bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract C118: Design of programmable peptide-guided oncoprotein degraders via generative language models
Authors: Bhat Suhaas , Brixi Garyk , Palepu Kalyan , Hong Lauren , Yudistyra Vivian , Chen Tianlai , Vincoff Sophia , Zhao Lin , Chatterjee Pranam
Published: December 2023

Targeted protein degradation of pathogenic proteins represents a powerful new treatment strategy for multiple cancers. Unfortunately, a sizable portion of these proteins are considered “undruggable” by standard small molecule-based approaches, including PROTACs and molecular glues, largely due to their disordered nature, instability, and lack of binding site accessibility. As a more modular strategy, we have developed a genetically-encoded protein architecture by fusing target-specific peptides to E3 ubiquitin ligase domains for selective and potent intracellular degradation of oncoproteins. To enable programmability of our system, we develop a suite of algorithms that enable the design of target-specific peptides via protein language model (pLM) embeddings, without the requirement of 3D structures. First, we train a model that leverages pLM embeddings to efficiently select high-affinity peptides from natural protein interaction interfaces. Next, we develop a high-accuracy discriminator, based on the contrastive language-image pretraining (CLIP) architecture underlying OpenAI's DALL-E model, to prioritize and screen peptides with selectivity to a specified target oncoprotein. As input to the discriminator, we create a Gaussian diffusion generator to sample a pLM latent space, fine-tuned on experimentally-valid peptide sequences. Finally, to enable de novo design of binding peptides, we train an instance of GPT-2 with protein interacting sequences to enable peptide generation conditioned on target oncoprotein sequences. Our models demonstrate low perplexities across both existing and generated peptide sequences, highlighting their robust generative capability. By experimentally fusing model-derived peptides to E3 ubiquitin ligase domains, we reliably identify candidates exhibiting robust and selective endogenous degradation of diverse, "undruggable" oncoproteins in cancer cell models, including tumorigenic regulators such as β-catenin and TRIM8, as well as oncogenic fusion proteins, such as EWS-FLI1, PAX3-FOXO1, and DNAJB1-PRKACA. We further show that our peptide-guided degraders have negligible off-target effects via whole-cell proteomics and demonstrate their modulation of transcriptional and apoptotic pathways, motivating further translation of our therapeutic platform. Together, our work establishes a CRISPR-analogous system for programmable protein degradation applications across the oncoproteome.

Citation Format: Suhaas Bhat, Garyk Brixi, Kalyan Palepu, Lauren Hong, Vivian Yudistyra, Tianlai Chen, Sophia Vincoff, Lin Zhao, Pranam Chatterjee. Design of programmable peptide-guided oncoprotein degraders via generative language models [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C118.
Abstract C137: Tumor-selective, chaperone-mediated targeting of ERK5 (MAPK7)
Authors: Foley Kevin P , Yang Xiangcai , Yin Wei , Xu Mengmeng , Wang Mingkai , Ding Qinglin , Dai Yan , Zhou Haoxin , Tusa Ignazia , Menconi Alessio , Lombardi Zoe , Tubita Alessandro , Prince Thomas L , Wang Guoqiang , Rovida Elisabetta , Ying Weiwen
Published: December 2023

Extracellular signal-regulated kinase 5 (ERK5 or MAPK7) belongs to the mitogen-activated protein kinase family and has been associated with a wide range of cellular functions, including cell proliferation, migration, differentiation and survival. ERK5 has also been implicated in the onset and progression of several types of cancer. Importantly, studies comparing pharmacological inhibition versus genetic deletion or knockdown of ERK5 have revealed that it also possesses kinase activity-independent functions, suggesting that an ERK5 protein degrader approach may be required to completely block all ERK5-regulated signaling. To this end, we have explored applying Chaperone-mediated Protein Degradation (CHAMP) technology to target ERK5 protein. CHAMPs are heterobifunctional small molecules that mediate protein degradation by inducing proximity between a target protein and the HSP90 chaperone complex, resulting in target ubiquitination and degradation by the proteasome. Due to HSP90 being highly activated in cancer cells, CHAMPs also preferentially accumulate in tumors relative to normal tissues, resulting in an improved therapeutic index versus typical inhibitors. In order to chemically induce ERK5 degradation, CHAMP compounds were synthesized by covalently coupling ERK5- and HSP90-binding moieties through a short linker. CHAMP treatment of cancer cell lines resulted in formation of an ERK5-CHAMP-HSP90 ternary complex and subsequent proteasome-dependent ERK5 degradation. This in turn resulted in inhibition of ERK5 downstream signaling, leading to cell growth inhibition, cell cycle arrest and apoptosis in a panel of cancer cell lines. Further, in mouse xenograft models, CHAMPs displayed prolonged pharmacokinetics in tumors relative to plasma and normal tissues and strongly inhibited tumor growth at tolerated doses. Based on these findings, ERK5-targeted CHAMPs represents a promising new approach to disrupt the entire function of ERK5 for the of treatment cancer.

