tbuckley/cabot-search huggingface dataset:
Abstract 6794: Elucidating mechanisms of cancer cell persistence to lorlatinib in ALK positive NSCLC
Authors: Toshio Fujino, Darlan C. Minussi, Christina L. Anastasia, Emily Hensley, Satoshi Yoda, Mari Mino-Kenudson, Wei Ping, Katya Marjon, Xinmeng J. Mu, Marco Maruggi, Aaron N. Hata
Journal: Cancer Research (2025)

Abstract ALK fusion-positive lung cancers exhibit deep and durable responses to ALK tyrosine kinase inhibitors (TKIs), however the emergence of acquired drug resistance is inevitable. Current targeted therapies are insufficient to eliminate all cancer cells within a tumor. So called drug tolerant “persister” cells (DTPCs) evade initial treatment, subsequently evolve mechanisms of acquired resistance, and drive disease relapse. Currently, our understanding of the underlying mechanisms driving DTPC survival and evolution in ALK+ fusion NSCLC, especially during treatment with the most advanced ALK lorlatinib, remains incomplete. To identify mechanisms and therapeutic vulnerabilities of DTPC survival in ALK+ NSCLC, we performed bulk and single-cell RNA-seq and ATAC-seq on ALK+ NSCLC patient-derived cell lines and PDX tumors before, during and after treatment with lorlatinib. Tumors exhibited robust initial responses to lorlatinib (&amp;gt; 50% of tumor reduction) followed by a stable residual disease phase and in some cases tumor regrowth after extended treatment, mimicking clinical treatment trajectories. Transcriptomic analysis revealed progressive upregulation of MAPK pathway signaling in DTPC cells in residual tumors and resistant cells in relapsing tumors. Furthermore, we discovered a sub-population of cells with stem-like features present in untreated and residual tumors, potentially representing a pre-existing cell state poised to evade lorlatinib treatment. Finally, we identified several tumor surface proteins upregulated in residual and relapsing tumors that could serve as potential targets for antibody drug conjugate therapies. These results reveal mechanisms driving survival and evolution of DTPCs and identify potential therapeutic targets to prevent resistance of ALK+ NSCLCs to lorlatinib. Citation Format: Toshio Fujino, Darlan C. Minussi, Christina L. Anastasia, Emily Hensley, Satoshi Yoda, Mari Mino-Kenudson, Wei Ping, Katya Marjon, Xinmeng J. Mu, Marco Maruggi, Aaron N. Hata. Elucidating mechanisms of cancer cell persistence to lorlatinib in ALK positive NSCLC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6794.
Abstract 6465: Development of triple co-culture spheroid models of lung and ovarian carcinomas for in vitro evaluation of antitumor therapies
Authors: Rock Pulak, Shrey Shah, Yongwoon Kim, Gerard G. D’Souza
Journal: Cancer Research (2025)

Tumor spheroids have emerged as superior in vitro models for studying solid tumors compared to monolayer cultures due to their ability to replicate key aspects of the tumor microenvironment (TME), including cell-cell interactions, extracellular matrix deposition, and nutrient and oxygen gradients. However, spheroids composed solely of tumor cells, i.e. monoculture spheroids, still lack the non-tumor cell components that contribute to additional in vivo TME complexity. This study focuses on developing triple co-culture spheroid models that integrate tumor cells, tissue-specific fibroblasts, and endothelial cells to better replicate the structural and functional features of the TME. Using an optimized liquid overlay technique, triple co-culture spheroids were successfully generated with drug-resistant lung and ovarian tumor cells. These spheroids demonstrated key tumor-like characteristics, such as extracellular matrix production and distinct spatial localization of cell types. Specifically, fibroblasts concentrated at the spheroid core during growth, while endothelial cells localized to the core only in the presence of fibroblasts. When treated with a liposomal formulation previously identified as selectively toxic to drug-resistant tumor cells in monolayer cultures, the triple co-culture spheroids exhibited reduced sensitivity to the treatment in a manner dependent on their composition. These results highlight the potential of triple co-culture spheroids as advanced in vitro models for investigating tumor biology and optimizing therapeutic strategies prior to in vivo evaluation. Citation Format: Rock Pulak, Shrey Shah, Yongwoon Kim, Gerard G. D’Souza. Development of triple co-culture spheroid models of lung and ovarian carcinomas for in vitro evaluation of antitumor therapies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6465.
Abstract 6803: RNF5-DNAJA1 axis dictates selinexor sensitivity of multiple myeloma by regulating mitochondrial function
Authors: Mengqi Wang
Journal: Cancer Research (2025)

