tbuckley/cabot-search huggingface dataset:
Abstract 3023: Master corepressor inactivation through oncogene suppressor RAI2 mediated polymerization
Authors: Nishit Goradia, Stefan Werner, Edukondalu Mullapudi, Gunhild von Amsberg, Klaus Pantel, Matthias Wilmanns
Journal: Cancer Research (2024)

Abstract Imbalanced transcription of a large number of genes can be caused at various levels, ranging from alterations in individual transcription factors to dysfunctional corepressor and coactivator complexes [1]. C-terminal binding proteins (CtBPs) are ubiquitous master transcriptional coregulators associated with the Polycomb Repressive Complex 2 (PRC2), with essential functions in the development and oncogenesis of various tumor entities, including breast cancer and prostate cancer (PC) [2,3]. As CtBPs bind to short linear PxDLS-like sequence motifs (SLiMs), the presence of such motifs in tandem on the putative metastasis suppressor RAI2 [4] suggested a previously undiscovered dual interaction with CtBPs. Here, we show that RAI2 induces CtBP polymerization through well-ordered filaments of stacked tetrameric CtBP layers, as illustrated by a high-resolution single particle cryo electron microscopy structure. These filaments are mirrored by RAI2-mediated CtBP nuclear foci and relief of CtBP corepressor function in RAI2-expressing cancer cells. Analyses of a diverse PC patient cohort revealed a substantial decrease in RAI2 in the aggressive subtypes, suggesting a pivotal role of RAI2 in the transition to androgen receptor signaling-independent progression. Taken together, our data demonstrate a previously unknown mechanism of multivalent short linear sequence motif-induced polymerization. As RAI2-like SLiM motifs are found in a wide range of organisms, including pathogenic viruses, our findings serve as a paradigm for diverse functional effects through multivalent interaction-mediated polymerization by disordered proteins in healthy and diseased conditions. The specific properties of these repeated interactions open up new therapeutic opportunities. References [1] Lee, T.I. &amp; Young, R.A. Transcriptional regulation and its misregulation in disease. Cell 152, 1237-51 (2013). [2] Di, L.J. et al. Genome-wide profiles of CtBP link metabolism with genome stability and epithelial reprogramming in breast cancer. Nat Commun 4, 1449 (2013). [3] Wang, R. et al. Role of transcriptional corepressor CtBP1 in prostate cancer progression. Neoplasia 14, 905-14 (2012). [4] Werner, S. et al. Suppression of early hematogenous dissemination of human breast cancer cells to bone marrow by retinoic Acid-induced 2. Cancer Discov 5, 506-19 (2015). Citation Format: Nishit Goradia, Stefan Werner, Edukondalu Mullapudi, Gunhild von Amsberg, Klaus Pantel, Matthias Wilmanns. Master corepressor inactivation through oncogene suppressor RAI2 mediated polymerization [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 3023.
Abstract 4209: Unraveling the effects of the microenvironment on glioblastoma multiforme invasiveness using a xeno-free 3D hydrogel platform
Authors: Alejandra I. Ferrer Díaz, John Huang
Journal: Cancer Research (2024)

