bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2851: Characterization of neogenes in desmoplastic small round cell tumors
Authors: Truong Danh , Magrath Justin , Lee Sean , Ludwig Joseph
Published: March 2024

Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, soft tissue sarcoma caused by the EWS::WT1 fusion protein (FP). The FP acts as an aberrant transcription factor with oncogenic properties. Recently, oncogenic chimeric transcription factors (OCTF), such as EWS::WT1, were discovered to induce the expression of novel transcripts in otherwise silent genomic regions. These neogenes (NGs) are highly specific to each OCTF and not detected in normal tissue. 37 NGs were found to be associated with the EWS::WT1 FP.We explored the NGs to characterize their expression and regulation in a cohort of MD Anderson Cancer Center patients. We annotated and counted the NGs from the bulk RNA-seq data of 37 specimens. After fusion detection, only 22/37 specimens harbored the EWS::WT1 FP. We found that only the same 22 specimens robustly expressed DSRCT-specific NGs. Interestingly the NGs were heterogeneously expressed, suggesting that there may be patient-specific differences. Single-nucleus RNA-sequencing (snRNA-seq) of Ewing sarcoma (ES), CIC::DUX4 sarcoma (CDS), DSRCT, and osteosarcoma revealed that only the three sarcomas driven by an OCTF robustly expressed NGs. Notably, the DSRCT-specific NGs were only expressed in DSRCT. Similarly, ES and CDS only expressed their subtype-specific NGs. Given the robust expression of the DSRCT-specific NGs in DSRCT, we asked if the EWS::WT1 FP regulated the expression of the NGs. Knockdown (KD) of the EWS::WT1 FP in four DSRCT cell lines showed a consistent reduction in DSRCT-specific NGs. While there was variability in NG expression and EWS::WT1 FP KD sensitivity, we identified seven NGs decreased by at least 75% in all four cell lines and an additional eight NGs with 75% reduction across three cell lines. BOD-DSRCT and SK-DSRCT2 had the largest number of NGs reduced after KD, with 25/37 and 20/37 NGs with 75% expression reduction, respectively. EWS::WT1 FP has two known isoforms generated by alternative splicing in the WT1 domain that includes or excludes three amino acids, lysine, threonine, and serine (KTS) between zinc fingers 3 and 4, producing E+KTS and E-KTS isoforms. By transducing one or both isoforms into the mesothelial cell line LP9, we found 3/37 NGs were induced by the E+KTS isoform and 17/37 were induced by the E-KTS isoform, suggesting that the E-KTS isoform is primarily responsible for NG expression. Current work is underway investigating the relationship between EWS::WT1 FP binding and NG expression and the potential for NG to produce novel peptides that could serve as DSRCT immunotherapy targets.

Citation Format: Danh Truong, Justin Magrath, Sean Lee, Joseph Ludwig. Characterization of neogenes in desmoplastic small round cell tumors [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 2851.
Abstract 2949: A flexible and efficient approach for single-cell CRISPR perturbation screens combined with targeted RNA-seq expression analysis
Authors: Tedesco Donato , Liu Tianbing , Makhanov Mikhail , Hu Dongfang , Isachenko Nadya , Diehl Paul , Chenchik Alex
Published: March 2024

This study presents a novel approach for performing 10X platform-based targeted single-cell RNA-seq analysis in combination with CRISPR perturbation screens. For the analysis, we constructed a custom sgRNA library focused on a small subset of genes associated with the TNFα response (i.e., NFκB pathway). We compared analysis of two targeted gene expression panels—the first, targeting all protein-coding genes (genome-wide) and the other, targeting a selected set of genes representing key hubs in signaling pathway modules. Narrowing down the analyzed gene set enhanced the efficiency of single-cell RNA-seq by reducing the associated next-generation sequencing (NGS) depth required for readout, and significantly streamlining data analysis. Comparing the analysis of the expression panels targeting all protein-coding genes with the smaller pathway-targeted set, we were able to assess the general flexibility of the novel approach for single-cell CRISPR perturbation screens. We evaluated the specific tradeoffs with regard to the size of the CRISPR library, the size of the panel of genes targeted for expression analysis, and NGS sequencing depth. This flexible, targeted approach not only refines the precision of RNA-seq but also provides a more cost-effective solution for comprehensive genomic analyses.

Citation Format: Donato Tedesco, Tianbing Liu, Mikhail Makhanov, Dongfang Hu, Nadya Isachenko, Paul Diehl, Alex Chenchik. A flexible and efficient approach for single-cell CRISPR perturbation screens combined with targeted RNA-seq expression analysis [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 2949.
Abstract 2963: Dihydromyricetin is a senomorphic agent to promote therapeutic outcome of age-related conditions including cancer and Alzheimer's disease
Authors: Xu Qixia , Li Zi , Jiang Zhirui , Campisi Judith , Sun Yu
Published: March 2024

