bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3470: Evaluation of the association between sickle cell disease and breast cancer using the All of Us Research Program dataset
Authors: Jubilee Ivan T. , Evans Lauren K. , Lemieux KiTani Parker
Published: March 2024

Background: The All of Us Research Program (AoURP) dataset was used to evaluate pharmacological treatment modalities in patients with both breast cancer (BC) and sickle cell disease (SCD). This study aims to identify treatment strategies for sickle cell patients with BC that may inform improved treatment options for patients living with either or both conditions, as there is an imminent need in this patient population.

Methods: We investigated the relationship between SCD and BC using the AoURP dataset. Criteria were female patients with a confirmed diagnosis of concomitant SCD and BC were selected. Hematologic, antineoplastics, and immunomodulating agents prescribed to patients were identified. Analysis was conducted in a Jupyter Notebook environment by way of R. Using FDA-approved and off-label indications, medication use patterns were used to reverse-engineer patient information and identify trends between SCD and BC.

Results: Nine female patients had concomitant diagnoses of SCD and BC, which aligned with the inclusion criteria. African Americans were significantly represented in this cohort, making up sixty-seven of patients. Twenty-two percent of patients did not indicate race, while eleven percent of patients identified as Caucasian. All patients included in the study were prescribed anemic therapy. Eleven percent of patients were prescribed an FDA-approved medication for SCD. Seventy-eight percent of patients were prescribed hormone-targeted BC medications. Thirty-three percent of patients were prescribed the immunotherapy regimen, Dinutuximab with adjunctive interferon-alpha. Eleven percent of patients were prescribed cytotoxic therapy.

Conclusion: Further investigation is warranted for dinutuximab use in BC treatment, specifically the triple negative subtype, as currently no targeted therapeutic options exist, and prognosis is poor. The data suggests dinutuximab with adjunctive interferon-alpha may be promising for triple-negative BC patients with SCD.

Citation Format: Ivan T. Jubilee, Lauren K. Evans, KiTani Parker Lemieux. Evaluation of the association between sickle cell disease and breast cancer using the All of Us Research Program dataset [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 3470.
Abstract 3515: SynAI: An AI-driven cancer drug synergism prediction platform
Authors: Yan Kuan , Jia Runjun , Guo Sheng
Published: March 2024

Introduction: The SynAI solution is an adaptive AI-driven in silico drug synergism screening solution aiming to discover the potential therapeutic value of compounds at an early development stage. Given one of both compound inputs in SMILE sequences, SynAI can predict the potential Bliss score of compounds in any given cell line without the need for compound synthesis or structural analysis.The evaluation version of SynAI is accessible at https://synai.crownbio.com

Methods: The AI core of SynAI was constructed using the MLP (multi-layer perceptron) network under the PyTorch machine learning framework. The AI core of SynAI was trained against NCI-Almanac and DrugCombDB datasets. In total, these datasets consist of over 12 million in vitro synergism tests across 150 cancer cell lines of different origins. On average, each cell line is tested against over 6000 two-compound combinations of FDA-approved cancer drugs. One MLP network was trained for each cell line. Essentially, these networks predict the Bliss score for any combination of SMILE-based feature sets known as molecular fingerprints. The networks were trained against the NCI Almanac set and verified against NCI and DrugCombDB using n-fold cross-validation to avoid model overfitting. During the training, a hyperparameter tuning (HT) study was performed for SynAI and other popular algorithms; allowing an objective comparison of SynAI performances.

Results: Compared to existing synergism prediction platforms, SynAI yields similar performance in all categories (cf. Table 1) but provides more flexibility for data input using SMILE sequences directly. In addition, the AI core of SynAI can be constantly updated with new inputs from different cell lines and drug combinations. Table 1. Pearson cross correlation (PCC) between measured and predicted Bliss scores of NCI test set

Conclusions: Its adaptive and dynamic nature allows SynAI to learn from new data feeds from future studies and has significant potential in reducing the time and cost of synergism screening.

PCC Score Cell Lines Algorithm MCF7 OVCAR-8 SK-MEL-5 SynAI 0.68 ± 0.02 0.56 ± 0.07 0.86 ± 0.02 RF 0.64 ± 0.02 0.55 ± 0.03 0.89 ± 0.02 GBX 0.66 ± 0.02 0.48 ± 0.05 0.88 ± 0.02 RNN 0.54 ± 0.12 0.43 ± 0.06 0.83 ± 0.08

Citation Format: Kuan Yan, Runjun Jia, Sheng Guo. SynAI: An AI-driven cancer drug synergism prediction 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 3515.
Abstract 3517: A deep learning-based virtual staining system with multimodal-attention for precision medicine
Authors: Zhou Zixia , Jiang Yuming , Li Ruijiang , Xing Lei
Published: March 2024

Purpose: This study introduces a novel multimodal-attention-based virtual mIF staining (MAS) system designed for efficient, reliable virtual mIF staining from label-free fluorescence images. Our goal was to overcome the performance bottleneck and time-cost limitations associated with traditional mIF techniques and thereby enhance their clinical utility.

Method and Materials: Our approach involved developing a cutting-edge MAS model. This model is built upon a sophisticated end-to-end generative convolutional neural network (CNN) architecture. It ingeniously leverages autofluorescence and 4',6-diamidino-2-phenylindole (DAPI) slides as inputs to generate mIF images. To achieve this, we equipped the model with feature extractors enhanced by pretrained masked auto-encoders (MAEs) and a self-attention combination strategy. These components worked harmoniously to extract antigen-label-related features and precisely locate specific cells within the images.

