Mol Cancer Ther Research Articles

Abstract B007: Unexpected synthetic lethality mechanisms in eIF4A-targeted therapy

Abstract BACKGROUND Dysregulation of mRNA translation, which is prevalent in cancer, presents an underexplored therapeutic vulnerability. The eukaryotic translation initiation factor 4A (eIF4A) promotes protein synthesis by unwinding secondary structures in the 5’-untranslated region of mRNAs to facilitate translation initiation. While perturbation of eIF4A minimally affects the health normal cells, it is crucial for the translation of many oncogenes and is considered essential in most cancer cell lines. Zotatifin, a first-in-class eIF4A inhibitor, is currently under evaluation in a Phase I/II clinical trial for KRAS-mutant tumors and ER+ breast cancers. In addition to the tumor-intrinsic effect, our recent publication in the Journal of Clinical Investigation revealed that pharmacological targeting of eIF4A not only affects tumor cells but also improves the tumor immune microenvironment. This results in tumor inhibition, heightened sensitivity to immune checkpoint blockade, and remarkable synergism with platinum in various preclinical triple-negative breast cancer mouse models. OBJECTIVES To investigate the mechanism underlying the synergy between eIF4A-targeted therapy and platinum. UNPUBLISHED RESULT Mass spectrometry proteomic analysis coupled with ELISA and qPCR analysis unveiled that eIF4A-targeted therapy promotes type I interferon (IFN) secretion and induces a robust type I IFN response both in vivo and in vitro. This suggests a tumor cell-autonomous effect of IFN induction by eIF4A inhibition. Combining platinum with eIF4A-targeted therapy further heightens the type I IFN response in vivo, leading to T cell-and macrophage-dependent synergistic tumor regression. Interestingly, this synergy was not observed in vitro, indicating the involvement of the host immune system in the efficacy of combination therapy. It is possible that platinum may stimulate certain immune populations to secrete IFN, which acts on tumor cells to upregulate their IFN response. CONCLUSION Activation of the type I IFN response by eIF4A inhibition combined with platinum in vivo can lead to synthetic lethality of tumor cells. These studies not only offer novel insights into eIF4A biology but also provide valuable guidance for ongoing and future clinical trials. Citation Format: Na Zhao, Elena Kabotyanski, Alexander Saltzman, Jeffrey Rosen. Unexpected synthetic lethality mechanisms in eIF4A-targeted therapy [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B007.

Abstract A001: KIF18A inhibition, via ATX020, leads to mitotic arrest and robust anti-tumor activity through a synthetic lethal interaction with chromosome instability

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR001) of the Conference Program/Proceedings. Citation Format: Maureen S. Lynes, Laura Ghisolfi, Sanjoy Khan, Taylor Hotz, Brian A. Sparling, Mary-Margaret Zablocki, Deepali Gotur, P. Ann Boriack-Sjodin, Kenneth W. Duncan, Stephen J. Blakemore, Serena J. Silver, Robert A Copeland. KIF18A inhibition, via ATX020, leads to mitotic arrest and robust anti-tumor activity through a synthetic lethal interaction with chromosome instability [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr A001.

Abstract B024: Leveraging synthetic lethality across EP300-mutant solid cancers through selective CBP degradation

Abstract CREB binding protein (CBP) and E1A binding protein P300 (EP300) are paralog histone acetyltransferases that can function as transcriptional coactivators to regulate diverse cellular processes. Mutations in CBP and EP300 have been implicated in the biology of various cancer types. Functional genomic screens have revealed a bidirectional synthetic lethal relationship between these paralogs in tumor cells, highlighting a therapeutic opportunity in targeting CBP selectively in EP300-mutant cancers while sparing other tissues in which EP300 is intact. This strategy would enable an improved therapeutic window beyond those observed with dual CBP/EP300 inhibitors, which exhibit hematological toxicities. However, due to the high degree of homology between the CBP and EP300 proteins, identifying chemical matter that selectively disrupts CBP activity has proven challenging. Here, we demonstrate selective and potent CBP degrader compounds that disrupt proliferation in EP300-mutant cancer cell line models. Notably, these degraders have little impact on cell lines with intact EP300. Moreover, in cell line-derived xenograft (CDX) tumor models, we achieve potent and sustained CBP degradation and associated tumor growth inhibition. Our CBP-selective protein degraders have the potential to be a first-in-class therapeutic option for patients with tumors harboring EP300 mutations. Citation Format: Darshan Sappal, Ammar Adam, Hafiz Ahmad, Benjamin Adams, Ketaki Adhikari, Wesley Austin, Breanna Bullock, Julie Di Bernardo, Thomas Dixon, Danette Daniels, Claudi Dominici, GiNell Elliott, Brian Ethell, Anais Gervais, Md Imran Hossain, David Huang, David Lahr, Laura La Bonte, Mei Yun Lin, David Mayhew, Karolina Mizeracka, Solymar Negretti, Tyler Nguyen, Olga Prifti, Shawn Schiller, Brenna Sherbanee, David Terry, Nihan Ucisik, Elizabeth Wittenborn, Molly M Wilson, Qianhe Zhou, Mark Zimmerman. Leveraging synthetic lethality across EP300-mutant solid cancers through selective CBP degradation [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B024.