Abstract Selinexor is a First-in-Class XPO1 Inhibitor approved for relapsed or refractory multiple myeloma (RRMM), but the overall response rate remains unsatisfactory. The main mechanism by which Selinexor kill MM cells is to suppress the export of tumor suppressor proteins and oncoprotein mRNAs, however other key underlying mechanisms need to be investigated. Here, using a proteomics of nucleocytoplasmic separation assay, we discover that a ring finger containing E3 ligase, RNF5, is a cargo substrate of XPO1 and its nuclear-cytoplasmic transport is correlated with poor clinical therapeutic response. In the interactome of XPO1, we identify that DNAJA1 is a new partner of RNF5 and catalyzes K29-linked polyubiquitination of DNAJA1, which strengthens the interaction between DNAJA1 and HSP70, consequently and antagonizes the interaction of HSP70 and HSF1, therefore activates UPRmt activation and mitochondrial protection. Thus, administration of RNF5 inhibitor inh-02 and DNAJA1 inhibitor 116-9e disrupts UPRmt balance and sensitizes selinexor in vitro culture cell lines and in the xenograft and Vk*Myc mouse models. Collectively, our study elucidates the machinery of XPO1-RNF5-DNAJA1 axis in regulating mitochondrial function, and sheds light on developing new strategies to improve the efficacy of treating RRMM patients. Citation Format: Mengqi Wang. RNF5-DNAJA1 axis dictates selinexor sensitivity of multiple myeloma by regulating mitochondrial function [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6803.
Abstract 6562: Bro1 proteins govern a multivesicular bodies fate switch to regulate exosome secretion, metastasis and tumor immune evasion
Authors: Nai Yang Yeat, Li-Heng Liu, Yu-Hsuan Chang, Charles Pin-Kuang Lai, Ruey-Hwa Chen
Journal: Cancer Research (2025)

Abstract Exosomes play pleiotropic tumor-promoting functions and are secreted by fusion of multivesicular bodies (MVBs) with the plasma membrane. However, MVBs are also directed to lysosomes for degradation and the mechanism controlling different fates of MVBs remains elusive. Here, we show that the pro-tumor protein WDR4 enhances exosome secretion through degrading the ESCRT-associated Bro1-family protein PTPN23. Mechanistically, PTPN23 and its paralog ALIX compete for binding to syntenin, thereby directing MVBs towards degradation and secretion, respectively. ALIX, but not PTPN23, recruits actin capping proteins CAPZA1/CAPZB to prevent branched F-actin accumulation around MVBs, thus enabling MVBs trafficking to cell periphery for secretion. Functionally, WDR4/ALIX dependent exosomes preferentially load a set of pro-tumor proteins to potentiate metastasis and immune evasion. Our study highlights a previously unprecedented coupling between biogenesis mechanism and fate decision of MVBs and its importance in exosome cargo landscape, which have potential broad impacts on boosting exosome production and devising cancer therapeutic strategy. Citation Format: Nai Yang Yeat, Li-Heng Liu, Yu-Hsuan Chang, Charles Pin-Kuang Lai, Ruey-Hwa Chen. Bro1 proteins govern a multivesicular bodies fate switch to regulate exosome secretion, metastasis and tumor immune evasion [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6562.
Abstract 4238: DNMT1 inhibition by SGI-1027 promotes neuroblastoma cell death through a p53-independent pathway
Authors: Farah Naz, Shyam Sundar Jaganathan, Umamaheswari Natarajan, Appu Rathinavelu
Journal: Cancer Research (2025)

