bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 4864: Epidemiological characteristics and treatment strategies of gastric cancer with neuroendocrine differentiation (NED)
Authors: Huang Zhen , Wei Jinlai , Shen Yifan , Zhang Jun
Published: March 2024

Background: Gastric cancer with neuroendocrine differentiation (NED) occurs in 10% to 40% of cases, a significant proportion that is under-researched. The lack of clinical guidelines for this subgroup necessitates the development of effective treatment protocols.

Methods: This study enrolled 149 gastric cancer patients, analyzing retained surgical wax blocks via immunohistochemistry for syn, CgA, and CD56 expressions. Patients were categorized into NED-positive and NED-negative groups for analysis, employing continuous variable analysis, categorical variable analysis, clustering, principal component analysis (PCA), feature importance analysis, heatmap analysis, and survival prognosis. Moreover, the clinical efficacy and safety of first-line (surufatinib + SOX + anti PD-1 antibody, n=3) and second-line (surufatinib + anti PD-1 antibody, n=3) treatments were observed in six advanced gastric cancer with NED patients, exploring the epidemiological characteristics, feasibility, and importance of clinical treatments for NED.

Results: The study revealed a 10.1% incidence of NED positivity in gastric cancer patients. NED-positive patients exhibited a rapid decline in early survival probability, with a median relapse-free survival of 32.4 months compared to 41.5 months in NED-negative patients, indicating a poorer prognosis for NED-positive patients. In-depth analysis suggested significant correlations between NED status and factors such as gender, tumor location, pathological type, and AJCC staging, with the most significant associations observed in males, stage IIIA, and gastric angle location. In the six advanced gastric cancer with NED cases, effective tumor reduction was observed in both first-line (100% tumor shrinkage rate, ORR 66.7%, DCR 100%) and second-line treatments (66.7% tumor shrinkage rate, ORR 33.3%, DCR 100%), showing sustained partial responses (PR) exceeding 10 months in two patients and 7 months in one patient, respectively. The major grade 3 or higher TEAEs being neutropenia and thrombocytopenia in the first-line, and hypertension and proteinuria in the second-line therapy.

Conclusion: This study provides pivotal epidemiological and clinical treatment evidence for gastric cancer with NED, underscoring the necessity of personalized treatment strategies for this subgroup. Future research should focus on refining treatment protocols to enhance the quality of life and overall prognosis for these patients.

Citation Format: Zhen Huang, Jinlai Wei, Yifan Shen, Jun Zhang. Epidemiological characteristics and treatment strategies of gastric cancer with neuroendocrine differentiation (NED) [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 4864.
Abstract 487: Peptide amphiphiles hitchhike on endogenous biomolecules for enhanced drug delivery
Authors: Fischer Jared M. , Stewart Morgan , Dai Mingchong , Drennan Samuel , Sabuncu Sinan , Kingston Benjamin , Dengos Isabel , Xiang Li , Bonic Karla , Yi Xin , Ranganathan Srivathsan , Branchaud Bruce , Yildirim Adem
Published: March 2024

Peptide amphiphiles (PAs) have been applied as building blocks for self-assembled nanostructures with various morphologies. These self-assembled nanostructures are promising drug delivery platforms as they are naturally biodegradable and biocompatible with low immunogenicity. One primary focus in drug delivery using the PA nanostructures has been to develop strongly assembled structures to avoid disassembly in the blood and allow them to carry payloads to their intended targets. In this work, rather than developing stable self-assembled PA structures, we focused on weakly assembled PA nanostructures to investigate their interactions with blood components and to understand how these interactions affect their biodistribution. We found that weakly assembled PA nanostructures (SA-E) quickly disassembled in plasma and reassembled with lipoproteins (LPs), which significantly prolonged the blood circulation of SA-E in mice. We showed that SA-E crossed the endothelial barriers through transcytosis only when they were assembled with LPs. Cellular uptake studies showed that SA-E accumulated in cancer cells through lipid-raft-mediated uptake. Interestingly, their cellular internalization was independent of LP receptors, suggesting that SA-E assembles with different endogenous biomolecules in vivo. By exploiting these endogenous interactions, SA-E demonstrated high tumor accumulation in a myriad of small animal tumor models of breast, colon, pancreatic, brain, skin, prostate, or lung cancers. SA-E demonstrated large tumor-to-background signal ratios in live animals (>5), extended retention (>2 weeks), and excellent tissue distribution (tumor to liver signal >3) in these tumor models. Encouraged by the excellent tumor accumulation of SA-E, we prepared SA-E drug conjugate using a highly potent and toxic chemotherapeutic agent, Monomethyl auristatin E (MMAE). SA-E-MMAE conjugate demonstrated strong antitumor efficacy in aggressive breast and glioma models in mice with reduced side effects. With its simple and modular design and universal tumor accumulation mechanism, SA-E represents a promising platform for broad applications in cancer therapy.