Abstract Glioblastoma multiforme (GBM) is a grade IV astrocytoma and the most common type of adult brain malignancy. The overall survival of patients diagnosed with GBM is less than 5 years. Therefore, it is imperative to understand the mechanisms contributing to GBM progression, invasiveness, and survival. This study aimed to evaluate the effect of the extracellular matrix (ECM) on GBM cell invasion by performing the traditional invasion assay as well as novel in vitro invasion assay strategies. A significant challenge with in vitro cell invasion assays is the use of animal-based ECM: the components of animal-based ECM are not characterized; the batch-to-batch variability of animal-based ECM can influence experimental findings and affect potential clinical applications; and the temperature-sensitive operation protocols make the use of animal-based ECM time-consuming and difficult for automated high-throughput assays. These challenges can be circumvented using VitroGel®, a synthetic xeno-free, bio-functional hydrogel resembling the physiological ECM with tunable biophysical and biochemical properties. In this study, we harnessed the properties of the synthetic xeno-free hydrogel system to examine how different mechanical strengths and functional ligands as well as cytokines and serum within the hydrogel matrices or in the outer well, affect GBM cell invasion. The results indicated that adjusting the mechanical strength of the ECM system affects GBM cell invasion. We further showed that the bio-functional ligands within the hydrogel matrix, such as matrix metalloproteinases, RGD peptide, and others, stimulated cell invasion. This finding exemplifies the importance of using a well-characterized ECM system given that it is difficult to evaluate how specific ECM components contribute to cell invasion using the undefined animal-based ECM. Since the composition of the hydrogel system is chemically defined, we could further control the cytokine milieu within the matrix to understand how the ECM composition affects cell migration. To demonstrate this, we added the cytokine TGF-β1 to the hydrogel and examined GBM cell invasion. Indeed, we showed that adding TGF-β1 to the synthetic VitroGel enhanced GBM cell invasion, thus illustrating that incorporating factors inside the matrix is a powerful method to evaluate chemotaxis. Altogether, this study demonstrates the potency and flexibility of using a xeno-free hydrogel for a myriad of invasion assay applications. Citation Format: Alejandra I. Ferrer Díaz, John Huang. Unraveling the effects of the microenvironment on glioblastoma multiforme invasiveness using a xeno-free 3D hydrogel platform [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 4209.
Abstract 4905: Multimodal transformer model improves survival prediction in lung cancer compared to unimodal approaches
Authors: Aakash Tripathi, Asim Waqas, Yasin Yilmaz, Ghulam Rasool
Journal: Cancer Research (2024)

Abstract Integrating multimodal lung data including clinical notes, medical images, and molecular data is critical for predictive modeling tasks like survival prediction, yet effectively aligning these disparate data types remains challenging. We present a novel method to integrate heterogeneous lung modalities by first thoroughly analyzing various domain-specific models and selecting the optimal model for embedding feature extraction per data type based on performance on representative pretrained tasks. For clinical notes, the GatorTron models showed the lowest regression loss on an initial evaluation set, with the large GatorTron-medium model achieving 12.9 loss. After selecting the top performers, we extracted robust embeddings on the full lung dataset built using the Multimodal Integration of Oncology Data System (MINDS) framework. MINDS provides an end-to-end platform for aggregating and normalizing multimodal patient data. We aligned the multimodal embeddings to a central pre-trained language model using contrastive representation learning based on a cosine similarity loss function. To adapt the language model to the new modalities, we employed a parameter-efficient tuning method called adapter tuning, which introduces small trainable adapter layers that leave the base model weights frozen. This avoids catastrophic forgetting of the pretrained weights. We evaluated our multimodal model on prognostic prediction tasks including survival regression and subtype classification using both public and internal lung cancer datasets spanning multiple histologic subtypes and stages. Our aligned multimodal model demonstrated improved performance over models utilizing only single modalities, highlighting the benefits of integrating complementary information across diverse lung data types. This work illustrates the potential of flexible multimodal modeling for critical lung cancer prediction problems using heterogeneous real-world patient data. Our model provides a strong foundation for incorporating emerging data types, modalities, and predictive tasks in the future. Citation Format: Aakash Tripathi, Asim Waqas, Yasin Yilmaz, Ghulam Rasool. Multimodal transformer model improves survival prediction in lung cancer compared to unimodal approaches [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 4905.
Abstract 1974: Discovery of TRX-211-399, a potent, CNS-penetrant, highly selective inhibitor of EGFR exon 20 insertion mutations
Authors: Kwangwoo Chun, Sumin Lim, Joohyun Lee, Seulgi Choi, Seongrak Kim, Youngil Choi, Areum Park, Bohee Kim, Yongseo Park, Eunhyun Choi, Sungwon Lee, Koo Lee
Journal: Cancer Research (2024)