Citation Format: Kevin P Foley, Xiangcai Yang, Wei Yin, Mengmeng Xu, Mingkai Wang, Qinglin Ding, Yan Dai, Haoxin Zhou, Ignazia Tusa, Alessio Menconi, Zoe Lombardi, Alessandro Tubita, Thomas L Prince, Guoqiang Wang, Elisabetta Rovida, Weiwen Ying. Tumor-selective, chaperone-mediated targeting of ERK5 (MAPK7) [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C137.
Abstract C140: BI 1810631 is a novel EGFR wild-type sparing, HER2-selective small molecule inhibitor that efficiently blocks HER2 mutant-driven lung cancer
Authors: Neumüller Ralph A. , Wilding Birgit , Scharn Dirk , Baum Anke , Augsten Martin , Waizenegger Irene , Kohsaka Shinji , Santoro Valeria , Chetta Paolo , Woelflingseder Lydia , Popow Johannes , Gerlach Daniel , Ettmayer Peter , Gerstberger Thomas , Fuchs Julian , Treu Matthias , Zahn Stephan , Pearson Mark , Petronczki Mark , McConnell Darryl B. , Kraut Norbert , Solca Flavio
Published: December 2023

Here we report pre-clinical characterization of the clinical compound BI 1810631, a HER2 specific, EGFR wild-type-sparing tyrosine kinase inhibitor (TKI). BI 1810631 has shown early signs of clinical activity in patients carrying tumors with HER2 aberrations [NCT04886804], mainly comprising HER2 mutations (Heymach et al. 2023). In non-small cell lung cancer, activating mutations in HER2 are found in 2-4% of patients and predominantly cluster in exon 20 within the tyrosine kinase domain (TKD), of which the most frequent variant is A775_G776insYVMA. Studies across tumor cell lines and xenograft mouse models show that BI 1810631 is a potent and selective inhibitor of HER2-driven oncogenic signaling. Compound-mediated reduction of cell growth and survival was observed in mutant HER2 driven Ba/F3 cell systems, in human tumor cell lines in vitro and translated into tumor regressions in a genome-engineered HER2-YVMA mutant xenograft model. The in vivo efficacy of BI 1810631 was further confirmed in HER2 exon 20 mutant patient-derived tumor models. Corresponding biomarker studies in vitro and in vivo showed modulation of pharmacodynamic markers, corroborating the on-target mechanism of action of the compound. These findings demonstrate that HER2 mutations can be effectively addressed by BI 1810631 and support the ongoing and future clinical trials.

Citation Format: Ralph A. Neumüller, Birgit Wilding, Dirk Scharn, Anke Baum, Martin Augsten, Irene Waizenegger, Shinji Kohsaka, Valeria Santoro, Paolo Chetta, Lydia Woelflingseder, Johannes Popow, Daniel Gerlach, Peter Ettmayer, Thomas Gerstberger, Julian Fuchs, Matthias Treu, Stephan Zahn, Mark Pearson, Mark Petronczki, Darryl B. McConnell, Norbert Kraut, Flavio Solca. BI 1810631 is a novel EGFR wild-type sparing, HER2-selective small molecule inhibitor that efficiently blocks HER2 mutant-driven lung cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C140.
Abstract C171: Immune desert microenvironment is associated with poor outcome in Wilms tumors
Authors: Su Xiaoping , Malouf Gabriel
Published: December 2023

Background: Presence of anaplasia is a potent marker for adverse outcome in patients with Wilms tumors with diffuse anaplasia (DAWT). Patients with WT with focal anaplasia (FAWT) are considered as intermediate risk. Besides TP53 mutations thought to arise in anaplastic components, the crosstalk between genomic alterations and immune landscape remains unknown.

Methods: We performed whole-exome and/or RNA sequencing on genomic DNA derived from 12 matched tumor-normal WTs and extended analysis in an independent dataset of 9 cases. TP53 mutations and tumor infiltrating lymphocytes (TILs: CD3, CD4 and CD8) were also assessed. Validation was performed using TARGET-WT (n=96) and GEO-WT (n=12) cohorts. Prognostic role of TILs was investigated in another 55 pre-treated WTs.

Results: TP53 (50%) and DROSHA (33.3%) were the sole recurrent mutations identified. TP53 mutations occurred in mutually exclusive manner with chromatin-modifying genes which were altered in both FAWT (100%) and DAWT (33.3%). Microenvironment analysis revealed a reproducible immune desert WTs with poor outcome that enriched in DAWT cases and TP53 mutation, which mirrored the inversion of CD4:CD8 ratio in TP53-mutated comparing to TP53-wild tumors (P=0.003). Immune desert WTs were also characterized by overexpression of DNA repair pathways, PRC2, HDCA, and polycomb targets of EZH2, leading to higher sensitivity to HDCA inhibitor of vorinostat. Additionally, the immunophenotypes were tightly associated with replication stress subtypes; WTs with high replication stress were susceptible to ATR and WEE1 inhibitors. High ratio of CD4/CD8 was considered as independent recurrence-free and overall survival factors for WTs (both P<0.05).

Conclusions: Our results reveal that WT with anaplastic features are characterized by either TP53 alterations or chromatin-modifying genes. These data implicate TP53 as a tumor cell-intrinsic driver of an immune desert phenotype, in contrast with adult TP53 tumors. TP53 inactivation might therefore causes epigenetic deregulation across cancer sites, and has implications for immunotherapy.