Citation Format: Jared M. Fischer, Morgan Stewart, Mingchong Dai, Samuel Drennan, Sinan Sabuncu, Benjamin Kingston, Isabel Dengos, Li Xiang, Karla Bonic, Xin Yi, Srivathsan Ranganathan, Bruce Branchaud, Adem Yildirim. Peptide amphiphiles hitchhike on endogenous biomolecules for enhanced drug delivery [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 487.
Abstract 4880: Identification and clinicopathological analysis of potential p73-regulated biomarkers in colorectal cancer via integrative bioinformatics
Authors: Bareja Chanchal , Dwivedi Kountay , Uboveja Apoorva , Mathur Ankit , Kumar Naveen , Saluja Daman
Published: March 2024

This work aims to decipher p73-regulated biomarkers for a prompt diagnosis of colorectal cancer (CRC) by employing a combination of integrative bioinformatics and expression profiling technologies. Transcriptome profile of HCT116 cell line p53−/− p73+/+ and p53−/− p73 knockdown was performed to identify differentially expressed genes (DEGs) followed by cross-checking with three CRC tissue expression datasets available in Gene Expression Omnibus. KEGG and Gene ontology were performed on differentially expressed transcripts obtained via the transcriptome profile and intersected genes. The PPI network was constructed via Cytoscape to extract hub genes. KM plots assisted in investigating the prognostic significance of the hub genes. The clinicopathological relevance was explored using the GEPIA and UALCAN databases. Finally, machine/deep learning algorithms were employed to perform TNM-stage classification. Transcriptome profiling revealed 1,289 upregulated and 1,897 downregulated genes. When intersected with employed CRC datasets, 284 DEGs were obtained. The analysis of gene ontology and KEGG showed enrichment of the DEGs in metabolic process, fatty acid biosynthesis, etc. The PPI network constructed using these 284 genes assisted in identifying 20 hub genes. Kaplan Meier, GEPIA, and UALCAN analyses uncovered the prognostic and diagnostic relevance of these hub genes. Conclusively, the deep learning model achieved TNM-stage classification accuracy of 0.78 and 0.75 using 284 DEGs and 20 hub genes, respectively. This is a novel study utilizing transcriptomics, publicly available tissue datasets, and machine learning to unveil key CRC-relevant genes. These genes are found relevant regarding the patients’ prognosis and diagnosis. The unveiled biomarkers are also found robust in TNM-stage prediction. This is the first study where transcriptomics, publicly available tissue datasets, and machine learning are altogether employed to reveal key genes in CRC pathogenesis. Our research highlights the robust analysis of four independent data sets to find the key hub genes, further predicting the performance of the key genes in stage-wise classification.

Citation Format: Chanchal Bareja, Kountay Dwivedi, Apoorva Uboveja, Ankit Mathur, Naveen Kumar, Daman Saluja. Identification and clinicopathological analysis of potential p73-regulated biomarkers in colorectal cancer via integrative bioinformatics [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 4880.
Abstract 4910: AI predicts drug response from the genomic features of cells and the kinase activity changes induced by compounds
Authors: Janssens Rens , Rizzolo Kimberly , Artin Erin , Wagner Joel , Riester Markus , Korn Joshua , Park Jisoo
Published: March 2024

Human protein kinases are playing an important role in various biological activities including tumorigenesis and cancer progression, and for this reason, many kinase inhibitors have been developed as promising targeted therapies for cancer. To date, there are 72 FDA-approved treatments targeting about two dozen different protein kinases; 3 of them were approved in 2022. However, there are still critical challenges that can be addressed to improve the robustness and selectivity of the kinase inhibitors such as drug resistance, toxicity and compromised efficacy. To gain a deeper understanding of the biological mechanisms underlying the resistance to kinase inhibitors, we hereby design and train an artificial intelligence (AI) model that predicts in-vitro cell response to various kinase inhibition from the integration of the genomic features of cancer cell lines and the biochemical profiles of kinase activities. The inner-working of an optimized model provides important insights on the relevant kinase activities for the cell response. A major challenge for training such a model is that the training data for biochemical kinase activity is very sparse; the kinase panels are not consistent across different sources and each dataset contains many missing values. To address this, we train a secondary AI model to predict all the missing values for the kinase activity in our training data using the combination of the compound chemical structure and the kinase structure. The secondary model is independently validated to ensure the quality of the training data for the drug response prediction model. An investigation of the secondary model’s inner mechanism sheds light on the kinase binding sites and which chemical substructures are important for its inhibition. The model accurately predicts the cell response to different CDK inhibition. A focused analysis of the model characterizes off-target effects of the CDK inhibitors which may be linked to the drug resistance mechanisms, suggesting ways to improve the inhibitors or potential targets for combination therapies.

Citation Format: Rens Janssens, Kimberly Rizzolo, Erin Artin, Joel Wagner, Markus Riester, Joshua Korn, Jisoo Park. AI predicts drug response from the genomic features of cells and the kinase activity changes induced by compounds [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 4910.
Abstract 4914: Mapping the cancer immune landscape in colorectal adenocarcinoma using multiplexed imaging and AI based analysis
Authors: Agrawal Vasundhara , Arvidson Lisa , Smith Michael J. , White Katie O. , Heil-Chapdelaine Richard A. , Jensen Samuel , Bose Arindam
Published: March 2024