Results: In our comprehensive study, we engaged 94 gastric cancer patients, utilizing the MAS system for automated virtual mIF staining of seven biomarkers, namely CD3, CD20, FOXP3, PD1, CD8, CD163, and PDL1, in both cancerous and non-cancerous tissues. Importantly, the MAS-produced virtual mIF stains matched the quality of traditional manual stains. Furthermore, we validated the prognostic accuracy for gastric cancer using these virtual mIF images, demonstrating their ability to provide clinical information that is as reliable and valuable as that obtained from manually stained mIF images.

Conclusions: Our study identifies the MAS system as an important advancement in mIF staining, enhancing personalized medicine with its efficiency and quality. This tool holds significant potential to enable personalized medicine efficiently and cost-effectively, streamlining the process of diagnosing diseases, making prognoses, and developing treatment plans.

Quantitative Comparison of Ablation Experiments for MAS system in predicting multiple biomarkers Biomarkers Index U-Net (Avg±Std) ReU-Net (Avg±Std) Att-ReU-Net (Avg±Std) MAS (Avg±Std) CD3 PSNR 27.053±4.10 27.419±4.15 28.073±4.00 28.546±4.40 CD3 SSIM 0.733±0.07 0.724±0.07 0.728±0.05 0.742±0.07 CD20 PSNR 28.835±4.66 29.244±4.76 28.672±4.52 29.243±4.99 CD20 SSIM 0.921±0.058 0.921±0.057 0.915±0.051 0.923±0.051 FOXP3 PSNR 31.769±3.29 31.838±3.10 31.098±3.20 31.862±3.11 FOXP3 SSIM 0.613±0.11 0.618±0.11 0.617±0.112 0.617±0.12 PD1 PSNR 27.908±4.47 27.950±4.43 30.283±4.37 31.717±4.17 PD1 SSIM 0.654±0.13 0.659±0.13 0.694±0.12 0.726±0.11

Citation Format: Zixia Zhou, Yuming Jiang, Ruijiang Li, Lei Xing. A deep learning-based virtual staining system with multimodal-attention for precision medicine [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 3517.
Abstract 3613: Screening iPSC lines for optimal characteristics of differentiation into immune effector cells for clinical programs
Authors: Morse Barry A. , Cogburn Amarin , Chialastri Alex , Hall Matthew S. , Manor Ohad , Lebid Andriana , Kim Dae Hwan , Cocka Luis , Perry Daniel J. , Budd Ciara , Kolluri Aarti , Campion Liam , Nishimura Toshinobu , Naso Michael , Levitsky Hyam
Published: March 2024

Engineered Induced Pluripotent Stem Cells (iPSCs) are the core foundational technology for Century Therapeutics. In our constant effort to identify iPSC lines with diverse functional activity, we have derived a large panel of clinical-grade peripheral blood mononuclear cell (PBMC)-derived and gamma-delta T cell-derived IPSC lines (PiPSCs and TiPSCs, respectively) from multiple donors. These lines have been screened by multiple criteria to select the top lines for clinical development in our iPSC-derived NK (iNK) and T cell (iT) programs. Initial screening included in-depth genomic and transcriptomic analysis of PiPSC and TiPSC lines to eliminate those with any unwanted genetic abnormalities, as well as to build multi-omics datasets for correlating gene polymorphisms and transcript variation to function. Next, all lines were differentiated to iNK or iT effector cells, and phenotypically characterized throughout the differentiation process. In those studies, 86.5% of PiPSCs and 69.2% of TiPSCs lines were compatible with our protocols and able to be successfully differentiated and acquire NK cell and gamma delta T cell phenotypes respectively. Yield and lineage commitment (%CD56+ for NK cells and %CD3+ for T cells) variability was found to be higher across clones than donors in this initial analysis. Finally, we evaluated in vitro cytotoxicity, cytokine secretion, and persistence for all clones that met differentiation thresholds (>90% lineage commitment). As part of that evaluation, 39 PiPSCs lines were differentiated to iNK cells. Cytotoxicity against tumor lines was observed to be consistently between 85-100% at an effector to target ratio of 1:1. Although no trends in functionality were found to be associated with the PBMC donor, iPSC lines derived from CD34+ enriched PBMCs exhibited higher levels of innate killing as compared to those derived from bulk PBMCs. For this presentation, we will present genetic, transcriptomic, and phenotypic correlations with favorable differentiation and functional efficacy and illustrate how our screening process enables efficient selection of founder lines with the highest therapeutic potential for allogeneic cell therapies.

Citation Format: Barry A. Morse, Amarin Cogburn, Alex Chialastri, Matthew S. Hall, Ohad Manor, Andriana Lebid, Dae Hwan Kim, Luis Cocka, Daniel J. Perry, Ciara Budd, Aarti Kolluri, Liam Campion, Toshinobu Nishimura, Michael Naso, Hyam Levitsky. Screening iPSC lines for optimal characteristics of differentiation into immune effector cells for clinical programs [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 3613.
Abstract 3640: RAB26 accelerates endometrial cancer cell progression by regulating the Hedgehog signaling pathway
Authors: Gao Chao , Liu Yanyan , Han Yanyan , Xue Fengxia , Wang Yingmei
Published: March 2024