Citation Format: Xiaoping Su, Gabriel Malouf. Immune desert microenvironment is associated with poor outcome in Wilms tumors [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C171.
Abstract C172: PTX3 blockade restores anti-tumor immunity through suppressing M2-like macrophages phenotypes in colon cancer
Authors: Chen Feng-Wei
Published: December 2023

The tumor microenvironment is a chronic inflammatory condition which is composed of various types of stromal cells, immune cells, and cytokines. Cancer-associated fibroblasts and M2-like macrophages are involved in enhancing malignancy of colon cancer progression, such as tumor growth and immunosuppression. Identifying the cross-talk mechanisms among cancer cells, cancer-associated fibroblasts, and M2-like macrophages is important for development of cancer therapy. Pentraxin 3 (PTX3) is a secretory factor that is rapidly responsive to exposure of proinflammatory cytokines. The function of PTX3 is known to regulate innate immunity and tissue remodeling. However, its role in tumor progression appears to be context-dependent and unclear. In this study, we found that PTX3 is silenced in colon cancer cells due to epigenetic regulation but is primarily expressed by fibroblasts in colon tumors. Clinically, higher PTX3 expression is positively correlated with fibroblast and inflammatory response signatures and associated with a poor survival outcome in colon cancer patients. Our results showed that PTX3 had no effect on cellular proliferation of fibroblasts or cancer cells in vitro, but blockade of PTX3 by specific monoclonal antibody significantly reduced stroma cell-mediated tumor growth in vivo. In addition, blockade of PTX3 reduced MC38 tumor growth in immunocompetent mice but had no effect in immunodeficient mice, suggesting the role of PTX3 in regulating tumor-immunity. Indeed, inhibition of PTX3 resulted in reduced numbers of M2-like macrophages and increased numbers of cytotoxic CD8 T cells in MC38 tumors. The expressions of cytotoxic markers in T cells were suppressed under exposure to conditioned media from PTX3-stimulated macrophages in vitro. We further revealed that PTX3 stimulated macrophage polarization toward an M2-like phenotype through activation of CREB/CEBPB axis. These findings suggest that PTX3 is involved in stroma cell-mediated protumoral immunity and targeting PTX3 by monoclonal antibody can be a potential therapeutic strategy in colon cancer treatment.

Citation Format: Feng-Wei Chen. PTX3 blockade restores anti-tumor immunity through suppressing M2-like macrophages phenotypes in colon cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C172.
Abstract C173: Negative selection of ligand-receptor interactions mediating lymphocyte infiltration confers melanoma resistance to Immune Checkpoint Blockade therapy by turning hot tumors to cold
Authors: Sahni Sahil , Wang Kun , Wang Binbin , Dhruba Saugato Rahman , Wu Di , Nagy Matthew , Ruppin Eytan
Published: December 2023

Immune checkpoint blockade (ICB) is a promising cancer therapy; however, response rates remain less than desired (less than ~40%) and resistance often develops. To learn more about ICB resistance mechanisms, we developed IRIS (Immunotherapy Resistance cell-cell Interaction Scanner), a machine learning method aimed at identifying candidate ligand-receptor interactions (LRI) that are likely to underlie ICB resistance in the tumor microenvironment (TME). Our approach considers two key components that such interactions should fulfill: they should be (1) differentially activated between the pre-treatment and post-treatment non-responderpatients, and (2) they should be predictive of ICB response in pre-treatment patients. We trained the model on the five largest publicly available melanoma bulk transcriptomics ICB cohorts and demonstrated its superior performance versus two states-of-the-art transcriptomics-based prediction methods (IMPRES and TIDE) in predicting ICB therapy response both in terms of RECIST criteria and patient survival. We further validated our identified resistance relevant LRIs in a melanoma single cell ICB cohort. Strikingly, LRIs highly activated in the pre-treatment group showed stronger predictive power for ICB response compared to the post-treatment non-responder group, which implies a potential negative selection of LRIs by tumors. Notably, many of these LRIs are mediating lymphocyte infiltration within the TME. Reassuringly, we further find a strong correlation between the activity of these LRIs and CD8+ T cells infiltration levels in the TME and are highly enriched in hot tumors in an independent cohort. Overall, these findings suggest that the tumor may develop resistance to ICB via inhibiting lymphocytes infiltration relevant ligand-receptor interactions, turning hot tumors to cold.

Citation Format: Sahil Sahni, Kun Wang, Binbin Wang, Saugato Rahman Dhruba, Di Wu, Matthew Nagy, Eytan Ruppin. Negative selection of ligand-receptor interactions mediating lymphocyte infiltration confers melanoma resistance to Immune Checkpoint Blockade therapy by turning hot tumors to cold [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C173.
Abstract C175: The potential effect of KRAS inhibitors on tumor microenvironments
Authors: Tanaka Noritaka , Sakamoto Takeharu
Published: December 2023