Abstract IA019: Identification of metabolic adaptation mechanisms that confer resistance to glutathione depletion in Ewing sarcoma

Abstract Aggressive cancer cells must overcome diverse stress forms in the tumor microenvironment and circulation, such as oxidative stress, to survive and metastasize. One adaptive process to counter oxidative stress is to upregulate glutathione (GSH), a tripeptide consisting of glutamate, cysteine, and glycine, which is a powerful antioxidant in cells, including in tumor cells. A rate-liming step in GSH production is the availability of the amino acid, cysteine. Tumor cells can either import cystine, a dimer of cysteine, through the xCT antiporter system, for conversion to the reduced cysteine monomer, or in some tumor types, they can synthesize cysteine de novo from methionine and serine through the transsulfuration pathway. GSH is not only critical for redox homeostasis, but is taken up into mitochondria where is acts as a source of sulphur to generate iron-sulphur (Fe-S) clusters that are essential for many mitochondrial enzymes including electron transport complexes. We wished to determine if Ewing sarcoma cells could tolerate reduced levels of GSH, using either xCT genetic or pharmacologic inhibition, or by blocking downstream enzymes in the GSH synthesis pathway, including GCLC using buthionine sulfoximine (BSO), or glutaminase using CB-839. To our surprise, we were able to generate BSO and CB-839 resistant cells with vanishingly low levels of GSH. These cells somehow maintained not only redox homeostasis, but also showed functional mitochondrial respiration (oxidative phosphorylation). We then performed CRISPR dropout screens to identify how these cells might be surviving in the absence of GSH, and to tease out specific dependencies of these BSO and CB-839 resistant cells. These studies revealed unexpected dependencies, and opportunities for synthetic lethal interventions, as will be discussed. Citation Format: Poul H. Sorensen, Hai-Feng Zhang, Christopher Hughes, Alberto Delaidelli, Samuel Aparicio. Identification of metabolic adaptation mechanisms that confer resistance to glutathione depletion in Ewing sarcoma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA019.

Abstract PR001: KIF18A inhibition, via ATX020, leads to mitotic arrest and robust anti-tumor activity through a synthetic lethal interaction with chromosome instability

Abstract KIF18A is a plus-end directed kinesin known to play a role in mitosis by facilitating chromosome alignment and spindle microtubule dynamics. Knockdown or knockout of KIF18A has been shown to inhibit proliferation in cells with whole genome doubling or aneuploidy, cellular states characterized by chromosomal rearrangements. These alterations render cells particularly vulnerable to disrupted mitosis upon KIF18A loss. As such, KIF18A is a compelling synthetic lethality target in a subset of tumors with chromosomal instability (CIN), which have ongoing chromosomal segregation defects. We have identified potent and selective small molecule inhibitors of KIF18A. A proprietary tool compound, ATX020, inhibits KIF18A ATPase activity with an IC50 of 0.014 µM; KIF18A is selectively inhibited over other kinesins including CENPE (IC50 > 10 µM) and EG5 (IC50 5.87 µM). ATX020 exhibits robust cellular activity, with anti-proliferative activity observed in chromosomally instable ovarian cancer cell lines such as OVCAR-3 (IC50 0.053 µM) and OVCAR-8 (IC50 0.54 µM). Upon treatment with ATX020, Annexin V is robustly induced in sensitive cell lines, demonstrating that KIF18A-dependent cell lines undergo apoptosis upon KIF18A inhibition. In KIF18Ai sensitive cells, a dose-dependent upregulation of phospho-Histone H3 and gamma-H2AX is observed upon ATX020 treatment in OVCAR-3 and OVCAR-8 cells, consistent with the induction of mitotic arrest and DNA damage. In these sensitive cell lines, ATX020 induces a dose-dependent cell cycle arrest in G2/M, consistent with the role of KIF18A in facilitating mitosis. OVCAR-3 cells treated with ATX020 exhibit fragmented nuclei and malformed mitotic spindles. In contrast, CIN negative Ovarian cancer cells that are insensitive to KIF18A loss, such as A2780 and OVK18, proliferate normally upon ATX020 treatment, cell division is unaffected, and no induction of Annexin V, phospho-Histone H3, and gamma-H2AX is observed. This selective dependency is also observed in vivo, where administration of ATX020 leads to dose-dependent tumor growth inhibition in an OVCAR-3 cancer cell line-derived xenograft model, with significant tumor regression observed at 100 mpk/day. In contrast, OVK18 tumors are unaffected by ATX020 administration, as expected based on the lack of cell cycle and proliferation effects in that cell line. Together, these data demonstrate a critical role for KIF18A in facilitating mitosis in a subset of chromosomally instable cells. These effects are selective, with KIF18A-independent cell lines proceeding through the cell cycle normally in the presence of inhibitors. Small molecule inhibition of KIF18A is therefore expected to have robust efficacy in solid tumors with high levels of chromosomal instability such as Ovarian cancer. Citation Format: Maureen S. Lynes, Laura Ghisolfi, Sanjoy Khan, Taylor Hotz, Brian A. Sparling, Mary-Margaret Zablocki, Deepali Gotur, P. Ann Boriack-Sjodin, Kenneth W. Duncan, Stephen J. Blakemore, Serena J. Silver, Robert A. Copeland. KIF18A inhibition, via ATX020, leads to mitotic arrest and robust anti-tumor activity through a synthetic lethal interaction with chromosome instability [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR001.

