bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 3277: PAI-1 mediates resistance to MET-targeted therapy in non-small cell lung cancer
Authors: Higashihara Tomoaki , Thu Yin Min , Suzawa Ken , Date Keiichi , Matsuoka Atsushi , Mizuno Daisuke , Yoshichika Ryo , Hayashi Naohiro , Mukohara Fumiaki , Yoshikawa Mao , Shien Kazuhiko , Yamamoto Hiromasa , Toyooka Shinichi 
Published: March 2024

Abstract
[Purpose] The mesenchymal epithelial transition factor receptor (MET) is a potential therapeutic target in various cancers, including non-small cell lung cancer (NSCLC). In NSCLC, the activation of MET pathway is thought to occur through diverse mechanisms that influence properties affecting cancer cell survival, growth, and invasiveness. These tumors show oncogene addiction to MET and exhibit remarkable responses to MET-Tyrosine Kinase Inhibitors (TKIs). However, the long-term effectiveness of MET-TKIs is usually limited due to acquired drug resistance. The mechanisms underlying primary and acquired resistance to MET-TKIs in the management of NSCLC remain unclear. In this study, we investigated the mechanisms acquired for crizotinib in MET-amplified lung carcinoma cell lines. [Experimental Designs] Two MET-amplified lung cancer cell lines, EBC-1 and H1993, were established for acquired resistance to MET-TKI crizotinib and were functionally elucidated. The factors contributing to the resistance mechanism were assessed by genomic and transcriptomic data, and the alterations hypothesized to confer resistance were validated. [Results] Multiple mechanisms underlay acquired resistance to crizotinib in MET-amplified lung cancer cell lines. In EBC-1-derived resistant cells, the drug resistance mechanism was mediated by the overexpression of SERPINE1, the gene encoding plasminogen activator inhibitor-1 (PAI-1). Crizotinib resistance was overcome by combination therapy with PAI-1 inhibitor and PAI-1 knockdown. Another mechanism of resistance in different subline cells of EBC-1 was evaluated as epithelial to mesenchymal transition (EMT) with the upregulation of antiapoptotic proteins. In the H1993-derived resistant cells, the phosphorylated forms of MEK and ERK were observed to be upregulated and MEK inhibitors could be a potential therapeutic strategy for overcoming the resistance. [Conclusions] In this study, we revealed the different mechanisms of drug resistance to MET-TKI treatment and presented some possible strategies to overcome the resistance.
Citation Format: Tomoaki Higashihara, Yin Min Thu, Ken Suzawa, Keiichi Date, Atsushi Matsuoka, Daisuke Mizuno, Ryo Yoshichika, Naohiro Hayashi, Fumiaki Mukohara, Mao Yoshikawa, Kazuhiko Shien, Hiromasa Yamamoto, Shinichi Toyooka. PAI-1 mediates resistance to MET-targeted therapy in non-small cell lung 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 3277.
Abstract 3325: HBW-012-D and HBW-012-E are novel, potent, selective, safe, and bioavailable KRAS G12D inhibitors with superior anti-tumor efficacy in mice
Authors: Lee Ning , Li Yingfu , Liu Guanfeng , Li Jiang , Ren Junfeng 
Published: March 2024

Abstract
Purpose: This study is to characterize newly identified KRAS G12D small molecule inhibitors HBW-012-D and HBW-012-E, both showing improved oral bioavailability than MRTX1133, the known clinical compound with poor bioavailability. Method: Through our medicinal chemistry efforts, we have aimed to design novel small-molecule KRAS G12D inhibitors that are orally bioavailable. The compounds were screened via pERK and cell viability (CTG) assays in multiple cell types. The optimized compounds were further evaluated based on their pharmacokinetic (PK) properties and toxicity. The anti-tumor efficacy of the leads was confirmed in the GP2D (colorectal carcinoma with KRAS G12D mutation) mouse xenograft tumor model. Result: As shown in the table, HBW-012-D and HBW-012-E have significantly better potency and PK characteristics than MRTX1133. In the mouse GP2D model, comparing head-to-head with the same vehicle and protocol (50 mg/kg, twice daily, orally), MRTX1133 hardly inhibited tumor growth, whereas HBW-012-D inhibited tumor growth well (58 % tumor growth inhibition), and HBW-012-E not only completely inhibited tumor growth but also further regressed tumor size by around 40%. Preliminary toxicity tests showed that HBW-012-D and HBW-012-E are safe: weak inhibition of CYP450 enzymes, negative mini-Ames test, excellent kinase selectivity, and no obvious abnormalities in the 14-day rat or mouse toxicity test. Conclusion: New KRAS G12D inhibitors, HBW-012-D and HBW-012-E, were identified. Their preclinical profile, including potency, efficacy, and PK data, are all superior to MRTX1133, and their safety meets the criteria of clinical development. They show potential as a preferred oral treatment option for patients with tumors mediated by the KRAS G12D mutation, such as pancreatic cancer that still lacks effective treatments.