Abstract Lung cancer is the leading cause of cancer-related deaths worldwide, accounting for approximately 2 million new cases and 1.8 million deaths annually. Various types of EGFR-activating mutations are one of the most important oncogenic drivers in non-small cell lung cancer (NSCLC). Among NSCLC patients with EGFR mutations, 5-10% of patients have EGFR exon 20 insertion (ex20ins) mutations that are insensitive to clinically available EGFR tyrosine kinase inhibitors (TKIs). Recently, as mobocertinib (EXKIVITY®) failed to improve progression-free survival in Phase 3 clinical trial, there remains a high unmet medical need to develop new drugs with wider therapeutic window to treat NSCLC harboring EGFR ex20ins mutations. Herein, we report a novel EGFR-TKI, TRX-211-399, specifically designed to target ex20ins mutations. TRX-211-399 potently inhibited the proliferation of not only Ba/F3 cells overexpressing near-loop (A767dupASV, S768dupSVD) and far-loop (H773insNPH, H773dupH) mutations but also patient-derived NSCLC cell line. In particular, TRX-211-399 demonstrated high selectivity against wild-type EGFR. With favorable DMPK profiles, once-daily oral administration of TRX-211-399 showed significant tumor regression in multiple Ba/F3 xenograft models carrying different EGFR exon20ins mutations. Furthermore, in a PC-9-luc cell intracranial xenograft model, TRX-211-399 induced substantial anti-tumor effects and prolonged survival without body weight loss. TRX-211-399 is currently undergoing further preclinical evaluation as a potential candidate for clinical development for patients with EGFR exon20ins mutations. Citation Format: Kwangwoo Chun, Sumin Lim, Joohyun Lee, Seulgi Choi, Seongrak Kim, Youngil Choi, Areum Park, Bohee Kim, Yongseo Park, Eunhyun Choi, Sungwon Lee, Koo Lee. Discovery of TRX-211-399, a potent, CNS-penetrant, highly selective inhibitor of EGFR exon 20 insertion mutations [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 1974.
Abstract 4557: Overexpressed CPAP promotes cancer stemness and enhances chemo-resistance in HCC
Authors: Liang-Yi Hung
Journal: Cancer Research (2024)

Abstract Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and is highly resistant to chemotherapy and targeted therapy. It was reported that HCC cancer stem cells (CSCs) are involved in chemo-drug resistance by regulating multidrug resistance (MDR) gene expression, such as ABC transporters. Our previous reports indicated that CPAP, a centrosomal protein, can promote HCC progression by up-regulating NF-κB and STAT3 transcriptional activities. Here, we demonstrated that overexpressed CPAP can increase cancer stemness features and CSCs-derived sorafenib resistance in HCC by up-regulating the transcriptional activities of NF-κB and β-catenin. Importantly, CPAP stably expressed HCC spheroids are significantly resistance to sorafenib in vitro and in vivo. Our results suggested that CD24 and ABCG2 are two potential downstream effectors in CPAP overexpressed HCC. CPAP can transcriptionally up-regulate CD24 and ABCG2 expression via Wnt/β-catenin and NF-κB signaling pathways, respectively; high CPAP/ABCG2/CD24 expression levels are negatively correlated with disease-specific survival rates in HCC patients. Combined treatment with sorafenib and Wnt/β-catenin pathway inhibitor PRI-724 significantly inhibited CPAP-overexpressing Hep3B spheroids-derived tumor growth in a xenograft mouse model. Our study highlights the oncogenic role of CPAP in promoting CSCs-induced sorafenib resistance in HCC and provides insights into potential therapeutic strategies. Citation Format: Liang-Yi Hung. Overexpressed CPAP promotes cancer stemness and enhances chemo-resistance in HCC [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 4557.
Abstract 4227: Human-derived hydrogels to support phenotypic changes in ER+ breast cancer cell line
Authors: Cecilia G. Sanchez, Katie Hamel, Emma Rogers, Jordan Robinson, Haley Lassiter, Trivia Frazier, Christopher Williams
Journal: Cancer Research (2024)