Aging is characterized by a progressive decline of organ function and gradual rise of susceptibility to multiple chronic disorders, with cancer being a primary cause of human morbidity and mortality worldwide. Cellular senescence represents a state of permanent cell cycle arrest and contributes to chronological aging and age-related diseases including Alzheimer's disease (AD), mainly through development of a distinct secretome termed the senescence-associated secretory phenotype (SASP). By screening a natural medicinal agent library, we noticed Rattan tea extract (RTE) has a prominent antiaging potential, wherein dihydromyricetin (DMY), the most abundant natural flavonoid in RTE, played a central role in suppressing the SASP expression of senescent cells. DMY enhanced total antioxidant capacity (T-AOC), increased catalase (CAT) and glutathione peroxidase (GSH-Px) activity, upregulated the expression of HO-1, NQO1, nuclear Nrf2 and phospho-ERK (p-ERK), but decreased malondialdehyde (MDA) level in senescent cells. Furthermore, DMY regulates PI3K/Akt/mTOR signaling pathway, NLRP3 inflammasome formation, the NF-κB complex activity and ER stress-response, each responsible for a full spectrum SASP development. Transcriptomic profiling suggested that DMY can dampen the genome-wide upregulation of pro-inflammatory factors produced by senescent cells, resulting in abrogated progression of cancer malignancy including elevated proliferation, migration, invasion and chemoresistance. Importantly, combination of DMY with classic chemotherapy significantly enhanced therapeutic efficacy, causing remarkable tumor regression and extending posttreatment survival. Alzheimer's disease (AD) is marked by the presence of amyloid plaques, neurofibrillary tangles, damaged neuronal macromolecules and redox sensitive ions. We found that DMY restrains inflammatory injury in microglial cells, reduces their apoptosis and inflammation, and inhibits TLR4 and MD2 expression. Results of small molecule-protein docking and pull-down assays indicated that DMY binds MD2 to suppress the formation of TLR4 complex. In AD mice, DMY improved the cognitive disorder of animals, suppressed inflammatory injury in brain and reduced TLR4 expression. Together, DMY represents a valid natural candidate that has senomorphic activity and can be applied for treatment of malignancies or neurodegenerative disorders such as AD, pathologies that frequently arise in late life of humans.

Citation Format: Qixia Xu, Zi Li, Zhirui Jiang, Judith Campisi, Yu Sun. Dihydromyricetin is a senomorphic agent to promote therapeutic outcome of age-related conditions including cancer and Alzheimer's disease [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 2963.
Abstract 3006: Morphogen-driven regulation of nuclear shape and its implication for colorectal cancer
Authors: Gendi Mona A. El , Hervé Solène , Gautam Sudeep , Miroshnikova Yekaterina A.
Published: March 2024

Colorectal cancer (CRC) is the second leading cause of cancer-related deaths worldwide despite improved rates of early detection and development of targeted treatments. Dysregulation of nuclear shape and the emergence of aberrant chromatin architecture correlate with cancer onset and progression, including CRC. Both extrinsic and intrinsic factors, most critically cytoskeletal and nucleoskeletal organization, chromatin architecture, and metabolic signaling, impact nuclear shape. Yet, what precisely determines nuclear shape in health and disease and how it is linked to cell fate and function remains a fundamental open question. In the case of over 75% of CRC cases, the first transformative genetic event is the loss of function in the tumor suppressor gene, adenomatous polyposis coli (APC). Mechanistically, perturbed APC signaling leads to aberrant activation of Wnt/beta-catenin signaling. This pathway is essential for intestinal homeostasis, as is the regulation of proper nuclear shape and function. Here, we aim to decipher the crosstalk between Wnt gradients and nuclear shape regulation in non-transformed and APC-mutated epithelial cells in vitro, as well as in WT and APC-mutant mouse colon tissues. The long-term goal of this work is to test whether a mechanistic link exists between Wnt-driven cellular transformation and the emergence of aberrant nuclear shape and function.

Citation Format: Mona A. El Gendi, Solène Hervé, Sudeep Gautam, Yekaterina A. Miroshnikova. Morphogen-driven regulation of nuclear shape and its implication for colorectal cancer [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 3006.
Abstract 304: The role of DDR1 mediated E-cadherin stability in collective colon cancer cell migration
Authors: Chen Hui-Chun , Wang Yu-Chun , Ching Yu-Chien , Cheng Chun-Pu , Ku Chia-En , Lee Shin-Ru , Chao Wei-Ting
Published: March 2024

In cancer metastasis, the mechanism of single cell migration and collective cell migration are investigated. The dynamics of E-cadherin is critical in collective cell migration as the important mechanism of metastasis. DDR1 (Discoidin Domain Receptor 1) has been shown to promote E-cadherin stability at adherens junction in epithelial cells by regulating endocytosis of E-cadherin. However, in the growth of epithelial cell cluster and collective cell migration, the role of DDR1 in the cell-cell contacts is not clear. In this study, HT-29 colon cancer cells with epithelial phenotype were used in the experiments. Cells were treated with epidermal growth factor to stimulate E-cadherin turnover or applied with lysosome inhibitor chloroquine to interfere cellular vesicle transport. DDR1 and E-cadherin were revealed by immuno-confocal microscopy. The immunostaining results showed DDR1 was localized at cell-cell contacts and co-localized with E-cadherin. When cells were treated with epidermal growth factor, the phosphor MAPK activity was increased and DDR1 was localized at cell-cell contacts intensively. When lysosome activity was blocked by chloroquine treatment. The cellular vesicle transport and collective cell migration was reduced and furthermore inhibited DDR1 translocation to the cell-cell contacts. This study demonstrated DDR1 co-localized with E-cadherin is responsible for epidermal growth factor stimulation in cell cohort. Lysosome activity is required for E-cadherin turnover and affected DDR1 translocation. Chloroquine maybe the potential drug to suppress tumor nest growth and collective cell migration by interfere DDR1 mediated E-cadherin stability.

