bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2315: AI-enabled precision oncology era: Advanced and interactive interpretation of next-gneneration sequencing (NGS) reports
Authors: Chen Hui , Xu Zanmei , Chen Lijuan , Wang Mingmin , Zhang Peng , Pang Fei , Wang Kai
Published: March 2024

Background: Next-generation sequencing (NGS) has been widely adopted in clinical practice, but there are still unmet needs among physicians regarding the interpretation and application of NGS reports. These needs include selecting multi-targeted and combination therapies, keeping up with evolving treatment options and clinical trial results, and incorporating personalized medicine based on real clinical cases.

Methods: To address these challenges, we propose using large language model (LLM) to analyze and interpret clinical questions, perform semantic searches in a high-quality database, and provide customized prompts and logical outputs. Our knowledge base includes diagnostic and treatment details for 600+ tumor subtypes, 620,000+ entries, 2,000+ drug details, and 440,000+ clinical trials. The database is updated automatically using a fact engine and medical literature sources. Personalized gene interpretation is incorporated using pretraining, cosine similarity, and context learning prompts.

Results: Our tool, named "SmartMTB", enables personalized interpretation of genomic testing reports for precision oncology. Users input the latest clinical features using a selection-based or question-and-answer approach. The tool identifies the treatment stage and genomic variations, provides information on mutation frequencies, sensitivity and resistance of targeted and immunotherapies, and priority selection strategies for multi-gene mutations. It matches similar clinical cases and provides real-time updates on treatment options and clinical trial literature. It also facilitates patient matching for clinical trials and considers economic factors.

Conclusion: We present a groundbreaking artificial intelligence (AI) tool in cancer care that revolutionizes precision oncology. This AI system, trained on extensive datasets, swiftly and accurately analyzes and interprets complex genomic and clinical data. It enables clinicians to make informed decisions about personalized treatment strategies, significantly improving patient outcomes in cancer therapy.

Citation Format: Hui Chen, Zanmei Xu, Lijuan Chen, Mingmin Wang, Peng Zhang, Fei Pang, Kai Wang. AI-enabled precision oncology era: Advanced and interactive interpretation of next-gneneration sequencing (NGS) reports [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 2315.
Abstract 2317: Development and validation of a colorectal cancer prediction model: A nationwide cohort-based study
Authors: Hayek Samah
Published: March 2024

Background: Colorectal cancer (CRC) ranks as the third most prevalent cancer globally and is a major cause of cancer-related mortality. Early diagnosis is critical to increase survival rates. While CRC screening has shown significant benefit, adherence remains low, and there is a need for better tools to identify high-risk patients. Risk prediction models were demonstrated to identify such patients.

Aim: To establish an individualized risk prediction model for CRC diagnosis based on Electronic Health Records (EHR).

Methods: This is a retrospective cohort study utilizing EHR data of Clalit Health Services (CHS) members aged 50-74 that were eligible for CRC screening, from January 2013 to January 2019. The model was trained to predict CRC diagnosis within two years using approximately 20,000 EHR features including socio-demographic information, laboratory results and medical history. Model performance, as a complementary screening method, was evaluated.

Results: The study included 2679 subjects with CRC diagnosis and 1,133,713 subjects without CRC diagnosis. The model was trained on subjects from 2013-2017, and performance was validated on subjects from 2019 and a cohort of subjects that underwent fecal occult blood test (FOBT). Incidence values of CRC among subjects in the top 1% risk scores were higher than baseline (2.3% vs. 0.3%; lift 8.38; P-value <0.001). Characteristics of subjects by risk scores percentiles are presented in Table 1. Cumulative event probabilities increased with higher model scores, indicating a correlation between predicted and actual risk of CRC diagnosis. Model-based risk stratification among subjects with a positive FOBT, identified subjects with more than twice the risk for CRC compared to FOBT alone.

Conclusions: We developed an individualized risk prediction model for CRC that can be utilized as a complementary decision support tool for healthcare providers to precisely identify patients at high risk for CRC and refer them to confirmatory testing.

Citation Format: Samah Hayek. Development and validation of a colorectal cancer prediction model: A nationwide cohort-based study [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 2317.
Abstract 2335: MultiNMF: multiview factorization for joint modeling of spatial multi-omics and histology images
Authors: Bowie William , Wang Stacy , Strope Benjamin , Zhu Qian
Published: March 2024

An increasing number of cancer research studies employ spatially resolved transcriptomics (SRT) to investigate the composition of tumor microenvironment in a cancer type of interest. These studies have defined tumor microenvironment (TME) states and spatial domains based on clustering spatial gene expression patterns in SRT in an unbiased manner, yet a more thorough delineation of TME states requires the incorporation of the tumor’s histology image. Here, we develop MultiNMF, a multiview factorization approach that is suitable for cancer research studies where joint profiles of spatial multi-omics and tumor histology images are available. We apply MultiNMF to analyze a set of TNBC SRT primary tumor samples and reveal TME states in the stromal, epithelial, and immune enriched compartments, defined by distinct histomorphological features. We further illustrate the ability of the approach to extend to paired spatial ATAC-seq and histology dataset that is recently published on HER2 breast cancer. MultiNMF thus permits an automated and data-driven decomposition of SRT and spatial ATAC data supported by histomorphological evidence.