Abstract Introduction: Neuroblastoma is an aggressive childhood cancer originating from neural crest cells, accounting for 700-800 new cases annually and cuases15% of pediatric cancer deaths in the U.S. Treatment for high-risk neuroblastoma includes chemotherapy, stem cell transplants, radiation, and immunotherapy. Recent evidence suggests that DNMTs inhibitors such as SGI-1027 and CM-272 can potentiate apoptosis via epigenetic modulation of critical regulatory pathways in cancers. Hence, we hypothesized that SGI-1027 can induce apoptosis in SK-N-SH neuroblastoma cells by upregulating p21 through DNMT1 inhibition. Our study aimed to elucidate the underlying mechanisms and assess the potential of using SGI-1027 for treating high-risk neuroblastoma. Methods: SK-N-SH cells were treated with 2 µM of SGI -1027 for 24 hrs. The cell viability was evaluated using Trypan Blue Dye Exclusion method, while apoptotic activity was quantified through a fluorescence assay using DEVD-amc substrate for measuring caspase-3/7 activation. qRT-PCR and Western Blot analyses were conducted to assess expression levels of the cell cycle, apoptotic, and epigenetic pathway-related markers such as p53, p21, PARP, BAX, BCL-XL, and DNMT1. Apoptotic changes in cells were further confirmed through Immunofluorescence studies. Results: Our study results confirmed that SK-N-SH cells treated with SGI-1027 showed significant cell death and enhanced fluorescence in the DEVD-amc, indicating activation of apoptotic activity. Consistent with our hypothesis, we observed an elevation in p21 levels, an increased BAX/BCL-XL ratio, and a downregulation in the levels of DNMT1, suggesting that SGI-1027 may be facilitating neuroblastoma cell death through a p21-driven mechanism that is independent of p53 pathway. Conclusion: This study highlights the potential of DNMT1 inhibitor SGI-1027 to induce apoptosis in neuroblastoma cells through upregulating p21 and modulating the BAX/BCL-XL ratio. Our findings suggest that targeting DNMT1 using SGI-1027 may offer an effective pathway for inducing cell death and controlling neuroblastoma growth. We are in the process of validating DNMT1 targeted therapies as a powerful addition for treating aggressive neuroblastoma. Acknowledgments: This project was supported by the National Pediatric Cancer Foundation (NPCF) and the Royal Dames of Cancer Research Inc., Fort Lauderdale, Florida. Citation Format: Farah Naz, Shyam Sundar Jaganathan, Umamaheswari Natarajan, Appu Rathinavelu. DNMT1 inhibition by SGI-1027 promotes neuroblastoma cell death through a p53-independent pathway [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4238.
Abstract 6455: Development of a H3K27M inducible and reversible model of diffuse midline glioma (DMG) to characterize tumor microenvironment and epigenetic memory
Authors: Niloofar Khairkhah, Sienna L. Galban, Megan Faunce, Rodrigo T. Cartaxo, Carl Koschmann, Yue Zhao, Stefanie Galban
Journal: Cancer Research (2025)

Diffuse Midline Gliomas (DMGs) with a lysine to methionine mutation in Histone 3 are lethal pediatric brain tumors. Despite ongoing efforts to develop new therapies, it remains unclear whether targeting this oncohistone or downstream epigenetic pathway activation are sufficient to halt and eradicate tumors. Here, we introduce a H3K27M inducible and reversible mouse model for DMG that allows precise control of oncohistone expression. This model enables us to study the effects of H3K27M activation, inactivation and re-activation on tumor growth and recurrence and additionally, characterize changes in the microenvironmental and epigenetic memory. We employed the in utero electroporation-based (IUE) delivery method to express the PiggyBac-based expression vectors mutant PDGFRA and dominant-negative TP53 and the newly designed tetracycline inducible H3K27M, along with the transposon. Upon tetracycline induced H3K27M activation, DMG tumors were detected and dissected to generate a new DMG cell line (PPiK27M), which can also be used for intracranial implantations in immunocompetent mice. In addition, we used two patient-derived DMG cell models wherein H3K27M was CRISPR edited (H3K27M-KO) to reintroduce the inducible and reversible H3K27M construct to provide an orthotopic model closely recapitulating human disease. We validated inducibility and reversibility of H3K27M by intracellular flow cytometry and western blotting in the murine and human cell models. We detected characteristic morphological changes and repression of astrocytic markers upon H3K27M re-expression in KO cells. In conclusion, our results indicate that the new inducible and reversible H3K27M IUE model and cells faithfully recapitulate DMG characteristics. We are currently performing single-cell RNA sequencing (scRNA-seq) of tumors to track cellular and molecular alterations in the surrounding tumor immune microenvironment. Additionally, we are characterizing the epigenome to understand whether transcriptional changes persist after inactivation of the oncohistone. Our study provides new tools to mechanistically decipher the role of the oncohistone, and potentially, identify new therapeutic targets for DMG. Citation Format: Niloofar Khairkhah, Sienna L. Galban, Megan Faunce, Rodrigo T. Cartaxo, Carl Koschmann, Yue Zhao, Stefanie Galban. Development of a H3K27M inducible and reversible model of diffuse midline glioma (DMG) to characterize tumor microenvironment and epigenetic memory [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6455.
Abstract 6795: Cystine deprivation overcomes protective effects of hypoxia on ferroptosis in high-grade serous ovarian cancer
Authors: Zonghao Tang, Anil Sood
Journal: Cancer Research (2025)