Citation Format: Hui-Chun Chen, Yu-Chun Wang, Yu-Chien Ching, Chun-Pu Cheng, Chia-En Ku, Shin-Ru Lee, Wei-Ting Chao. The role of DDR1 mediated E-cadherin stability in collective colon cancer cell migration [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 304.
Abstract 3105: Computational integration with phage library to optimize clones of DEFB4A antibodies for cancer diagnostics and therapeutics
Authors: Guo Yichen , Yom Jina , Han Andy (Xi) , Guo Zhaoying , Zewdu Eden , Gonzalez Rachel , Qu Tianli , Gilmore Bailey , Liu Xuan , Fu Wei , Hu Xiaomin
Published: March 2024

DEFB4A, a human beta-defensin, functions as a potential cancer biomarker, with elevated expression observed in various cancers, making it a candidate for diagnostic and prognostic applications. Additionally, its role in immune modulation suggests that DEFB4A may hold promise as a target for novel cancer treatments, particularly in the context of immunotherapy. This study aimed to develop a stable and high-affinity DEFB4A antibody for clinical and pre-clinical use.

To achieve this, a combination of high-diversity phage libraries and computation-assisted analysis was employed to generate single-chain variable fragments (ScFv) clones specifically targeting DEFB4A. This research presents a robust approach for the generation of DEFB4A-targeting single-chain variable fragments (ScFv) from a phage library characterized by a high diversity of 109 unique clones and high titer of 1013 cfu/mL. Computational optimization was then applied to enhance the affinity, stability, and expression of these candidates through rational design and virtual mutagenesis programs. The binding activity of the optimized mutants was validated using biophysical methods such as surface plasmon resonance (SPR) and thermal stability assays. The process showed a remarkable 100-fold increase in affinity and stability. Additionally, the selected ScFv clone was further employed in immunohistochemistry (IHC) to detect DEFB4A in breast, prostate, and gastric cancers, showing higher expression levels compared to initial clones.

This study highlights the synergy of high-diversity phage libraries and computational methods in crafting DEFB4A antibodies with enhanced affinity, stability, and expression. The findings advance the field of antibody engineering, emphasizing the crucial integration of experimental and computational approaches. This work lays the groundwork for the development of high-performance biologics with diagnostic and prognostic applications across diverse cancer types. Furthermore, it demonstrates the possibility of integrating computational approaches in antibody development, offering the promise of expediting the process in the future.

Citation Format: Yichen Guo, Jina Yom, Andy (Xi) Han, Zhaoying Guo, Eden Zewdu, Rachel Gonzalez, Tianli Qu, Bailey Gilmore, Xuan Liu, Wei Fu, Xiaomin Hu. Computational integration with phage library to optimize clones of DEFB4A antibodies for cancer diagnostics and therapeutics [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 3105.
Abstract 3112: Colorectum metabolome map revealed etiological and survival heterogeneity in cancers of different subsites: Challenging the proximal versus distal classification
Authors: Jain Abhishek , Johnson Caroline , Berardi Domenica , Khan Sajid , Morris Montana
Published: March 2024

Objective: Colorectal cancer (CRC) is usually classified as proximal, distal and rectal cancer. clinicopathological, molecular features and risk factors do not change abruptly and variations exist even among the refined subsites, which may contribute to the failure of mechanism-targeted therapies for CRC and poor accuracy of potential CRC biomarkers. We generated a CRC metabolome map describing etiological and survival heterogeneity in cancers of different subsites of the colorectum.

Design: Utilizing 372 tumor tissues with matched normal mucosa liquid chromatography-mass spectrometry was applied to examine metabolomics profiles along 7 subsites of the colorectum: cecum (n=63), ascending colon (n=44), transverse colon (n=32), descending colon (n=28), sigmoid colon (n=75), rectosigmoid colon (n=38) and rectum (n=92). Linear regression showed distribution of metabolites along the subsites. Survival heterogeneity along subsites were statistically tested by cox regression analysis. Metabolome profiles were obtained from invitro cultures of 310 human microbial species.

Results: 40 and 76 significantly altered metabolites (including bile acids, lysoPCs and LysPEs) among tumors and normal mucosa showed metabolic heterogeneity existed among CRC subsites. Gradual changes in metabolites abundance with significantly linear trend from cecum to rectum: 23 metabolites in tumor, 30 metabolites in normal mucosa and 15 metabolites in both tumor and normal mucosa, revealed concentration gradient depends on the disease status. Exclusively significant alteration of metabolites only in one subsite showed the differences in cancers among the 7 subsites of colorectum. We identified the metabolites associated with survival were different and unique to each subsite. Integration of microbial metabolome with CRC metabolome revealed microbial metabolites contributed to etiological and survival heterogeneity among CRC subsites.