Abstract Adipose tissue plays a critical role in breast cancer incidence, progression, and response to therapy. The development of human derived 3D culture systems can accelerate the understanding of the role of environmental factors in the progression of Breast cancer as well as a model for preclinical studies during drug development. MCF-7 spheroids were cultured in Obatala Sciences’ Obavate and human-derived hydrogels ObaGel® and ObaGel®-ECM and control media. Organoid structure and phenotypic changes were analyzed via live cell imaging on the Incucyte S3. Migration studies were performed and gene expression analysis of EMT markers. Finally, adipocyte-breast cancer cell crosstalk was evaluated using pooled adipocytes co-cultured with MCF-7 spheroids. The results demonstrated that ObaGel® and ObaGel®-ECM 3D cultures support the growth and proliferation of MCF-7 tumorspheres during an extended culture period. In addition, MCF-7 cells exhibit the characteristic morphology of tumorsphere-forming cells when cultured in Obavate, with morphological changes in the ObaGel® and ObaGel®-ECM 3D. ObaGel® and ObaGel®-ECM differentially supports MCF-7 migratory behavior and phenotypic changes characteristic of EMT. Conclusions: Human derived hydrogels are developed to support 3D culture of breast cancer cells and to recapitulate the phenotypic changes associated with their metastatic potential. Furthermore, the use of a human derived 3D coculture system provides a platform for the understanding of adipose tissue-breast cancer cell interactions as it relates to breast cancer initiation, progression, and treatment response. Defining these interactions will support the development of a tool for future use in patient stratification and precision medicine in identifying underlying causes of breast cancer progression and response to treatments. Citation Format: Cecilia G. Sanchez, Katie Hamel, Emma Rogers, Jordan Robinson, Haley Lassiter, Trivia Frazier, Christopher Williams. Human-derived hydrogels to support phenotypic changes in ER+ breast cancer cell line [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 4227.
Abstract 4575: FGFR3 altered bladder cancer exhibits a lineage-dependent vulnerability
Authors: Mohamad Karim Koleilat, Yan Zhu, Lawrence Kwong
Journal: Cancer Research (2024)

Abstract Fibroblast Growth Factor 3 (FGFR3) genomic alterations are oncogenic drivers in ~15% of bladder cancer patients. A novel FGFR inhibitor, Erdafitinib, was FDA approved in 2019 based off a Phase II trial with an overall response rate of 40%. However, the majority of patients rapidly relapse at a median of 6 months, requiring combination therapies to prevent drug resistance. We hypothesized that a genome-wide CRISPR screen would identify Erdafitinib-sensitizing co-targets. We screened UM-UC-14, an S249C FGFR3 mutated bladder cancer cell line, and identified Cyclin C as a top hit in addition to known MAPK effectors such as ERK2 and SHP2. Cyclin C is a non-cell cycle related cyclin and part of the CDK8/19 kinase module of Mediator. Pharmacological validation in 4 FGFR3 altered cell lines confirmed a high degree of synergy between Erdafitinib and the CDK8/19 inhibitor Sel120, while no effect was seen in 2 wildtype cell lines, suggesting strong specificity. Moreover, the synergy in FGFR3-mutant cells was superior to that of SHP2 inhibitor SHP099 or the ERK inhibitor BVD-523. Similarly, GATA3 and PPARG also scored highly in our CRISPR screen. These transcription factors have been shown to be sufficient to enforce a luminal identity but not necessarily to maintain it. We validated these 3 genes as sensitizers and show in luminal cells that loss of either GATA3 or PPARG leads to loss of luminal markers and gain of basal markers. In contrast, cells treated with Sel120 showed, on RNAseq, an increase in basal markers without loss of luminal markers. Interestingly, our data suggests that the gain of basal markers, commonly associated with a worse prognosis, is associated with a strong sensitization to FGFR inhibition in FGFR3 alteration driven bladder cancer. We conducted a xenograft experiment confirming that mice responded well to single agent Erdafitinib, but without frank tumor regression. By contrast, Sel120+Erdafitinib induced complete responses in 8/10 mice compared to 6/10 mice for SHP099+Erdafitinib. Remarkably, after 60 days of daily drugging and a 20-day washout, the tumors did not grow back in the complete responders. Importantly, no loss of body weight or other signs of morbidity were found. Our results suggest an immediate and promising benefit in combining either CDK8/19 or SHP2 inhibitors with Erdafitinib in treating patients with FGFR3 alteration driven bladder cancers. Furthermore, we identified a strategy in targeting lineage modulators as sensitizers to existing therapies. Citation Format: Mohamad Karim Koleilat, Yan Zhu, Lawrence Kwong. FGFR3 altered bladder cancer exhibits a lineage-dependent vulnerability [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 4575.
Abstract 4559: SMAD3 mediates oxaliplatin resistance in esophageal adenocarcinoma
Authors: Farah Ballout, Heng Lu, Nadeem Bhat, Lei Chen, Dunfa Peng, Zheng Chen, Alexander Zaika, Oliver McDonald, Wael El-Rifai
Journal: Cancer Research (2024)