Abstract B023: Nimbolide targets RNF114 to induce the trapping of PARP1 and synthetic lethality in BRCA-mutated cancer

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR002) of the Conference Program/Proceedings. Citation Format: Peng Li, Yuanli Zhen, Chiho Kim, Zhengshuai Liu, Jianwei Hao, Heping Deng, Hejun Deng, Min Zhou, Xu-Dong Wang, Tian Qin, Yonghao Yu. Nimbolide targets RNF114 to induce the trapping of PARP1 and synthetic lethality in BRCA-mutated cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B023.

Abstract PR013: Detecting pairwise and higher-order antagonistic epistatic effects among somatic cancer genotypes to discover synthetic lethality

Abstract The mutual exclusivity of somatic variants in cancer suggests that current somatic variants can exert antagonistic epistatic effects on the selection of new mutations, contributing to a complex landscape of evolutionary trajectories. However, quantifying pairwise and higher-order epistatic effects—which are essential to estimation of the trajectory of likely cancer genotypes—has been a challenge. We have developed a continuous-time Markov chain model that enables the estimation of mutation origination and fixation, dependent on somatic cancer genotype. We coupled the continuous-time Markov chain model with an approach that deconvolutes the underlying mutation rates and selection intensities across trajectories of oncogenesis. By elucidating the routes of variant evolution and the strengths of selective forces at play, our approach lays the groundwork for quantifying antagonistic epistatic effects of specific somatic genotypes. We applied our approach to report the variant mutation rates, selection intensities, and consequent substitution rates for lung adenocarcinoma, comparing smoker and nonsmoker tumor cohorts. We describe the distinct influences of smoking on underlying mutation rates and on physiology affecting the selective regime of lung tissue. Inference of the most likely routes of site-specific variant evolution, as well as estimation of the selection strength operating on each step along the route represents a key component for prioritization, development, and implementation of personalized cancer therapies that target synthetic lethality. Citation Format: Jorge A. Alfaro-Murillo, Krishna Dasari, Jeffrey P. Townsend. Detecting pairwise and higher-order antagonistic epistatic effects among somatic cancer genotypes to discover synthetic lethality [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR013.

Abstract PR011: Inhibiting eIF4E phosphorylation sensitizes triple-negative breast cancer to CDK4/6 inhibition

Abstract Despite significant progress in breast cancer treatment, Triple-Negative Breast Cancer (TNBC) presents a unique challenge due to the absence of three conventional drug targets found in other breast cancer subtypes, highlighting an urgent need for novel therapeutic strategies. A critical element of TNBC pathogenesis is the dysregulation of mRNA translation, a critical process required by rapidly dividing cancer cells to synthesize proteins as building blocks. This hallmark positions mRNA translation as a promising target for therapeutic intervention. At the forefront of regulating mRNA translation, is the mRNA cap-binding protein, eukaryotic initiation factor 4E (eIF4E). While its role in general mRNA translation initiation is crucial, eIF4E phosphorylation by the MNK1/2 [MAPK (Mitogen-Activated Protein Kinase)-Interacting Kinase1/2] has been implicated in tumorigenesis. Specifically, phosphorylated eIF4E (p-4E) selectively enhances the translation of mRNAs encoding proteins critical for cancer cell survival and metastasis, such as myeloid cell leukemia-1 (MCL1) and matrix metalloproteinase-3 (MMP3). Yet, inhibiting eIF4E phosphorylation markedly impairs TNBC metastasis without affecting the primary tumor’s growth rates in vivo, emphasizing its specific role in metastatic progression. To dissect the mechanism of p-4E in TNBC, we performed an in vitro shRNA synthetic lethal screen in TNBC cells to identify genes whose knockdown synergizes with p-4E inhibition to limit cell growth. A small-molecule inhibitor of MNK1/2, eFT508, was utilized to mitigate p-4E level during the screen. This screen uncovered that knockdown of cyclin-dependent kinase 4 (CDK4), known primarily for its role in cell cycle regulation, synergizes with p-4E inhibition. Through validation using various cell proliferation assays and three different FDA-approved CDK4/6 inhibitors (palbociclib, ribociclib, and abemaciclib), we demonstrated a strong synergy between CDK4/6 inhibition and eFT508 in reducing cell growth. The synergy between CDK4/6 and p-4E inhibition not only impaired TNBC cell proliferation, but also significantly reduced eIF4E activity and mRNA translation. Additionally, our findings reveal a novel role for CDK4/6 inhibitors in modulating mRNA translation via mTORC1 signaling pathways, extending beyond their canonical role in cell cycle regulation. This discovery suggests a potential combinatorial therapeutic approach for TNBC treatment involving MNK1/2 and CDK4/6 inhibitors. Such a strategy could exploit the vulnerabilities in TNBC’s dysregulated mRNA translation machinery, offering a promising direction in treating this aggressive breast cancer subtype. Citation Format: Qiyun Deng, Mehdi Amiri, Anastasija Ana Piric, Yasaman Bagherian, Zilan Li, Sidong Huang, Michael Pollak, Nahum Sonenberg. Inhibiting eIF4E phosphorylation sensitizes triple-negative breast cancer to CDK4/6 inhibition [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr PR011.