in vitro data IC 50 (nM) MRTX1133 HBW-012-D HBW-012-E AGS (G12D, stomach, pERK) 1 0.8 0.46 AsPC-1 (G12D, pancreas, 3D CTG) 10.88 3.09 GP2D (G12D, colon, 3D CTG) 1.38 0.67 0.69 MKN-1 (WT, stomach, 3D CTG) &gt;3000 Rat PK @ 100 mg/kg oral Cmax (ng/mL) 9 82 1444 AUC0~t (mg.h/mL) 20 258 5724
Citation Format: Ning Lee, Yingfu Li, Guanfeng Liu, Jiang Li, Junfeng Ren. HBW-012-D and HBW-012-E are novel, potent, selective, safe, and bioavailable KRAS G12D inhibitors with superior anti-tumor efficacy in mice [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 3325.
Abstract 3446: Associations of non-steroidal anti-inflammatory drug use and circulating inflammatory proteins with gallbladder dysplasia
Authors: Rosa Lorena , Cook Paz , Pfeiffer Ruth M. , Kemp Troy J. , Hildesheim Allan , Pehlivanoglu Burcin , Adsay Volkan , Bellolio Enrique , Araya Juan Carlos , Pinto Ligia , Ferreccio Catterina , Aguayo Gloria , Viñuela Eduardo , Koshiol Jill 
Published: March 2024

Abstract
Background: Most gallbladder cancer (GBC) cases arise from the metaplasia-dysplasia-GBC sequence, and chronic inflammation has been associated with its development. The use of non-steroidal anti-inflammatory drugs (NSAIDs) has been associated with reduced risk of GBC; however, little is known about these associations with preneoplastic lesions. We thus aimed to study the associations of the use of NSAIDs and inflammatory proteins with gallbladder dysplasia, a precursor to GBC.
Methods: Associations of NSAIDs and gallbladder dysplasia were evaluated in 1,925 Chilean cholecystectomy patients, 82 with dysplasia and 1,843 with gallstones but not dysplasia. In addition, we measured 33 circulating inflammatory proteins in a subsample of 68 dysplasia cases diagnosed at the time of sample selection and 136 gallstone controls. Age- and sex-adjusted odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated, and associations of inflammatory proteins and gallbladder dysplasia were analyzed.
Results: NSAID use was inversely associated with gallbladder dysplasia (OR: 0.48, 95% CI: 0.26-0.83). Comparing the highest versus lowest category of each immune-related protein, eight proteins were inversely associated with dysplasia with ORs ranging from 0.30 (95%CI: 0.12-0.77) for IL-33 to 0.76 (95%CI: 0.59-0.99) for MIP-1B. Of those, GRO remained associated with dysplasia (OR: 0.64, 95%CI: 0.45-0.91) and BCA-1 was borderline-associated (OR: 0.74, 95%CI: 0.54-1.01) in the multivariable logistic regression model additionally adjusted for sex, age and NSAID use.
Conclusion: NSAID users were less likely to have gallbladder dysplasia, suggesting that NSAIDs might be beneficial for gallstones patients. Prospective studies are needed to understand the inverse association of immune-related markers and dysplasia, and to evaluate the biological effect of NSAIDs in GBC.
Research supported by general funds from the Intramural Research Program of the US National Institutes of Health, National Cancer Institute, Division of Cancer Epidemiology and Genetics, and the Office of Research on Women’s Health, National Institutes of Health.
Citation Format: Lorena Rosa, Paz Cook, Ruth M. Pfeiffer, Troy J. Kemp, Allan Hildesheim, Burcin Pehlivanoglu, Volkan Adsay, Enrique Bellolio, Juan Carlos Araya, Ligia Pinto, Catterina Ferreccio, Gloria Aguayo, Eduardo Viñuela, Jill Koshiol. Associations of non-steroidal anti-inflammatory drug use and circulating inflammatory proteins with gallbladder dysplasia [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 3446.
Abstract 3486: Triple hormone receptor signatures as novel prognostic markers in breast cancer
Authors: Omar Mohamed , Harrell J. Chuck , Tamimi Rulla M. , Marchionni Luigi , Ince Tan 
Published: March 2024

