bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 3378: Acinar cell susceptibility for tumor development in the pancreas: Targeting the critical regulators for therapy
Authors: Pan Zhaolong , Bossche Jan-Lars Van den , Rodriguez-Aznar Eva , Janssen Pauline , Lara Olaya , Ates Gamze , Massie Ann , De Paep Diedert Luc , Houbracken Isabelle , Mambretti Marco , Rooman Ilse
Published: March 2024

Acinar to ductal metaplasia (ADM) or acinar cell dedifferentiation is one of the most notable features of chronic pancreatitis. It is also considered the initial step of pancreatic cancer development when oncogenic mutations accumulate. However, its precise mechanism and regulatory pathways remain unclear. This study profiled the transcriptome of dedifferentiated acinar cells from both humans and mice. Differential expression analysis integrated with a systematic literature search revealed several potential regulators (e.g., GDF15, GFRA1, MXRA5, CXCL17), of which the expression pattern over time was validated by qRT-PCR. We also focused on multiple conserved pathways of cell survival, among which SLC7A11 (xCT) is transiently upregulated in both species. The xCT subunit, integral to the cystine/glutamate antiporter system xc-, plays a critical role in cell survival across various cell types. To elucidate its role in acinar dedifferentiation, we employed gene silencing, pharmacological inhibition, and a knock-out mouse model. Acinar cells with diminished xCT function exhibit increased ferroptosis linked to lipid peroxidation. Antioxidants such as N-acetylcysteine and ferroptosis inhibitors like Ferrostatin-1 can mitigate lower glutathione levels and lipid ROS accumulation. Similarly, in mouse acute pancreatitis, xCT prevents lipid peroxidation. Our findings indicate that xCT fuels the glutathione pool and maintains ROS balance during ADM, thereby preventing pancreatic acinar cells from ferroptosis, a form of cell death rarely reported in relation to ADM. Next to xCT, a future and similar comprehensive study of the aforementioned genes could provide valuable insights into the dynamic changes that occur during acinar cell dedifferentiation and pave the way to the discovery of new intervention targets to suppress tumorigenesis in chronic pancreatitis.

Citation Format: Zhaolong Pan, Jan-Lars Van den Bossche, Eva Rodriguez-Aznar, Pauline Janssen, Olaya Lara, Gamze Ates, Ann Massie, Diedert Luc De Paep, Isabelle Houbracken, Marco Mambretti, Ilse Rooman. Acinar cell susceptibility for tumor development in the pancreas: Targeting the critical regulators for therapy [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 3378.
Abstract 339: Universal synthetic TCR/BCR spike-in controls to evaluate immune receptor profiling assay and next-generation sequencing performance
Authors: Chenchik Alex , Liu Tianbing , Makhanov Mikhail , Hu Dongfang , Ghias Khadija , Diehl Paul
Published: March 2024

Adaptive immune receptor (AIR) repertoire diversity assays are susceptible to biases arising from variations in conditions in the RT-PCR and next-generation sequencing (NGS) steps. We designed synthetic TCR and BCR spike-in controls to mitigate these biases and to serve as universal standards for any PCR-based immune receptor profiling assay. We synthesized 48 BCR constructs representing different IGH, IGK, and IGL genes and 39 TCR constructs for TRB, TRA, TRG, and TRD genes. The spike-in controls were tested as (16 × 3) BCR constructs and (13 × 3) TCR Triplex isoform pools added to multiple samples in the same batch to detect cross-contamination across samples. We successfully discriminated between controls and background sequences by combining a unique molecular identifier (UMI)-based correction strategy with spike-in controls at the data analysis step. We also tested 48 BCR and 39 TCR Premixed Controls by spiking into peripheral blood mononuclear cells (PBMC) RNA samples before reverse transcription using Cellecta’s DriverMap™ Adaptive Immune Receptor Profiling Assay that uses a multiplex RT-PCR approach with gene-specific primers and UMIs. We successfully used it to evaluate assay performance by adding premixed controls at different concentrations. Results showed a linear trend as the number of spike-in molecules increased. Our analysis revealed an average sequencing error rate of 0.4%-0.8% per base, aligning with the reported error rate range of Illumina sequencing. This suggests the reliability of our spike-in controls, which can be used to rectify biases in the AIR protocol and accurately estimate error and mutation rates for the DriverMap AIR assay or any other sequencing-based immune receptor profiling assay. This innovative approach enhances the robustness of immune receptor profiling technology, facilitating more accurate assessments of repertoire diversity.