Abstract IA009: Single strand DNA GAP accumulation as a functional biomarker for DNA Repair Inhibitors

Abstract Deficiency of homologous recombination (HR)-mediated DNA repair occurs through genetic or epigenetic inactivation of the BRCA1 and BRCA2 (BRCA1/2) genes. HR-deficiency also provides unique opportunities for targeted therapy, through the mechanism of synthetic lethality, as exemplified by the hypersensitivity of BRCA1/2-mutated tumors to PARP inhibitors (PARPi). To date, several PARP inhibitors have been approved for clinical use. The promising clinical response of patients with germline BRCA1/2-mutations prompted the use of PARPi for patients with somatic BRCA1/2 mutations as well. In addition, these results extended the use of PARPi for various types of ovarian, breast, pancreatic, and prostate tumors with HR defects. PARPi resistance is emerging as the major obstacle to clinical effectiveness in patients with HR-deficient tumors. PARPi resistance results from several independent mechanisms, leading to the restoration of Homologous Recombination and/or Replication Fork stabilization. The absence of alternative options for patients with tumors with innate or acquired resistance underlines the urgency to develop additional therapeutics. More recent studies have identified new synthetic lethal opportunities for BRCA1/2 deficient tumors. Knockout of the genes for POLQ (DNA polymerase theta) or for USP1 (Ubiquitin Specific Protease 1) results in killing of these tumors, and inhibitors of these enzymes are emerging as promising agents for HR-deficient tumors. POLQ and USP1 expression is particularly high in subtypes of breast and ovarian tumors with defects in HR. As a result, POLQi or USP1i in HR-deficient tumors induces cell death. POLQi or USP1i can synergize with PARPi in killing HR-deficient tumors or PARPi-resistant tumors. BRCA1/2 deficient tumors have an increase in single strand DNA gaps (ssGAPs) near replication forks. Treatment with PARPi results in an increase in the size and number for these ssGAPs, ultimately leading to DSBs and cell death. Interestingly, PARPi resistance results, at least in part, from the ability of resistant cells to close the ssGAPs through enhanced POLQ and USP1 activity, thereby providing a rationale for the combination of PARP1, POLQi, and USP1 in HR-deficient cancers. USP1 inhibition was synergistic with PARP and POLQ inhibition in BRCA1-mutant cells, with enhanced ssDNA gap accumulation. Moreover, this synergy was observed in a set of patient-derived ovarian cancer organoids (PDOs), thus confirming the sensitivity of BRCA1-deficient cells to inhibition by these agents. The accumulation of ssDNA gaps after treatment with a USP1i, PARP, or POLQi correlated with the sensitivity to these drugs in all models tested. Ovarian cancer PDOs provide a powerful tool for detecting drug synergy and for rapid in vitro sensitivity testing. The detection of ssDNA gap accumulation may be a useful predictive biomarker for response to DNA Repair inhibitors as monotherapy or in combination in ongoing clinical trials. Citation Format: Alan D. D'Andrea. Single strand DNA GAP accumulation as a functional biomarker for DNA Repair Inhibitors [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA009.

Abstract B011: Detecting pairwise and higher-order antagonistic epistatic effects among somatic cancer genotypes to discover synthetic lethality

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR013) of the Conference Program/Proceedings. Citation Format: Jorge A. Alfaro-Murillo, Krishna Dasari, Jeffrey P Townsend. Detecting pairwise and higher-order antagonistic epistatic effects among somatic cancer genotypes to discover synthetic lethality [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B011.

Abstract IA002: Overcoming the K-Ras inhibitor resistant cell state in PDAC with molecular glues.

Abstract K-Ras inhibitor resistance in PDAC is associated with metabolic reprogramming towards a high OXPHOS state. Existing inhibitors of components of the electron transport chain have on-target toxicities that limit their use in the clinic, highlighting an opportunity to develop mechanistically orthogonal approaches. In this talk, I discuss our development of molecular glue degraders that target metabolic vulnerabilities in K-Ras inhibitor resistant PDAC. Citation Format: Fleur M. Ferguson. Overcoming the K-Ras inhibitor resistant cell state in PDAC with molecular glues [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA002.