Context

In SRT by 10X Visium, the hematoxylin eosin (H&E) staining image is automatically aligned to the slide where the tissue section is mounted. Image patches can be easily extracted from areas under the SRT barcoded spots. For these images, I will apply a pre-trained convolutional neural network (CNN) model to extract high dimensional features from spot images. The image features can be added as a second view after gene expression view for joint analysis under MultiNMF.

Results

MultiNMF can factorize the SRT data into components well-supported by histological evidence. It has identified T-cell infiltrating regions, and EMT-enriched regions with distinct immune and stroma morphological characteristics. The T-cell infiltration neighbors a region that has an appearance of necrosis according to the pathologist evaluation. These domains further demonstrate enrichments of modules with motif enrichment (known as regulons) according to SCENIC analysis. Analysis of spatial ATAC illustrates not only HER2 but also its amplicon amplification. From MultiNMF components of spatial ATAC, we derive regulatory regions for T-cell/B-cell marker genes. Overall, MultiNMF is a novel model that has not been applied to SRT field. It provides an multiomic extension to the traditional NMF.

Citation Format: William Bowie, Stacy Wang, Benjamin Strope, Qian Zhu. MultiNMF: multiview factorization for joint modeling of spatial multi-omics and histology images [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 2335.
Abstract 2371: BGB-B167, a first-in-class 4-1BB/CEACAM5 bispecific antibody, exhibits potent in vitro and < for vivo antitumor activity and < for superior safety profile in preclinical models
Authors: Li Zhuo , Qu Liang , Chen Xin , Xue Liu , Li Jie , Liu Qi , Sun Jian , Sun Hanzi , Chen Yun , Xie Yuanyuan , Wang Wanyi , Zhu Lin , Wang Penghao , Zhou Xiaosui , Hou Hongjia , Chen Jie , Liu Xinyi , Zhang Yilu , Liu Ning , Liang Xinyi , Zhang Shuo , Tang Xiaoyan , Song Jing , Zhang Tong , Song Xiaomin , Liu Xuesong , Li Kang , Huang Chichi
Published: March 2024

4-1BB (CD137) is a key costimulatory immunoreceptor and a promising therapeutic target in cancer. CEACAM5 (CEA) is a well-established tumor associated antigen overexpressed in many cancers, including colorectal, gastric, lung, pancreatic cancer, liver, breast and thyroid cancers. BGB-B167 is a novel immunoglobulin G (IgG)-based bispecific antibody targeting 4-1BB and CEA and is under clinical development for the treatment of advanced or metastatic solid tumors in humans. BGB-B167 binds to its target proteins with high specificity and affinity. Potent and CEA-dependent functional activities were demonstrated using peripheral blood mononuclear cell (PBMC)-based immune cell activation and cytotoxicity assays. In humanized 4-1BB knock-in mice bearing human CEA-expressing tumors, BGB-B167 exhibited potent, dose-associated single-agent efficacy as well as synergistic antitumor activity in combination with anti-PD-1 antibody. BGB-B167 was well tolerated in 1-month repeat-dose toxicology study in cynomolgus monkeys. Here, we describe the characterization of BGB-B167 with regard to preclinical proof-of-concept and basic drug-like properties. The combined dataset provides an overview on the design, mode of action, preclinical pharmacology and safety profile of BGB-B167.

Citation Format: Zhuo Li, Liang Qu, Xin Chen, Liu Xue, Jie Li, Qi Liu, Jian Sun, Hanzi Sun, Yun Chen, Yuanyuan Xie, Wanyi Wang, Lin Zhu, Penghao Wang, Xiaosui Zhou, Hongjia Hou, Jie Chen, Xinyi Liu, Yilu Zhang, Ning Liu, Xinyi Liang, Shuo Zhang, Xiaoyan Tang, Jing Song, Tong Zhang, Xiaomin Song, Xuesong Liu, Kang Li, Chichi Huang. BGB-B167, a first-in-class 4-1BB/CEACAM5 bispecific antibody, exhibits potent in vitro and < for vivo antitumor activity and < for superior safety profile in preclinical models [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 2371.
Abstract 2410: Comparative genomic profiling of unresectable NSCLC patients in the U.S. and China using a globally harmonized liquid biopsy assay platform
Authors: Tang Haoran , Jia Cancan , Xie Feng , Zhang Yue , Dong Xiaoxi , Huang Yong , Jia Shading
Published: March 2024

Background: Non-Small Cell Lung Cancer (NSCLC), accounting for over 80% of all lung cancers, benefits from targeted therapies based on genetic tests like EGFR, KRAS, ALK, and ERBB2. While prior studies focused on molecular characteristics through tissue biopsies, limited research has explored NSCLC molecular profiles via liquid biopsy, especially across different human races. This study presents a comprehensive genomic profiling analysis of unresectable NSCLC patients in the U.S. and China, using a globally harmonized liquid biopsy assay.

Methods: As part of Predicine's Phoenix Program, a global molecular biomarkers screening initiative, 61 patients in the U.S. and 352 patients in China with unresectable advanced NSCLC were enrolled. All were treatment-naïve or recurred after 1st-line targeted therapies. Blood samples (10ml) were tested using PredicineCARE, an NGS-based liquid biopsy assay, to profile somatic mutations, copy number variations, and gene fusions.