Abstract
Background: Tumor phenotype across various cancers, including breast cancer, is predominantly shaped by a synergy between genomic alterations and the cell-of-origin from which the tumor originates. These elements collectively influence crucial aspects like tumor aggressiveness, treatment response, and patient prognosis. While existing research highlights that the role of cell-of-origin in shaping the molecular architecture of breast cancer, leveraging this information for actionable clinical insights has proven challenging. Here, we introduce two robust models leveraging cellular ancestry signatures of breast luminal cells to improve patient stratification and outcome prediction.
Methods: In this study, we developed a unique gene signature anchored in the expression levels of triple hormone receptors (THR)—namely androgen (AR), estrogen (ER), and vitamin D (VDR)—in breast cancer cells. Building on this, we formulated two distinct mRNA markers, THR-50 and THR-70, aimed at categorizing breast tumors based on their THR expression profiles. These markers were rigorously validated across 65 independent breast cancer studies, involving a total of 6,679 patients, utilizing Kaplan-Meier survival curves, Cox proportional hazards models, and unsupervised clustering analyses.
Results: Our findings indicate that both THR-50 and THR-70 are robustly associated with overall survival and recurrence-free survival in breast cancer patients across all datasets evaluated. Importantly, these THR signatures demonstrate broad applicability across various breast cancer subtypes, grades, and treatment phases—unlike existing prognostic markers that tend to be subtype-specific. Additionally, the THR signatures have revealed four unique patient clusters with divergent survival outcomes, three of which are ER-positive and one is ER-negative. Additionally, we developed an immune-based signature (i20) which can further categorize patients within the ER-negative cluster into two subgroups: one with a highly favorable prognosis, comparable to the ER-positive subtypes, and another that is characterized by exceedingly poor survival outcomes.
Conclusion: The THR-based cellular ancestry signatures open a new avenue in understanding the intricacies of breast cancer biology. These signatures offer a robust and stable framework for developing other prognostic markers, thus providing an enhanced stratification of existing breast cancer categories as well as creating new classifications with more distinct survival estimates.
Citation Format: Mohamed Omar, J. Chuck Harrell, Rulla M. Tamimi, Luigi Marchionni, Tan Ince. Triple hormone receptor signatures as novel prognostic markers in breast 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 3486.
Abstract 3496: EpigenPlot: A tool for the gene-level methylation analysis of colorectal tumors
Authors: Müller Dalma , Gyorffy Balazs 
Published: March 2024

Abstract
Introduction. Aberrant DNA methylation patterns are frequent in colorectal adenocarcinoma (CRC) tissues. The investigation of this layer of epigenetic regulation holds the promise of a better understanding of tumour progression and the identification of novel biomarker candidates.
Purpose. Our goal was to collect and analyse publicly available DNA methylation data of colorectal samples and create a user-friendly tool for exploring and visualizing the CRC methylome.
Methods. We used Illumina Infinium Methylation Arrays, which is a popular platform for genome-wide methylation analysis of large cohorts. Gene Expression Omnibus database (GEO) and TCGA-COAD (The Cancer Genome Atlas Colon Adenocarcinoma) datasets including normal colorectal mucosa, adenoma, and adenocarcinoma samples were systematically collected and filtered. Differentially methylated regions were identified using the Kruskal-Wallis test. Genes with significant methylation changes were further analysed using ROC (Receiver Operator Characteristic) analysis. Finally, we established a web application using the shiny R package.
Results. We assembled a database including methylation data of 2,586 samples. Adenoma and adenocarcinoma samples were globally hypomethylated. Hypermethylation (p &lt; 0.05, Δβ &gt;= 0.2) in adenocarcinoma samples was predominantly present in regions near proximal promoters. Out of the 74 previously proposed biomarkers examined, 50 had a cross-validated AUC of over 0.8. FDA-approved biomarkers BMP3, NDRG4, and SEPT9 have shown the highest performance in the TSS200 region (cvAUC = 0.8, 0.83, and 0.76, respectively). Genes with the highest performance were ITGA4 (5’UTR, first exon: cvAUC = 0.9), MDFI (5’UTR: cvAUC = 0.9), CNRIP1 (5’UTR, first exon: cvAUC = 0.89). The established web application can visualize methylation at CpG sites and gene regions, and KEGG pathway genes. The platform is available at https://epigenplot.com.
Conclusion. We collected and analysed a sizeable database of colorectal tissue data. Gene regions with the best performance include previously proposed and novel diagnostic biomarker candidates. The web platform provides an tool for the efficient exploration of the assembled data.
Citation Format: Dalma Müller, Balazs Gyorffy. EpigenPlot: A tool for the gene-level methylation analysis of colorectal 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 3496.
Abstract 3580: Understanding and overcoming innate and acquired resistance to type I and II RAF inhibitors in anaplastic thyroid cancer using translational functional genomics
Authors: Zeng Peter , Meens Jalna , Barrett John , Cecchini Matthew J. , Ryan Sarah B. , Pan Nachuan , Karimi Amir , Jarycki Laura , Dawson Alice E. , Shaikh Mushfiq , Palma David , Winquist Eric , Boutros Paul C. , Ailles Laurie , Nichols Anthony C. 
Published: March 2024