Colorectal cancer is a high burden cancer in the United States, leading to the second highest cause of cancer deaths. Despite chemotherapeutic intervention and surgical resection, recurrent disease may occur in some patients and typically, has a poorer prognosis. Thus, there is a demand for advanced therapies such as immunotherapies for improved clinical outcomes. An in-depth understanding of the colon cancer microenvironment is necessary to improve outcome in this subset of patients. Spatial biology approaches are well positioned to comprehensively uncover the molecular and biological mechanisms of cancer cell aggression in colorectal cancer. Here, we visualized nearly 30 biomarkers in colon adenocarcinoma (CAC) tissue using the Cell DIVE multiplexed imaging workflow and validated antibodies from Cell Signaling Technology (CST®). Using this approach, we were able to probe multiple pathways of interest in cancer progression, such as vascularization of tumor tissue, immune cell responses, and cell proliferation. Together, these data allow the creation of a spatial map of tumor cell aggression and offer predictive value for the progression of the disease. Deep molecular and architectural insights on this level are possible only with a spatial biology approach and offer multiple downstream hypotheses to further understand cancer progression and interrogate the heterogeneity within the tumor microenvironment.

Citation Format: Vasundhara Agrawal, Lisa Arvidson, Michael J. Smith, Katie O. White, Richard A. Heil-Chapdelaine, Samuel Jensen, Arindam Bose. Mapping the cancer immune landscape in colorectal adenocarcinoma using multiplexed imaging and AI based 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 4914.
Abstract 4956: A fast and efficient bioinformatics analysis workflow for processing reads from single-cell multiomics assays captured on a microwell-based platform
Authors: Padmanabhan Raghavendra , Weichel Brent , Radenbaugh Amie , Jiang Yuefu , Weeks Charles , McCarthy Thomas , Kim Youngsook , Berno Anthony , Jensen Devon
Published: March 2024

Here, we present a significant update: version 2.0 of our sequencing analysis, it is a comprehensive primary analysis workflow that is up to 7X faster and consumes 2X less disk space than the previous release. We used it to process a library with 20,000 human PBMCs sequenced to a depth of 1.2 billion reads in 2.5 hours of wall-clock time. The pipeline can be used with reads from single-cell whole transcriptome, targeted mRNA, surface antigens (AbSeq), TCR/BCR and Sample Tag libraries captured on the BD Rhapsody™ System platform. The major processing steps include Quality Filtering, Cell Barcode Identification, Read Alignment, Feature Assignment, UMI Error Correction, Identification of Putative Cells, Sample De-Multiplexing, Dimensionality Reduction for Visualization and VDJ Contig Assembly and Annotation. Output files and metrics are available in easy-to-digest formats, including an html report with dynamic visualization. Integrated outputs in Seurat and Scanpy formats combine expression matrices and all cell annotation metadata (e.g., predicted cell type, sample assignment, TCR/BCR sequence and gene segments). These pre-generated files are ready to load into popular single-cell analysis tools. The pipeline uses CWL as the workflow manager and makes use of custom code written in C++ and Python along with various open-source packages for data processing. The pipeline can also process reads from non-human species and includes built-in support for specifying and building custom reference genome indices. In support of high-throughput multiomic discovery studies enabled by the BD Rhapsody™ HT Xpress System, this pipeline has been tested with datasets containing more than 800,000 putative cells and 14.5 billion reads.

For Research Use Only. Not for use in diagnostic or therapeutic procedures. BD, the BD Logo and BD Rhapsody are trademarks of Becton, Dickinson and Company or its affiliates. © 2023 BD. All rights reserved. NPM-2535 (v1.0) 1023

Citation Format: Raghavendra Padmanabhan, Brent Weichel, Amie Radenbaugh, Yuefu Jiang, Charles Weeks, Thomas McCarthy, Youngsook Kim, Anthony Berno, Devon Jensen. A fast and efficient bioinformatics analysis workflow for processing reads from single-cell multiomics assays captured on a microwell-based 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 4956.
Abstract 4989: Targeting IL-1β mitigates radiation induced MDSC expansion & improves survival in glioblastoma
Authors: Ghosh Subhajit , Huang Jiayi , DeNardo David , Hallahan Dennis , Jaboin Jerry , Thotala Dinesh
Published: March 2024

Background: Our previous research demonstrated that radiation therapy (RT) for glioblastoma (GBM) induces aberrant myelopoiesis, increasing production of myeloid derived suppressor cells (MDSCs) and exacerbating T-cell suppression. However, the precise biological mechanisms underlying this phenomenon remain unclear. This study aims to elucidate the role of the pro-inflammatory cytokine interleukin-1beta (IL-1β) in RT-induced myelopoiesis and its correlation with poor prognosis in GBM patients.

Methods: We conducted an extensive analysis of circulatory immune cells and pro-inflammatory cytokines in GBM patients treated with chemoradiotherapy. Using an orthotopic mouse model of GBM, we investigated the impact of IL-1β on myelopoiesis and survival. Functional assays were employed to examine MDSC expansion. Multi-color flow cytometry was used for immune profiling.

Results: We found that RT elevated the plasma IL-1β concentration in both GBM patients and GBM-bearing mice, which also corresponded with an increase of MDSC in blood. In the murine GBM model, RT appeared to promote hematopoietic stem (HSPC) differentiation towards myelopoiesis. This led to increased MDSC precursor cells in the bone marrow, elevated circulating MDSCs in blood, and more infiltration of MDSCs in the tumor microenvironment (TME). Similar effects were observed in GBM-bearing mice following the administration of exogenous IL-1β. In contrast, inhibition of IL-1β using anti-IL-1β antibody during RT led to reduced myelopoiesis. When anti-IL-1β antibody was combined with functional inhibition of MDSCs using phosphodiesterase-5 inhibitor-tadalafil during RT, we observed decreased MDSC infiltration and increased CD8+ T cell infiltration in the TME. The combination approach also extended the survival of GBM-bearing mice after RT longer than either drug alone.

