It has been shown that PRMT5 inhibition by small molecules can selectively kill cancer cells with homozygous deletion of the MTAP gene if the inhibitors can leverage the consequence of MTAP deletion, namely, accumulation of the MTAP substrate MTA. Herein, we describe the discovery of TNG908, a potent inhibitor that binds the PRMT5·MTA complex, leading to 15-fold-selective killing of MTAP-deleted (MTAP-null) cells compared to MTAPintact (MTAP WT) cells. TNG908 shows selective antitumor activity when dosed orally in mouse xenograft models, and its physicochemical properties are amenable for crossing the blood–brain barrier (BBB), supporting clinical study for the treatment of both CNS and non-CNS tumors with MTAP loss.
Abstract MTA-cooperative PRMT5 inhibitors are an emerging treatment option for patients with one of the 10-15% of all human cancers harboring MTAP homozygous deletion. To identify potential regulators of sensitivity to PRMT5 inhibitors, we performed genome-wide CRISPR knockout screens in the presence and absence of an MTA-cooperative PRMT5 inhibitor. Knockout of CAAP1 and AKAP17A were among the strongest sensitizing hits across multiple MTAP-deleted cancer cell lines representing different histologies. Strikingly, the CAAP1 gene co-localizes with MTAP and CDKN2A on chromosome 9p21. Co-deletion of CAAP1 is reported in 20 percent of MTAP-deleted cancers in the TCGA PanCancer Atlas. CAAP1 or AKAP17A knockout in MTAP-deleted cancer cell lines sensitized the cells to PRMT5 inhibitors including the clinical stage MTA-cooperative inhibitors, TNG908 and TNG462, and the non-MTA-cooperative inhibitor, GSK3326595. Moreover, we discovered that CAAP1 and AKAP17A protein levels are interdependent, as knockout of either gene caused decreased protein levels for the other. Consistent with this finding, CAAP1 reconstitution in CAAP1-deleted cell lines led to increased AKAP17A levels. Endogenous CAAP1 and AKAP17A protein levels are positively correlated across a panel of cancer cell lines and MTAP-deleted patient-derived xenograft models. Consistent with a previous report (Ni et al., 2023), exogenous CAAP1 and AKAP17A co-immunoprecipitation studies suggest that the proteins form a protein complex. AKAP17A and CAAP1 are not well-characterized proteins, but PRMT5 inhibitors induce global alternative splicing events (ASEs) in cancer cells, and based on preliminary studies a possible function for the CAAP1/AKAP17A complex could be to mitigate ASEs induced by PRMT5 inhibition. Collectively, these data indicate that CAAP1 and AKAP17A exist interdependently and mediate sensitivity to PRMT5 inhibitors. The colocalization and 20 percent incidence of CAAP1 deletion in the setting of MTAP deletion may suggest that such patients will have improved responses to PRMT5-targeted therapy. S. Yoda and M. R. Tonini contributed equally. Citation Format: Satoshi Yoda, Matthew R. Tonini, Hilary E. Nicolson, Samuel Poleretzky, Silvia Fenoglio, Steven Lombardo, Lauren Grove, Samuel R. Meier, Ashley Choi, Yi Yu, Kevin M. Cottrell, John P. Maxwell, Teng, Jannik N. Andersen, Kimberly J. Briggs. Genome-wide drug anchor screens identify CAAP1 and AKAP17A as regulators of PRMT5 inhibitor sensitivity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4636.
Abstract TNG908 is an investigational PRMT5 inhibitor with a novel MTA-cooperative binding mechanism designed to leverage the synthetic lethal interaction between PRMT5 inhibition and MTAP deletion. MTAP deletion occurs in 10-15% of all human cancer representing multiple histologies. MTA is a negative regulator of PRMT5 that accumulates as a result of MTAP deletion. TNG908 selectively binds the PRMT5-MTA complex driving selective inhibition of PRMT5 in MTAP-null cancers, which is postulated to create a large therapeutic index relative to PRMT5 inhibitors currently in clinical development. TNG908 is 15X selective for MTAPnull cell lines over isogenic MTAPWT cell lines, and has marked selectivity for MTAP-deleted cancer cell lines independent of lineage in a large, diverse cell line panel. In vitro mechanistic studies confirm that MTAPnull-selective PRMT5 inhibitors can selectively target MTAPnull cancer cells in either an admixture of MTAPnull and MTAPWT cells, or with intracellular MTA accumulation 2-5X relative to basal levels in MTAPWT cells. Oral administration of TNG908 drives dose-dependent, MTAPnull-selective antitumor activity in multiple xenograft models, including tumor regressions in models representing non-small cell lung cancer (adenocarcinoma and squamous), cholangiocarcinoma, urothelial carcinoma, and others. Preclinical studies suggest clinical combinations that leverage PRMT5 biology and/or concurrent oncogenic driver mutations, such as KRASG12C. In summary, TNG908 is a novel, potent PRMT5 inhibitor with excellent drug-like properties and strong preclinical activity in multiple xenograft models that has the potential for histology-agnostic clinical development in MTAP-deleted solid tumors. Citation Format: Kimberly J. Briggs, Kevin M. Cottrell, Matthew R. Tonini, Erik W. Wilker, Lina Gu, Charles B. Davis, Minjie Zhang, Doug Whittington, Deepali Gotur, Matthew J. Goldstein, Heather DiBenedetto, Marc S. Rudoltz, Alan Huang, John P. Maxwell. TNG908 is an MTAPnull-selective PRMT5 inhibitor that drives tumor regressions in MTAP-deleted xenograft models across multiple histologies [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 3941.