As one of the most common gynecological malignant tumors, endometrial cancer (EC) is continuously being studied since its etiology is still not clear. RAB26, a member of the RAB family, has been shown to influence cell proliferation, metastasis and other malignant phenotypes in several cancers. However, whether and how RAB26 plays roles in EC remain unknown. Our previous study showed that RAB26 was related to the cell cycle-associated protein IK, which has been shown to contribute to carcinogenesis. Herein, we further explored the clinical significance and biological function of RAB26 in EC. Immunohistochemical staining of 615 endometrial tissue samples was conducted to explore whether RAB26 expression was related to the clinicopathological characteristics of EC. In vitro and in vivo experiments were used to evaluate the role of RAB26 in EC and investigate the underlying mechanism. RAB26 expression was higher in EC than in normal endometrium (NE), hyperplastic endometrium (HE) and atypical hyperplastic endometrium (AHE). High RAB26 expression was positively correlated with tumor histological grade (P=0.010), FIGO stage (P=0.042) and tumor size (P=0.003) in EC. RAB26 attenuation inhibited cell proliferation and metastasis but promoted cell apoptosis and caused G0/G1 arrest. After RAB26 attenuation, RNA sequencing data showed that the Hedgehog signaling (SHH) pathway was enriched. Further western blot results confirmed that the levels of SHH pathway proteins (SHH, PTCH1, smo and Gli1) decreased as RAB26 expression was attenuated. Moreover, an agonist of the SHH pathway, purmorphamine, blocked the inhibitory effect of RAB26 attenuation on EC progression. The results of an in vivo study also showed that RAB26 attenuation exerted a significant antitumor effect. Accordingly, RAB26 may act as an oncogenic protein to promote EC progression through the SHH pathway. RAB26 may be a potential target for the treatment of EC patients.

Citation Format: Chao Gao, Yanyan Liu, Yanyan Han, Fengxia Xue, Yingmei Wang. RAB26 accelerates endometrial cancer cell progression by regulating the Hedgehog signaling pathway [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 3640.
Abstract 3667: Nucleic acid quantification in uveal melanoma aqueous humor
Authors: Chang Christina , Pike Sarah , Reid Mark , Peng Chen-Ching , Xu Benjamin , Berry Jesse , Xu Liya
Published: March 2024

Introduction: Uveal melanoma (UM) is the most common primary adult intraocular cancer. Though radiation brachytherapy is often employed for UM treatment, half of UM patients develop systemic metastases. In large tumors with macular involvement, the disease and its treatment can lead to blindness. Clinically, UM prognosis is estimated by tumor size, location, American Joint Cancer Commission (AJCC) staging, and histologic findings. Prognostic UM biomarkers have been established but lesions <2 mm in height, particularly near the fovea, are difficult to biopsy, and thus physicians often do not perform biopsies on such tumors. Therefore, the use of aqueous humor (AH) as a liquid biopsy is a promising methodology. The purpose of the study was to quantify analytes in AH samples collected at diagnosis and post-brachytherapy from UM eyes with varying tumor sizes and AJCC Stages to analyze correlations between analyte (dsDNA, microDNA, and protein) concentrations and tumor features.

Methods: This case series study included 119 UM AH samples from 66 UM eyes and 16 control AH samples collected from age-matched non-UM glaucoma (GLC) eyes analyzed for unprocessed analytes using Qubit fluorescence assays.

Results: Most UM AH samples contained quantifiable analyte concentrations (dsDNA: 94.1%, miRNA: 88.0%, protein: 95.2%) and at higher concentrations than GLC controls (dsDNA, P=0.008; miRNA, P<0.0001; protein, P=0.007). In samples taken at diagnosis, concentrations were higher at more advanced AJCC stages; comparing most advanced Stage III (n=8) to least advanced Stage I (n=24), median dsDNA was 4 times greater (P<0.0001), protein was 3 times greater (P<0.0001), and miRNA was 2 times greater (P=0.001). Analytes were quantifiable in >70% of pre-brachytherapy samples from eyes with tumors <2 mm tall (n=17). Height was positively associated with analyte concentrations at diagnosis (dsDNA: R=0.43, P=0.0007; miRNA: R=0.35, P=0.01; protein: R=0.39, P=0.005). In paired samples (n=53), all analyte concentrations were significantly higher post-therapy compared to diagnosis pre-therapy (Ps<0.01).

Conclusions: Although AH analytes were also quantifiable in smaller, less advanced tumors, AH samples from eyes with larger, more advanced tumors had higher analyte concentrations. The detection of prognostic biomarkers in AH may allow for early UM recognition and guide personalized treatment.

Citation Format: Christina Chang, Sarah Pike, Mark Reid, Chen-Ching Peng, Benjamin Xu, Jesse Berry, Liya Xu. Nucleic acid quantification in uveal melanoma aqueous humor [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 3667.
Abstract 3669: Clinical application of urinary DNA methylation biomarkers for identifying patients with non-muscle invasive bladder cancer
Authors: Bonora Giancarlo , Zhu Ziqi , Gould Billie , Xiang Binggang , Zhou Kemin , Jia Shidong , Li Roger , Du Pan
Published: March 2024

Introduction

Differences in DNA methylation along cell-free DNA (cfDNA) fragments are known to exist between cancer patients and healthy individuals. Profiling these aberrant methylation patterns in urinary cfDNA (ucfNDA) holds great promise for the non-invasive detection and monitoring of bladder tumors, including non-muscle invasive bladder cancer (NMIBC). Here, we analyzed fragment-level DNA methylation patterns in urine samples obtained prior to repeat transurethral resection of a bladder tumor (reTURBT) from a cohort of NMIBC patients. The results were compared to traditional clinical disease assessment and mutation-based tumor fractions. We found a strong concordance between DNA methylation abnormality and clinical diagnosis, as well as tumor fractions, highlighting the potential of epigenetic alterations as a non-invasive indicator of bladder cancer status.