Abstract Iron is known to be crucial for high-grade serous ovarian cancer (HGSC) proliferation. HGSC tumors exhibit elevated iron levels compared to normal tissues, making it more susceptible to ferroptosis. Previous studies have shown that ferroptosis inducers can reduce both tumor growth and metastasis in ovarian cancer mouse models. Hypoxia is a prevalent feature of the tumor microenvironment and may protect HGSC from ferroptosis. Induction of ferroptosis can be triggered by inhibitors of GPX4 (GPX4i) or xCT (xCTi), prompting us to consider whether hypoxia may abrogate the induction of ferroptosis in HGSC cells. We tested multiple ovarian cancer cell lines (e.g., OVCAR3, OVCAR4, and OVCAR8) under normoxia and hypoxia. We used both hypoxia chamber (1% oxygen) and CoCl2 to mimic hypoxic conditions and found that both methods significantly inhibited GPX4i-induced ferroptosis by more than twofold (e.g. 5uM RSL3 decreased OVCAR4 cell viability by 80% under normoxia but only 50% under hypoxia), while only having a minimal effect on xCTi-induced ferroptosis. Given that xCTi blocks cystine import, we also examined whether hypoxia affects cystine deprivation-induced ferroptosis. Hypoxia did not protect HGSC cells from cystine deprivation-induced ferroptosis. In conclusion, our study suggests that hypoxia selectively blocks GPX4i-induced ferroptosis in HGSC, while cystine deprivation-induced ferroptosis remains effective, highlighting the potential of targeting cystine import as a more robust approach for treating HGSC. Citation Format: Zonghao Tang, Anil Sood. Cystine deprivation overcomes protective effects of hypoxia on ferroptosis in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6795.
Abstract 6862: Preclinical evaluation of drugs for the treatment of MTAP-deficient cancers
Authors: Qin Li, Jie Yang, Feifei Fan, Jian Xiang, Yajie Xiong, Ying Tong, Shuai Zhao, Qingyang Gu
Journal: Cancer Research (2025)