Conclusions: Gradual changes of metabolites from cecum to rectum and the association of different metabolites with CRC risk and survival in each subsite of colorectum, revealed the differences in cancers along the colorectum and challenge the simple classification of CRC in LCC, RCC and rectum. Human microbial metabolites contributed to etiological and survival heterogeneity among CRC subsites.

Citation Format: Abhishek Jain, Caroline Johnson, Domenica Berardi, Sajid Khan, Montana Morris. Colorectum metabolome map revealed etiological and survival heterogeneity in cancers of different subsites: Challenging the proximal versus distal classification [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 3112.
Abstract 3170: Epigenetic identification and functional characterization of a novel RING finger protein tumor suppressor in nasopharyngeal carcinoma and esophageal carcinoma
Authors: Chai Xiaoxue , Luo Feifei , Bao Shujie , Meng Liuzhen , Chan Anthony T. , MA Brigette B. , Tao Qian , LiLi li
Published: March 2024

RING finger proteins play crucial roles in normal physiology and pathophysiology as important regulators of ubiquitin-dependent proteasomal protein degradation. Many RING finger proteins have also been implicated in tumorigenesis either as oncogenes or tumor suppressors. Through cancer CpG methylome studies, we identified RING finger protein 150 (RNF150) as a methylated target gene in nasopharyngeal carcinoma (NPC) and esophageal carcinoma (ESCC). RNF150 was found to be ubiquitously expressed in human normal tissues but frequently downregulated in NPC and ESCC cells due to its promoter methylation. Its downregulation is associated with poor survival in patients with head and neck cancer and esophageal cancer. We also found that RNF150 is a functional tumor suppressor by inhibiting tumor cell growth and inducing cell cycle arrest in NPC and ESCC cells. Furthermore, ectopic expression of RNF150 inhibited NPC and ESCC cell migration/invasion by suppressing epithelial-mesenchymal transition (EMT) through upregulation of epithelial marker E-cadherin and downregulation of mesenchymal markers (vimentin, N-cadherin, Snail, and Slug). RNF150 is located in the cytoplasm and represses several oncogenic signaling pathways including the Wnt/β-catenin and NF-kB signaling pathways. Liquid chromatography-mass spectrometry (LC-MS) was performed to elucidate RNF150 binding proteins. KEGG enrichment analysis showed that glycolysis/gluconeogenesis, pyruvate metabolism, central carbon metabolism in cancer, and AMPK signaling were the top 4 pathways with significant enrichment, suggesting potential targeting of metabolic molecules by RNF150. Thus, our results provide insights into a new ring finger protein member, RNF150, as a functional tumor suppressor for NPC and ESCC. Our study also suggests a potential epigenetic biomarker for the early dection of NPC and ESCC.

Citation Format: Xiaoxue Chai, Feifei Luo, Shujie Bao, Liuzhen Meng, Anthony T. Chan, Brigette B. MA, Qian Tao, li LiLi. Epigenetic identification and functional characterization of a novel RING finger protein tumor suppressor in nasopharyngeal carcinoma and esophageal carcinoma [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 3170.
Abstract 3189: A novel monoclonal antibody targeting TM4SF4 enhances antitumor activity through regulation of cellular levels of immune checkpoint ligands and antibody dependent cellular cytotoxicity
Authors: Kim Rae Kwon , Heo Chang-Kyu , Kahm Yeon-jee , Jung Uhee , Shin Byung-Chul , Kim Won-Yong , Kim Bum-Jin , Kim Sung-Chul , Ryu Chun-jeih , Cho Eun-Wie , Kim In-Gyu
Published: March 2024

Transmembrane 4 super family member 4(TM4SF4) protein has been shown to be involved in EMT-associated stemness through autocrine of insulin-like growth factor 1(IGF1) and osteopontin(OPN) in non-small cell lung cancer(NSCLC) cells. However, its potential as a therapeutic target has not been evaluated. In this study, anti-human TM4SF4 monoclonal antibodies(anti-hTM4SF4 mAbs) were prepared in mouse as part of a strategy for developing anticancer drug using humanized antibody. A synthetic peptide(15 mer, 126-140th AA) derived from the extracellular loop(ECL) 2 of human TM4SF4 exposed on outer cell surface was used as an immunization antigen. Among the selected anti-hTM4SF4 mAbs, ECL-2B7 and ECL-12A8 showed the best affinity for the antigen(Kd), approximately 2.66 nM and 8.34 nM, as determined by surface plasmon resonance analysis. Using mouse xenograft of NSCLC cell line, it was confirmed that ECL-2B7 was superior to ECL-12A8 in producing humanized antibody. ECL-2B7 inhibited EMT-associated stemness of TM4SF4 positive cancer cells by blocking cellular signaling events such as IGF1Rβ and CD44 and their downstream signals, PI3K/AKT/GSK3β/NF-κB and JAK2/STAT3 pathways. ECL-2B7 also enhanced antitumor activity by downregulating cellular and exosomal level of PD-L1 and B7-H4, immune-checkpoint ligands that elicit immunosuppression of T cell, and by mediating antibody-dependent cellular cytotoxicity. Treatment with OPN- and IGF1-neutralizing antibodies suppressed intracellular PD-L1 and B7-H4 level. It means that the regulation of PD-L1 and B7-H4 levels by TM4SF4 is closely related to the autocrine action of OPN and IGF1 induced by TM4SF4. Using patient-derived xenograft model, it was confirmed that the ECL-2B7 has excellent antitumor activity that effectively inhibits tumor progress. These results strongly suggest that it is necessary to construct humanized antibody based on ECL-2B7 to confirm its potential as a novel anticancer drug.