Methods

Patients with high-risk NMIBC (n = 30) were prospectively enrolled prior to reTURBT. The PredicineEPIC™ genome-wide methylation analysis and PredicineBEACON™ MRD profiling was performed on pre-repeat TURBT urine samples. Abnormally methylated genomic fragments were detected against a background model built from a panel of plasma samples from healthy donors.

Results

DNA methylation abnormality was significantly higher (p = 4.8 × 10−6) in samples classified as NIMBC positive by a clinical pathologist (n = 19) compared to negative samples (n = 11), as well as compared to hold-out healthy donor samples (n=24; p = 7.0 × 10−9). Classifying the samples based on a DNA methylation score cut-off derived from healthy donor samples, 24/30 samples showed concordant disease status. Furthermore, DNA methylation abnormality scores correlated positively with mutation-based tumor fractions (r = 0.62), with higher grade samples showing a stronger correlation (r = 0.81; n = 13) than lower grade samples (r = 0.54; n = 17).

Conclusion

We demonstrate the utility of methylation patterns extracted ucfDNA samples obtained prior to reTURBT to detect and monitor NMIBC. Urinary DNA methylation patterns were highly concordant with clinical pathology status and as well as tumor fractions determined from mutation analysis.

Citation Format: Giancarlo Bonora, Ziqi Zhu, Billie Gould, Binggang Xiang, Kemin Zhou, Shidong Jia, Roger Li, Pan Du. Clinical application of urinary DNA methylation biomarkers for identifying patients with non-muscle invasive bladder 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 3669.
Abstract 3733: Gut microbiota-dependent bile acidtaurodeoxycholic acid, TDCAfacilitates anti-tumor immune responses by modulating cytotoxic CD8 T cell immunity
Authors: li Wenng , Wang Hesuiyuan , Coughlin Laura , Poulides Nicole , Valle Priscilla Del , Lichterman Jake , Zhan Xiaowei , Liao Chen , Palmer Suzette N. , Li Xin , Koh Andrew Y.
Published: March 2024

Gut microbiota are critical for effective immune checkpoint blockade therapy (ICT) for cancer. However, the underlying mechanisms by which gut microbiota and/or microbiota-derived metabolites augment antitumor response are largely unknown. Here, we utilized a preclinical melanoma (B16-F10) model and treated groups of mice (Jackson, C57BL/6J, female, 6-8 wks, n=14-26 per group) with seven distinct antibiotic treatments to induce unique gut microbiomes and metabolomes. Mice were then treated with ICT (anti-PD-1 and anti-CTLA-4), resulting in markedly heterogeneous tumor phenotypes (tumor volume and weight) as dictated by the specific antibiotic treatment. Using machine learning (e.g. random forest classifier), we identified metabolite candidates most strongly associated with ICT response (i.e. tumor volume and weight).One metabolite candidate, the bile acid taurodeoxycholic acid, TDCA, had previously been identified by my group as associated with anti-PD-1/anti-CTLA-4 response in human melanoma patients (PMID 28923537). Administration of TDCA alone is sufficient to overcome antibiotic-induced ICT hyporesponsiveness in mice. Utilizing both in vitro/ex vivo immune cell assays and in vivo preclinical models, we have validated that TDCA treatment directly boosted the antitumor cytotoxic CD8+ T cell responses (i.e. IFN-gamma production, anti-tumor cytotoxicity, tumor growth, etc.) without affecting innate immune responses. Bulk RNAseq of CD8 T cell analysis indicated that TDCA modulate CD8 T cell function through IFN pathway. Together, our findings suggest that the gut microbial metabolite TDCA could promote immunotherapy efficacy through regulation of CD8+ T cell immunity and has the potential to be utilized as a novel therapeutic agent to enhance ICT efficacy.

Citation Format: Wenng li, Hesuiyuan Wang, Laura Coughlin, Nicole Poulides, Priscilla Del Valle, Jake Lichterman, Xiaowei Zhan, Chen Liao, Suzette N. Palmer, Xin Li, Andrew Y. Koh. Gut microbiota-dependent bile acidtaurodeoxycholic acid, TDCAfacilitates anti-tumor immune responses by modulating cytotoxic CD8 T cell immunity [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 3733.
Abstract 3735: Combinatorial targeting of tumor-microenvironment together with antigen vaccination using innovative nano-immuno-gel for enhanced cancer-immunotherapy
Authors: Sunilkumar Anjali Kozhissery , Salvi Margaux , Mohammed Saira Nujoom , Zakkariya Zahara Thaivalappil , Cadena Alejandra Gomez , Chappan Shalin , Radhakrishnan Sreedevi Panachithanathu , Manohar Maneesh , Keechilat Pavithran , Nair Shantikumar , Romero Pedro , Jandus Camilla , Koyakutty Manzoor
Published: March 2024