Results: The assay, validated in both regions using the same reference materials, achieved a Limit of Detection (LOD) of 0.25% mutation allele frequency, with a positive predictive value exceeding 99%. Profiling NSCLC patients in the U.S. and China revealed common genes like TP53, CDKN2A, EGFR, KRAS, RB1, and PIK3CA. TP53 and PIK3CA variations showed equivalent prevalence. However, EGFR variations were significantly higher in China (p<0.05), while CDKN2A (p<0.001), KRAS (p<0.01), and RB1 (p<0.01) variations were notably higher in the U.S.

Conclusions: This study unveils the mutational landscape of advanced NSCLC through liquid biopsy. Unique prevalence patterns between U.S. and China cohorts suggest novel biomarkers for clinical diagnosis and provide insights for targeted therapy mechanism studies.

Citation Format: Haoran Tang, Cancan Jia, Feng Xie, Yue Zhang, Xiaoxi Dong, Yong Huang, Shading Jia. Comparative genomic profiling of unresectable NSCLC patients in the U.S. and China using a globally harmonized liquid biopsy assay platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2410.
Abstract 2443: Improved detection of low frequency mutations in ovarian and endometrial cancers by utilizing a highly accurate sequencing platform
Authors: Revil Timothée , Pezeshkian Nairi , Gilbert Lucy , Sockell Alexandra , Ragoussis Jiannis
Published: March 2024

Ovarian and endometrial cancers come within the top-4 for incident cancers as well as deaths in North American women. Cure rates have not improved in 30 years as high-grade subtypes continue to be diagnosed in Stage III/IV. Attempts at early diagnosis have failed because high-grade cancer cells exfoliate and metastasize while the primary cancer is small and undetectable by existing tests based on imaging and blood-based tumor markers. DOvEEgene (Detecting Ovarian and Endometrial cancers Early using genomics) is a genomic uterine pap test developed by a McGill team to screen and detect these cancers while they are confined to the gynecologic organs and curable by surgery. The test identifies pathogenic somatic mutations in uterine brush samples. Here we tested the Onso system, a highly accurate sequencing technology from PacBio in order to potentially increase sensitivity while driving down sequencing costs by reducing required sequencing depth vs the current NGS standard. A highly sensitive, error-correcting capture technology (DOvEEgene-SureSelectHS) utilizing duplex error correction sequencing interrogated the exons of 23 genes involved in the development of sporadic and hereditary ovarian and endometrial cancers. We applied a combination of germline gene panel testing on saliva samples with deep duplex sequencing to detect somatic mutations at <0.1% VAF, interrogation of microsatellite loci for instability, and low coverage WGS for copy number analysis of uterine brush samples. We sequenced 20 duplex Illumina sequencing libraries produced using the DovEE assay at PE 100bp mode and compared Onso data in non- duplex sequencing mode as well as duplex sequencing mode to the original Illumina duplex sequencing method. Here, we present this comparison and highlight the benefits of high accuracy sequencing for the detection of very low frequency (<0.1%) somatic mutations. We observed improved mismatch rates for Onso data compared to Illumina, even after duplex error correction was applied. In addition, we found that more individuals are called as displaying microsatellite instablity from the Onso data, which may be due to improved sequencing performance in repetitive regions for Onso. Finally, we observed fewer potential false positive variant calls in the Onso data, highlighting the value of improved sequencing accuracy for rare variant detection.

Citation Format: Timothée Revil, Nairi Pezeshkian, Lucy Gilbert, Alexandra Sockell, Jiannis Ragoussis. Improved detection of low frequency mutations in ovarian and endometrial cancers by utilizing a highly accurate sequencing platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2443.
Abstract 2550: Investigating glutathione peroxidases as potential prognostic factors in uterine corpus endometrial cancer
Authors: Dukesherer Alexis , Davison-Versagli Calli A.
Published: March 2024

Introduction: Uterine corpus endometrial cancer (UCEC) is one of the deadliest women’s reproductive cancers in the United States, and mortality rates have not improved in the last 30 years due to poor prognostic methodologies. Altered expression patterns of Glutathione Peroxidases (GPX1-8) have been connected to the outcome of many cancers. Still, GPX expression patterns and their use as prognostic biomarkers in UCEC have yet to be explored. This project aimed to evaluate the potential utility of GPX1-8 as prognostic biomarkers for UCEC.

Methods: To identify GPX1-8 expression alterations in UCEC tumors, the UCEC tissue samples (n=543) from the Cancer Genome Atlas Database (TCGA) dataset were analyzed using the University of Alabama at Birmingham Cancer Data Analysis portal (UALCAN) software to statistically compare mRNA levels between UCEC tumor samples and non-tumorigenic uterine tissue. To determine the impacts of GPX1-8 expression on overall survival (OS) and relapse-free survival (RFS), the UCEC TCGA dataset was analyzed using the pan-cancer RNA seq platform using Kaplan-Meier Plotter (KM plotter). The patient cohort was split into groups according to high GPX expression status and low GPX expression status using the trichotomization function in KM plotter. Hazard ratio (HR), 95% confidence interval (95% CI), and log-rank P value were calculated using the KM plotter platform.