Abstract 5-Methylthioadenosine phosphorylase (MTAP), a key enzyme in the methionine salvage pathway that plays a vital role in cell apoptosis, proliferation, differentiation and inflammatory response, is frequently deleted in human cancers, approximately 15% of total tumors, including 53% of glioblastomas, 33% of bladder cancers, 26% of pancreatic cancers, and other tumor types. Deficiencies in MTAP lead to the accumulation of 5'-methylthioadenosine (MTA), which subsequently inhibits protein arginine methyl transferase 5 (PRMT5). This mechanism facilitates the development of therapeutics that selectively target MTA-bound PRMT5 (PRMT5: MTA) in MTAP-deficient tumors, while sparing normal tissues expressing wild-type MTAP. Numerous studies have demonstrated that MTAP-deficient cells exhibit heightened sensitivity to methionine depletion and inhibitors of purine synthesis, rendering PRMT5 and MAT2A promising therapeutic targets for MTAP-deficient tumors. In this study, we presented our preclinical research focusing on MTAP related models. We assessed the mRNA expression of MTAP in over 700 human cancer cell lines and more than 1, 400 patient-derived xenograft (PDX) models. Subsequently, with in vitro viability assay we showed that the two PRMT5 inhibitors, GSK3326595 and MRTX1719 exhibited strong anti-proliferative effects against MTAP-deficient cells. In vivo, we proved that GSK3326595 showed a significant antitumor activity against MTAP-deficient models. Additionally, immunohistochemistry (IHC) staining was performed to assess the MTAP protein levels in forty PDX models, which covering pancreatic, colon, and bladder cancers types. Models harboring moderate PRMT5 expression but lacking MTAP were selected for efficacy study with MRTX1719. This selective PRMT5 inhibitor developed a superior anti-tumor effect, achieving a tumor growth inhibition of over 100% after three weeks of treatment. In summary, our findings may advance the development of novel therapeutic strategies for MTAP-deficient cancers. Citation Format: Qin Li, Jie Yang, Feifei Fan, Jian Xiang, Yajie Xiong, Ying Tong, Shuai Zhao, Qingyang Gu. Preclinical evaluation of drugs for the treatment of MTAP-deficient cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6862.
Abstract 6540: Lung adenocarcinoma cancer cells that metastasize to the brain bring their own soil
Authors: Alejandro Bernardo Suárez, Gabriela Caballero, Iban Aldecoa Ansorregui, Natalia Isabel Diaz-Valdivia, Patricia Fernandez-Nogueira, Noemi Reguart, Jordi Alcaraz Casademunt
Journal: Cancer Research (2025)

Abstract Lung adenocarcinoma (LUAD) is the most common histologic subtype of non-small cell lung cancer (NSCLC). Unlike other prevalent NSCLC subtypes, LUAD is characterized by an early dissemination, most frequently to the brain, particularly in patients harboring EGFR mutations. Although the mechanisms underlying LUAD metastasis to the brain are poorly understood, tumor-associated fibroblasts (TAFs) are increasingly recognized as major drivers of tumor progression and have also been hypothesized to contribute to tumor dissemination and metastasis. However, current experimental evidence of TAFs in brain metastasis is very limited. To address this gap of knowledge, we aimed to analyze retrospectively common markers of immunosuppressive TAFs phenotypes in LUAD in patient biopsies from primary tumors and paired brain metastases (n=17). These markers included α-SMA, FAP and MYH11, and were analyzed by immunofluorescence. We confirmed the presence of TAFs that were positive for these markers in primary tumors, although α-SMA+ TAFs were dominant, in line with previous observations. Notably, our preliminary analysis in brain metastases revealed numerous cells exhibiting an elongated nuclear morphology comparable to that found in fibroblasts in LUAD primary tumors; moreover, these cells were also positive for either α-SMA, FAP and MYH11 or a mixture of these markers. In further agreement with the primary tumor, α-SMA+ TAFs were dominant, whereas FAP+ TAFs were patient dependent and MYH11+ TAFs accounted for a smaller TAF population. In contrast, these TAF-like cells were negative for standard markers of activated astrocytes and pericytes. Moreover, brain metastasis showed patterns of T-cell exclusion similar to those reported in primary tumors. Because the normal brain is devoid of fibroblasts, these preliminary observations strongly support the presence of bona fide TAFs in brain metastasis. Moreover, the striking similarities between major immunosuppressive TAFs populations in the primary tumors and brain metastases support that disseminated cancer cells from LUAD patients bring their own soil during brain metastasis. Future analysis should validate these observations to ultimately define major immunosuppressive TAFs populations in brain metastasis, which could be used to design more specific therapeutic approaches against these populations. Citation Format: Alejandro Bernardo Suárez, Gabriela Caballero, Iban Aldecoa Ansorregui, Natalia Isabel Diaz-Valdivia, Patricia Fernandez-Nogueira, Noemi Reguart, Jordi Alcaraz Casademunt. Lung adenocarcinoma cancer cells that metastasize to the brain bring their own soil [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6540.