Successful cancer-immunotherapy need to address three critical factors: a) Relieving the immuno-suppressive tumor microenvironment (TME) b) expanding antigen specific, functionally avid effector T cells, c) triggering systemic immunity with a balanced innate-adaptive response for continued effector cell-feeder supply-chain and memory generation. Combinatorial engagement of such multi-elemental components demands smart, engineered immunotherapy systems compared to conventional vaccines. Here, we report an injectable Nano-Immuno-Gel (NIG) that can neutralize immunosuppressive components (e.g., myeloid derived suppressor cells (MDSCs), M2 macrophages (Mϕ) in TME, together with generating strong effector T cells by nano-vaccination, and sustained release of cytokines to enhance systemic immunity against tumor. In a proof-of-concept study, we show that sustained-release of myeloid-suppressive drug from NIG depot efficiently inhibited MDSCs and M2 Mϕ, not only in TME, but also in the circulation and in peripheral systems, thus creating a conducive, hot TME infiltrated with CD8 effector cells. Follow-up antigen vaccination with novel nano-adjuvant enhanced DC-T cell engagement and sustained IL15 release from NIG provided systemic NK/T cell activation, rendering significant control of the tumor growth. Our data demonstrate the potential of rationally engineered multi-functional nano-immuno-gels (NIG) to combine sequential neutralization of the suppressive TME, antigen vaccination, and concurrent systemic immune activation for highly effective combinatorial cancer immunotherapy.

Citation Format: Anjali Kozhissery Sunilkumar, Margaux Salvi, Saira Nujoom Mohammed, Zahara Thaivalappil Zakkariya, Alejandra Gomez Cadena, Shalin Chappan, Sreedevi Panachithanathu Radhakrishnan, Maneesh Manohar, Pavithran Keechilat, Shantikumar Nair, Pedro Romero, Camilla Jandus, Manzoor Koyakutty. Combinatorial targeting of tumor-microenvironment together with antigen vaccination using innovative nano-immuno-gel for enhanced cancer-immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3735.
Abstract 3916: TNG260, a small molecule CoREST inhibitor, sensitizes STK11-mutant NSCLC to anti-PD1 immunotherapy
Authors: Patel Ayushi , Sahu Soumyadip , Geng Ke , Punekar Salman , Stephens Janaye , Deng Jiehui , Chen Ting , Ahronian Leanne , Zhang Minjie , Andersen Jannik , Haines Brian , Wong Kwok-Kin
Published: March 2024

Loss of function (LOF) of the serine-threonine kinase STK11/LKB1, which has been reported in ~15% of non-small cell lung cancer (NSCLC), drives resistance to immune checkpoint therapies such as PD1. In vivo CRISPR screens in tumor-bearing immune competent mice identified the Corepressor of Repressor Element 1 Silencing Transcription (CoREST) complex as a synthetic lethal immune evasion target for STK11- mutant tumors. Here, we demonstrate that TNG260, a small molecule drug specifically targeting the CoREST complex, can sensitize STK11 mutant lung cancers to anti-PD1 immunotherapy. Combination treatment with TNG260 and anti-PD1 arrested KRAS/STK11 mutant NSCLC tumor growth with no major toxicity observed, as confirmed in both allograft and genetically engineered mouse models (GEMMs) of STK11 mutant NSCLC. Further transcriptional analysis via bulk RNA-seq revealed that treatment of KRAS/STK11 mutant lung tumors with TNG260 promotes genes related to inflammatory responses and suppresses genes related to cell cycle and mitotic checkpoint(s). This phenotype was not observed in STK11 wildtype KRAS/P53 mutant lung tumors. Furthermore, combinational treatment of TNG260 with PD1 antibody showed increased macrophages, neutrophils and dendritic cells signatures in vivo. Our data suggests that epigenetic reprogramming via TNG260 sensitizes STK11 mutant NSCLC tumors to anti- PD1 treatment via targeting of the CoREST complex. This work identifies new vulnerabilities in STK11 LOF cancers that can be exploited therapeutically. TNG260 is currently being investigated in combination with pembrolizumab for the treatment of STK11-mutant cancer (NCT05887492), including NSCLC.

Citation Format: Ayushi Patel, Soumyadip Sahu, Ke Geng, Salman Punekar, Janaye Stephens, Jiehui Deng, Ting Chen, Leanne Ahronian, Minjie Zhang, Jannik Andersen, Brian Haines, Kwok-Kin Wong. TNG260, a small molecule CoREST inhibitor, sensitizes STK11-mutant NSCLC to anti-PD1 immunotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3916.
Abstract 393: RAS and PI3K activation promote glioblastoma progression and ischemia-associated tumor cell death
Authors: Kim Soo Yeon , Tang Miaolu , Chih Stephen , Thorpe Jessica , Lu Tong , Wang Hong-Gang , Li Wei
Published: March 2024