Abstract A022: Synthetic lethality of ERBB2 and CCND1 in breast cancer at scale

Abstract Introduction: Synthetically lethal mutations offer unique molecular targets for oncologic therapy. At scale, synthetic lethality (SL) is observed when alterations to one gene alone do not correspond with worse overall survival (OS), but simultaneous expression with another gene does correspond with worse OS. Mutually exclusive gene expression is not a requirement for SL. Existing breast cancer (BC) literature suggests synthetic lethality between CKS1B and PLK1, as well as BRCA1/BRCA2 and PARP1. Unaltered RB1 and altered CCND1 are also known to exhibit SL in the HER2-deficient environment of triple-negative BC. CCND1 and ERBB2 are typically amplified in invasive ductal carcinoma, with ERBB2 amplifications correlating to larger tumor size. This relationship is not observed in invasive lobular carcinoma, although expression of E2F1, a downstream transcription factor of CCND1, is inversely correlated with tumor grade. Methods: Our in silico approach investigated SL between ERBB2 and CCND1 in breast invasive carcinoma without distinction to lobular or ductal origin (TCGA, PanCancer Atlas 2018). We identified 17 genes of interest based on molecular alterations present in >10% of the sample (n=1084) and common mentions in BC literature. SL was determined if alterations to one gene alone did not significantly worsen OS, while alterations to two genes corresponded with worse OS. Results: Twenty-three SL interactions were observed. CCND1 and ERBB2 were selected because neither gene significantly worsened OS alone (p=0.915 & p=0.0951 respectively). However, patients with alterations to both genes had significantly worse OS compared to those with alterations to one gene alone. CCND1 and ERBB2 alterations were present in 14.9% and 13.7% of the sample, respectively. HR=2.568 (p=0.0138) for SL patients compared to those with CCND1 alterations alone; HR=2.244 (p=0.0497) for SL patients compared to those with ERBB2 alterations alone. Mutual exclusivity was not significantly observed (p=0.084). Multivariate analysis was performed using Cox regression models; neither age (older or younger than 55 years) nor race (White, Black, Asian) confounded our results due to p>0.05. Conclusion: Our findings support potential therapeutic use of CCND1 targets in HER2+ BC, specifically for patients with SL between CCND1 and ERBB2. These include PLK1 inhibitors, commonly used in estrogen receptor-positive patients with CDK4/6 inhibitor resistance, along with HER2 inhibitors. A combination of MAP2K and PIK3CA inhibitors should also be investigated in HER2+ BC patients with CCND1 amplification, since HER2+ colorectal cancer patients have been demonstrated to fare better with this treatment. Citation Format: Rishi Nair, Evan P. White, Roy Khalife, Anthony M. Magliocco. Synthetic lethality of ERBB2 and CCND1 in breast cancer at scale [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr A022.

Abstract IA003: Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase

Abstract The WRN helicase serves as a key target in the treatment of cancers characterized by microsatellite instability (MSI) because it plays a crucial role in resolving harmful non-canonical DNA structures that arise in cells with defective mismatch repair systems. Despite the critical functions of human DNA and RNA helicases, no drugs targeting these enzymes have been approved, largely due to the difficulties in identifying potent and selective inhibitors. In this study, we present the chemoproteomics-based identification of a clinical-stage, covalent allosteric inhibitor of WRN, VVD-133214. This inhibitor specifically interacts with a cysteine residue (C727) within the helicase domain, which undergoes inter-domain movement during the DNA unwinding process. VVD-133214 reacts with the WRN protein in a nucleotide cooperative manner, promoting stable, compact structures that impede the enzyme's dynamic flexibility essential for its helicase activity. Inhibition of WRN by VVD-133214 leads to extensive double-stranded DNA breaks, nuclear enlargement, and ultimately cell death, specifically in MSI-high cells but not in microsatellite stable cells. The inhibitor demonstrated good tolerance in mice and significant tumor reduction in various MSI-high colorectal cancer cell lines and patient-derived xenograft models. Our findings highlight an allosteric strategy to inhibit WRN function that avoids interference from the endogenous ATP cofactor in cancer cells and positions VVD-133214 as a promising therapeutic candidate for patients with MSI-high cancers. Citation Format: Matthew P. Patricelli, Kristen A. Baltgalvis, Kelsey N. Lamb, Kent T. Symons, Chu-Chiao Wu, Melissa A. Hoffman, Aaron N. Snead, Xiaodan Song, Thomas Glaza, Shota Kikuchi, Jason C. Green, Donald C. Rogness, Betty Lam, Maria E. Rodriguez-Aguirre, David R. Woody, Christie L. Eissler, Socorro Rodilles, Seth M .Negron, Steffen M. Bernard, Eileen Tran, Jonathan Pollock, Ali Tabatabaei, Victor Contreras, Heather N Williams, Martha K. Pastuszka, John J. Sigler, Piergiorgio Pettazzoni, Markus G. Rudolph, Moritz Classen, Doris Brugger, Christopher Claiborne, Jean-Marc Plancher, Isabel Cuartas, Joan Seoane, Laurence E. Burgess, Robert T. Abraham, David S. Weinstein, Gabriel M. Simon, Todd M. Kinsella. Chemoproteomic discovery of a covalent allosteric inhibitor of WRN helicase [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA003.