Results: GPX1, GPX2, GPX4, GPX7, and GPX8 were differentially expressed in UCEC tumor tissue compared to non-cancerous uterine tissue. However, unfavorable OS in patients associated with low GPX4 expression in UCEC tumor samples (P=0.0043, HR=0.39, 95% CI=0.2-0.76) only. Unfavorable RFS in UCEC patients only correlated with low GPX1 expression (P=0.019, HR=0.43, 95% CI=0.21-0.89) or high GPX6 expression (P=0.0032, HR=2.37, 95% CI=1.31-4.27) in UCEC tumor samples.

Conclusion: Low GPX1 and GPX4 expression and high GPX6 expression may be novel unfavorable UCEC prognostic markers.

Citation Format: Alexis Dukesherer, Calli A. Davison-Versagli. Investigating glutathione peroxidases as potential prognostic factors in uterine corpus endometrial 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 2550.
Abstract 2581: Measuring interstitial fluid flow to predict and optimize spatial CAR-T dynamics in the clinic
Authors: Woodall Ryan T. , Esparza Cora , Brown Christine C. , Munson Jennifer M. , Rockne Russell C.
Published: March 2024

Interstitial fluid flow dynamics in brain tumors are known to be an important indicator for tumor invasion into healthy tissue, as cancerous cells follow the interstitial flow towards tumor-stimulating chemokines. These flow gradients not only carry tumor-stimulating chemokines, but also carry cytokines secreted by immune response. CAR-T cells are known to also depend highly on the cytokines present in the CSF and serum. For these reasons, we have developed a novel method, Localized Convolutional Function Regression (LCFR) for measuring interstitial fluid flow, perfusion, and diffusion using dynamic contrast-enhanced MRI. LCFR works by applying the known physics of contrast agent transport, and fitting the observed contrast agent dynamics to the known physics. From LCFR, we can recover standard Tofts-Kety perfusion dynamics, including Ktrans and Vp, and also recover the underlying flow field and diffusivity. These new measurements allow for the prediction of where tumors invade, and allow for us to model how CAR-T cells move within a tumor. In a case study, we model the spatial distribution of CAR-T cells and glioblastoma cells over time, assuming that the fluid velocity field drives CAR-T spread throughout the tumor. Using multiple delivery locations, we identify the optimal catheter placement to optimally distribute CAR-T cells through the tumor, improving the 50% kill rate of simulated tumor cells by over 25% from a naive delivery strategy. Further, we collect longitudinal cytokine levels from patients undergoing CAR-T therapy, allowing us to understand how interstitial flow, CAR-T dynamics, and tumor dynamics interact with each other. We report a case study wherein a patient is longitudinally followed through their treatment with CAR-Ts. Perfusion imaging reveals that the patient experienced a steady increase in perfusion and decrease in fluid leakage into surrounding tissue. VEGF and IL12 levels are observed to increase as tumor volume increases. To better understand this patient's dynamics, we use the fluid velocity field measured by LCFR to simulate the development of CAR-T cells within the tumor, using the cytokine profile as a surrogate measurement of CAR-T population. These results demonstrate the importance of fluid flow and cytokines in understanding how brain tumors develop and respond to treatment.

Citation Format: Ryan T. Woodall, Cora Esparza, Christine C. Brown, Jennifer M. Munson, Russell C. Rockne. Measuring interstitial fluid flow to predict and optimize spatial CAR-T dynamics in the clinic [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 2581.
Abstract 26: An HLA-class II restricted HPV18 E7 specific TCR cloned from a long-term surviving cervical cancer patient
Authors: Long Jianting , Chen Xihe , Ou Shudan , Ma Minjun , Chu Junjun , Han Yanyan
Published: March 2024

T cell receptor (TCR)-engineered T cell therapy is a promising approach for the treatment of solid malignancy, with multiple clinical trials reporting impressive responses using affinity-matured TCRs. However, artificially mutated TCRs can increase the risk of off-target toxicities due to unexpected cross-reactions, which limits the overall safety of this approach. To tackle this challenge, we have developed a novel strategy for cloning tumor-specific endogenous therapeutic TCRs from long-term surviving patients who have responded to immunotherapy. Specifically, we have identified a TCR (10F04) that is specific to human papillomavirus type 18 (HPV18) E784-98 and restricted to human leukocyte antigen (HLA) class II molecular DRA/DRB1*09:01 from the peripheral blood of a patient with HPV-positive metastatic cervical cancer who received multiple antigens stimulating cellular therapy (MASCT) and exhibited sustained T-cell immunological responses. Upon transduction into human T cells, the 10F04 TCR demonstrated robust antitumor activity in both in vitro and in vivo models. Notably, the TCR effectively redirected both CD4 and CD8 T cells to specifically recognize tumor cells and induced multiple cytokine secretion along with durable antitumor activity. Importantly, no cross-reactivity was detected in toxicity studies. As a result, this TCR is currently being investigated in a phase I clinical trial for treating HPV18-positive cancers (NCT05787535). The first-in-human infusion had been just completed. No severe adverse event had been observed, while an early proliferation of TCR-T was detected several days after infusion. Our approach of cloning tumor-specific and safe endogenous therapeutic TCRs from long-term surviving patients offers a promising strategy for developing safe and effective TCR-engineered T-cell therapies for solid tumors. These findings provide important insights into the potential of HLA class II-restricted TCR-T therapy as a novel cancer treatment modality.

