tbuckley/cabot-search huggingface dataset:
Abstract 5531: A 3D CRISPR screening identified RET-TKI resistance through MIG6 loss in RET rearranged NSCLC
Authors: Xinzhao Wei, Ken Uchibori, Makoto Nishio, Ryohei Katayama
Journal: Cancer Research (2025)

RET-fusion positive non-small cell lung cancer (NSCLC) accounts for 1-2% of total population of NSCLC. RET selective tyrosine kinase inhibitors (TKIs) have demonstrated remarkable efficacy, and 2 RET-TKIs have been approved for the treatment of RET-rearranged NSCLC. However, the emergence of acquired resistance which remains unclear largely. To better simulate in vivo tumor conditions, we employed a 3D culture system using LC2/ad (CCDC6-RET) and LCC190 (CCDC6-RET, originally established from RET-TKI naïve patient’s pleural effusion) cell lines. RET-TKIs showed significant increased efficacy in this 3D system compared to standard 2D cultures with increased apoptosis pathway and reduced ERBB-mediated MAPK and PI3K/Akt/mTOR signaling pathways.Further, we conducted a genome-wide CRISPR/Cas9 screening in the 3D condition in LCC190, which identified multiple candidate genes including ERRFI1 (MIG6) contributor to drug-tolerant persister (DTP) cell survival during RET-TKI treatment. Knockout of MIG6, a negative regulator of EGFR signaling, induced significant EGFR activation in the presence of extreme low ligand concentrations (1 ng/mL), leading to resistance through the activation of MAPK and PI3K/Akt/mTOR pathways. These findings highlight the critical role of regulation of MIG6 on EGFR in bypassing RET inhibition. Notably, combining RET-TKIs with EGFR inhibitors (afatinib or cetuximab) markedly reduced the survival of DTP cells in vivo and in vitro suggesting a potential combination strategy to overcome such resistance. Conversely, overexpression of MIG6 restored sensitivity to RET-TKIs under conditions of low EGFR ligands with reduced level of phosphorylation of EGFR. In conclusion, this study identifies MIG6 as a critical mediator of RET-TKI resistance in NSCLC and highlights the utility of 3D culture systems in uncovering key resistance mechanisms in RET-fusion positive NSCLC. Targeting EGFR in combination with RET-TKIs presents a promising therapeutic strategy to overcome drug-tolerant persistence and improve treatment outcomes in RET-rearranged NSCLC. Besides MIG6, we have also found several candidate genes related to DTP cell survival or RET-TKI resistance from the genome-wide Crispr screening. Further studies are needed to clarify the mechanisms of resistance induced by loss of these candidate genes to comprehensively understand the mechanisms how DTP cells survive against TKI treatment and how such resistance could be overcome by novel treatment methods. Citation Format: Xinzhao Wei, Ken Uchibori, Makoto Nishio, Ryohei Katayama. A 3D CRISPR screening identified RET-TKI resistance through MIG6 loss in RET rearranged 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 5531.
Abstract 5680: MPSA-AB5000: a high-throughput membrane proteins screening array for therapeutic biologics specificity profiling
Authors: Liping Wang, Yuanyuan Sun, Guoqian Wang, Jinying Ning, Feng Hao
Journal: Cancer Research (2025)

Abstract Antibody drug development is lengthy and complex, often hindered by various challenges in clinical advancement. Reports indicate that off-target binding of antibodies may be a significant issue, with approximately 25% of preclinical candidates potentially experiencing these off-target problems. With the rise of new modalities such as CD3 bispecific antibodies, ADCs, and CAR-T therapies, preliminary off-target screening of antibodies has become increasingly important. Despite the use of techniques like immunohistochemistry, ELISA, and flow cytometry (FACS) for off-target testing of antibodies, these methods still exhibit limitations in sensitivity, specificity, and throughput. To address the need for antibody target deconvolution and receptor identification, we developed a novel membrane protein screening array (MPSA) AB5000. MPSA-AB5000 is a high-throughput, cell-based platform for identifying antibody targets and off-targets, enhancing antibody specificity screening and reducing development risks. The MPSA-AB5000 covers diverse human membrane proteins, expressed in live cells to preserve native conformations. C-terminal epitope-tagged clones allow for expression confirmation and cellular localization. To provide the highest level of sensitivity, MPSA-AB5000 uses luciferase reporter cell line detection. The wash-free strategy reduces false negatives, and signal amplification makes remarkable discrimination. Compared to similar technologies, we possess significant advantages in the following aspects: a. High sensitivity and sigh throughput: our technology platform offers not only high sensitivity, capable of detecting subtle interactions but also supports high-throughput screening, allowing for the evaluation of a large number of samples in a short timeframe. b. Avoidance of false negative signals: by eliminating washing steps, our method reduces the risk of false negative signals, ensuring reliable detection of non-specific binding. c. Comprehensive validation approaches: we employ various validation methods such as FACS and ELISA to eliminate false positive signals, enhancing the accuracy and credibility of our results. All the advantages ensure that MPSA-AB5000 is more rapid, simple, and highly sensitive than traditional assays. Citation Format: Liping Wang, Yuanyuan Sun, Guoqian Wang, Jinying Ning, Feng Hao. MPSA-AB5000: a high-throughput membrane proteins screening array for therapeutic biologics specificity profiling [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 5680.
Abstract 5708: Investigating the role of SMYD3 in medulloblastoma progression and treatment response: Implications for targeted therapy
Authors: Swapna Asuthkar, Erick Benjamin Saldes, katherine Shishido, Ilango Balakrishnan, Sujatha Venkataraman
Journal: Cancer Research (2025)