Abstract A016: Companion Diagnostics (CDx) to identify hallmarks of Alternative Lengthening of Telomeres (ALT)

Abstract Maintenance of telomeres in the absence of telomerase is known as Alternative Lengthening of Telomeres (ALT), which is prevalent in 10-15% of all cancers. Tessellate BIO targets ALT mechanisms to drive cell death by synthetic lethality. To identify patients who will benefit from our therapy, we are developing companion diagnostics (CDx). In this study, established hallmarks of ALT are investigated as CDx target in tissue-derived samples. In fresh and FFPE tumor tissue, presence and abundance of different ALT hallmarks were measured, including RPA phosphorylation, C-circles and telomeric single stranded DNA. While not all markers pass the stringent requirements of a CDx, C-circles prove to be a reliable biomarker. To measure C-circles, a robust and scalable PCR-based protocol was developed, facilitating easy implementation in the clinic. Utilizing this protocol, C-circles were successfully measured across different tissue types. Further, the protocol allowed for C-circle quantification in cell lines, showcasing its utility across matrices of varying complexity. Successful development of the C-circle CDx enables patients selection based on ALT mechanisms herewith improving the response rate of targeted therapies in patients and accelerating new discoveries in the ALT space. Citation Format: Ganesh Kadamur, Dalia Tarantino, Freddie Grogono, Patrick Von Morgen, Salvina Tammaccaro, Diana Zatreanu, Donata Federici Canova, Jana Wolf, Corne van den Kieboom, Katie Chapman, Joris Schuurmans, Jurgen Moll. Companion Diagnostics (CDx) to identify hallmarks of Alternative Lengthening of Telomeres (ALT) [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr A016.

Abstract B015: Combinatorial genetic screens to map synthetic lethal interactions and identify new cancer drug targets in KRAS mutant cancers

Abstract This abstract is being presented as a short talk in the scientific program. A full abstract is printed in the Proffered Abstracts section (PR014) of the Conference Program/Proceedings. Citation Format: Rand Arafeh, Laura Chang, Lydia Sawyer, Helen Wang, James McFarland, Joshua Dempster, Peter DeWeirdt, John Doench, William C Hahn. Combinatorial genetic screens to map synthetic lethal interactions and identify new cancer drug targets in KRAS mutant cancers [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr B015.

Abstract A024: SOX11: An Achilles heel of mantle cell lymphoma enhancing sensitivity to DNA damaging agents by impairing DNA repair

Abstract Mantle cell lymphoma (MCL) is an aggressive malignancy with mature B-cell differentiation and a median overall survival of 5 years. A characteristic hallmark of MCL is the aberrant expression of the transcription factor sex determining region on Y chromosome (SRY)-related and high mobility group (HMG) domain containing protein 11 (SOX11) in approximately 90% of the cases. The role of SOX11 in MCL pathogenesis has been attributed to transcriptional dysregulation, ultimately driving malignant gene expression profile of MCL. However, little is known about the potential transcription factor-independent modes of action of SOX11. Our co-immunprecipitation and proteomic analysis showed that SOX11 binds to factors of DNA damage response (DDR), nucleosome remodeling and chromatin regulation, among others. Sterile Alpha motif and HD domain containing protein 1 (SAMHD1) is top-listed among the SOX11 binding partners in MCL. We recently showed that SOX11 binds via its HMG domain to SAMHD1, disturbing its homo-tetramerization. A growing body of evidence unveiled the implication of SAMHD1 in DDR, particularly in promoting homologous recombination. Immunofluorescent imaging showed that SOX11 impairs homologous recombination in MCL, evidenced by reduced accumulation of RAD51 foci upon chromatin in response to treatment with the topoisomerase1 inhibitor camptothecin (CPT). This was further consistent with abrogated phosphorylation of DNA-break binding protein RPA32 (S4/8), but not total RPA32, in response to CPT treatment in SOX11-positive conditions. Inducing SOX11 expression in SOX11-negative MCL cell line (JVM-2) resulted in increased accumulation of cytosolic single-stranded DNA upon CPT treatment. This was translated in an enhanced sensitivity to CPT in SOX11-expressing MCL cell lines as compared to SOX11-negative conditions. Moreover, this enhanced sensitivity was reflected in increased levels of cleaved PARP1, cleaved caspase 3 and persistent γ-H2A.X in SOX11-positive cells. Simian Immunodeficiency Virus protein (Vpx)-mediated depletion of SAMHD1 yielded a similar, yet attenuated, sensitive phenotype to CPT compared to SOX11 induction in JVM-2. SAMHD1 depletion in addition to SOX11 induction showed no significant additional impact on the response to CPT in JVM-2 under the conditions tested. Intriguingly, T592 phosphorylation of SAMHD1 was reduced upon inducing SOX11 expression in JVM-2, suggesting a mode of action by which SOX11 inhibits SAMHD1. However, the mechanism behind increased levels of SAMHD1 post-translational modification upon SOX11 induction requires further investigation. Altogether, our findings suggest that SOX11 may impair homologous recombination, at least in part, through inhibiting SAMHD1. These results highlight SOX11 as an Achilles heel that renders MCL vulnerable to DNA damaging and suggest that incorporating DNA damaging agents including topoisomerase inhibitors or anthracyclines into currently used treatment modalities for MCL might be clinically beneficial. Citation Format: HA Morsy, Virginia Amador, Birger Christensson, Nikolas Herold, Birgitta Sander. SOX11: An Achilles heel of mantle cell lymphoma enhancing sensitivity to DNA damaging agents by impairing DNA repair [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr A024.