Abstract
Anaplastic thyroid cancer (ATC) is one of the most lethal human cancers, with some patients succumbing to the disease within weeks of diagnosis. Despite a subset of BRAFV600E mutant ATC patients responding to monomeric type I RAF inhibitor (RAFi) dabrafenib in combination with MEK inhibitor (MEKi) trametinib, almost all patients rapidly develop adaptive or acquired resistance. These patients, along with those who do not harbor the BRAFV600E alteration, have limited treatment options. To understand the mechanism of resistance to dabrafenib and trametinib, we utilized multi-region whole genome sequencing and single nuclei profiling of ATC patient tumors to unravel genomic, transcriptomic, and microenvironmental evolution during type I RAFi and MEKi therapy. Single-cell nuclei sequencing of matched primary and resistant ATC patient tumors identified transcriptomic reactivation of MAPK-pathway, along with immunosuppressive macrophage proliferation, underlie the development of acquired resistance. Our translation genomics led us to hypothesize that deeper inhibition of the MAPK-pathway can be efficacious in overcoming treatment resistance. Screening of a panel of type II RAFis revealed that ATC cell lines are exquisitely sensitive to the type II RAFi naporafenib. We further demonstrate that naporafenib in combination with MEKi trametinib can durably and robustly overcome both innate and acquired treatment resistance to dabrafenib and trametinib using ATC cell lines and patient-derived xenograft models, including in a PDX model from an ATC patient who developed acquired resistance to dabrafenib and trametinib. Finally, we describe a novel mechanism of acquired resistance to type II RAF inhibitor and MEK inhibitor through compensatory mutations in MAST1. Taken together, our work using translational and functional genomics have unraveled the differential mechanisms of treatment resistance to type I and type II RAFi in combination with trametinib, and rationalizes the clinical investigation of type II RAFi in the setting of thyroid cancer.
Citation Format: Peter Zeng, Jalna Meens, John Barrett, Matthew J. Cecchini, Sarah B. Ryan, Nachuan Pan, Amir Karimi, Laura Jarycki, Alice E. Dawson, Mushfiq Shaikh, David Palma, Eric Winquist, Paul C. Boutros, Laurie Ailles, Anthony C. Nichols. Understanding and overcoming innate and acquired resistance to type I and II RAF inhibitors in anaplastic thyroid cancer using translational functional genomics [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 3580.
Abstract 3590: Tumor intrinsic production of glucocorticoids in ovarian carcinoma
Authors: Hanjra Pahul , Stur Elaine , Cole Steven , Lutgendorf Susan , Sood Anil 
Published: March 2024