Conclusions: Irradiation of GBM appears to induce IL-1β to promote aberrant myelopoiesis and MDSC expansion. A multi-pronged approach to inhibit MDSC production using IL-1β inhibitor and MDSC function using tadalafil during RT may be a promising approach to overcome the immune-suppressive TME of GBM.

Citation Format: Subhajit Ghosh, Jiayi Huang, David DeNardo, Dennis Hallahan, Jerry Jaboin, Dinesh Thotala. Targeting IL-1β mitigates radiation induced MDSC expansion & improves survival in glioblastoma [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 4989.
Abstract 5007: Ex vivo evaluation of mRNA lipid nanoparticle cancer vaccines
Authors: Lidström Tommy , Arauzo Mara Blanco , Karlowatz Nickolas , Johansson Mikael , Forsell Mattias , Nilsson Jonas
Published: March 2024

Lipid nanoparticle vaccines have recently been developed broadly against pathogens and recently, in precision medicine targeting mutations in different tumors. Evaluating vaccine candidates typically require animal models using orthotopic or allogenic transplantations to evaluate efficiency. Evaluating vaccine efficacy using ex vivo systems is faster and less technically demanding. Here we aim to develop individualized cancer vaccines based on neoantigen identified within established human organoids or directly from patient tissue. The selected neoantigens are enriched for epitopes identified on gene fusions. Identified gene fusions encoding predicted immunogenic proteins are inserted into a vaccine backbone and used to make mRNA lipid nanoparticle vaccines. The neoantigen candidates are then evaluated in a personalized ex vivo testbed. Within the ex vivo testbed personal tumor neoantigens are tested on the patients own isolated CD8+ T cells and monocytes. Monocytes are in vitro differentiated into monocyte derived dendritic cells (moDCs), which specialize in antigen cross presentation. The moDCs are inoculated with mRNA lipid nanoparticle vaccines or loaded with peptides. The moDCs are then co-cultured with syngeneic T cells. Vaccine candidates are evaluated based on CD8+ T cell activation and cytotoxicity in the co-culture ex vivo testbed. Our pipeline offers a fast and efficient means of evaluating individualized vaccine candidates. Effective vaccines developed through this process can be administered as a standalone therapy or in combination with checkpoint inhibitors, to generate a strong durable immune response against a variety of solid tumor types.

Citation Format: Tommy Lidström, Mara Blanco Arauzo, Nickolas Karlowatz, Mikael Johansson, Mattias Forsell, Jonas Nilsson. Ex vivo evaluation of mRNA lipid nanoparticle cancer vaccines [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 5007.
Abstract 504: Anticancer effects of kaempferol through cell cycle arrest and the inhibition of proliferation in genetically distinct triple-negative breast cancer cells
Authors: Kaur Sukhmandeep , Mendonca Patricia , Soliman Karam F. A.
Published: March 2024

Triple-negative breast cancer (TNBC) is one of the most known aggressive subtypes of breast cancer, affecting 1 in 3 newly diagnosed cancers in women. TNBC affects African-American women disproportionally in comparison to Caucasian women. Due to the lack of estrogen receptors (ER), progesterone receptors (PR), and human epidermal growth factor receptors (HER-2), it poses direct challenges to the efficacy of standard hormonal therapies. The current TNBC treatments present higher toxicity and multiple side effects. An alternative would be using natural compounds that have emerged as potential anticancer agents. Kaempferol is a major flavonoid aglycone found in many fruits, vegetables, and herbs, including grapes, tomatoes, broccoli, tea, and ginkgo biloba leaves. In this study, we investigated the differential effect of kaempferol on cell toxicity, cell growth, and underlying mechanisms in inducing cell cycle arrest in genetically different TNBC cells from Caucasian (MDA-MB-231) and African American (MDA-MB- 468) women. Kaempferol significantly inhibited cell growth in both the cell lines with a more profound effect against MDA-MB-231 (IC50: 43.86 µM) compared to MDA-MB-468 cells (IC50: 53.47 µM). Also, kaempferol treatment induced cell cycle arrest at S-phase in both cancer cell subtypes. The MDA-MB-231 cells showed a kaempferol effect at lower concentrations (6.25µM and 12.5µM), while MDA-MB-468 cells showed the same effect at higher concentrations (25µM and 50µM). Kaempferol also modulated CDK gene expression associated with cell cycle progression in breast cancer cells. The inhibition at S-phase is important in cancer treatment because it targets the highly proliferative nature of cancer cells characterized by uncontrolled cell division. This study indicates that, by inducing cell cycle arrest at the S-phase, kaempferol may interfere with cancer cell growth and proliferation by inhibiting DNA replication, offering potential therapeutic benefits. This approach could reduce side effects and increase treatment efficacy, providing hope for more effective interventions in the fight against TNBC.