Abstract Background: Resistance to conventional treatments is a significant barrier to esophageal adenocarcinoma (EAC) therapy. TGF-β signaling appears to be important for EAC tumorigenesis; however, its role in EAC chemoresistance remains understudied. This study investigates the role of SMAD3 in EAC resistance to the frontline chemotherapeutic drug oxaliplatin. Methods: Publicly available datasets were analyzed to determine SMAD3 expression in EAC versus normal samples. Western blot, quantitative real-time polymerase chain reaction, immunofluorescence staining, and flow cytometric analyses were utilized to validate bioinformatic results. Human EAC cell lines (OE33 and OE19) were treated with pharmacologic inhibitors or transfected with small interfering RNA and assessed for DNA damage and apoptotic cell death. Patient-derived organoids and patient-derived xenograft models of EAC were used to confirm our findings in vivo. Results: SMAD3 was significantly upregulated in EAC versus normal tissue samples. Total and phosphorylated SMAD3 protein levels were upregulated in EAC tissues accompanied by increased expression of several genes regulated by SMAD3. Notably, oxaliplatin-resistant EAC cells exhibited overexpression of SMAD3. Chemotherapy non-responding patients showed enrichment of SMAD3 gene expression when compared to responders in the clinical dataset GSE165252. Knockdown or inhibition of SMAD3 hindered DNA repair and sensitized EAC cells to oxaliplatin treatment in vitro and in vivo. Mechanistically, SMAD3 promoted ATM phosphorylation by interacting with protein phosphatase 2A (PP2A) and sequentially inhibiting the binding of PP2A to ATM. Conclusion: Our results reveal a pivotal role for SMAD3 in mediating oxaliplatin resistance in EAC and thus hold a significant potential in guiding future drug development and combination strategies. Citation Format: Farah Ballout, Heng Lu, Nadeem Bhat, Lei Chen, Dunfa Peng, Zheng Chen, Alexander Zaika, Oliver McDonald, Wael El-Rifai. SMAD3 mediates oxaliplatin resistance in esophageal adenocarcinoma [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 4559.
Abstract 4238: Modeling<i>RET</i>-rearranged non-small cell lung cancer (NSCLC): Generation of lung cell progenitors from patient-derived induced pluripotent stem cells (iPSCs)
Authors: Paul Marcoux, Jinwook Hwang, Christophe Desterke, Jusuf Imeri, Annelise Bennaceur Griscelli, Ali Turhan
Journal: Cancer Research (2024)

Abstract Rearranged during Transfection (RET) oncogenic rearrangements can occur in 1-2% of lung adenocarcinomas. While RET-driven NSCLC models have been developed using various approaches, no model based on patient-derived induced pluripotent stem cells (iPSCs) has been described yet. Patient-derived iPSCs hold great promise for disease modeling. However, generating iPSCs with specific oncogenic drivers, like RET rearrangements, presents challenges due to reprogramming efficiency and genotypic variability within tumors. To address this issue, we aimed to generate lung progenitor cells (LPCs) from patient-derived iPSCs carrying the somatic mutation RETC634Y which is commonly associated with hereditary medullary thyroid carcinoma. Additionally, we have established a RETC634Y knock-in iPSC model to validate the effect of this oncogenic mutation during LPC differentiation. We successfully generated LPCs from RETC634Y iPSCs using a 16-days protocol and showed an overexpression of cancer-associated markers as compared to control iPSCs. Transcriptomic analysis revealed a distinct signature of NSCLC tumor repression, suggesting a lung multilineage lung dedifferentiation, along with an upregulated signature associated with RETC634Ymutation potentially linked to poor NSCLC prognosis. These findings were validated using the RETC634Y knock-in iPSC model, highlighting key cancerous targets such as PROM2 and C1QTNF6, known to be associated with poor prognostic outcomes. Furthermore, the LPCs derived from RETC634Y iPSCs exhibited a positive response to the RET inhibitor Pralsetinib, evidenced by the downregulation of the cancer markers. This study provides a novel off-the-shelf iPSC model of RET-driven NSCLC, paving the way for exploring the molecular mechanisms involved in RET-driven NSCLC to study disease progression and to uncover potential therapeutic targets. Citation Format: Paul Marcoux, Jinwook Hwang, Christophe Desterke, Jusuf Imeri, Annelise Bennaceur Griscelli, Ali Turhan. ModelingRET-rearranged non-small cell lung cancer (NSCLC): Generation of lung cell progenitors from patient-derived induced pluripotent stem cells (iPSCs) [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 4238.