Abstract Loss of function mutations in Serine Threonine Kinase 11 (STK11) occur in 15% of lung adenocarcinoma and have been shown to drive resistance to immune checkpoint blockade clinically, as well as in preclinical models. Though STK11 is commonly inactivated in human cancer with strong implications for treatment outcomes, few STK11 mutations identified from tumor samples have been functionally characterized. TNG260 is an inhibitor of CoREST that is currently being investigated in combination with pembrolizumab for the treatment of STK11-mutant cancer (NCT05887492). Patients are eligible for enrollment in the TNG260 phase 1/2 trial if their tumor contains a deleterious STK11 mutation. To begin classifying non-annotated variants, over 2,000 distinct mutations in the STK11 gene were identified from STK11 literature or public repositories of tumor sequencing data such as AACR Project GENIE and ClinVar. Where possible, loss-of-function annotations were captured from literature or predictive tools such as PolyPhen-2. However, many STK11 variants, particularly missense mutations, have never been functionally characterized. We developed a functional screening approach to characterize STK11 alterations using the lung adenocarcinoma cell line A549. A549 cells contain homozygous loss of STK11 via a truncation mutation at Q37, and re-expression of wild-type STK11 in these cells strongly impairs their growth in vitro and in vivo. We created a library of STK11 variant cDNAs, each containing a unique barcode. This library was expressed in A549, and cells were maintained in vitro or in vivo to allow for positive selection of STK11 loss-of-function variants and depletion of variants that behave like wild-type STK11. At the end of the screen, variants were quantified by NGS using each mutant cDNA’s unique barcode and compared to well-annotated controls. These data were assembled to generate TNG260mutationfinder.com – the first website to curate STK11 variants with functional annotations. Citation Format: Leanne G. Ahronian, Preksha Shahagadkar, Lauren Flynn, Lauren Grove, Shangtao Liu, Samuel R. Meier, Binzheng Shen, Hannah Stowe, Hsin-Jung Wu, Yi Yu, Andre Mignault, Iga Sienczylo, Heather DiBenedetto, Silvia Fenoglio, Teng. Experimental ‘loss-of function’ annotation of STK11 mutations with prognostic and therapeutic implications (TNG260mutationfinder.com) [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 5584.

Background Loss of function mutations in STK11 drive immune evasion and cause resistance to immune checkpoint blockade. TNG260 is a small molecule inhibitor of the CoREST complex that increases the expression of immune-related genes in STK11-deficient cancer cells. TNG260 reverses the immune evasion phenotype caused by STK11 loss and induces tumor regressions in STK11-deficient models in combination with anti-PD1. Methods We discovered and developed TNG260, a small molecule which selectively inhibits the CoREST complex and spares the other Class I HDAC complexes, NCoR, NuRD, and Sin3 (with 500-fold selectivity). Previous reports have shown that combining an LSD1 inhibitor with anti-PD1 results in improved antitumor responses. Since LSD1 is a member of the CoREST complex, the combination of an LSD1 inhibitor with anti-PD1 was evaluated to determine if an LSD1 inhibitor can replicate the effects of TNG260 in an STK11-deficient mouse model that is typically resistant to anti-PD1 monotherapy. We also profiled an AXL inhibitor, which is currently in development for STK11-mutant cancer as a combination approach with pembrolizumab. To determine the mechanism of the TNG260 immunomodulatory effect on tumors, we performed RNA-sequencing and cytokine profiling of STK11-mutant cancer cell lines after treatment with TNG260. Results TNG260 with anti-PD1 induced tumor regressions in 75% of animals with STK11-deficient tumors. In contrast, an LSD1 inhibitor in combination with anti-PD1 provided limited tumor growth inhibition compared to anti-PD1 alone in an STK11-deficient syngeneic model. Similarly, the AXL inhibitor, bemcentinib, provided a minor enhancement to the tumor growth inhibition seen with anti-PD1 as a single agent in this model. These data suggest that TNG260 outperforms other anti-PD1-based combination therapies in development for STK11-deficient cancer. TNG260 causes transcriptional changes in STK11-mutant cancer cells such as up-regulation of genes involved in antigen presentation and interferon gamma pathway signaling. These results are consistent with cytokine profiling studies which show that TNG260 causes an increase in T cell activity when tumor cells are co-cultured with PBMCs. These findings support previous experiments which demonstrate that TNG260 is an immunomodulatory compound. Conclusions TNG260 alters expression of immunomodulatory genes in STK11-deficient cancer cells via inhibition of the CoREST complex. Unlike other small molecules being combined with anti-PD1 for STK11-deficient NSCLC, the combination of TNG260 with anti-PD1 drives tumor regressions in STK11-deficient models that are typically resistant to anti-PD1 monotherapy. TNG260 is under investigation in a Phase 1/2 study as a single agent and in combination with pembrolizumab for patients with STK11-mutated, advanced solid tumors.