Abstract Medulloblastoma (MB), the most prevalent malignant brain tumor in children, presents significant treatment challenges, particularly in the aggressive Group 3 subtype, which is associated with poor prognosis. Current therapeutic strategies, including surgery, chemotherapy, and radiotherapy, often result in severe side effects and inadequate long-term outcomes. This study investigates the role of SMYD3, a histone methyltransferase known for its overexpression in various cancers, in mediating radioresistance in MB. We analyzed SMYD3 expression levels in MB cell lines and patient samples, revealing a notable overexpression in Group 3 MB, which correlated with diminished patient survival rates. Notably, ionizing radiation exposure resulted in a dose-dependent increase in SMYD3 expression, suggesting a potential adaptive response to treatment. Inhibition of SMYD3 using the small molecule BCI-121 significantly reduced cell viability and enhanced radiosensitivity in vitro. Preliminary in vivo studies utilizing a BALB/c nude mouse orthotopic MB model demonstrated promising outcomes, indicating that targeting SMYD3 may improve therapeutic efficacy. Our findings underscore the critical role of SMYD3 in promoting radioresistance in MB and suggest that SMYD3 inhibition could be a viable strategy to enhance the effectiveness of radiotherapy, particularly in aggressive MB subtypes. Further investigations are warranted to elucidate the underlying mechanisms and to explore the potential for combination therapies aimed at improving treatment outcomes in MB. Citation Format: Swapna Asuthkar, Erick Benjamin Saldes, katherine Shishido, Ilango Balakrishnan, Sujatha Venkataraman. Investigating the role of SMYD3 in medulloblastoma progression and treatment response: Implications for targeted therapy [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 5708.
Abstract 5522: Cell state modulates the KRASG12C proximal proteome
Authors: Anurima Majumder, Liznair Bridenstine, Denis Imbody, Kiah Bowers, Dalia Ercan, Bin Fang, Eric Haura
Journal: Cancer Research (2025)