Abstract IA005: Therapeutic vulnerabilities of cohesin-mutant myeloid malignancies

Abstract Splicing modulation is a promising treatment strategy pursued to date only in splicing-factor mutant cancers; however, its therapeutic potential is poorly understood outside of this context. Like splicing factors, genes encoding components of the cohesin complex are frequently mutated in myeloid malignancies, including 15-20% of myelodysplastic syndromes (MDS) and secondary acute myeloid leukemia (AML), where they are associated with poor outcomes. I will discuss our recent findings identifying cohesin mutations as biomarkers of sensitivity to drugs targeting splicing-factor SF3B1 (H3B-8800 and E-7107) and describe the mechanism by which drug-induced alterations in splicing of DNA repair genes, such as BRCA1 and BRCA2, underlie this sensitivity. We have demonstrated that treatment of cohesin-mutant cells with SF3B1 modulators results in impaired DNA damage response, accumulation of DNA damage, and increased sensitivity to PARP inhibitors and a panel of chemotherapeutic agents in vitro and in vivo, using AML cell lines and patient-derived xenograft models. Furthermore, we identified RAD51 foci formation as a predictive biomarker of sensitivity to SF3B1 splicing modulation alone or followed by sequential treatment with PARP inhibition and chemotherapy, and have identified additional non-cohesin mutant subtypes of MDS/AML and ovarian and breast cancer which are sensitive to this therapeutic approach. Our findings expand the potential therapeutic benefits of SF3B1 splicing modulators to include cohesin-mutant MDS/AML and we propose this as broader strategy for therapeutic targeting of other DNA damage-repair deficient cancers. Citation Format: Zuzana Tothova. Therapeutic vulnerabilities of cohesin-mutant myeloid malignancies [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA005.

Abstract A012: Targeting proteasome vulnerabilities for the treatment of monosomy 7 associated blood disorders

Abstract Monosomy 7 is among the most frequent cytogenetic abnormalities in hematological disorders and is associated with short survival and drug resistance. Despite its high prevalence and detrimental impact, the therapeutic vulnerabilities underlying monosomy 7-associated blood disorders remain largely elusive, impeding progress toward improved patient care. The homeostatic cellular requirement for a normal dosage of essential genes creates an opportunity to target vulnerabilities that arise due to reduced levels of proteins encoded by a haploinsufficient essential gene. Briefly, the loss of one copy of a dosage-sensitive essential gene (gene X), in combination with the inhibition of itself or a related gene (gene Y), or an associated pathway results in lethal consequences for cells. The remarkable and selective clinical efficacy of lenalidomide for the treatment of del(5q) MDS has demonstrated how allelic haploinsufficiency underlies the sensitivity to this drug by synthetic lethality. Differential expression analysis of gene and protein expression in primary AML samples with monosomy 7 revealed significant downregulation of multiple proteasome pathway members at the protein level, but not at the RNA level. Primary AML samples with -7/del(7q) exhibited increased sensitivity (low IC50) to the proteasome inhibitor bortezomib, as evidenced by two independent ex vivo drug screening cohorts (the Beat AML and the FIMM study). Chromosome 7 harbors four proteasome subunits, PSMA2, PSMC2, PSMG3, and SEM1. We performed gene expression, protein expression, copy number analysis, and individual gene knockout experiments. The results have revealed PSMA2 to be a haploinsufficient essential gene on chromosome 7. PSMA2 knockout confers leukemia a growth disadvantage for multiple AML cell clines in both TP53 wild-type and knockout backgrounds. We generated PSMA2 isogenic hemizygous deletion and diploid single-cell clones. PSMA2 hemizygous deletion cells exhibited approximately half the protein expression compared to diploid controls, confirming that PSMA2 is a haploinsufficient gene. PSMA2hemizygous deletion single-cell clones showed significantly enhanced sensitivity to all three evaluated proteasome inhibitors (bortezomib, ixazomib, and carfilzomib), aligning with the sensitivity observed in primary -7/del(7q) leukemia samples. PSMA2 hemizygous deletion cell clones displayed increased p38 and decreased pERK levels upon treatment with proteasome inhibitors, potentially contributing to their increased sensitivity to proteasome inhibitors. Proteomics analysis and in vivo validation is ongoing. As such, we have identified haploinsufficient essential gene PSMA2 mediated proteasome pathway vulnerability in monosomy 7 associated leukemia and further showed that proteasome inhibitors as promising therapeutic approaches for treating hematological disorders associated with monosomy 7. Citation Format: Haijiao Zhang, Basil Allen, Daniel Bottomly, Peter Ryabinin, Schannon K. Targeting proteasome vulnerabilities for the treatment of monosomy 7 associated blood disorders [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr A012.