Citation Format: Jianting Long, Xihe Chen, Shudan Ou, Minjun Ma, Junjun Chu, Yanyan Han. An HLA-class II restricted HPV18 E7 specific TCR cloned from a long-term surviving cervical cancer patient [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 26.
Abstract 2606: Targeting mesothelin on tumor cells with a novel, completely human fusion construct delivering the serine protease granzyme B
Authors: Mohamedali Khalid A. , Cheung Lawrence H. , Iurascu Mihai G. , DePalatis Louis R. , Thuning-Roberson Claire , Rosenblum Michael G.
Published: March 2024

Mesothelin is a cell-surface antigen identified as an excellent cancer-associated target upregulated on numerous tumors, including pancreatic and ovarian cancers, as well as mesotheliomas and lung cancers. Granzyme B is a highly cytotoxic serine protease nominally delivered by immune effector cells to target cells, resulting in induction of cell death pathways that are both caspase-dependent and -independent. We developed a fusion protein (GrB-Fc-SD1) composed of GrB and containing SD1, a novel human single-domain antibody that uniquely targets Region III of the mesothelin glycoprotein. The SD1 and GrB domains are tethered by a human IgG heavy chain fragment which enables dimerization. The fusion protein was transiently expressed in HEK-293E cells in serum-free conditions with a final yield of 5 mg/L. Western blot analysis confirmed the expression of this construct as a homodimer. The GrB enzymatic activity in GrB-Fc-SD1 was similar to that of commercially available human granzyme B. ELISA studies confirmed the specific recognition of the SD1 antibody to mesothelin extra-cellular domain. Biacore analysis confirmed binding of GrB-Fc-SD1 with a dissociation constant between 10−7 and 10−8 M. In vitro cytotoxicity against a limited panel of lung, pancreatic and ovarian cancer cell lines expressing surface mesothelin indicate cytotoxicity in the nanomolar range, while cytotoxicity against mesothelin-negative cells was at micromolar levels. Ex vivo serum stability studies showed excellent stability of GrB-Fc-SD1 at both 4°C and -20°C over ninety days and a half-life of approximately three days at elevated temperatures (37°C). In vivo efficacy studies against Capan-2 xenografts in nude mice using both weekly x 5 and QOD x 5 doses of GrB-Fc-SD1 (130 mg/mg total dose, delivered IP) indicated highly significant efficacy in both dose regimens, with p < 0.001 compared to vehicle-treated mice. Mouse body weights were not impacted at the efficacy doses used in this study, indicating that this dose was non-toxic. Histopathology studies revealed a significant decrease in the percentage of Ki-67+ nuclei in treated tumors compared to controls. These data warrant continued investigation of the protein as a therapeutic candidate. Research supported by H2Biologics. Research conducted, in part, by the Clayton Foundation for Research.

Citation Format: Khalid A. Mohamedali, Lawrence H. Cheung, Mihai G. Iurascu, Louis R. DePalatis, Claire Thuning-Roberson, Michael G. Rosenblum. Targeting mesothelin on tumor cells with a novel, completely human fusion construct delivering the serine protease granzyme B [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 2606.
Abstract 2609: Vesicular LGALS3BP is a neuroblastoma biomarker and a therapeutic target for combination therapy with antibody-drug conjugate and checkpoint inhibitors
Authors: Sala Gianluca , Capone Emily , Cela Ilaria , Lovato Giulio , Lamolinara Alessia , Iezzi Manuela , Rossi Cosmo , De Laurenzi Vincenzo , Ippoliti Rodolfo , Iacobelli Stefano
Published: March 2024

We have recently shown that targeting circulating LGALS3BP with a maytansinoid-based non-internalizing antibody-drug conjugate (ADC) resulted in tumor eradication of high-risk NMYC-amplified neuroblastoma patient-derived xenografts. LGALS3BP is a high molecular weight, hyperglycosylated and secreted protein which is enriched at the surface of cancer-derived extracellular vesicles (EVs). Here, using a neuroblastoma pseudometastatic preclinical model, we extended our previous work demonstrating that EVs-associated LGALS3BP strictly correlates with disease progression and dissemination. Moreover, to investigate whether LGALS3BP ADC, named 1959sss/DM4, possesses immune-modulating properties, we analyzed DM4 ability to induce immunogenic cell death (ICD). Interestingly, using NXS2 murine neuroblastoma cells, we found that DM4 induced a time-dependent surface expression of three different ICD marker, i.e. calreticulin, HSP70 and HSP90. As it was recently demonstrated that to limit immune surveillance NXS2 cells increase PD-L1 expression in response to IFNγ production in the tumor immune infiltrate, we evaluated potential synergism between LGALS3BP targeting ADC and an anti-PD1 immune check-point inhibitor. To this aim, we genetically manipulated NXS2 cells which resulted nearly negative for murine LGALS3BP expression. Therefore, using a lentivirus-based gene transduction system, we obtained NXS2 cells producing large amounts of vesicular human LGALS3BP. Of note, the vesicular LGALS3BP could be quantified by ELISA and imaged by confocal microscopy using 1959 antibody. Strikingly, while single agent treatment showed a limited antitumor activity in NXS2-LGALS3BP syngeneic model, the LGALS3BP ADC/anti-PD1 combination resulted in a marked inhibition of tumor growth, which was followed by a prolonged survival. In conclusion, our findings establish that vesicular LGALS3BP is a potential biomarker for liquid biopsy and reveals this protein as a suitable target for therapeutic strategy that combines 1959sss/DM4 ADC with immune checkpoint blockade for the treatment of LGALS3BP expressing neuroblastoma.