Citation Format: Rae Kwon Kim, Chang-Kyu Heo, Yeon-jee Kahm, Uhee Jung, Byung-Chul Shin, Won-Yong Kim, Bum-Jin Kim, Sung-Chul Kim, Chun-jeih Ryu, Eun-Wie Cho, In-Gyu Kim. A novel monoclonal antibody targeting TM4SF4 enhances antitumor activity through regulation of cellular levels of immune checkpoint ligands and antibody dependent cellular cytotoxicity [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 3189.
Abstract 3230: Discovery of selective BRM (SMARCA2) ATPase inhibitors for the treatment of BRG1 (SMARCA4) mutant cancers
Authors: Lee Janice Y. , Brooks Nathan , Antonakos Brandon , Perria Bryan , Langan Candace , Jones Bonita D. , Flack Robert Stephen , Li Zhifang , Terry David , Wallace Ross , Bondi Robert , Sis Gereint , Baracani Ronee , McVean Maralee , Kolakowski Gabrielle , Osimboni Dayo , Wilson Kevin
Published: March 2024

BRM (SMARCA2) and BRG1 (SMARCA4) are highly homologous ATPases that are members of the BAF (also known as the mSWI/SNF) chromatin remodeling complex. BRM and BRG1 are mutually exclusive enzymatic subunits of BAF complexes, and functional genomic screens have shown a synthetic lethal relationship between the two genes. BRG1 is frequently mutated in cancer, including in approximately 10% of non-small cell lung carcinomas. Selective inhibition of BRM is a mechanism by which BRG1-mutated cancer cell growth would be affected by losing BRM function, while normal tissues should be spared as they still express functional BRG1. Given that the ATPase domains of BRM and BRG1 are 92% identical, the identification of selective enzymatic inhibitors of BRM has been challenging. Here, we report the discovery of novel, highly potent compounds that selectively inhibit BRM over BRG1 as seen in cell-based transcription and proliferation assays, that also possess excellent oral pharmacokinetics. Our lead compounds inhibit BRM in a cell-based reporter assay with an unbound IC50 of 1 nM and are greater than 20-fold selective over BRG1. They are also selective against other helicases and do not show any significant activity in off-target screening panels. Dosing of mice carrying BRG1-mutant xenografts causes target gene modulation that is correlated with compound exposure. Treatment of A549 and RERF-LC-AI xenografts with lead compounds led to tumor growth inhibition of 87% and 96%, respectively, at well-tolerated doses, and significant tumor growth inhibition was also achieved in multiple other BRG1-mutant models. The results suggest that our compounds have first-in-class potential as potent and selective BRM ATPase inhibitors for the treatment of BRG1-mutated cancers, and we are planning to file an IND in 2024.

Citation Format: Janice Y. Lee, Nathan Brooks, Brandon Antonakos, Bryan Perria, Candace Langan, Bonita D. Jones, Robert Stephen Flack, Zhifang Li, David Terry, Ross Wallace, Robert Bondi, Gereint Sis, Ronee Baracani, Maralee McVean, Gabrielle Kolakowski, Dayo Osimboni, Kevin Wilson. Discovery of selective BRM (SMARCA2) ATPase inhibitors for the treatment of BRG1 (SMARCA4) mutant cancers [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 3230.
Abstract 3261: Improving targeted therapy in female patients with lung squamous cell carcinoma
Authors: Momcilovic Milica , Shackelford David
Published: March 2024

Non-small cell lung cancer (NSCLC) will claim the lives of ~60,000 female patients in the US in 2023. Lung squamous cell carcinoma (LUSC) is a subtype of Non-Small Cell Lung Cancer (NSCLC) that comprises ~30% of NSCLC and is characterized by high metabolic activity. Specifically, LUSC typically exhibits elevated rates of both glucose and glutamine metabolism driven by the PI3K-AKT-mTOR and KEAP1/NRF2 pathways. Further, a paucity of identifiable genetic drivers in LUSC has resulted in a lack of effective targeted therapies for patients with this devastating disease. Despite recent advances in therapy, the 5-year survival rate for patients with advanced NSCLC is 6%, underscoring the need for better treatment options. Importantly, no significant sex bias is seen in the newly diagnosed cases of lung cancer (~50%M/~50%F) (American Cancer Society, 2023), yet there are no sex-specific therapeutic approaches in clinical use. We demonstrated that the catalytic mTOR kinase inhibitor TAK228 can be utilized to effectively treat LUSC tumors via inhibition of glycolysis, an approach that is currently being evaluated on two phase I/II clinical trials (NCT02417701, NCT04250545), launched as a direct result of our pre-clinical work. However, our pre-clinical data suggests that despite the potential benefit of TAK228 inhibition in LUSC, a subset of tumors are resistant to TAK228 despite on-target activity of mTOR inhibitor, leading to the rationale of the current hypothesis, namely the possibility that sex-specific differential effects of TAK228 may exist. To evaluate this hypothesis, we have generated preliminary data demonstrating that sex is a determinant of TAK228 response in LUSCs, whereby male mice are significantly more sensitive to mTOR inhibition than females. Follow-on experiments have demonstrated that the anti-estrogen therapy (Letrozole) sensitized previously resistant female mice bearing LUSCs to TAK228, suggesting an estrogen-related link to TAK228 resistance in females. Additionally, RNASeq and biochemical analyses identified pathways that are upregulated in TAK228 resistant female mice with LUSC tumors. These results suggest that the estrogen may play a key role in the observed pattern of female resistance to mTOR inhibition. As such, the goal of the current proposal is to evaluate the catalytic mTOR kinase inhibitor TAK228, in combination with anti-estrogen therapy as a therapeutic strategy to treat LUSC in females.