Abstract IA008: Exploiting tumor selective vulnerabilities with structure based drug design

Abstract It is well appreciated that the integrity of both pluripotent and terminally differentiated cellular genomes is under constant pressure from damage provoked by cell-intrinsic and environmental factors. As such, defects in the cellular machinery preserving genomic integrity lead to the accumulation of variants that can promote cancer, but they also confer tumor-cell specific vulnerabilities that present synthetic-lethal therapeutic opportunities. The deepening mechanistic appreciation of tumor-selective pressure on DNA replication-fork fidelity, namely oncogene-induced replication stress, has provoked great interest in the prosecution of drug targets within the cellular machinery that otherwise supports replication fork stability. Poly (ADP-Ribose) glycohydrolase (PARG) is an enzyme with a unique role in the resolution of DNA damage repair and DNA replication fork restart through hydrolysis of Poly (ADP-ribose) (PAR) chains. IDE161 is a potent, selective small molecule inhibitor of PARG that is being developed as an anti-cancer therapeutic for patients with advanced or metastatic cancer harboring defects in homologous recombination repair. In culture, the accumulation of PAR chains upon PARG inhibition causes delayed repair of DNA breaks, replication stress and mitotic catastrophe in settings with collateral liabilities in DNA damage repair and/or replication fork stability. Genome-wide CRISPR-mediated fitness screens across multiple genetic backgrounds revealed strong synthetic lethal interactions of IDE161 with otherwise non-essential components of cellular machinery supporting base excision repair, homologous recombination repair and replication fork stability. In addition, evaluation of IDE161 antiproliferative activity across a panel of 350 molecularly characterized cancer cell lines returned a response profile that was only partially overlapping with that observed with PARPi and was enriched for models harboring vulnerabilities associated with replication stress and/or defects in DNA repair. Notably, many homologous recombination deficient (HRD) cell models display differential dependency on PARG activity vs PARP1/2 activity, suggesting PARG inhibition as a potential therapeutic strategy distinct from PARP inhibitors. In vivo assessment of IDE161 anti-tumor activity in CDX and PDX models mirrored these mechanistic relationships. A number of HRD PDX models displayed a superior response to IDE161 versus PARPi, including robust regressions selectively observed with IDE161 versus niraparib in BRCA2 altered ER+, HER2-breast cancers. Thus, IDE161 has potential as novel targeted therapy that exploits the synthetic lethal relationship between PARG and genomic instability, leading to selective anti-proliferative activity in tumors harboring defects in DNA repair and replication fidelity. Citation Format: Reeja Maskey, Diana Munoz, Megan Conway, Arjun Rao, Vidhya Nagarajan, Ivan Shabalin, Kelly Trego, Jonathan Ryan, Peter Teriete, Christian Frey, Josh Taygerly, Paul Barsanti, Claire Neilan, Jasgit Sachdev, Michael White. Exploiting tumor selective vulnerabilities with structure based drug design [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr IA008.

Abstract A007: Assessment of metabolic vulnerabilities of breast cancer brain metastasis

Abstract The metastasis of cancer to the brain is a major contributor to patient morbidity and mortality. Prior work suggests that there is therapeutic potential in targeting metabolic processes within brain metastatic cancer, however how best to identify novel targets and select patient populations remains unclear. In this study, we determine what nutrients are available to breast cancer cells in the brain and how those nutrients are used. We also engineer breast cancer cells that are auxotrophic for specific nutrients and assess how this impacts tumor growth in the brain using various approaches. These methodologies include direct implantation into the brain and introduction into the circulation to evaluate tumor formation as brain metastases. Unexpectedly, we find that no single approach, including assessment of brain nutrient availability, tumor biosynthetic activity, and evaluation of genetic dependencies using in vivo CRISPR screens reliably predicts metabolic dependencies that broadly extend across models of breast cancer brain metastasis. Our findings underscore the necessity of a holistic approach in considering how best to identify and prioritize new targets for treating metastatic cancer. Citation Format: Keene L. Abbott, Sonu Subudhi, Raphael Ferreira, Yetiş Gültekin, Sophie C. Steinbuch, Sophie E. Honeder, Ashwin S Kumar, Michelle Wu, Diya Ramesh, Jacob Hansen, Lisa M. Riedmayr, Mark Duquette, Ahmed Ali, Nicole Henning, Sharanya Sivanand, Tenzin Kunchok, Millenia Waite, Brian T. Do, Virginia Spanoudaki, Francisco J. Sánchez-Rivera, George M. Church, Rakesh K Jain, Matthew G. Vander Heiden. Assessment of metabolic vulnerabilities of breast cancer brain metastasis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Expanding and Translating Cancer Synthetic Vulnerabilities; 2024 Jun 10-13; Montreal, Quebec, Canada. Philadelphia (PA): AACR; Mol Cancer Ther 2024;23(6 Suppl):Abstract nr A007.