Citation Format: Gianluca Sala, Emily Capone, Ilaria Cela, Giulio Lovato, Alessia Lamolinara, Manuela Iezzi, Cosmo Rossi, Vincenzo De Laurenzi, Rodolfo Ippoliti, Stefano Iacobelli. Vesicular LGALS3BP is a neuroblastoma biomarker and a therapeutic target for combination therapy with antibody-drug conjugate and checkpoint inhibitors [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 2609.
Abstract 2637: Super-enhancer-related m6A modification promotes immune escape in hepatocellular carcinoma associated with metabolic dysfunction-associated fatty liver disease via CCL4 signaling pathway inhibition
Authors: Xu Liangliang
Published: March 2024

The incidence and mortality rates of hepatocellular carcinoma caused by metabolic dysfunction-associated fatty liver disease (MAFLD) have been increasing in recent decades, emphasizing the urgent need for new therapeutic approaches. Emerging evidence suggests that approximately 80% of super-enhancer RNAs (seRNAs) undergo selective m6A modifications. seRNA and m6A modifications have been implicated in the progression of various cancers, making them potential targets for therapeutic intervention. Based on our previous research, we hypothesize that the lack of m6A modification on the super-enhancer of CCL4 may contribute to the reduced expression of the CCL4 gene in HCC.To validate our hypothesis, we employ nano-chromatin immunoprecipitation combined with high-throughput sequencing (nano-ChIP-seq), m6A-seq (m6A-seq), single-cell RNA sequencing (scRNA-seq) on multiple models including clinical samples, cell lines, and mouse models. Interestingly, we have made a significant discovery that overexpression of CCL4 in tumor cells enhances the infiltration of CD8+ T cells, which are crucial for anti-tumor immune responses. In contrast, normal tissue cells undergo m6A modification on the CCL4 seRNAs, while this modification is notably absent in cancerous tissue. Consequently, the reduced expression of CCL4 could impair the tumor-killing capabilities of CD8+ T cells and facilitate immune evasion by the tumor.Furthermore, our results shed light on the underlying molecular mechanisms involving super-enhancers and m6A modifications in the regulation of immune escape in MAFLD HCC. We identify the specific super-enhancer and downstream regulatory genes influenced by m6A modification in MAFLD-associated HCC, providing valuable insights and novel targets for the treatment of this condition.

Citation Format: Liangliang Xu. Super-enhancer-related m6A modification promotes immune escape in hepatocellular carcinoma associated with metabolic dysfunction-associated fatty liver disease via CCL4 signaling pathway inhibition [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 2637.
Abstract 2675: A new dual-targeting anti-immune checkpoint therapeutic approach for the treatment of “hot” and “cold” tumors
Authors: Moutuou Moutuaata M. , DeLuce Nora , Creton Elodie , Lucchi Honorine , Accolas Julien , Savatier Alexandra , Léonetti Michel
Published: March 2024

Anti-Immune Checkpoint (ICP) antibody approaches provided a major breakthrough in the field of cancer therapy. However, their efficiency is mainly restricted to patients with “hot” tumors characteristics, which limits the breadth of their use. To tackle this limit, we developed a new strategy aimed at amplifying anti-ICP antibody ability to activate immune cells. This approach is based on antibodies engineered to make them able to target both an ICP receptor and a co-receptor often involved in receptor-mediated activation, namely Heparan Sulfate Proteoglycan.

The dually-targeting engineered anti-ICP antibodies were produced in eukaryotic cells. They were purified to homogeneity using two chromatographic steps and remain stable for months in frozen conditions. A first engineered antibody-derived construct was assessed for its ability to impact immune cell activation and tumor-growth. It is able to stimulate subsets of immune cells from mouse splenocytes as well as from human peripheral mononuclear cells, in vitro. In addition, its injection in healthy mice triggers activation of T-cells. Last, in mice previously implanted with different types of cancer cells it impacts growth of “hot” as well as “cold” tumors. Immune profiling in a “cold” cancer model shows that the treatment decreases the proportion of MDSCs and increase that of CD8+ T-cells and NK-cells in tumor microenvironment making it close of that found in “hot” tumors. Altogether, our data indicate that our first engineered antibody-derived construct presents an attractive immunotherapeutic potential for a large variety of cancers paving the way for its evaluation in clinical phases.