Citation Format: Milica Momcilovic, David Shackelford. Improving targeted therapy in female patients with lung squamous cell carcinoma [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 3261.
Abstract 3278: Analysis of the mechanism of resistance to selpercatinib in thyroid cancer cells with RET/PTC1 fusion gene
Authors: Amitani Masatsugu , Ito Ken-ichi
Published: March 2024

Purpose: Precision oncology, in which molecularly targeted drugs are selected based on genetic mutations, has begun in thyroid cancer, and drugs targeting BRAF, RET, and NTRK are already in clinical use. However, as with previous therapeutic agents for malignant tumors, there have been cases of resistance to these drugs either initially or during treatment, and the mechanisms of drug resistance need to be elucidated. So far, little is known about the mechanisms of resistance to molecularly targeted drugs in thyroid cancer. To overcome resistance to the RET inhibitor, selpercatinib (SEL), and to consider next therapeutic strategies, we aimed to elucidate the mechanisms of resistance to SEL.

Method: We used papillary carcinoma cell lines TPC-1 and CUTC48, which harbor the RET/PTC1 fusion gene. We established an SEL-resistant subline (TPC-1/SELR) in TPC-1 by long-term exposure to SEL. The growth inhibitory effect of drugs was analyzed using the WST assay. The alteration of intracellular signal transduction was analyzed by western blotting.

Result: The 50% inhibitory concentration (IC50) for SEL in the parental TPC-1 was 3 nM, while growth inhibition in TPC-1/SELR did not reach 50% even at more than 100 nM of SEL. On the other hand, growth inhibition by SEL in CUTC48 did not reach 50% even at more than 100 nM of SEL. The sensitivity to SEL in CUTC48 was comparable to that in TPC-1/SELR, and CUTC48 showed an intrinsic resistance to SEL. TPC-1/SELR showed increased phosphorylation of EGFR, Erk, Akt, and mTOR compared to TPC-1. In CUTC48, phosphorylation of EGFR and Erk was not increased compared to that of TPC-1, while phosphorylation of Akt and mTOR was increased. We investigated the growth inhibitory effect of an mTOR inhibitor everolimus and found that TPC-1 (IC50: 1.3 nM), TPC-1/SELR (5 nM), and CUTC48 (9.4 nM) were all highly sensitive to everolimus.

Discussion: Our results showed that Akt and mTOR phosphorylation were elevated in the SEL-resistant TPC-1/SELR and the SEL-intrinsic resistant CUTC48 in common, suggesting the involvement of activation of the Akt-mTOR pathway in SEL resistance in thyroid cancer. The inhibition of the Akt-mTOR pathway in parallel with RET may have therapeutic potential to overcome SEL resistance in thyroid cancer.

Citation Format: Masatsugu Amitani, Ken-ichi Ito. Analysis of the mechanism of resistance to selpercatinib in thyroid cancer cells with RET/PTC1 fusion gene [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 3278.
Abstract 3434: Effect modification by levels of sex hormones in the association between adiposity and cancer incidence in the UK Biobank
Authors: Lucas LeeAnn , Lu Yujia , Giovannucci Edward L. , Song Mingyang
Published: March 2024

Introduction: The association between adiposity and cancer risk differs between sexes for some cancer types.

Methods: We prospectively examined adiposity in relation to cancer incidence according to sex hormones in the UK Biobank. Adiposity was assessed by body mass index (BMI) and visceral adipose tissue (VAT), the latter predicted using determinants of age, height, weight, hip circumference, waist circumference, and race. Serum sex hormone binding globulin (SHBG), testosterone, and estradiol were measured using a biochemistry assay and were classified as high or low based on median levels. Cancer incidence was ascertained using ICD-10 codes through cancer registry linkage. For cancer types showing a sex difference in the association between adiposity and cancer incidence, we assessed multiplicative and additive interaction with sex hormones in men and women separately and corrected for multiple testing using false discovery rate. We used Cox regression to calculate the multivariable hazard ratio (HR) of cancer per increase between the 90th to 10th percentile of adiposity (BMI or predicted VAT).