Glioblastoma multiforme (GBM) is the most common and aggressive brain tumor in adults. Despite the association of tumor necrosis and a poor prognosis in GBM, the mechanisms underlying tumor necrosis formation remain unclear, likely due to the lack of appropriate experimental models to examine the development of tumor necrosis. In our study, we developed mouse models with tumor necrosis by intracranially injecting human GBM cells expressing KRAS or PI3K active mutants into immunodeficient mice. Surprisingly, despite all tumors displayed similar sizes, the control tumors expressing an empty vector (EV) did not exhibit tumor necrosis. This intriguing observation led us to explore the potential role of KRAS and PI3K in promoting cell death within the tumor microenvironment. Ischemia, which is characterized by insufficient nutrients and hypoxia, is often found in GBM. Under an in vitro ischemia mimetic condition, we found that the KRAS or PI3K activated GBM cells showed more cell death compared to EV cells. Mechanistically, ischemia activates the p38 MAPK-MK2 pathway to induce cell death, a process further enhanced by KRAS or PI3K. Notably, we observed elevated expression of p-MK2 in the peri-necrotic areas of GBMs harboring KRAS or PI3K mutants compared to the cellular tumor zones. Moreover, we revealed that ischemia induces the unfolded protein response (UPR) pathway. Among UPR-related molecules, KRAS and PI3K upregulate ERN1, which encodes the transmembrane protein kinase IRE1, in ischemic conditions. Inhibition of ERN1 not only prevented ischemia-induced cell death but also inhibited the p38 MAPK-MK2 pathway. Furthermore, we observed an increase in the expression of pro-inflammatory cytokine IL-8 under ischemic conditions, a response that was prevented by inhibitors of p38 MAPK or MK2. Lastly, we found that ischemia induces ATP release and calreticulin exposure, indicating the cell death possessing certain immunogenic cell death features. In summary, our findings revealed a pivotal role of KRAS and PI3K in inducing cell death in the ischemic GBM tumor microenvironment through activating the IRE1-p38 MAPK-MK2 pathway. The cell death under this circumstance displays pro-inflammatory and immunogenic properties. Therefore, the IRE1-p38 MAPK-MK2 pathway may be exploited for the treatment of GBM in which RAS or PI3K is activated.

Citation Format: Soo Yeon Kim, Miaolu Tang, Stephen Chih, Jessica Thorpe, Tong Lu, Hong-Gang Wang, Wei Li. RAS and PI3K activation promote glioblastoma progression and ischemia-associated tumor cell death [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 393.
Abstract 3950: Dedifferentiation unveils origin of Ewing sarcoma
Authors: Kapoor Utkarsh , Hafemeister Christoph , Shaw Lisa , Muelbacher Karin , Moldaschl Julia , Egger Dominik , Toegel Stefan , Kasper Cornelia , Farlik Matthias , Halbritter Florian , Kovar Heinrich
Published: March 2024

Ewing sarcoma (ES) is an aggressive pediatric bone tumor in adolescents primarily driven by the expression of the fusion oncogene EWS::FLI1. Although the etiology of ES remains controversial, human mesenchymal stem cells (hMSCs) are considered to be the likely cell of origin. This is not only due to their ability to tolerate ectopic EWS::FLI1 expression, but also because the transcriptome of EWS::FLI1 expressing hMSCs is highly similar to that of primary Ewing tumors. However, to date a cellular differentiation-based model of ES does not exist. With the intent to understand ES histogenesis, this study aims to establish the first comprehensive single-cell differentiation atlas (both transcriptome and epigenome) of juvenile bone marrow-derived hMSCs with and without EWS::FLI1 expression. We sought to study the consequences of inducing the EWS::FLI1 oncogene expression at various time points of hMSC differentiation into adipo-, chondro-, osteo- and neuro-genic lineages. Our workflow utilizes physiology-mimicking conditions including serum-free differentiation, hypoxia, and growth/differentiation as spheroids. We pooled bone marrow-derived hMSCs isolated from eleven healthy juvenile donors, engineered them to conditionally express EWS::FLI1, and carried out multi-lineage differentiation for 10 days where EWS::FLI1 was induced daily for 24h or 72h. This temporally resolved atlas of 105 samples representing normal and perturbed differentiation allowed us to map ES patient tumor data to multiple lineages and time-points across stages of lineage commitment. Single-cell RNA-seq analysis of ~271,000 transcriptomes revealed an apparent and dynamic dedifferentiation in the presence of EWS::FLI1 across all four lineages. Preliminary analysis of genes detected in the EWS::FLI1 high cluster uncovers a specific lineage preference and time window that shares the transcriptomic signature with tumor cells, indicating the potential cell/stage of tumor-origin. Our results provide new insight into the enigmatic cell of origin of Ewing sarcoma, laying the foundation for the development of much-needed pre-clinical models for tailoring therapies. This study is supported by a generous grant (#20) of the Alex’s Lemonade Stand Foundation (ALSF) Crazy8 Program.

Citation Format: Utkarsh Kapoor, Christoph Hafemeister, Lisa Shaw, Karin Muelbacher, Julia Moldaschl, Dominik Egger, Stefan Toegel, Cornelia Kasper, Matthias Farlik, Florian Halbritter, Heinrich Kovar. Dedifferentiation unveils origin of Ewing sarcoma [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 3950.
Abstract 4086: ABN202 (anti-Trop-2-interferon-beta mutein): A potent antibody-cytokine fusion protein for the treatment of Trop-2 positive solid tumors
Authors: Park Hee Geon , Lee Hyun Kyung , Seo Myeung Ryun , Kim Daa Eun , Bang Sang Beom , Lee Ji Yang , Hong Sung Youl , Song Kyoung , Lee Chan Gyu , Jeong Hae Min , Lee Sae Hyung , Kim Na Young , Choi Jun Young , Shin Young Kee
Published: March 2024