Citation Format: Moutuaata M. Moutuou, Nora DeLuce, Elodie Creton, Honorine Lucchi, Julien Accolas, Alexandra Savatier, Michel Léonetti. A new dual-targeting anti-immune checkpoint therapeutic approach for the treatment of “hot” and “cold” 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 2675.
Abstract 2680: Knockout on enhancer of zeste homolog 2 in triple-negative breast cancer model alters immune signaling and decreases tumor progression and lung metastasis
Authors: Monterroza Lenore , Parrilla Maria , Samaranayake Sarah , Rivera Dormarie , Dobosh Brian , Selvaraj Periasamy , Tirouvanziam Rabindra M.
Published: March 2024

Triple-negative breast cancer (TNBC) is an aggressive and highly metastatic subtype of breast cancer. Lack of known targets, patient-to-patient variations of target antigens and resistance to immune checkpoint inhibitors make TNBC one of the most challenging cancers to treat. TNBC is enriched in tumor-infiltrating neutrophils (TINs). TINs are key contributors to pro-tumorigenic processes linked to “immunologically cold” tumors, in part by preventing recruitment of T-lymphocytes (TILs). Prior studies identified the Enhancer of zeste homolog 2 (EZH2) as a prominent methyltransferase expressed in primary and metastatic TNBC cells. EZH2 is an upstream regulator of the stimulator of interferon genes (STING), a critical innate sensor mediating anti-tumor responses that is inhibited in cold tumors. To date, EZH2/STING signaling in TINs is relatively unknown. Here, we hypothesized that EZH2 inhibition and subsequent STING activation could exert anti-tumor activity by modulating TINs. We derived EZH2-knockout (KO) and EZH2-overexpressed (OX) cell lines from the well-established 4T1 TNBC mouse cell line. We demonstrate a 10-fold decrease in lung metastasis and significant reduction of 4T1 EZH2 KO tumor growth compared to the parent 4T1 cell line. Concomitantly, the TIN:TIL ratio was significantly reduced in 4T1 EZH2 KO vs. control tumors. Overexpression of EZH2 in 4T1 TNBC cells did not affect the primary tumor growth or lung metastasis. A therapeutic study using the repeated injection of the STING agonist MSA-2 after tumor engraftment in vivo also demonstrated a decrease in lung metastasis and tumor growth in MSA-2 vs. vehicle injection with both 4T1 parent and EZH2 KO cell lines. Together, our findings suggest a key role for STING pathway modulation and TIN/TIL poise in primary TNBC progression and lung metastasis.

Citation Format: Lenore Monterroza, Maria Parrilla, Sarah Samaranayake, Dormarie Rivera, Brian Dobosh, Periasamy Selvaraj, Rabindra M. Tirouvanziam. Knockout on enhancer of zeste homolog 2 in triple-negative breast cancer model alters immune signaling and decreases tumor progression and lung metastasis [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 2680.
Abstract 2687: NK cell plasticity in SCLC is linked to tumor transcriptional diversity
Authors: Malin Justin , Zhuang Sophie , Sharma Ajit Kumar , Clara Joseph , Thomas Anish
Published: March 2024

Natural Killer (NK) cells are innate lymphoid cells that are pivotal in the body’s response to cancer. To harness their cytotoxicity in clinical interventions, it is critical to understand their biology, which is highly tissue- and tumor-specific. In Small Cell Lung Cancer (SCLC), reports have described widely divergent levels of NK activity in neuroendocrine (NE) and non-neuroendocrine (non-NE) subtypes. Diminished self-antigen presentation by MHC-I is a classic trigger of NK cell activity but, counter-intuitively, NK cells exhibit reduced cytotoxicity in MHC-I downregulated NE SCLC.

To explore potential causes for depressed NK activity in NE SCLC relative to non-NE, we applied scRNA-Seq to 45 SCLC patient biopsies and rapid autopsies, and identified 4000 NK cells based on gene expression signature. There was a notable dip in NK cell infiltration in NE tumors compared to non-NE tumors. Tumor cell-surface ligands recognized by activating and, unexpectedly, inhibitory NK cell receptors were generally both more highly expressed in non-NE tumors. While inhibitory NK receptors were comparable in NE and non-NE tumors, activating NK receptors were expressed significantly, though modestly, higher in non-NE. We observed tumor site-specific gene expression patterns in NK cells from different metastatic sites. Overall, there were a remarkably high number of differentially expressed genes (>1k) between NK cells from NE and non-NE tumors, even after controlling for tumor site. Together, our work suggests that NK cell plasticity is manifest at the level of SCLC transcriptional subtypes.