Citation Format: Sukhmandeep Kaur, Patricia Mendonca, Karam F. A. Soliman. Anticancer effects of kaempferol through cell cycle arrest and the inhibition of proliferation in genetically distinct triple-negative breast cancer cells [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 504.
Abstract 5050: Germline variants in CDKN2A wild-type melanoma prone families
Authors: Knappskog Stian , Iversen Gjertrud T. , Loeng Marie , Holth Amalie L. , Lonning Per E. , Geisler Jurgen
Published: March 2024

The presence of germline pathogenic variants in CDKN2A is a well-established underlying cause of familial malignant melanoma. While pathogenic variants in several other genes have also been linked to melanoma development, many familial cases remain unexplained. We analyzed for pathogenic germline variants in a panel of 360 cancer related genes in a set of 56 Norwegian melanoma prone families. The index cases and families were selected based on familial history of melanoma and/or multiple primary melanomas in the same individual, along with previous negative tests for pathogenic CDKN2A variants. We found 6 out of 56 index individuals to carry germline pathogenic or likely pathogenic variants. These variants were found in BRCA2, MRE11, ATM, MSH2, CHEK2 and AR. In addition, one family member with a melanoma diagnosis (not index case) carried a pathogenic variant in MAP3K6. In genes typically linked to xeroderma pigmentosum, we found a high fraction of variants previously considered benign and/or as variants of uncertain significance. In particular the XPCL48F variant was found in 8 out of 56 indexes, thus, the allele fraction (0.07) was significantly higher than in comparable healthy populations (p-values from 0.007 to 0.014). Similarly, we found presumed benign or uncertain variants in MC1R to be significantly enriched or numerically higher in index cases versus comparable healthy populations (p-values from 0.009 to 0.1). The common MC1RArg151Cys variant was highly enriched in our cohort (p=0.001).In conclusion, we found that several melanoma prone families harbored pathogenic variants in genes not usually linked to melanoma.

Citation Format: Stian Knappskog, Gjertrud T. Iversen, Marie Loeng, Amalie L. Holth, Per E. Lonning, Jurgen Geisler. Germline variants in CDKN2A wild-type melanoma prone families [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 5050.
Abstract 5069: Retrospective analysis of acute myeloid leukemia using next generation cytogenomics identifies variants missed at diagnosis
Authors: Eacker Stephen , Malig Maika , Wood Mary , Muratov Alexander , Sala-Torra Olga , Liachko Ivan , Yeung Cecilia , Radich Jerald
Published: March 2024

Cytogenetics forms the cornerstone of diagnostic genetic testing in leukemia, providing both prognostic and diagnostic information to help guide treatment. Currently, standard-of-care cytogenetics in acute myeloid leukemia (AML) is composed of a combination of karyotyping, FISH testing, and in some cases chromosomal microarray analysis, each test offering a unique combination of advantages and weaknesses. A particular challenge for this combination of tests is the delivery of results in a timely and comprehensive manner. To overcome these limitations, we have developed OncoTerra, a proximity-ligation-sequencing based method which can rapidly detect all classes of variants detected by cytogenetics tests in a single assay. We applied OncoTerra to a cohort of more than 100 samples from a SWOG AML trial (S0106), benchmarking sensitivity and specificity of the variants. We observed an overall >0.95 sensitivity and a specificity of 1 for the variants identified by cytogenetics and identified numerous cryptic variants. Overall, we identified variants that changed the diagnostic risk stratification of 15% of the patient involved in the trial based on the ELN 2022 criteria. This translated into better overall prediction of outcomes of patients in the trial and has identified both known and novel variants missed by standard-of-care tools.

Citation Format: Stephen Eacker, Maika Malig, Mary Wood, Alexander Muratov, Olga Sala-Torra, Ivan Liachko, Cecilia Yeung, Jerald Radich. Retrospective analysis of acute myeloid leukemia using next generation cytogenomics identifies variants missed at diagnosis [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 5069.
Abstract 5243: CAR B cells to accelerate antigen presentation in cancer
Authors: Molloy Mary Ellen , Balero Jessica , Contreras-Sandoval Ana , Selby Mark , Park Hangil , Kothakota Srinivas , Boyle Kathleen , Romano Rosa , Rajendiran Smrithi , Hernandez Moises , Pios Ariel , Williams Rusty
Published: March 2024

Engineered B cells hold promise for multiple therapeutic applications. Walking Fish Therapeutics is engineering B cells to produce replacement proteins for deficiency diseases, antibodies of defined specificity and effector function, and Chimeric Antigen Receptor (CAR) B cells with and without therapeutic payloads for use in the oncology setting. B cells are professional antigen presenting cells (APCs) with the ability to present antigen to CD4+ T cells. Recent studies have found the presence of tumor infiltrating B cells are associated with favorable outcomes across multiple cancer types. Adoptive transfer of B cells has demonstrated antitumor activity in a syngeneic mouse model. B cells from OVA-vaccinated transgenic luciferase mice were adoptively transferred to mice bearing EG7.OVA-tumors. We observed B cells migrating to the tumor and tumor draining lymph node (TDLN), locations where B cells can engage with antigen. Further, we observed a strong anti-tumor response in mice receiving B cells from OVA-vaccinated donors. Based on these results, we hypothesized that B cells engineered to target tumor specific antigens may engage and activate the immune system leading to an enhanced antitumor immune response. We generated CAR B cells expressing synthetic BCRs with tumor-antigen specific scFvs fused to designated B cell signaling motifs. Expression of different CAR constructs were confirmed in both human and mouse B cells. Upon antigen engagement CAR B cells release pro-inflammatory cytokines. Importantly, we demonstrate in vitro that antigen-specific CAR B cells can recognize cognate cell surface antigen, leading to uptake, processing, and presentation on MHCII as detected by activation of peptide-specific CD4+ T cells. When administered in vivo by IV administration, we observed a significant increase in mouse CAR B cells at the tumor site compared to unengineered B cells. We are currently investigating additional CAR formats that may lead to enhanced anti-tumor activity.