Citation Format: Alex Chenchik, Tianbing Liu, Mikhail Makhanov, Dongfang Hu, Khadija Ghias, Paul Diehl. Universal synthetic TCR/BCR spike-in controls to evaluate immune receptor profiling assay and next-generation sequencing performance [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 339.
Abstract 3393: Deciphering colorectal cancer: A model to study sex-based differences and role of estrogen amidst obesity
Authors: Wele Prachi , Shi Haifei , Wu Xian
Published: March 2024

Worldwide statistics indicate that obesity is increasing globally, mostly due to the consumption of Western diet. The literature points out that obesity is a potent risk factor for the development of colorectal cancer (CRC). Interestingly, CRC incidence is higher in men compared to women, and the sex hormone estrogen protects reproductive-age females from CRC despite obesity. In this project, we aim to understand the sex-based differences and protective role of estrogen in obesity-influenced CRC. An improved mouse model was devised where the effects of obesity and estrogen in CRC could be meticulously studied. We deployed 4-5-week-old male and female FVB/NJ mice and performed either sham surgery (males and females) or bilateral ovariectomy (OVX) (females). Post one week of recovery, all mice were randomly sub-grouped into either low-fat diet (LFD, 10% fat) or high-fat diet (HFD, 60% fat) groups, weekly injected with a colon-specific carcinogen azoxymethane (AOM; 5 mg/kg for week 1, 10 mg/kg for weeks 2-6), and cyclically every 4-5 days injected 17-beta-estradiol (E2; 4 μg/mouse) to a group of OVX mice for the study period of 22 weeks. The body weight of all mice was tracked every week. A whole-body composition analysis after 22 weeks showed that males and OVX females are more obese compared to females with sham surgery and OVX females with E2 injection (OVX+E2), respectively. Additionally, mice on HFD had a higher body weight compared to those on LFD; however, the absence of estrogen in OVX females led them to have higher body weight compared to sham and OVX+E2 females. Moreover, a significant difference was observed in the tumor size between males and females, females and OVX females, and OVX and OVX+E2 females. Study models have rarely incorporated both sex-dependent differences and diet-induced obesity in understanding CRC. With the current study model, it is anticipated to learn more about these differences at molecular, cellular, and metabolic levels. Acknowledgments: 1) NIH/NCI R15 [To HS, XW]; 2) Miami University CFR Faculty Research Grants [To HS, XW, JZ]; 3) Miami University's College of Education, Health, and Society Interdisciplinary Research Seed Grant [To HS, XW, JZ]; 4) Sigma Xi Grants in Aid Research [To PW]; and 5) We thank Jazzminn Hembree (Director of Laboratory Animal Resources, Miami University) and Laboratory Animal Resources, Dr. Jiangjiang Zhu (Department of Human Sciences, Ohio State University), Dr. Jing Zhang (Department of Statistics), and Dr. Ramiro Malgor (Director of Histology Core Facility, Ohio University)

Citation Format: Prachi Wele, Haifei Shi, Xian Wu. Deciphering colorectal cancer: A model to study sex-based differences and role of estrogen amidst obesity [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 3393.
Abstract 3395: Polyisoprenylated cysteinyl amide inhibitors: Effects on RAS signaling pathway intermediates and viability of mutant KRAS African American lung cancer cell line
Authors: Mensah-Mamfo Justin K. , Ofosu-Asante Kweku , Lazarte Jassy Mary , Burra Amarender Goud , Lugo Sofia A. , Huang Yong , Offringa Ite A. , Lamango Nazarius S.
Published: March 2024