Abstract
Background: Cortisol is a glucocorticoid (GC) known to be produced by the hypothalamic-pituitary-adrenal (HPA) axis. Dysregulation of the HPA axis is prevalent in patients with ovarian cancer. These patients have elevated nighttime levels of cortisol and increased tumoral expression of the glucocorticoid receptor (GR); both of which correlate with shortened overall survival (OS). We hypothesize that outside the HPA axis, ovarian cancer may have tumor-intrinsic production of GC. In this study, we examined whether 11 beta-hydroxysteroid dehydrogenase 1 (11β-HSD1; enzyme which activates cortisone to cortisol) has steroidogenic activity in the ovarian cancer tumor microenvironment (TME).
Methods: We used the Genotype-Tissue Expression (GTex) Portal and the Cancer Cell Line Encyclopedia (CCLE) to determine expression of steroidogenic enzymes in the ovary and ovarian cancer cell lines. We further performed UMAP analysis of a single-cell RNA-seq dataset of tumor samples from patients with ovarian carcinoma to cluster for cell type. ELISAs were performed to quantify cortisol production and secretion by cells stimulated with metabolite, cortisone. Subcellular fractionation and Western blotting were performed to measure protein expression of 11β-HSD1, GR, and phospho-Ser 211 GR.
Results: HSD11B1 mRNA (which encodes 11β-HSD1) is detectable in bulk ovarian tissue at a median expression of 78.19 transcripts per million (TPM) as measured in the GTex data. In vitro, primary human ovarian fibroblasts express functional 11β-HSD1 and produce and secrete cortisol upon cortisone stimulation in a time-dependent manner, with a mean total secretion of 17.91 ± 0.21 ng/ml at 12 hours. Analysis of scRNA-seq data identifies that cancer-associated fibroblasts (CAFs) may be a source of HSD11B1 in the ovarian TME, with roughly 9% of CAFs expressing HSD11B1. In HeyA8 ovarian cancer cells (positive for 11β-HSD1), cortisone stimulation in vitro results in cortisol production with a mean total secretion of 22.04 ± 5.46 ng/ml at 12 hours. Moreover, this cortisol results in GR activation in an 11β-HSD1-dependent manner.
Discussion: We identify 11β-HSD1 as a potential mechanism of GC production within ovarian cancer, with CAFs being a putative source. We further show that 11β-HSD1 activity can lead to activation of the GR within cancer cells.
Citation Format: Pahul Hanjra, Elaine Stur, Steven Cole, Susan Lutgendorf, Anil Sood. Tumor intrinsic production of glucocorticoids in ovarian 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 3590.
Abstract 3612: Preclinical & clinical activity of autologous mRNA engineered chimeric antigen receptor monocytes for targeted cancer immunotherapy
Authors: Wang Yuxiao , Gerber Michele , Gorgievski Michael , D'Alessandro Josephine , Diwanji Neha , Vale Ronald , Mukherjee Siddhartha , Getts Daniel 
Published: March 2024

Abstract
Introduction: The tumor microenvironment (TME) is a dynamic and multifaceted system that comprises largely myeloid lineage immune cells including neutrophils, macrophages, dendritic cells and monocytes. When activated, these cells are can effectively infiltrate TME and orchestrate anti-tumor immune response. Reprogramming myeloid cells by arming them with a tumor specific chimeric antigen receptor (CAR) presents an attractive strategy to overcome current limitations in solid tumor treatment. In this study, we present the isolation and mRNA-based engineering of monocytes with chimeric antigen receptors (CARs), followed by their in vivo application for cancer treatment in rodent models and in human T cell lymphoma patients.
Results: Engineered monocytes demonstrated the abilities to infiltrate the TME, undergo activation, and differentiate into macrophages and dendritic cells. Upon CAR activation, these reprogrammed myeloid cells utilized both direct and indirect mechanisms to eliminate tumor cells. This included direct tumor cell killing through phagocytosis and TNF-associated mechanisms. Furthermore, engineered monocytes exhibited the capacity to recruit natural killer (NK) cells and T cells to the TME. In the case of T cells, these engineered myeloid cells facilitated the presentation of neoantigens to T cells and stimulate an adaptive immune response. In patients with T cell lymphoma, treatment with engineered monocytes expressing a CAR targeting CD5 exhibited a favorable safety profile and was associated with TME remodeling, expansion of novel T cell clones, and promising survival outcomes.
Conclusions: These findings underscore the potential of reprogrammed myeloid cells as a novel avenue for cancer immunotherapy, offering hope for improved treatments and outcomes in the fight against cancer.
Citation Format: Yuxiao Wang, Michele Gerber, Michael Gorgievski, Josephine D'Alessandro, Neha Diwanji, Ronald Vale, Siddhartha Mukherjee, Daniel Getts. Preclinical & clinical activity of autologous mRNA engineered chimeric antigen receptor monocytes for targeted cancer immunotherapy [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 3612.