KRAS is one of the most common driver oncogenes among various cancer types. Researches aiming to develop KRAS inhibitors has been surging recently and the first clinical KRAS inhibitor sotorasib was approved for non-small cell lung cancer in the US and Japan. As KRAS activity has been reported to have certain effects on tumor microenvironments, KRAS inhibitor could potentially induce collateral outcomes on tumor microenvironment. Therefore, I have analyzed the potential influences of resistance to KRAS inhibitors on the tumor microenvironment. At first, I have established pancreatic cancer cell line MIA-Paca2 that acquired resistance to sotorasib, MIA/AMG-R, by continuously exposing them to sotorasib (1 µmol/L). An RNA sequencing analysis were performed with MIA/AMG-R and revealed that a gene set related to hypoxia were upregulated. When non-small cell lung cancer cell line NCI-H358 cells were exposed to sotorasib (1 µmol/L) for 4 hrs, the protein levels of HIF-1A decreased while that in MIA Paca-2 cells were unaffected. To evaluate at which steps of protein synthesis from gene transcription to through protein degradation of HIF-1A, NCI-H358 cells were treated with transcription inhibitor actinomycin D, translation inhibitor cycloheximide or proteasome inhibitor MG-132. The treatment of transcription inhibitor actinomycin D on NCI-H358 cells for 6 hrs did not lead to the decrease of HIF-1A protein level however, translation inhibitor cycloheximide induced drastic decrease in HIF-1A protein. Although exposure of NCI-H358 cells to MG-132 increased the expression level of HIF-1A, the combinational treatment of sotorasib and MG-132 still led to slight decrease in HIF-1A protein level. Also, MG-132 failed to recover the protein expression level decreased by cycloheximide treatment. In total, the cellular expression level of HIF-1A is possibly dependent on translation activity and KRAS inhibitor potentially affect the HIF-1A expression through the regulation of its translation. Conclusively, KRAS inhibitors could potentially be used to reprogram the hypoxic tumor microenvironments besides its primary effect against the downstream signaling of KRAS.

Citation Format: Noritaka Tanaka, Takeharu Sakamoto. The potential effect of KRAS inhibitors on tumor microenvironments [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C175.
Abstract IA002: Inference of intercellular signaling activities in tumor spatial and single-cell transcriptomics, with applications in identifying cancer immunotherapy targets
Authors: Jiang Peng
Published: December 2023

My talk will present three computational frameworks we developed to study cytokine signaling activities and cell-cell communications during the antitumor immune response, using tumor single-cell and spatial transcriptomics. The basic immunology tool to study cytokine signaling mostly measures cytokine release, which is transient and does not represent downstream target activities. Therefore, we first developed the CytoSig platform, providing a database of target genes modulated by cytokines and a predictive model of cytokine signaling cascades from transcriptomic profiles. We collected 20,591 transcriptome profiles for human cytokine, chemokine, and growth factor responses. This atlas of transcriptional patterns induced by cytokines enabled the reliable prediction of signaling activities in distinct cell populations in infectious diseases, chronic inflammation, and cancer using bulk and single-cell transcriptomic data. CytoSig revealed previously unidentified roles of many cytokines, such as BMP6 as an anti-inflammatory factor. Then, based on CytoSig, we developed Tres, a computational model utilizing single-cell transcriptomic data to identify signatures of T cells that are resilient to immunosuppressive signals, such as TGF-β1, TRAIL, and prostaglandin E2. Tres reliably predicts clinical responses to immunotherapy in multiple cancer types using bulk T cell transcriptomic data from pre-treatment patient tumors or infusion/pre-manufacture samples for cellular immunotherapies. Further, Tres identified FIBP as a candidate immunotherapy target to potentiate adoptive cell therapy efficacies. FIBP knockout in T cells enhanced adoptive cell therapy by down-regulating T cells' cholesterol metabolism. Last, I will briefly show our SpaCET framework for deconvolving cell fractions and identifying cell-cell interactions in tumor spatial transcriptomics data. SpaCET resolved several challenges in spatial transcriptomics analysis that previous methods did not address sufficiently. Through coupling cell fractions with ligand-receptor co-expression analysis, SpaCET reveals that intercellular interactions tend to be located at the tumor-immune boundaries.

Citation Format: Peng Jiang. Inference of intercellular signaling activities in tumor spatial and single-cell transcriptomics, with applications in identifying cancer immunotherapy targets [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr IA002.
Abstract IA004: Preclinical development of DuoBody®-CD3xB7H4, a novel CD3 bispecific antibody for the treatment of solid cancers
Authors: Koopman Louise A , Alemdehy Farshid , Paauwe Madelon , Vries Laura Smits-de , Karaiskaki Frosso , Brandhorst Marcel , Franken Patrick , Plantinga Theo S , Houtkamp Mischa A , de Poot Stefanie A.H. , Breij Esther C.W.
Published: December 2023