Results: During a median follow-up of 13.1 years, we documented 23,964 and 21,045 incident cancer cases among 217,460 men and 256,163 women, respectively. Adiposity showed a much stronger association with higher risk of colorectal, esophageal, and liver cancers in men than women. In men, BMI was more strongly associated with higher risk of colorectal cancer in low vs. high levels of SHBG (HR (95%CI) of 1.47 (1.31-1.64) vs. 1.12 (0.94-1.33) (adjusted Pinteraction = 0.027). In contrast, BMI showed a stronger association in high vs. low levels of SHBG with esophageal (HR = 2.39 vs. 1.62) and liver cancers (HR = 3.24 vs 1.96) in men (adjusted Pinteraction = 0.038 and 0.027, respectively). Among women, BMI was associated with a higher risk of esophageal cancer in those with low SHBG (HR=1.68) but not in those with high SHBG (HR=0.64) (adjusted Pinteraction = 0.025). Similar patterns were observed for predicted VAT. Men with high SHBG levels and high adiposity (BMI and predicted VAT) had 7.63 (5.08-11.46) and 8.92 (5.72 to 13.90), respectively, times higher risk of liver cancer compared to men with low SHBG levels and low adiposity. No effect modification by estradiol or testosterone was detected for any of the cancers studied.

Conclusions: The association between adiposity and colorectal, esophageal, and liver cancer differed by sex. SHBG may be an important factor underlying these differences.

Citation Format: LeeAnn Lucas, Yujia Lu, Edward L. Giovannucci, Mingyang Song. Effect modification by levels of sex hormones in the association between adiposity and cancer incidence in the UK Biobank [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 3434.
Abstract 3509: Using generative AI for filtering and comprehension of drug target discovery screen results
Authors: Rech Andrew , Goltsev Yury , Samusik Nikolay , Kaznadzey Anna
Published: March 2024

Recent advancements in generative AI, including models such as GPT-4 and LLAMA2, have been rapidly integrated into cancer research. Cellformatica, Inc. has developed a pipeline designed to enhance the accuracy of functional and genomic drug target discovery screens by reducing the incidence of false positives and refining the interpretation process. This pipeline is capable of conducting comprehensive investigations, including genome-wide analyses, and is accessible via web and API interfaces. At the core of the pipeline is the use of the extensive global corpus of scientific literature to assess the relevance of each gene within the context defined by the experimental design of the screen. To address the issue of AI-generated inaccuracies, often referred to as 'hallucinations,' the pipeline incorporates a custom-tuned language model (LLM) component within the generative AI framework. This fine-tuning process is specifically tailored to the gene set under investigation. The pipeline's multi-agent architecture is a distinctive feature. It scores candidates based on three orthogonally-tuned criteria: effectiveness, confidence, and novelty. In benchmarking tests, this multi-agent scoring system has outperformed GPT-4 and has proven particularly adept at identifying candidate targets that may have been overlooked in previous research. These candidates are recognized for their significant therapeutic potential and are corroborated by existing scientific findings. The versatility of the Cellformatica pipeline is demonstrated through its application in three distinct areas of cancer research. First, it has been employed to optimize chimeric antigen receptor (CAR) T-cell therapies, a form of immunotherapy for cancer treatment. Second, the pipeline has been used to elucidate the network of chemotactic molecules that orchestrate immune cell infiltration and tissue remodeling in the lungs of patients with COVID-19. Third, it has been used to spatially define signaling pathways in humanized xenograft murine tumor experiments, for which existing cross-species database knowledge is limited. These applications underscore the pipeline's potential to contribute to the understanding and treatment of complex diseases.

Citation Format: Andrew Rech, Yury Goltsev, Nikolay Samusik, Anna Kaznadzey. Using generative AI for filtering and comprehension of drug target discovery screen results [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 3509.
Abstract 3611: A patient-derived organoid platform to assess the effectiveness of γδTCR cell therapy in solid tumors
Authors: Bisso Andrea , Overmeer Rene , Baardman Sjoerd , Coomans Chris , Oyarce Cesar , Boj Sylvia F.
Published: March 2024

Recent advances in cancer immunotherapy have positively impacted the life expectancy of patients for an extensive range of clinical indications. With new treatment strategies and druggable targets being identified at an increasing pace, the number of patients eligible for cancer immunotherapy is expected to expand steadily. However, promising therapeutic developments face hurdles in translating preclinical findings into therapy since conventional 2D cancer models hold low clinical predictive value. HUB developed an innovative alternative, building on the discovery that adult stem cells proliferate and organise into three-dimensional organotypic structures when embedded into the extracellular matrix. Patient-derived organoids are generated from healthy and malignant tissues, and they recapitulate complex characteristics of the original parental tissue, including molecular heterogeneity and morphological and functional traits. Cell therapies have achieved positive results in treating haematological cancers. Recently, the unique tumour-targeting properties of γδ T cell receptors have been leveraged to develop safer and more effective strategies. HUB and Gadeta joined efforts to explore the therapeutic potential of GDT002 - i.e. αβ T cells engineered with a Gadeta proprietary new γδTCR - to target solid cancers. A preclinical basket trial was performed using patient-derived organoids from several tumour types (colorectal, breast, head and neck, ovarian cancers) cocultured with GDT002. The results showed broad reactivity of GDT002 against solid tumor PDOs. Interestingly, GDT002 was particularly efficient at killing ovarian cancer-derived PDOs, allowing Gadeta to move GDT002 to clinical trials for this indication confidently. This study reveals that our tumor organoid co-culture with engineered T cells platform holds significant value for the preclinical development of cellular therapies.