Citation Format: Justin Malin, Sophie Zhuang, Ajit Kumar Sharma, Joseph Clara, Anish Thomas. NK cell plasticity in SCLC is linked to tumor transcriptional diversity [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 2687.
Abstract 2756: Single cell analysis reveals treatment response-associated plastic cell state and lineage switching in aggressive variant prostate cancer
Authors: Guo Shuai , Subramani Elavarasan , Frigo Daniel E. , Pilié Patrick G. , Goswami Sangeeta , Soundararajan Rama , Aparicio Ana , Wang Wenyi
Published: March 2024

Prostate cancer (PCa) is a common malignancy in men over 65, ranking as the second leading cause of cancer-related deaths among men in the United States. While most prostate cancers respond to androgen receptor (AR) targeting therapies, Aggressive Variant Prostate Cancers (AVPCs), characterized by RB1, Tp53, and/or PTEN alterations, do not. AVPCs exhibit lineage plasticity in preclinical models, enabling the expression of non-prostate epithelial lineage markers to adapt to therapeutic pressures. However, a measurable definition of lineage plasticity as a potential therapeutic target for clinical trials is currently lacking. To arrive at said definition, we perform single-nuclei RNA sequencing (snRNA-seq) on lymph node metastases from twelve AVPC patients with matched sample pairs of both pre- and post-treatment. Additionally, we include snRNA-seq data from eight non-AVPC patients as a baseline. Expanding upon our prior establishment of tumor-specific total mRNA expression (TmS) as an indicator of tumor cell lineage plasticity (Nature Biotechnology, PMID: 35697807), we employ unique molecular identifier (UMI) counts from individual cells to quantify this plasticity. We reveal a distinct cluster of tumor cells with notably high UMI counts in resistant samples, indicative of a less differentiated state and increased transcriptional diversity. This high-UMI cluster is marked by significant enrichment in pathways associated with epithelial-mesenchymal transition (EMT), stemness, one-carbon metabolism, and arginine metabolism pathways. Concurrently, there is a reduction in activity within the androgen receptor (AR) and DNA damage repair pathways. These characteristics suggest an enhanced capacity for lineage switching in AVPC tumor cells, potentially contributing to evasion from targeted therapies. Moreover, immune components within resistant samples consistently display lower UMI counts, indicating a diminished propensity for lineage plasticity. In conclusion, we present a better understanding of lineage switching in therapeutic resistance in AVPCs, paving the way for novel treatment strategies in PCa management.

Citation Format: Shuai Guo, Elavarasan Subramani, Daniel E. Frigo, Patrick G. Pilié, Sangeeta Goswami, Rama Soundararajan, Ana Aparicio, Wenyi Wang. Single cell analysis reveals treatment response-associated plastic cell state and lineage switching in aggressive variant prostate 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 2756.
Abstract 2820: The effect of Pten haploinsufficiency on genomic and transcriptomic profiles in combined genetically-engineered mouse models for colonic neoplasia based on Apc inactivation
Authors: Sada Haruki , Niitsu Hiroaki , Nakahara Hikaru , Sakamoto Naoya , Tashiro Hirotaka , Ohdan Hideki , Hinoi Takao
Published: March 2024

Background and Aim: We have reported genetically-engineered mouse models for colonic neoplasia by using our novel CDX2P-Cre mice, in which Cre is restrictedly expressed in colonic epithelial cells. Although colonic tumors are generated in CDX2P-Cre;Apcflox/+ (CPC;Apc) mice with highly penetrant rate, greater number and deeper invasion of colonic tumors were observed in CDX2P-Cre;Apcflox/+;Ptenflox/+ (CPC;Apc+Pten), possibly resulting from haploinsufficiency of Pten gene. We have also confirmed shorter lifespan in CPC;Apc+Pten than that in CPC;Apc (AACR Annual Meeting 2018). Here, we test if these phenotypes come from one copy loss of Pten itself or secondary genetic and/or transcriptomic alterations induced by Pten loss by using whole genome sequence (WGS) and RNA sequence from macroscopically-dissected colonic tumors (bulk RNA-seq).

Methods: WGS for five tumors and five livers as counterpart controls in each mouse model was performed by DNBSEQ platforms. Bulk RNA-seq was performed for three tumors in each model.

Results: In the analysis using B-allele frequency, copy-neutral LOH occurred in chromosome 18 including Apc loci specifically in colonic neoplasia in both CPC;Apc and CPC;Apc+Pten mice. In contrast, LOH was not observed in chromosome 19 including Pten loci in CPC;Apc+Pten mice. We also confirmed remarkably decreased coverage of reads in reference mapping in Apc locus, and there was a slight decrease of coverage in Pten locus. There were no additional driver gene mutations in CPC;Apc or CPC;Apc+Pten in WGS. All these results suggested just one copy loss of Pten resulting in aggressive tumor phenotype in CPC;Apc+Pten mice. In RNA-seq and subsequent GSEA comparing colonic tumors in CPC;Apc+Pten with those in CPC;Apc revealed upregulation of some signal pathways including mTORC1. Supporting this observation, number of colon tumors, especially adenocarcinomas, were decreased by rapamycin administration to CPC;Apc+Pten. Similarly, rapamycin was more effective in tumorids from CPC;Apc+Pten those from CPC;Apc.

Conclusion: WGS reveals one copy loss of Pten locus is the only genetic alteration in CPC;Apc+Pten when compared with CPC;Apc. One copy loss of Pten is sufficient to upregulate mTORC1 pathway in a CPC;Apc+Pten mouse model, resulting in promotion of tumor formation and invasion.

Citation Format: Haruki Sada, Hiroaki Niitsu, Hikaru Nakahara, Naoya Sakamoto, Hirotaka Tashiro, Hideki Ohdan, Takao Hinoi. The effect of Pten haploinsufficiency on genomic and transcriptomic profiles in combined genetically-engineered mouse models for colonic neoplasia based on Apc inactivation [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 2820.