Several clinical trials are currently underway to investigate the effectiveness of CD3 bispecific antibodies (bsAb) in solid tumors. Given the number of approved CD3 bsAb therapies thus far, the development of these bsAbs appears to be more challenging in solid cancer compared to hematological malignancies. The choice of an appropriate tumor-specific target and CD3 affinity are important considerations for the development of effective and safe CD3 bsAbs. The immune checkpoint protein B7H4 is differentially expressed between normal and tumor tissue, showing high expression in various solid cancers. Therefore, B7H4 provides an attractive target for a CD3 bsAb. We explored the preclinical mechanism of action (MoA) and pharmacodynamic (PD) markers of two B7H4-targeting CD3 bsAbs with different CD3 affinities. By crosslinking CD3 on T cells with B7H4 on tumor cells, CD3xB7H4 bsAbs will induce T-cell mediated cytotoxicity in B7H4-expressing tumor cells, associated with T-cell activation and cytokine production. In comparative preclinical characterization studies in vitro, we showed that both bsAbs induced target-specific, dose-dependent, and complete tumor cell kill in a panel of tumor cell lines expressing varying levels of B7H4, albeit with different potency. Moreover, both molecules demonstrated an acceptable safety profile in cynomolgus monkeys. DuoBody-CD3xB7H4 (GEN1047), the variant with lower CD3 affinity, was selected as clinical candidate, to leverage its observed propensity for lower cytokine production. In a patient-derived xenograft model of ovarian cancer in NCG-HIS mice examined in vivo, DuoBody-CD3xB7H4 showed dose-dependent antitumor activity, which was associated with increased numbers of intratumoral T cells and with peripheral PD biomarkers of T-cell activation and cytokine production. Currently, DuoBody-CD3xB7H4 is being investigated in a first-in-human clinical trial for the treatment of solid tumors known to express B7H4 (NCT05180474), in which the MoA and PD, including biomarkers of response, will be clinically explored.

Citation Format: Louise A Koopman, Farshid Alemdehy, Madelon Paauwe, Laura Smits-de Vries, Frosso Karaiskaki, Marcel Brandhorst, Patrick Franken, Theo S Plantinga, Mischa A Houtkamp, Stefanie A.H. de Poot, Esther C.W. Breij. Preclinical development of DuoBody®-CD3xB7H4, a novel CD3 bispecific antibody for the treatment of solid cancers [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr IA004.
Abstract IA009: Antibody-lectin chimeras for glyco-immune checkpoint blockade
Authors: Stark Jessica
Published: December 2023

Despite the curative potential of checkpoint blockade immunotherapy, a majority of patients remain unresponsive to existing treatments. Glyco-immune checkpoints – interactions of cell-surface glycans with lectin, or glycan binding, immunoreceptors – have emerged as prominent mechanisms of immune evasion and therapeutic resistance in cancer. Here, we describe antibody-lectin chimeras (AbLecs), a modular platform for glyco-immune checkpoint blockade. AbLecs are bispecific antibody-like molecules comprising a tumor-targeting arm as well as a lectin “decoy receptor” domain that directly binds tumor glycans and blocks their ability to engage lectin receptors on immune cells. AbLecs enhanced cancer cell killing in vitro via macrophage phagocytosis and NK cell and granulocyte cytotoxicity compared to their parent monoclonal antibodies. AbLec treatment reduced tumor burden in vivo compared to treatment with the parent antibody in a humanized model of metastatic HER2+ cancer. Furthermore, AbLecs synergized with blockade of the “don’t eat me” signal CD47 for enhanced tumor killing. AbLecs can be readily designed to target numerous tumor-associated antigens and glyco-immune checkpoint ligands, and therefore represent a new modality of cancer immunotherapy.

Citation Format: Jessica Stark. Antibody-lectin chimeras for glyco-immune checkpoint blockade [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr IA009.
Abstract IA010: Engineering human sialidase as novel cancer therapeutics by targeting sialoglycans
Authors: Peng Li
Published: December 2023

Immune checkpoint blockade has revolutionized cancer treatment, but resistance remains a significant hurdle for many patients. Sialoglycans, as new immune checkpoints on tumors, present a promising therapeutic opportunity to enhance immune response. Cleaving off sialoglycans from tumors using a tumor-associated antigen (TAA) targeted antibody-bacterial sialidase conjugate has shown antitumor activity in preclinical models. Recognizing the immunogenicity risk of bacterial enzymes, we've engineered a human sialidase for therapeutic development. By investigating the roles of sialoglycans on immune cells, we've found that cleaving T cell surface sialoglycans boosts antitumor immunity. Additionally, we've demonstrated the efficacy and tolerability of the untargeted engineered human sialidase Fc fusion (Bi-Sialidase) as a potential immunotherapy. These advancements have led to the development of the EAGLE (enzyme antibody glycan editing) technology platform, which restores antitumor immunity by stripping sialic acids from immunosuppressive sialoglycans on both tumor and immune cells.

Citation Format: Li Peng. Engineering human sialidase as novel cancer therapeutics by targeting sialoglycans [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr IA010.
Abstract LB_A04: Quantitative digital spatial protein profiling of non-small cell lung cancer brain metastasis
Authors: Kim Tae Jung
Published: December 2023

Metastatic brain tumor is the most common form of adult central nervous system (CNS) tumor, and the majority of the cerebral metastasis originate from lung cancer. Along with recent combination strategies applying immune checkpoint inhibitor, evaluating tumor microenvironment of the brain metastasis (BM) needs to be unveiled. In this study, we tried to disclose immune context information of BM of non-small cell lung cancer (NSCLC) by using highly multiplex NanoString digital spatial profiling (DSP) method. Seven cases of NSCLC and metastatic brain tumor were evaluated. To detect proteins at quantitative and high multiplex with spatial resolution, NanoString optical barcoding technology was used to digitally profile protein expression in FFPE samples. Immuno-oncology protein targets, including immune cell markers and checkpoint proteins are included. DSP identified differentially expressed proteins between primary NSCLC and BM. Proteins associated with immune regulation, evasion, and adaptive immunity, such as IDO-1, PD1, PDL1, STAT3, PTEN, and CD44 revealed decreased expression in patients with BM (P<0.01). The expression of pS6 was significantly increased in BM (P<0.01), which is associated with activation induced T-cell death. This study demonstrated differentially expressed proteins in BM associated with immune regulation and evasion via NanoString DSP platform. This study highlighted the localized expression of immune-related proteins of BM in patients with NSCLC. Moreover, our results presented the possibility of using digitally quantified and spatially allocated novel method in BM eliminating the subjectivity and variability associated with the immunohistochemistry techniques.