Trop-2, trophoblast cell-surface antigen 2, is a type 1 transmembrane glycoprotein overexpressed in many solid cancers, including breast, lung, pancreatic, bile duct and bladder cancer. Overexpression of Trop-2 in cancer patients is associated with disease progression and poor prognosis. The antibody-drug conjugate (ADC) targeting Trop-2, Sacituzumab-govitecan (Trodelvy®), is approved for patients with triple-negative breast cancer (TNBC) and bladder cancer. However, Trop-2 targeting ADCs exhibit a high frequency of grade 3/4 adverse events and a short duration of response. Therefore, there is an unmet medical need for new treatment strategies beyond ADCs. In a previous study, we designed ABN202 (αTrop-2) to comprise a Trop-2 targeting antibody (Sacituzumab) and IFN-β mutein (ABN102) for the Trop2-positive tumor-specific delivery of ABN102. We confirmed anti-cancer activities of ABN202 against Trop-2 positive bladder cancer. In this study, we evaluated in vitro and in vivo anti-cancer efficacy of ABN202 (αTrop-2) in Trop-2 positive TNBC, bile duct cancer and bladder cancer cell lines. To identify response biomarkers for ABN202 (αTrop-2), we analyzed cell lines exhibiting both response and non-response to ABN202 (αTrop-2). In conclusion, ABN202 (αTrop-2) demonstrated potent anti-cancer efficacy compared to Trodelvy®. Our results support ABN202 (αTrop-2) as a promising drug candidate against Trop2-positive solid tumors.

Citation Format: Hee Geon Park, Hyun Kyung Lee, Myeung Ryun Seo, Daa Eun Kim, Sang Beom Bang, Ji Yang Lee, Sung Youl Hong, Kyoung Song, Chan Gyu Lee, Hae Min Jeong, Sae Hyung Lee, Na Young Kim, Jun Young Choi, Young Kee Shin. ABN202 (anti-Trop-2-interferon-beta mutein): A potent antibody-cytokine fusion protein for the treatment of Trop-2 positive solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4086.
Abstract 417: Chromosomal instability leads to durable tumor suppression upon macrophage-checkpoint disruption, with induction of anti-tumor IgG
Authors: Discher Dennis E.
Published: March 2024

Solid tumors generally exhibit chromosome copy number variation caused by chromosomal instability (CIN) in mitosis, and the resulting aneuploidy associates with poor prognosis in various cancer types and poor Tcell checkpoint blockade response in melanoma. In such contexts, however, macrophages and the SIRPa-CD47 checkpoint are understudied. Here, CIN is induced pharmacologically in poorly immunogenic B16F10 mouse melanoma cells, generating micronuclei plus diverse aneuploidy and skewing macrophages towards an anti-cancer phenotype based on markers and short-term tumor studies. Mice bearing CIN-afflicted tumors with wild-type CD47 levels survive only slightly longer compared to chromosomally stable controls, but long-term survival can be maximized when anti-tumor IgG opsonization is combined with adoptive transfer of macrophages with SIRPa blockade or with CD47 knockout of the B16F10. Multi-epitope, de novo anti-cancer IgG in survivors promote phagocytosis of CD47 knockout B16F10 cells by macrophages and suppress tumoroids in vitro and growth of tumors in vivo. An unexpected benefit of pairing CIN with maximal macrophage anti-cancer activity is thus an anti-cancer vaccination-like response that can lead to durable cures and potentiate cell-mediated acquired immunity.

Citation Format: Dennis E. Discher. Chromosomal instability leads to durable tumor suppression upon macrophage-checkpoint disruption, with induction of anti-tumor IgG [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 417.
Abstract 4192: In-depth evaluation of chemotherapy-induced mucositis in intestinal organoids using holotomography
Authors: Lee Mahn Jae , Lee Jaehyeok , Park Weisun , Kim Geon , Kim Hye-Jin , Park YongKeun
Published: March 2024

Intestinal mucositis is a prevalent adverse event associated with antineoplastic therapies, such as chemotherapy, which still lacks a targeted and effective treatment regimen. The difficulty in preclinical prediction and prevention of drug-induced intestinal mucositis is attributed to the intricate underlying mechanisms of its onset and the broad spectrum of patient-specific responses to chemotherapeutic agents. Advancements in regenerative medicine have enabled the generation of intestinal organoids from adult stem cells, serving as a personalized model to emulate disease pathology and simulate individual drug responses. Various imaging techniques are employed to evaluate the responses of the organoids to pharmacological agents, but the inherent complexity of their three-dimensional (3D) architecture poses significant challenges in organoid imaging. These challenges are exacerbated by the standard preparation processes for imaging, including fixation and staining, which do not allow for the observation of dynamic, real-time effects of drugs on living organoids. In this study, we focused on meticulously examining the histopathological alterations in small intestinal organoids subjected to chemotherapeutic agents that induce mucositis, specifically 5-fluorouracil and irinotecan. Employing holotomography, a label-free real-time 3D imaging technology, we were able to visualize the destructive processes affecting the intestinal organoids, including the breakdown of the epithelial lining, the exfoliation of dead cells, and the alteration of the villus/crypt structure. Furthermore, we propose a novel methodology for quantifying the viability of intestinal organoids. This quantification is essential for assessing the extent of damage caused by the chemotherapeutic agents and for determining the maximum drug concentrations that can be deemed safe for use, thereby minimizing the risk of inducing mucositis while maintaining therapeutic efficacy. These results provide new insights into the toxic mechanisms of chemotherapeutic drugs and highlight the importance of using organoid models in drug safety evaluation throughout the development phase.