Abstract Homozygous deletion of the MTAP gene occurs in 10-15% of all human cancers. To benefit this large and diverse patient population, MTA-cooperative PRMT5 inhibitors, including TNG908 and TNG462, have been developed to leverage the synthetic lethal relationship between MTAP deletion and PRMT5 inhibition. MTA-cooperative PRMT5 inhibitors selectively bind the PRMT5-MTA complex driving selective inhibition of PRMT5 in MTAP-deleted cancers while sparing normal, MTAP-proficient cells. Our PRMT5 inhibitors are currently in Phase I/II clinical trials (NCT05275478 and NCT05732831), and eligibility is restricted to patients with tumors with confirmed MTAP loss either detected by next-generation sequencing (NGS) or immunohistochemistry. MTAP gene loss occurs in cancers because of its chromosomal proximity to one of the most common genetically altered tumor suppressor genes, CDKN2A, but the chromosomal 9p breakpoints for the co-deletion are not uniform. Indeed, while clinical NGS testing and preclinical data confirm that homozygous intragenic MTAP breakpoints occur, the functional consequence of any given breakpoint on MTAP enzymatic activity and protein function remains unknown. Given the potential implications for homozygous intragenic MTAP deletions to impact the clinical response to MTA-cooperative PRMT5 inhibitors, we have started to evaluate the loss-of-function phenotype of various MTAP truncations to determine whether they retain MTAP activity. Here, we present our initial functional genomics analysis of this important diagnostic biomarker using in vitro cDNA reconstitution approaches for MTAP activity combined with analysis of PRMT5 inhibitor sensitivity. Ultimately, these data may help refine patient enrollment on clinical trials to drive the maximum benefit for patients with MTAP-deleted cancers. Citation Format: Matthew R. Tonini, Andre A. Mignault, Douglas A. Whittington, Steven A. Lombardo, Binzhang Shen, Hannah Stowe, Satoshi Yoda, Shangtao Liu, Minjie Zhang, Kevin M. Cottrell, Samuel R. Meier, Heidi Rego, Jennifer Morawiak, Ellen Hooper, Yi Yu, Heather DiBenedetto, Adam S. Crystal, Teng, Kimberly Briggs. Evaluation of the impact of homozygous MTAP truncations on the activity and selectivity of MTA-cooperative PRMT5 inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4631.
Significance Systems for degrading proteins at will are useful for a variety of biological experiments. Although a number of such systems have been described, they vary widely in terms of complexity, ease of obtaining the necessary reagents, and costs. Moreover, no one system seems to work for all proteins, and the ideal system often must be determined empirically. Thalidomide-like drugs (IMiDs) reprogram the ubiquitiously expressed cereblon ubiquitin ligase complex to degrade the lymphocyte transcription factors IKZF1 and IKZF3. Here, we show that an IKZF3-derived 25mer constitutes a modular degron that can be used to target heterologous proteins for destruction by IMiDs, which are widely available and cross the blood–brain barrier, in cell culture and in mouse experiments.
Significance Spontaneous overexpression of endogenous IRIS, an alternatively spliced product of the tumor suppressor gene BRCA1 , allows it to function as an oncoprotein that stimulates a potentially lethal outcome, i.e. metastasis of human cancer cells to tissues served, in part, by the arterial circulation. It does so by suppressing phosphatase and tensin homolog (PTEN) mRNA synthesis, thereby stabilizing and activating HIF-1α in normoxic cells. Thus, this study provides a strong rationale for exploring the therapeutic value of interfering with spontaneously overexpressed IRIS function in multiple types of tumors that can naturally overexpress it.