Citation Format: Tae Jung Kim. Quantitative digital spatial protein profiling of non-small cell lung cancer brain metastasis [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_A04.
Abstract LB_A21: NCI60 HTS384: The next phase of the NCI60 screen
Authors: Teicher Beverly A , Kunkel Mark W , Morris Joel , Taylor Ronald C , Dexheimer Thomas S , Coussens Nathan P , Doroshow James H
Published: December 2023

The NCI60 human tumor cell line screen, which has operated as a free service to the cancer research community for over 20 years, has proven to be an important drug discovery tool. The screen has operated using cutting-edge technology of the 1990s including a 96-well microplate format, a 2-day drug exposure period and following cell fixation, and a visible absorbance endpoint by the protein-staining dye sulforhodamine B (SRB). The SRB endpoint determines cell density based on protein content with a lower resolution limit of 1,000 – 2,000 cells. This report describes the next phase of this important cancer research tool, the NCI60 HTS384 screen format. While the cell lines remain the same, the screen is performed using 384-well microplates with a 3-day compound exposure period and a CellTiter-Glo luminescence endpoint. The CellTiter-Glo endpoint determines cell number based upon ATP content with a lower resolution limit of <10 cells. To develop a baseline comparison, data were generated from a library of 1,000 FDA-approved and investigational small molecule anticancer agents by the two assay formats. Although the mean-graph patterns and COMPARE analyses are very similar for many compounds, there is a divergence between the two screens for some molecular targets. Within subsets of approved and investigational agents directed toward the same target (e.g., EGFR, BRAF/MEK/ERK, and PI3K inhibitors), the clustering of compound data from the NCI60 HTS384 screen is qualitatively similar to the clustering of compound data from the classic NCI60 SRB screen and there is a strong COMPARE correlation between the two screens. However, for some drug targets there is very little or no clustering between data from the two screens, although the clustering within each screen is moderate-to-good. Examples include mTOR rapalogs, BET bromodomain and NAMPRTase inhibitors. Differences in data between the two screens might be partially attributed to increases in the assay endpoint sensitivity and compound exposure time of the NCI60 HTS384 assay. Compounds submitted for NCI60 screening after September 30, 2023, will be tested in the modernized NCI60 HTS384 format. This project was funded in part with federal funds from the NCI, NIH, under contract no. HHSN261201500003I and by the Intramural Research Program of the NIH, National Cancer Institute.

Citation Format: Beverly A Teicher, Mark W Kunkel, Joel Morris, Ronald C Taylor, Thomas S Dexheimer, Nathan P Coussens, James H Doroshow. NCI60 HTS384: The next phase of the NCI60 screen [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_A21.
Abstract LB_B08: The SRG OncoRat supports tumors derived from several RAS mutant cell lines for pre-clinical testing of RAS-inhibitors
Authors: Walton Grace , Begemann Diane , Dunn Cynthia , Steffey Valeriya , Brenzel Christopher , Noto Fallon
Published: December 2023

RAS family proteins have emerged as important molecular targets in multiple cancer therapeutics due to their role in hypertrophic and pro-mitotic signaling. KRAS is a small GTPase that is activated in response to growth factors including HGF, TGFα, and EGF. KRAS then activates the MAP kinase (MAPK; RAF/MEK/ERK) signaling pathway, driving ERK translocation to the nucleus, and resulting in transcription of pro-mitotic and hypertrophic genes. Furthermore, KRAS contributes to PI3K/AKT/mTOR signaling, leading to transcriptional activation as well as protein synthesis via mTOR. We validated several RAS mutant cell-derived tumor xenograft models in the SRG OncoRat. Cells were inoculated subcutaneously in the flank of SRG rats. To date, we have validated tumor growth using the HT-1080 fibrosarcoma NRAS mutant (Gln61Lys (c.181C>A)) cell line. We have also validated a suite of KRAS mutant lines in the SRG OncoRat, including: A-549 lung adenocarcinoma (Gly12Ser (c.34G>A)); NCI-H2122 NSCLC adenocarcinoma (Gly12Cys (c.34G>T)); MIA PaCa-2 pancreatic ductal adenocarcinoma and H-358 NSCLC adenocarcinoma (Gly12Cys (c.34G>T)); Capan-2 pancreatic ductal adenocarcinoma (Gly12Val (c.35G>T)); NCI-H441 NSCLC papillary adenocarcinoma (Gly12Val (c.35G>T)); NCI-H1734 NSCLC adenocarcinoma (Gly13Cys (c.37G>T)); and MDA-MB-231 breast adenocarcinoma (Gly13Asp (c.38G>A)). All cell lines showed robust and consistent tumor growth when injected subcutaneously into the SRG OncoRat. These models provide valuable tools for pre-clinical testing of RAS inhibition.