Abstract Background: KRAS mutations occur in ∼25% of lung adenocarcinomas (LUAD), with KRASG12C being the most common. There has been limited clinical success with KRAS inhibitors due intrinsic/acquired resistance. EMT is a known mechanism by which cancer cells become resistant to targeted therapy. Here, we aim to map protein interactors of KRASG12C in lung cancer cells using proximity-dependent biotin labeling (BioID) to gain insights into key regulators/effectors of oncogenic signaling and therapy resistance. Methods: Dox-inducible fusion of KRASG12C with the BirA biotin ligase was expressed in H358 LUAD cells. To determine alterations in KRASG12C interactome induced by EMT, BioID/mass spectrometry was performed on BirA-KRASG12C expressing cells, with or without chronic TGF-β treatment (to induce EMT). Transduced H358 cells treated either with Biotin or Dox alone were used as controls for the BioID experiment. Results: BioID analysis identified 144 proteins as potential proximal interactors for KRASG12C, which include known effectors of RAS signaling, such as NF1, RAF1, RASA1, MTOR, as well as novel ones, such as KEAP1, ASAP1, CRIP2, CRK, GULP1, AFDN. Pathway analysis suggests that these proximal proteins are involved in regulation of actin cytoskeleton, RAP1, PI3K-Akt, focal adhesion, and Ras signaling pathways. Our data also shows that TGF-β induced EMT reduces KRASG12C’s interaction with several of these known effectors, such as MTOR, RICTOR, and RAF1, while gaining new interactors, such as SPRED2, NOTCH2, DEPC1B and F11R. We also observe a reduction in RAS activity, RAS-RAF proximity and pERK/pRSK in TGF-β induced cells compared to parental cells. Conclusions: We show that BioID system can identify KRASG12C interactome proteins in a cell line model of LUAD. Our data suggests that upon undergoing TGF-β induced EMT, the KRASG12C interactome in these cells alter and now couple less with RAS/MTOR signaling effectors. We also observe similar change in sotorasib-resistant H358 cells showing EMT features, where KRASi no longer suppresses ERK signaling. These studies can understand variations in KRASG12C interactome under epithelial vs mesenchymal state and potentially identify new therapeutic vulnerabilities for cells that have undergone EMT. Citation Format: Anurima Majumder, Liznair Bridenstine, Denis Imbody, Kiah Bowers, Dalia Ercan, Bin Fang, Eric Haura. Cell state modulates the KRASG12C proximal proteome [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 5522.
Abstract 5709: Furin drives colorectal cancer progression and chemoresistance through the TGF-β/ERK signaling pathway
Authors: Abdul K. Siraj, Pratheesh Kumar Poyil, Sandeep Kumar Parvathareddy, Saravanan Thangavel, Fouad Al-Dayel, Khawla S. Al-Kuraya
Journal: Cancer Research (2025)

Abstract Furin, a key member of the pro-protein convertase (PC) family, is unfavorably involved in the proteolytic activation of various precursor proteins. While aberrant expression of furin has been extensively documented in multiple malignancies, its functional significance and mechanistic role in colorectal cancer remain inadequately characterized. We analyzed furin expression in a comprehensive cohort of Middle Eastern colorectal cancer (CRC) patient samples and investigated its functional role and underlying mechanisms using in vitro studies with CRC cell lines. Furin over-expression was noted in 46.9% (530/1131) of CRC cases. A significant association was noted between Furin over-expression and older age at diagnosis of CRC (&amp;gt;50 years; p = 0.0156), but no significant association was noted with other clinico-pathological characteristics. However, Furin over-expression was found to be associated with phosphor-ERK1/2 (p &amp;lt; 0.0001) and TGFβ (p &amp;lt; 0.0001). For in vitro analysis, we selected three chemosensitive CRC cell lines—HCT116, DLD1, and LOVO—and generated chemoresistant cells by treating them to prolonged low-dose 5-fluorouracil (5-FU). Our results revealed that 5-FU-resistant CRC cell lines exhibited elevated furin expression, accompanied by increased levels of TGF-β protein and phosphorylated ERK1/2 (pERK1/2). Notably, furin knockdown restored chemosensitivity, highlighting its critical role in drug resistance. Furthermore, we demonstrated that TGF-β treatment upregulated furin and pERK1/2 expression, while forced furin overexpression similarly induced TGF-β and pERK1/2 expression. Collectively, these findings suggest that furin plays a pivotal role in CRC progression and chemoresistance by activating the TGF-β/ERK signaling pathway. Citation Format: Abdul K. Siraj, Pratheesh Kumar Poyil, Sandeep Kumar Parvathareddy, Saravanan Thangavel, Fouad Al-Dayel, Khawla S. Al-Kuraya. Furin drives colorectal cancer progression and chemoresistance through the TGF-β/ERK signaling 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 5709.
Abstract 5694: Targeting NAD(P)H: Quinone oxidoreductase 1 (NQO1) for colorectal cancer diagnosis and therapy
Authors: Chaithanya Ganji, Santosh Behera, Lakkakula V. Bhaskar, Mehmet Akce, Bassel F. El-Rayes
Journal: Cancer Research (2025)