Citation Format: Mary Ellen Molloy, Jessica Balero, Ana Contreras-Sandoval, Mark Selby, Hangil Park, Srinivas Kothakota, Kathleen Boyle, Rosa Romano, Smrithi Rajendiran, Moises Hernandez, Ariel Pios, Rusty Williams. CAR B cells to accelerate antigen presentation in 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 5243.
Abstract 5278: Immunological control by PARP inhibitors for successful immunotherapy in metastatic ovarian carcinoma
Authors: Holicek Peter , Vosahlikova Sarka , Moserova Irena , Orsulic Sandra , Mikyskova Romana , Hensler Michal , Kasikova Lenka , Lanickova Tereza , Novotny Ondrej , Reinis Milan , Drozenova Jana , Ryska Ales , Laco Jan , Rob Lukas , Halaska Michael , Cibula David , Spisek Radek , Fucikova Jitka
Published: March 2024

Epithelial ovarian carcinoma (EOC) is among the top five causes of cancer-related death in women. Most women with EOC achieve indeed complete remission after primary or interval cytoreductive surgery combined with chemotherapy based on a platinum-taxane doublet. Homologous recombination (HR) defects imposed by germline or somatic BRCA1 DNA repair-associated (BRCA1) or BRCA2 mutations are not only key determinants of platinum sensitivity in EOC patients but also provide a strong rationale for maintenance therapy based on poly(ADP-ribose) polymerase (PARP) inhibitors, which is generally associated with improved progression-free survival (PFS). Besides direct cytotoxic and cytostatic properties, PARPi have been shown to mediate multipronged immunostimulatory effects, largely reflecting their ability to inhibit DNA repair in malignant cells and indicating the possibility to synergy with immune-check point inhibitors (ICIs). Here, using multiparametric flow cytometry, multiplex immunostaining, single cells transcriptomics and functional studies in experimental syngeneic BR5Brca1-/- mouse model and EOC tumor samples, we discuss PARPi immunomodulatory activity, with a specific focus on molecular and cellular pathways that can be harnessed to develop superior combinatorial regimens for clinical management. Thus, PARPi might enhance the mutational load of EOCs as consequence of unrepaired DNA damage and DAMPs exposure, favoring T cell infiltration, but also appear to drive robust type I IFN secretion downstream of cyclic GMP-AMP synthase and stimulator of IFN response cGAMP interactor 1 activation. In addition, the combination of PARPi with ICIs positively regulate the balance between adaptive anti-tumor immunity and innate myeloid components and significantly improve the cytotoxic T cell profile as shown in both experimental mice model and HGSOC tumor samples. We surmise that rationally designed combinations of PARPi and immunotherapeutic agents might be critical to unlock immunosuppression in the EOC microenvironment in support of clinical efficacy.

Citation Format: Peter Holicek, Sarka Vosahlikova, Irena Moserova, Sandra Orsulic, Romana Mikyskova, Michal Hensler, Lenka Kasikova, Tereza Lanickova, Ondrej Novotny, Milan Reinis, Jana Drozenova, Ales Ryska, Jan Laco, Lukas Rob, Michael Halaska, David Cibula, Radek Spisek, Jitka Fucikova. Immunological control by PARP inhibitors for successful immunotherapy in metastatic 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 5278.
Abstract 5304: ABL407, a LILRB4x4-1BB bispecific antibody with a wild type Fc, exhibits potent antitumor activity by modulating immune system in multiple ways involving T cells, myeloids, and regulatory T cells
Authors: Seon Minkyu , Lee Yangsoon , Youn Hyunseong , Park Yelim , Kim Sora , Park Kyungjin , Won Jonghwa
Published: March 2024