Citation Format: Andrea Bisso, Rene Overmeer, Sjoerd Baardman, Chris Coomans, Cesar Oyarce, Sylvia F. Boj. A patient-derived organoid platform to assess the effectiveness of γδTCR cell therapy in solid tumors [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 3611.
Abstract 362: Arsenic sulfide triggers ferroptosis in hepatocellular carcinoma cells via TRPC6/GPX4 signaling
Authors: Lu Shumin , Cai Yu , Zhu Chuanying , Feng Zhuowei , Chen Shuxian , Chen Siyu
Published: March 2024

Background: Ferroptosis is critically involved in the pathological process of various human diseases, including cancer. Due to this, ferroptosis-inducing drugs are gaining more attention for the clinical treatment of tumors.

Methods: The cell counting kit-8 (CCK-8) assay was conducted to observe cell viability of hepatocellular carcinoma (HCC) cell lines. Ferroptosis was determined by levels of Fe2+, lipid reactive oxygen species (ROS), malondialdehyde (MDA) and transmission electron microscopy. Enzyme-linked immunosorbent assay (ELISA), western blot, quantitative polymerase chain reaction and immunofluorescence staining were utilized to evaluate glutathione peroxidase 4 (GPX4) and transient receptor potential channel 6 (TRPC6). Co-immunoprecipitation assay was conducted to determine the binding between GPX4 and TRPC6.

Results: Arsenic sulfide initiated ferroptotic cell death in HCC cells, which was concomitant with ROS accumulation, lipid peroxidation, and GSH depletion. Arsenic sulfide -mediated cell death in HCC cells was blocked by ferroptosis inhibitors ferrostatin-1 (Fer-1), but not Z-VAD-FMK, necrosulfonamide, or chloroquine, suggesting that ferroptosis contributed to arsenic sulfide -induced cell death. Furthermore, TRPC6 expression was notably inhibited under arsenic sulfide intervention and the overexpression of TRPC6 rescued the effects of arsenic sulfide on cell viability and ferroptosis of HCC cells. Furthermore, GPX4 was identified to interact with TRPC6 through confocal microscopy images and co-immunoprecipitation assay.

Conclusion: Our findings led us to conclude that arsenic sulfide could be considered as a prospective drug for liver cancer treatment.

Citation Format: Shumin Lu, Yu Cai, Chuanying Zhu, Zhuowei Feng, Shuxian Chen, Siyu Chen. Arsenic sulfide triggers ferroptosis in hepatocellular carcinoma cells via TRPC6/GPX4 signaling [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 362.
Abstract 3656: Target enrichment of methylated circulating tumor DNA for colorectal cancer detection
Authors: Huang Hsiao-Yun , Satya Ravi Vijaya , Chan Wen-Ching , Atolia Esha , Babiarz Joshua , Zimmermann Bernhard , Kawli Trupti
Published: March 2024

Aberrant DNA methylation changes are one of the earliest signatures of cancer development. Methylation profiling of circulating tumor DNA (ctDNA) from plasma has emerged as a promising approach for early cancer detection (ECD). However, the set of methylation targets that can successfully distinguish cancer through liquid biopsy will vary depending on cancer type and subtype. Here, we explored a methylation target enrichment workflow and developed a methylation-based classification model to distinguish between patients with colorectal cancer (CRC) and healthy individuals. First, CRC-specific CpG targets were identified by comparing the methylation landscape of CRC and normal samples (tissue and blood) available in The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) datasets. This analysis resulted in >800 CRC-specific CpG targets for initial evaluation. To develop and test the classification model, CRC patients and healthy individuals with plasma samples were included. A machine learning model was used to evaluate the highest performing CpG targets that effectively discriminated between CRC patients with detected ctDNA (“CRC ctDNA-positive”) and healthy individuals. Correlation between methylation levels of the high performing CpG targets and the variant allele frequency (VAF) among CRC ctDNA-positive patients was calculated. In total, 86 patients were included in this proof of concept study (mean age, 62 ±12 years; male, 55%). 50 CRC ctDNA-positive patients (24% stage I, 40% stage II, 24% stage III, and 12% stage IV) and 36 healthy normals were included in the analysis. We investigated this cohort to identify the highest performing CpG targets among the >800 potential CpG targets that provided effective discrimination between CRC patients and healthy individuals. Using the highest performing CpG targets, observed methylation level was correlated with VAF of single nucleotide variants detected by ctDNA testing (R2: 0.8). In summary, we developed a cost-effective methylation target enrichment workflow and utilized machine-learning algorithms to demonstrate the potential use of ctDNA methylation markers in early detection. Additional studies are needed to confirm that these and other markers can accurately distinguish between patients with CRC and healthy individuals.

Citation Format: Hsiao-Yun Huang, Ravi Vijaya Satya, Wen-Ching Chan, Esha Atolia, Joshua Babiarz, Bernhard Zimmermann, Trupti Kawli. Target enrichment of methylated circulating tumor DNA for colorectal cancer detection [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 3656.