STK11 loss of function mutations occur in 12-15% of lung adenocarcinoma and have been shown to drive resistance to immune checkpoint blockade in patients and preclinical models. STK11-deficient syngeneic mouse tumor models reflect this biology and are insensitive to anti-PD1 treatment. Informed by in vivo CRISPR-based screens, histone deacetylase 1 (HDAC1) was identified as a target gene, which when knocked out in tumor cells, reverses anti-PD1 resistance driven by STK11 tumor suppressor gene loss. Here, we describe the discovery and development of TNG260 as a potent and selective inhibitor of the HDAC1-containing complex CoREST. TNG260 inhibits CoREST deacetylase activity with 500-fold selectivity over the other HDAC1-containing complexes, NuRD and Sin3, and the HDAC3-containing complex NCoR. In preclinical studies, selective CoREST inhibition by TNG260 results in transcriptional reprogramming of STK11-mutant tumor cells, altering tumor cell cytokine secretion and markedly reducing recruitment of suppressive Treg cells to STK11-mutant tumors. Moreover, TNG260, in combination with anti-PD1 treatment, drives durable tumor regressions in multiple syngeneic STK11-mutant xenograft models. TNG260 has no anti-tumor efficacy in athymic mice, indicating the responses with TNG260 are mediated by T cells. Unlike previously developed pan-HDAC inhibitors, which are directly cytotoxic to cancer (and immune) cells, IND-enabling toxicology studies in rat and dog showed that TNG260 was well-tolerated at exposures predicted to be efficacious in humans, with bone marrow suppression only detectable at doses where TNG260 is no longer selective for CoREST inhibition. TNG260 clinical development will be among the first to combine the power of genetic patient selection and immunotherapy, evaluating patients with STK11 mutant cancers in a trial combining TNG260 and a checkpoint inhibitor. Citation Format: Leanne G. Ahronian, Minjie Zhang, Chengyin Min, Alice W. Tsai, Jacques Ermolieff, Patrick McCarren, Margaret Wyman, David Guerin, Ye Wang, Alborz Bejnood, Kenjie Amemiya, Brian McMillan, Nikitha Das, Preksha Shahagadkar, Brian Doyon, Andre Mignault, Colin Liang, Vassil Elitzin, Samuel R. Meier, Ashley Choi, Yi Yu, John P. Maxwell, Brian B. Haines, Jannik N. Andersen, Heather DiBenedetto, Aaron Weitzman, Alan Huang, Xinyuan Wu. TNG260: A novel, orally active, CoREST-selective deacetylase inhibitor for the treatment of STK11-mutant cancers [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 ND12.

Abstract STK11 loss of function mutations occur in 12-15% of lung adenocarcinoma and have been shown to drive resistance to immune checkpoint blockade in patients and preclinical models. STK11-deficient syngeneic mouse tumor models reflect this biology and are insensitive to anti-PD1 treatment. Informed by in vivo CRISPR-based screens, histone deacetylase 1 (HDAC1) was identified as a target gene, which when knocked out in tumor cells, reverses anti-PD1 resistance driven by STK11 tumor suppressor gene loss. Here, we describe the discovery and development of TNG260 as a potent and selective inhibitor of the HDAC1-containing complex CoREST. TNG260 inhibits CoREST deacetylase activity with 500-fold selectivity over the other HDAC1-containing complexes, NuRD and Sin3, and the HDAC3-containing complex NCoR. In preclinical studies, selective CoREST inhibition by TNG260 results in transcriptional reprogramming of STK11-mutant tumor cells, altering tumor cell cytokine secretion and markedly reducing recruitment of suppressive Treg cells to STK11-mutant tumors. Moreover, TNG260, in combination with anti-PD1 treatment, drives durable tumor regressions in multiple syngeneic STK11-mutant xenograft models. TNG260 has no anti-tumor efficacy in athymic mice, indicating the responses with TNG260 are mediated by T cells. Unlike previously developed pan-HDAC inhibitors, which are directly cytotoxic to cancer (and immune) cells, IND-enabling toxicology studies in rat and dog showed that TNG260 was well-tolerated at exposures predicted to be efficacious in humans, with bone marrow suppression only detectable at doses where TNG260 is no longer selective for CoREST inhibition. TNG260 clinical development will be among the first to combine the power of genetic patient selection and immunotherapy, evaluating patients with STK11 mutant cancers in a trial combining TNG260 and a checkpoint inhibitor. Citation Format: Leanne G. Ahronian, Minjie Zhang, Chengyin Min, Alice W. Tsai, Jacques Ermolieff, Patrick McCarren, Margaret Wyman, David Guerin, Ye Wang, Alborz Bejnood, Kenjie Amemiya, Brian McMillan, Nikitha Das, Preksha Shahagadkar, Brian Doyon, Andre Mignault, Colin Liang, Vassil Elitzin, Samuel R. Meier, Ashley Choi, Yi Yu, John P. Maxwell, Brian B. Haines, Jannik N. Andersen, Heather DiBenedetto, Aaron Weitzman, Alan Huang, Xinyuan Wu. TNG260: A novel, orally active, CoREST-selective deacetylase inhibitor for the treatment of STK11-mutant cancers [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 ND12.