Tumor-associated myeloid cells such as myeloid-derived suppressor cells (MDSC) accumulate in the tumor microenvironment (TME) and suppress anti-tumor immune responses in a broad range of cancers. LILRB4 (Leukocyte Immunoglobulin-Like Receptor Subfamily B Member 4), an emerging myeloid target, is specifically expressed in tumor-associated myeloid cells and suppresses the immune response, thus promoting cancer progression and metastasis. ABL407 is a First-in-Class bispecific antibody designed to simultaneously target LILRB4 and 4-1BB, enabling LILRB4 expression-dependent 4-1BB activation. By antagonizing LILRB4 signaling, ABL407 inhibited LILRB4 mediated immunosuppression, restoring T cell activity. In addition, ABL407 inhibited fibronectin, a potential LILRB4 ligand, -mediated suppression of myeloid cells. To evaluate the efficacy of ABL407, we established EL4 murine tumor model overexpressing LILRB4 (EL4/LILRB4) in h4-1BB transgenic mice and hLILRB1/4-h4-1BB triple transgenic mice. We observed LILRB4 was overexpressed in M-MDSC in the blood and liver-metastasized tumors. A significant decrease of M-MDSC population and tumor growth inhibition was observed in mice treated with anti-LILRB4 antibody and ABL407. ABL407 treatment resulted in a proportion increment of T cells. However, the percentage of Treg cells and M-MDSC in the liver and blood was reduced by ABL407 treatment in hLILRB1/4-h4-1BB triple transgenic mice. Mice with complete remission (CR) were further protected from the rechallenge of previously exposed tumor after 3 months of cessation of ABL407 treatment, implicating that immunological memory might be generated. In conclusion, our findings suggest that ABL407, LILRB4x4-1BB bispecific antibody, may be a promising strategy for the treatment of cancer. It can be applied as a "LILRB4 antagonist" as well as a "LILRB4-dependent 4-1BB agonist" across a broad spectrum of cancers.

Citation Format: Minkyu Seon, Yangsoon Lee, Hyunseong Youn, Yelim Park, Sora Kim, Kyungjin Park, Jonghwa Won. ABL407, a LILRB4x4-1BB bispecific antibody with a wild type Fc, exhibits potent antitumor activity by modulating immune system in multiple ways involving T cells, myeloids, and regulatory T cells [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 5304.
Abstract 535: Resistant PDO models: Unraveling drug resistance mechanisms for discovering new drug targets
Authors: Abouleila Yasmine , Doorn Mayke , Verkerk Roel , Maas Joris , Verissimo Carla , Boj Sylvia
Published: March 2024

Resistance to cancer treatment remains a significant obstacle in curing patients with cancer. Despite recent advancements in novel drug targets for cancer therapeutics, patients often develop treatment resistance even after initial disease remission, leading to tumor relapse. To investigate the mechanisms responsible for developing resistance to standard-of-care therapies, it is essential to gain insights into the stepwise progression leading to complete resistance. Recent research has revealed that cancer cells can evade the effects of chemotherapy and targeted therapy by entering a reversible and slow proliferation state known as the drug-tolerant persister (DTP) state. This DTP state allows cancer cells to survive drug therapy long enough for additional mechanisms of acquired drug resistance to develop. HUB Organoids® or patient-derived organoid (PDO) models are derived from patient tissues, making them more physiologically relevant than traditional cell lines. Thus, studying drug persistence and resistance in PDO models is more likely to reflect in vivo conditions. This study demonstrates the successful development of persistent and resistant CRC PDO models to standard-of-care therapies. All models were characterized using whole exome sequencing and RNA sequencing to confirm their persistent or resistant state and to identify possible pathways involved in developing therapy resistance, as well as potential new drug targets. In conclusion, developing persistent and resistant PDO models is crucial for understanding drug resistance mechanisms, enabling the development of more effective and personalized cancer treatments, and advancing our overall knowledge of how resistance develops in cancer patients.

Citation Format: Yasmine Abouleila, Mayke Doorn, Roel Verkerk, Joris Maas, Carla Verissimo, Sylvia Boj. Resistant PDO models: Unraveling drug resistance mechanisms for discovering new drug targets [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 535.
Abstract 536: Breaking through ADCs resistance: Constructing preclinical enhertu-induced resistant model
Authors: Fang Yuan , Wang Huiyi , Xing Jun , Yang Lu , Zhao Jing , Gao Xiang , Ju Cunxiang
Published: March 2024

Antibody-drug conjugates (ADCs) are compounds that combine the specificity of monoclonal antibodies (mAbs) with the cytotoxic payload of toxic substances. In recent years, ADCs have rapidly developed in the field of cancer therapy, particularly in the treatment of HER2-positive breast cancer. One representative example is Trastuzumab deruxtecan (Enhertu), which has become a new benchmark for anti-HER2 ADCs due to its excellent performance in clinical trials. Despite the impressive clinical outcomes of ADCs, some tumors in patients may still develop resistance to these drugs. Therefore, it is crucial to understand the mechanisms of resistance and develop strategies to overcome ADCs resistance. To achieve these goals, it is essential to establish and utilize preclinical models to study these resistance mechanisms. Preclinical models of resistance to ADCs have mainly been generated using human cultured cell lines. JIMT-1 is a HER2-positive breast cancer cell line that exhibits primary resistance to the anti-HER2 antibody trastuzumab and also shows resistance to trastuzumab-derived ADC T-DM1. However, we found that Enhertu significantly inhibited tumor growth in JIMT-1 xenograft models. We subjected JIMT-1 tumor tissues to continuous passage in mice and administered long-term drug induction. The tumor growth rate gradually increased, and the drug sensitivity decreased, resulting in the acquisition of an Enhertu-resistant tumor model. The obtained resistant tumor tissues not only include tumor cells themselves but also comprise fibroblasts, extracellular matrix, and other cellular components, enabling a more comprehensive investigation into the interactions between different cells within the tumor microenvironment (TME). We believe that the establishment of preclinical Enhertu-resistant models helps predict resistance that has not yet emerged clinically and provides references for future drug development.