Citation Format: Grace Walton, Diane Begemann, Cynthia Dunn, Valeriya Steffey, Christopher Brenzel, Fallon Noto. The SRG OncoRat supports tumors derived from several RAS mutant cell lines for pre-clinical testing of RAS-inhibitors [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_B08.
Abstract LB_B10: Non-V600 BRAF mutants and their precise targeting
Authors: Hu Jiancheng
Published: December 2023

Hyperactive RAS/RAF/MEK/ERK signalling is responsible for a large portion of cancers and targeting this signalling pathway has achieved a promising outcome in clinic cancer treatment.  However,  significant challenges such as drug resistance are still existing. To resolve these problems, we need a deeper understanding of the regulatory mechanism and hence develop better targeting approaches against this signalling pathway. In this study, we investigated the molecular mechanism that controls that activity of BRAF, a key component of this signalling pathway, and found that BRAF cycled between inactive monomeric status and active dimeric status, which is coordinatively regulated by Cdc37/Hsp90 chaperone and 14-3-3 scaffold. Further, we found that most non-V600 mutations of BRAF in cancer genomes undermined this regulatory mechanism through disturbing the association of BRAF with Cdc37/Hsp90 chaperone or 14-3-3 scaffold and hence trapped BRAF in active dimeric status.  Given the high dimer affinity of these non-V600 BRAF mutants, we next examined whether their activity could be inhibited effectively RAF dimer breaker PLX8394 in vitro and in vivo. Indeed, we found that in contrast to clinic RAF inhibitor Vemurafenib (PLX4720), PLX8394 strongly inhibited the activity of non-V600 BRAF mutants and induced a rapid regression of fibroblastomas driven by non-V600 BRAF mutants. Together, our data clearly illustrates how oncogenic non-V600 mutations break down the regulation of BRAF by Cdc37/Hsp90 chaperone and 14-3-3 scaffold, and how these BRAF mutations could be precisely targeted by RAF dimer breaker, which has important implications for anti-BRAF cancer therapy.

Citation Format: Jiancheng Hu. Non-V600 BRAF mutants and their precise targeting [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_B10.
Abstract LB_B22: DrugMap: A quantitative pan-cancer analysis of cysteine ligandability
Authors: Bar-Peled Liron
Published: December 2023

Cysteine-focused chemical proteomic platforms have expanded the repertoire of protein targets for covalent inhibitors. However, it remains unknown how cysteine targeting varies across multiple cancer contexts. To address this question, we compiled an atlas of cysteine ligandability across 417 cancer cell lines. We unexpectedly find that cysteine ligandability fluctuates across cancers, which we attribute to differences in cellular redox state, protein complex formation and mutation. Focusing on lineage-restricted liganding, we identify highly actionable cysteines in SOX10, leveraging this information to develop covalent inhibitors. We find the SOX10 ligand functions as a covalent molecular glue and disrupts transcriptional activity in a dominant negative manner. Our findings reveal pervasive heterogeneity  in cysteine ligandability across cancer, pinpoint cell-intrinsic features driving cysteine targeting, and exemplify the use of covalent probes to disrupt [BPL2] oncogenic transcription factor activity.

Citation Format: Liron Bar-Peled. DrugMap: A quantitative pan-cancer analysis of cysteine ligandability [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_B22.
Abstract LB_C11: Small-molecule bifunctional inhibitors of PARP1/2 and HDAC enzymes
Authors: Truong Sarah , Ramos Louise , Zhai Beibei , Joshi Jay , Ghaidi Fariba , Marzban Mona , Adomat Hans , Chen Charles , Langlands John , Brown Dennis , Bacha Jeffrey , Collins Colin , Sorensen Poul , Shen Wang , Daugaard Mads
Published: December 2023

Background: Poly(ADP-ribose) polymerase (PARP) plays a major role in DNA repair and PARP inhibitors (PARPi) have shown promise for the treatment of cancers with DNA damage repair defects, such as BRCA mutations. PARPi are currently approved for treatment of BRCA-mutated cancers and as a maintenance therapy for patients who have responded to platinum-based chemotherapy. To improve efficacy, overcome resistance, and expand the usage of PARPi to non-BRCA mutated disease, combination therapies with PARPi have emerged as an area of interest. Histone deacetylases (HDACs) play a major role in DNA repair and inhibition of HDACs has been shown to reduce tumor growth. PARPi combined with HDACi has shown enhanced efficacy in pre-clinical studies in various cancers, and a clinical trial of olaparib and vorinostat against metastatic breast cancer is ongoing. However, combination therapies can be limited clinically due to overlapping toxicities and differing pharmacokinetics. Here, we report the efficacy of a novel class of bifunctional small-molecule compounds (kt-3000) with both PARP1 and PARP2 inhibitory and HDAC inhibitory activities.