Citation Format: Mahn Jae Lee, Jaehyeok Lee, Weisun Park, Geon Kim, Hye-Jin Kim, YongKeun Park. In-depth evaluation of chemotherapy-induced mucositis in intestinal organoids using holotomography [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 4192.
Abstract 4284: Macrophage reprogramming and immune suppression through extracellular vesicles loaded eIF4A1in ovarian cancer
Authors: Mittal Sonam , Kadamberi Ishaque Pulikkal , Kumar Sudhir , George Jasmine , Singh Mona , Geethadevi Anjali , Chaluvally-Raghavan Pradeep , Pradeep Sunila
Published: March 2024

Background- In ovarian carcinoma (OvCa), macrophages are reprogrammed toward pro-tumorigenic phenotypes, including releasing anti-inflammatory cytokines and expressing immunosuppressive molecules. However, how these macrophages acquire their phenotype remains largely unexplored. To understand the mechanism driving pro-tumorigenic phenotype in macrophages, we studied the role of tumor cell-derived extracellular vesicles (EVs) in the cross-talk with macrophages in OvCa. We found that EVs from ovarian cancer cells contain eukaryotic translation initiation factor 4A1 (eIF4A1). eIF4A1 containing EVs from ovarian cells enhanced macrophage translational activity and PD-L1 expression. However, the detailed mechanism that explains how eIF4A1-packaged EVs induce immunosuppressive phenotype in macrophages is necessary to develop novel immunotherapy strategies for advanced OvCa treatment.

Methods- We performed SUnSET assay (surface sensing of translation) to determine whether eIF4E-EVs affect global translation in macrophages. SILAC (Stable isotope labeling by amino acids) based mass spectrometry was used to identify the downstream targets of eIF4A1 in macrophages. We isolated murine peritoneal macrophages from naïve C57BL/6 female mice and co-cultured the macrophages with EVs derived from ovarian cancer cell lines. The expression of PD-L1, CD206, interleukin-6 (IL-6), and other inflammatory cytokines on EVs treated macrophages was evaluated using flow cytometry and a cytokine array kit. Further, we created a Rab27aKO ovarian cancer in vivo model to study the effect of eIF4A1 packaged EVs on the immune suppressive ability of macrophages and tumor progression.

Results- Our study shows that tumor cells employ EVs to deliver eIF4A1 to the tumor microenvironment, facilitating the release of cytokines such as IL-6 and the expression of PD-L1 on macrophages and supporting tumor growth. In addition, our data shows that eIF4A1-EVs enhance protein synthesis in macrophages. Our data show that in the Rab27aKO ovarian cancer in vivo mouse model, intravenous injection of eIF4A1-packaged EVs increased the tumor burden, metastasis, and ascites accumulation as compared to PBS control. eIF4A1-EVs treatment increased the infiltration of tumor-associated macrophages (TAM) in ascites. We also found increased expression of PD-L1 and CD206 on TAM isolated from ascites

Citation Format: Sonam Mittal, Ishaque Pulikkal Kadamberi, Sudhir Kumar, Jasmine George, Mona Singh, Anjali Geethadevi, Pradeep Chaluvally-Raghavan, Sunila Pradeep. Macrophage reprogramming and immune suppression through extracellular vesicles loaded eIF4A1in ovarian 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 4284.
Abstract 4287: Serological quantification of fibroblast activation protein (FAP) cleaved type III collagen: A biomarker for FAP activity
Authors: Pedersen Rasmus Sund , Karsdal Morten , Willumsen Nicholas
Published: March 2024

Introduction: Fibroblast activation protein (FAP) has unique proteolytic activity with very low expression in healthy tissues, while being upregulated in diseased tissues including many types of cancer for example non-small cell lung cancer (NSCLC). The disease specific expression and unique proteolytic activity have made FAP an interesting protein to be utilized for drug targeting purposes. Therefore, it is important to identify the patients with FAP activity. The aim of the study was to develop a tool to non-invasively quantify FAP activity and investigate its potential as a biomarker for patients with NSCLC.

Methods: We developed an ELISA (named C3F), with monoclonal antibodies raised against a FAP generated fragment of type III collagen that was identified by MS, to quantify FAP-mediated cleavage of type III collagen in serum to reflect proteolytic activity of FAP. We confirmed that the biomarker reflects proteolytic activity of FAP by incubating type III collagen with or without FAP and measured C3F. In addition, we confirmed elevated FAP expression in NSCLC (adenocarcinoma and squamous cell carcinoma) compared to healthy tissue and correlation between FAP and COL3A1 expression using data from The Cancer Genome Atlas (TCGA). The comparisons between FAP expression in healthy and cancer tissue was done using one-way ANOVA and correlation between FAP and COL3A1 was done using Spearman correlation. Lastly, C3F was measured in serum samples from patients with NSCLC (n = 109) and healthy controls (n = 42) and the two groups was compared using Mann Whitney test and area under receiver operating characteristic curves (AUROCs).

Results: A C3F signal only appeared after type III collagen incubation with FAP, supporting that C3F reflects FAP proteolytic activity. C3F was significantly elevated in serum from patients with NSCLC compared to healthy controls (p < 0.0001, AUROC = 0.78). In support, FAP expression (TCGA) was significantly elevated in NSCLC tissue compared to normal lung tissue (p < 0.0001) and FAP expression correlated with expression of COL3A1 (persons r = 0.83).

Conclusion: The FAP-cleavage mediated type III collagen fragment C3F reflects FAP activity and can be quantified non-invasively in serum. In this study we show C3F as promising diagnostic biomarker in NSCLC, however as the biomarker reflects FAP activity the optimal use is more is potentially as a predicter of treatment response from FAP-based drug delivery systems.

Citation Format: Rasmus Sund Pedersen, Morten Karsdal, Nicholas Willumsen. Serological quantification of fibroblast activation protein (FAP) cleaved type III collagen: A biomarker for FAP activity [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 4287.