Citation Format: Yuan Fang, Huiyi Wang, Jun Xing, Lu Yang, Jing Zhao, Xiang Gao, Cunxiang Ju. Breaking through ADCs resistance: Constructing preclinical enhertu-induced resistant model [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 536.
Abstract 5364: Progesterone receptor modulates the antigen processing and presentation machinery decreasing MHC class I expression on tumors
Authors: Tinoco Julio , Werner Lauryn , Chowanec Eilidh , Saunders Harmony , Xiaopeng Sun , Gertz Jay , Balko Justin , Hartman Zachary C. , Hagan Christy
Published: March 2024

Hormone receptor (HR) positive breast cancers, which account for approximately 75% of all breast cancers and express both estrogen receptor (ER) and progesterone receptor (PR), have been the subject of much research. As such, successful anti-estrogen/ER-based therapies have been very successful in the treatment of HR+ breast cancer. Despite this success, over 1/3 of patients will eventually progress on current ER/estrogen-targeted therapies, underscoring the need for new targeted therapies in HR+ breast cancer. Unlike ER, the role of PR in breast cancer progression has received far less attention. In a previous study, we found that a mouse mammary tumor cell line E0771, modified to express the mouse progesterone receptor (mPR) and the OVA peptide, demonstrated decreased T cell-mediated cell death when treated with progesterone compared to the control group. Progesterone-mediated protection from T-cell death was only observed in mPR+ cell lines. Flow analysis of the E0771-Ova-mPR cells also revealed a decrease in MHC Class I presentation in progesterone-treated cells compared to a vehicle control. To further explore the role of the machinery required for antigen processing and presentation of MHC Class I molecules, we conducted additional experiments using the E0771 cell line. Our results showed that treatment with progesterone led to a reduction in RNA levels of all the machinery required for antigen processing and presentation (APP). Based on these findings, we hypothesize that activation of the progesterone receptor by progesterone may decrease MHC Class I expression by regulating APP. Our results showed that treatment with progesterone resulted in a reduction in RNA levels of Tap1, Tap2, Tapbp, Nlrc5, B2m, and Psmb8, which are essential for APP. We therefore propose that activation of the progesterone receptor by progesterone may decrease MHC Class I expression by directly modulating the APP pathway. The findings of this study may have significant implications for our understanding of how breast cancer cells evade T-cell mediated cytotoxicity.

Citation Format: Julio Tinoco, Lauryn Werner, Eilidh Chowanec, Harmony Saunders, Sun Xiaopeng, Jay Gertz, Justin Balko, Zachary C. Hartman, Christy Hagan. Progesterone receptor modulates the antigen processing and presentation machinery decreasing MHC class I expression on 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 5364.
Abstract 5366: ATR promotes extracellular matrix stiffness mediated cytoskeleton remodeling and immunosuppression
Authors: Tu Xinyi , Lou Zhenkun , Mutter Robert
Published: March 2024

The stiffening of the extracellular matrix (ECM), a phenomenon that often promotes metastasis and immunosuppression in many cancers, is a process that is not yet fully understood. Our study reveals that ATR, a molecule primarily recognized for its role in maintaining the genome, plays a crucial role in ECM stiffness-induced immune evasion and metastasis in triple negative breast cancer (TNBC) through DNA repair independent manner. In response to ECM stiffness, ATR activates SUN2, a component of the linker of nucleoskeleton and cytoskeleton (LINC) complex. This activation enhances the interaction of SUN2 with outer nuclear membrane proteins KASH1 and KASH2. The interaction between SUN2 and KASH1/2 facilitates the nuclear localization of β-catenin, which in turn promotes epithelial mesenchymal transition (EMT) and reduces the expression of E-cadherin. E-cadherin is essential for attracting CD103+ immune cells that perform anti-tumor immunity. Interestingly, inhibiting ATR reduces EMT in tumor cells, leading to an increase in CD103+ dendritic cell infiltration while decreasing neutrophil and polymorphonuclear myeloid-derived suppressor cell (PMN-MDSC) infiltration. Further, we found that ATR levels are inversely correlated with immunotherapy response rates in patients. The alteration in immune cell composition sensitizes tumors to immunotherapy, thereby suppressing tumor growth and metastasis. In conclusion, the role of ATR in remodeling the immune environment could be crucial for optimizing the clinical use of ATR inhibitors. This makes ATR a promising target for overcoming immunotherapy resistance. We suggest early or prolonged treatment with an ATR inhibitor to potentially reduce metastasis rates and improve the prognosis of TNBC patients. Furthermore, we suggest using ATR levels as a marker to predict response rates and prognosis in TNBC patients. For patients with higher ATR expression levels, combination treatment with ATR inhibitors and immunotherapy may yield better outcomes. Enhanced anti-tumor immunity could increase the chances for patients to eliminate cancer cells and help end breast cancer. Finally, our research suggests the combined treatment of ATR inhibition and immunotherapy for patients without necessarily applying DNA damage stimulation. This approach could potentially reduce toxicity while still benefiting patients.

Citation Format: Xinyi Tu, Zhenkun Lou, Robert Mutter. ATR promotes extracellular matrix stiffness mediated cytoskeleton remodeling and immunosuppression [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 5366.