. Prognosis for this subtype of cancer is especially dire due to the absence of Estrogen (ER), Progesterone and Human Epidermal Growth Factor receptors, usually targeted by neoadjuvant therapies like Tamoxifen. Myrothamnus flabellifolius (MF), a well-studied South African medicinal herb, has shown significant potency against TNBC with minimal effect on normal cells. In this study, we use miRNA profiling, Ingenuity Pathway Analysis (Qiagen), MTT, immunoblots and immunofluorescence to characterize the targeted cytotoxic mechanism of MF in TNBC. We found deregulation in the expression of several oncogenic and anti-cancer miRNAs in TNBC post MF treatment. Using Ingenuity Pathway Analysis to analyze the miRNA expression profiles of the treated cells, we determined Estrogen Signaling as a pathway significantly affected by MF in TNBC. Immunoblots confirmed increase of the ERa/ERß ratio in TNBC, a well-studied marker for Tamoxifen-therapy sensitivity in TNBC. MTT cell viability assay and Annexin V staining confirmed increased sensitivity to Tamoxifen post treatment with low doses of MF, with up to 70% cell death at half the IC50 of Tamoxifen in TNBC. This study establishes a potential non-toxic therapeutic to supplement Estrogen-receptor targeting therapies in TNBC by increasing the ERa/ERß ratio. The data also evaluates the ERa/ERß ratio as a potential target for combination therapies in TNBC.

Citation Format: Fultang N, Klase Z, Mercier I, Peethambaran B. MicroRNA-mediated restoration of tamoxifen sensitivity in triple negative breast cancer through modulation of estrogen receptor alpha/beta ratio using Myrothamnus flabellifolius [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P5-07-13.