Background/Objective: Colorectal cancer (CRC) is the third most common cancer in the United States and is associated with poor outcomes. NAD(P)H: Quinone Oxidoreductase 1 (NQO1), an enzyme, shown to contribute to chemoprotection for CRC. This meta-analysis aims to examine the association between NQO1 C609T polymorphisms and CRC risk. Furthermore, the study explores the binding capacity and efficacy of BBI 608 against NQO1 in CRC through molecular docking. The inhibitor will then be tested in vitro. Methods: PubMed, Web of Science, and Google Scholar were used in bibliographic searches. For the NQO1 C609T analysis, 18 studies were used. Data was gathered and subsequently calculated using the pooled odds ratio (OR) (95% confidence interval, CI). Molecular docking, Western Blot, and QRT-PCR were used to determine the molecular function of BBI 608 and NQO1. Results: The relation between NQO1 polymorphism and CRC risk (TT + CT vs. CC: OR=1.19, 95% CI =1.06-1.34, p&amp;lt;0.001) was significant. Furthermore, stratified investigation based on ethnicity indicated a significant association between NQO1 polymorphism and CRC risk (TT + CT vs. CC: OR=1.17, 95% CI =1.08-1.27, p&amp;lt;0.001). This study indicates that the C609T polymorphism of NQO1 is linked with CRC risk in Asians and Caucasians. Computational approaches were applied to observe the molecular properties of BBI 608 (NQO1 inhibitor) and analyze the exact mechanism of NQO1 on CRC. This investigation provides a detailed understanding of the interaction between NQO1 and BBI 608 and its implication in CRC therapy. In vitro studies were performed to support this computational analysis. BBI 608 creates higher cytotoxicity in a dose-dependent manner in CRC cell lines. BBI 608 treatment significantly (p&amp;lt;0.001) reduced the NQO1 expression at protein and RNA levels in both CRC (HCT 116 and RKO) cell lines. Conclusion: Based on meta-analysis and a computational approach, NQO1 is a viable biomarker and a possible molecular target in CRC. In vitro, results showed that inhibiting NQO1 by BBI 608 decreased cell proliferation in both CRC cell lines. Knockout, overexpression, or site-directed mutagenesis is essential for a better understanding of BBI 608-targeted NQO1 and its amino acids. Citation Format: Chaithanya Ganji, Santosh Behera, Lakkakula V. Bhaskar, Mehmet Akce, Bassel F. El-Rayes. Targeting NAD(P)H: Quinone oxidoreductase 1 (NQO1) for colorectal cancer diagnosis and therapy [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 5666.
Abstract 5698: Opposing roles of HOXC6 isoforms in promoting head and neck squamous cell carcinoma
Authors: Ishita Gupta, Subhendu Roy Choudhury, Anirudh Saxena, Madeleine Ndahayo, Vera Mukhina, Andrey Loginov, Nadya Vorobyeva, Daria A. Gaykalova
Journal: Cancer Research (2025)

Abstract HOXC6, a member of the homeobox (HOX) family is a homeoprotein transcription factor regulating embryonic development, differentiation, and pathways like TGF-β/smad, PI3K/Akt, and Wnt. Although aberration in HOXC6 promotes onset and progression of several cancers, our previous study indicated an oncogenic role of HOXC6 in head and neck squamous cell carcinoma (HNSCC). Despite its role in HNSCC progression, the specific role of HOXC6 in HNSCC lies nascent. Emerging evidence suggests that alternative splicing events of HOXC6 generate distinct isoforms with diverse biological functions. While the HOXC6 transcript variant 1 encodes the primary isoform, variant 2 differs in the 5' UTR coding region and produces a shorter N-terminal isoform. In this study, we performed in-silico analysis alongside in vitro functional studies to delineate the roles of the primary and short isoforms in HNSCC progression. In-silico analysis revealed isoform-specific expression patterns across HNSCC and correlated with clinical outcomes. Our in vitro data demonstrated that the primary isoform enhances cell proliferation and migration by activating oncogenic pathways, while the shorter isoform counteracts these effects by inhibiting cell proliferation and suppressing metastatic potential. These findings highlight the impact of alternative splicing in modulating HNSCC function and reveal the opposing roles of its isoforms in HNSCC progression. This study underscores the importance of targeting isoform-specific mechanisms for developing biomarkers and therapeutic strategies in HNSCC. Citation Format: Ishita Gupta, Subhendu Roy Choudhury, Anirudh Saxena, Madeleine Ndahayo, Vera Mukhina, Andrey Loginov, Nadya Vorobyeva, Daria A. Gaykalova. Opposing roles of HOXC6 isoforms in promoting head and neck squamous cell carcinoma [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 5698.
Abstract 6896: A pan-KRAS degrader for the treatment of KRAS-mutant cancers
Authors: Mu-Sheng Zeng, Jie Yang, Qiao-Li Wang Wang, Guan-Nan Wang, Jia-Cong Ye, Zi-Qian Li, Jing-Yun Wang, Zhao-Hui Liang, Shu-Xin Li, Cong Sun, Wen-Ting Liao, Yi-Jun Gao, Jing Wang, Yong Mao, Chunjing Yu, Guo-Kai Feng
Journal: Cancer Research (2025)