Methods: PARP1 and PARP2 activity was measured using Trevigen Universal Colorimetric PARP Assay kit and BPS Bioscience PARP2 Colorimetric Assay kit respectively. HDAC activity was measured using HeLa nuclear extracts and a fluorogenic peptide-based biochemical assay. In vitro metabolism was determined by HPLC after incubation with human liver microsomes for up to 45 mins. Pharmacokinetic profiling was examined in mice up to 6 h after oral/intraperitoneal (IP) dosing.

Results: kt-3000 compounds showed potent inhibition of PARP1 and PARP2 activity with IC50 values comparable to olaparib (low nM) and inhibition of HDACs with IC50 values in the low µM range. Metabolic and pharmacokinetic profiling suggest drug-like qualities in the class.

Conclusion: kt-3000 molecules demonstrate potent inhibition of PARP1/2 and HDAC activities, with suitable pharmacokinetic properties for oral delivery. Further refinement and development of these bifunctional single-molecule inhibitors may offer a novel therapeutic opportunity for treatment of cancers with and without DNA damage repair defects.

Citation Format: Sarah Truong, Louise Ramos, Beibei Zhai, Jay Joshi, Fariba Ghaidi, Mona Marzban, Hans Adomat, Charles Chen, John Langlands, Dennis Brown, Jeffrey Bacha, Colin Collins, Poul Sorensen, Wang Shen, Mads Daugaard. Small-molecule bifunctional inhibitors of PARP1/2 and HDAC enzymes [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_C11.
Abstract LB_C19: Suppression of the antitumoral activity of natural killer cells by cancer-associated fibroblasts in a pancreatic TIME-on-Chip model
Authors: Kim Hyun-Ah , Kim Hyunsoo , Nam Min-Kyung , Park Jong Kook , Lee Moo-Yeal , Chung Seok , Lee Kyung-Mi , Kuh Hyo-Jeong
Published: December 2023

Background: Recently, natural killer (NK) cells emerged as a treatment option for various solid tumors. However, the immunosuppressive tumor immune microenvironment (TIME) can reduce the cytotoxic ability of NK cells in pancreatic ductal adenocarcinoma. Cancer-associated fibroblasts within the tumor stroma can suppress immune surveillance by dysregulating factors involved in the cellular activity of NK cells. Herein, the effect of activated pancreatic stellate cells (aPSCs) on NK cell-mediated anticancer efficacy under three-dimensional (3D) coculture conditions was investigated.

Methods: 3D cocultures of PANC-1 tumor spheroids (TSs) with aPSCs and NK-92 cells in a collagen matrix were optimized to identify the occurring cellular interactions and differential cytokine profiles in conditioned media using microchannel chips. PANC-1 TSs and aPSCs were indirectly cocultured, whereas NK-92 cells were allowed to infiltrate the TS channel using convective medium flow.

Results: Coculture with aPSCs promoted PANC-1 TSs growth and suppressed the antitumor cytotoxic effects of NK-92 cells. Mutual inhibition of cellular activity without compromising migration ability was observed between aPSCs and NK-92 cells. Moreover, the reduced killing activity of NK-92 cells was found to be related with reduced granzyme B expression in NK cells.

Conclusions: Herein, a novel TIME-on-chip model based on the coculture of PANC-1 TSs, aPSCs, and NK-92 cells was described. This model may be useful for studying the detailed mechanisms underlying NK cells dysregulation and for exploring future therapeutic interventions to restore NK cell activity in the tumor microenvironment.

Citation Format: Hyun-Ah Kim, Hyunsoo Kim, Min-Kyung Nam, Jong Kook Park, Moo-Yeal Lee, Seok Chung, Kyung-Mi Lee, Hyo-Jeong Kuh. Suppression of the antitumoral activity of natural killer cells by cancer-associated fibroblasts in a pancreatic TIME-on-Chip model [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_C19.
Abstract LB_C22: Dynamic interactions of disordered N-terminal domain of p53 in cancer
Authors: Wang Chunyu , Christopher Baines , Chen Jianhan , Loh Stewart
Published: December 2023

TP53 is mutated in over half of all human cancers, making it the most important tumor suppressor. p53 sequence includes an N-terminal domain (NTD), a DNA binding domain (DBD), and others. NTD is intrinsically disordered and interacts with many proteins, acting as a hub for cellular signaling. Using a combination of computational and experimental approaches, we show NTD have dynamic interactions with cyclophilin D (CypD), a mitochondria proline isomerase with key roles in cellular necrosis and mitochondrial energy metabolism. We show that a subset of p53 truncation mutations can promote cancer cell proliferation and mitochondrial metabolism in a CypD-dependent manner. Although dynamic interfaces are often considered “undruggable”, we have demonstrated that EGCG, the active ingredient of green tea, can bind to NTD and disrupt NTD-CypD interaction, inhibiting the effects of p53 truncation mutants. Our studies point to a novel mechanism for p53 gain-of-function (GOF) mutations through NTD interaction with mitochondrial CypD. Our data also provide novel insights into dynamic interactions of intrinscially disordered proteins and small molecule engagement of such challenging drug targets, with important implications for cancer treatment.

Citation Format: Chunyu Wang, Baines Christopher, Jianhan Chen, Stewart Loh. Dynamic interactions of disordered N-terminal domain of p53 in cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr LB_C22.