Background Histone deacetylase 1 (HDAC1) was identified from a novel in vivo CRISPR screening platform as a target gene whose inhibition reverses α-PD1 resistance driven by loss of STK11. Histone deacetylases are a well-studied class of oncology drug targets, but existing non-isoform-selective HDAC inhibitors have few approved clinical applications due to toxicities that limit sufficient exposure in solid tumors. Our data suggest that HDAC3, an essential gene, is a primary driver of bone marrow toxicity caused by HDAC inhibitors that target multiple isoforms. Methods We discovered and developed TNG260, a small molecule which inhibits HDAC1 with 10-fold selectivity over HDAC3 in cells, and 500-fold selectivity for the CoREST complex over the other HDAC1-containing complexes, NuRD and Sin3. Due to its CoREST-selective deacetylase inhibition, we have termed TNG260 a CoreDAC inhibitor. Results Treatment of an α-PD1 resistant STK11-mutant MC38 syngeneic tumor model with TNG260 re-sensitizes this model to treatment with α-PD1. The combination of TNG260 and α-PD1 led to durable complete tumor regressions in the majority of treated animals. All mice with complete responses remained tumor-free until tumor rechallenge (21 days) and rejected engraftment of tumor cells. Unlike previously developed HDAC inhibitors designed for tumor cell cytotoxicity, TNG260 has no anti-tumor efficacy in immunocompromised mice, indicating the tumor cell killing with TNG260 is immune-mediated and not due to direct cell killing. Immune profiling of tumors following treatment with TNG260 and α-PD1 showed a decoupling of Teffector and Tregulatory cell recruitment caused by α-PD1 monotherapy, leading to a more active immune microenvironment. TNG260 also decreased intratumoral infiltration of neutrophils, an immune suppressive cell type associated with STK11-mutant NSCLC. Toxicity profiling of TNG260 shows it has less viability impact on erythroid and myeloid cells in vitro than other HDAC inhibitors, and in vivo toxicity studies showed bone marrow suppression only at TNG260 doses that are no longer selective for HDAC1/2. Conclusions TNG260 is a potent, highly selective small molecule CoreDAC inhibitor with good drug-like properties. It reverses the immune evasion phenotype caused by loss of STK11 and induces tumor regressions in an STK11-mutant model in combination with α-PD1. The TNG260 clinical development plan will be among the first to combine the power of genetic patient selection and immunotherapy, evaluating patients with STK11 mutant cancers in a trial combining TNG260 and a checkpoint inhibitor.

Background Multiplexed ion beam imaging (MIBI) combines time-of-flight secondary ion mass spectrometry (ToF-SIMS) with metal labeled antibodies to image 40+ proteins in a single scan at subcellular spatial resolution. Here, we show that the recently released MIBIscope provides improved sensitivity for detecting immune checkpoint markers and offers greater throughput at higher resolution than the alpha instrument. Methods Serial sections from three FFPE NSCLC samples, in addition to a control slide consisting of various unremarkable tissues, were stained with a panel of 25 metal labeled antibodies. The tissue was imaged at subcellular resolution using the MIBIscope and the alpha instrument. Masses of detected species were assigned to target biomolecules given the unique label of each antibody and multi-step processing was used to create images. Cell classification was performed using two complementary methods that differed in the need for cell segmentation to phenotypically characterize the tissue environments and quantify marker expression. Results Replicate regions of interest (ROIs) were collected on both instruments with similarly sized ROIs acquired in 17 minutes with the MIBIscope compared to 280 minutes with the alpha instrument. Fourier Ring Correlation (FRC) showed the resolution to be greater on the MIBIscope as compared to the alpha instrument with FRC also demonstrating uniform resolution across an ROI 2.5X greater in size. Even with the 16X greater speed of the MIBIscope, the signal of the 25 markers across replicate ROIs was increased (y=x^1.07) and showed similar expression patterns to those observed on the alpha instrument (figure 1). This resulted in greater sensitivity to markers with low expression, such as checkpoint markers. Eleven cell populations were classified across the ROIs utilizing two methods, with both methods showing a similar frequency of tumor cells and B, T, and myeloid cell subsets between instruments. Segmentation enabled the number of cells within a population to be calculated but defining boundaries is laborious and signal from neighboring cells can result in misclassification. Performing classification at the pixel level, without segmentation, enabled the fraction of the tissue that is tumor or any other cell type to be rapidly determined. Conclusions The MIBIscope enables the phenotypic characterization of tumor and non-tumor microenvironments. Co-expression of markers can be used to classify tumor and immune populations and to quantify the expression of markers associated with immune suppression. The increased sensitivity and throughput of the MIBIscope, in combination with the 40-parameter capability and subcellular resolution, provides a platform uniquely suited to understanding the complex tumor immune landscape.