Abstract KRAS mutations are highly prevalent in a wide range of lethal cancers, and these mutant forms of KRAS play a crucial role in driving cancer progression and conferring resistance to treatment. While there have been advancements in the development of small molecules to target specific KRAS mutants, the presence of undruggable mutants and the emergence of secondary mutations continue to pose challenges in the clinical treatment of KRAS-mutant cancers. In this study, we developed a novel molecular tool called tumor-targeting KRAS degrader (TKD) that effectively targets a wide range of KRAS mutants. TKD is composed of a KRAS-binding nanobody, a cell-penetrating peptide selectively targeting cancer cells, and a lysosome-binding motif. Our data reveal that TKD selectively binds to KRAS in cancer cells and effectively induces KRAS degradation via a lysosome-dependent process. Functionally, TKD suppresses tumor growth with no obvious side effects and enhances the antitumor effects of the PD-1 antibody and cetuximab. This study not only provides a strategy for developing drugs targeting “undruggable” proteins but also reveals that TKD is a promising therapeutic for treating KRAS-mutant cancers. Citation Format: Mu-Sheng Zeng, Jie Yang, Qiao-Li Wang Wang, Guan-Nan Wang, Jia-Cong Ye, Zi-Qian Li, Jing-Yun Wang, Zhao-Hui Liang, Shu-Xin Li, Cong Sun, Wen-Ting Liao, Yi-Jun Gao, Jing Wang, Yong Mao, Chunjing Yu, Guo-Kai Feng. A pan-KRAS degrader for the treatment of KRAS-mutant 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 6896.
Abstract 6901: Imipridones (ONC201, ONC206 and ONC212) modulate MGMT and ClpX expression in DIPG cell lines
Authors: Lanlan Zhou, Shengliang Zhang, Wafik S. El-Deiry
Journal: Cancer Research (2025)

Abstract The first-in-class small-molecule imipridone ONC201/Dordaviprone targets mitochondrial protease ClpP to disrupt oxidative phosphorylation and trigger integrated stress response (ISR), TRAIL/DR5, and tumor cell death. ONC201 and analog ONC206 and ONC212 are blood-brain barrier penetrant. Temozolomide (TMZ) is an oral alkylating agent that is generally well tolerated. Epigenetic transcriptional silencing of O6-methylguanine-DNA methyltransferase (MGMT) mediated by MGMT gene promoter methylation is associated with response to TMZ treatment. TMZ has been used in combination with Radiation Therapy (RT) as standard of care for glioblastoma (GBM) with a methylated MGMT promoter since 2005. Our previous studies demonstrated that ONC201/ONC206 synergized with standard-of-care GBM therapies TMZ and RT in GBM cell lines and orthotopic GBM mouse model. Diffuse Intrinsic Pontine Gliomas (DIPG) is a fast growing and highly aggressive pediatric central neural system tumor that starts in the brain stem's glial cells and has a dismal prognosis. DIPG has been recognized to be molecularly distinct from both adult high-grade glioma (HGG) and other non-midline pediatric high-grade gliomas (pHGG). DIPG has almost universally unmethylated MGMT promoters and TMZ has no role in the treatment of this disease. We reported earlier that ONC201 suppresses oxygen consumption rate observed with TMZ alone in DIPG cells, and TMZ has effects on T-cells killing solid tumor cells with high expression of MGMT. In this study we discover that imipridones (ONC201, ONC206 and ONC212) reduce expression of MGMT in DIPG cell lines following treatment with Imipridones -/+ TMZ. ClpX levels were reduced in all glioma cells treated and served as a biomarker of imipridone target engagement. The change of MGMT has the same trend as that of ClpX. These novel findings suggest a potential mechanism of synergy between imipridones and TMZ through suppression of MGMT protein expression in DIPG cells that typically have unmethylated MGMT promoter and are resistant to effects of TMZ. We are going to test this mechanism of synergy and therapeutic efficacy in vivo by treating orthotopic DIPG mouse models with imipridones -/+ TMZ. Our results support further studies combining imipridones (ONC201, ONC206 and ONC212) with TMZ and RT as a reasonable and safe therapeutic option for DIPG. Citation Format: Lanlan Zhou, Shengliang Zhang, Wafik S. El-Deiry. Imipridones (ONC201, ONC206 and ONC212) modulate MGMT and ClpX expression in DIPG cell lines [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 6901.