Mutated KRAS is the most common cancer driver gene in lung adenocarcinomas in all racial and ethnic groups, including Blacks/African Americans (B/AAs). Drugs developed to combat KRAS-driven cancers become less effective due to intrinsic changes in the cells resulting in resistance and relapse. Due to the enormous challenges encountered in developing direct KRAS inhibitors, agents targeting alternative downstream RAS mediator kinase enzymes of the MAPK and PI3K/AKT signaling pathways have been developed. However, other avenues that directly target KRAS and similar cancer drivers must be explored to obtain alternative effective therapies. PCAIs constitute a group of potential anticancer agents that we developed to specifically disrupt and suppress signaling by hyperactive G-proteins such as mutated KRAS. In previous studies, PCAIs stimulated MEK1/2, ERK1/2, p90RSK and AKT phosphorylation resulting in cell death. The present study aims to determine whether specific inhibitors of the kinases can reverse PCAIs-stimulated phosphorylation and cell death. PCAIs were thus tested against the KRAS mutant NCI- cell line H23 (from a B/AA patient) and compared to KRASG12C inhibitor Sotorasib and other kinase inhibitors drugs. The EC50 values for the PCAIs NSL-YHJ-2-27 and NSL-AB-45 were 4.1 ± 0.3 and 5.5 ± 0.1 μM, respectively, compared to Gefitinib (EGFR), Sotorasib (KRASG12C), Dabrafenib (BRAF), Selumetinib (MEK1/2), Ulixertinib (ERK1/2) and Ipatasertib (AKT) whose EC50 values were 83 ± 12.9 μM, 38 ± 5.5 μM, 33 ± 1.2 μM, 71 ± 5.3 μM, 11 ± 0.2 μM, 12 ± 1.0 μM, respectively. The results indicate that the PCAIs are more effective against NCI-H23 than the other kinase inhibitor drugs. Future work will determine the effects of co-treating cells with the PCAIs and the respective kinase inhibitors on cell viability and PCAIs-induced phosphorylation of the kinases. Supported by grants U54CA233396, U54CA233444, and U54CA233465 from the National Institutes of Health (NIH)/National Cancer Institute (NCI) and the Norris Comprehensive Cancer Center core grant, award number P30CA014089 from the NIH/NCI

Citation Format: Justin K. Mensah-Mamfo, Kweku Ofosu-Asante, Jassy Mary Lazarte, Amarender Goud Burra, Sofia A. Lugo, Yong Huang, Ite A. Offringa, Nazarius S. Lamango. Polyisoprenylated cysteinyl amide inhibitors: Effects on RAS signaling pathway intermediates and viability of mutant KRAS African American lung cancer cell line [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 3395.
Abstract 3457: Distinct signatures of tumor-associated macrophage subpopulations predict survival in renal cell carcinoma
Authors: Han Youngsoo , Shen Aidan , Wang Zhaohui , Garrett Aliesha , Jiang Chongming
Published: March 2024

Background: Comprising 90% of renal cancer cases in adults, renal cell carcinoma (RCC) is marked by significant heterogeneity in its tumor microenvironment. This study aims to test the hypothesis that tumor-associated macrophages (TAMs) play a role in modulating RCC progression and patient response to treatment. We explored the prognostic implications of TAM signatures on RCC survival, leveraging immunomics to decipher TAM-related alterations in the tumor microenvironment.

Methods: Utilizing independent single-cell RNA-seq data from human RCC samples, we crafted 8 distinct RCC TAM signatures reflective of TAM presence. A LASSO Cox regression model was developed to prognosticate survival, tested against the TCGA dataset and independently validated across multiple RCC cohorts. Model performance was corroborated through Kaplan-Meier survival plots, receiver operating characteristic (ROC) curves, principal component analysis, and t-SNE analyses.

Results: We identified two TAM signatures that correlate positively with patient survival, indicative of the abundance of specific subsets of TAMs in RCC. These signatures showed a strong association of specific TAM markers and macrophage infiltration. Survival analysis demonstrated that specific TAM signature gene expressions are significant prognostic markers. Forest plots underscored their prognostic relevance. A 32-gene risk score model was established, successfully stratifying patients into distinct risk categories, with low-risk patients exhibiting markedly improved overall survival.

Conclusions: The study underscores the positive association between abundance of specific TAM subsets of and RCC patient survival. The precision of our LASSO Cox regression model, informed by novel abundance markers of specific TAM subsets, advances our understanding of TAM roles in TIME and RCC progression. These TAM signatures could potentially provide additional insights and targets to enhance the efficacy of RCC treatments.

Keywords: Tumor associated macrophage, renal cell carcinoma, prognosis, tumor microenvironment, immunomics.

Citation Format: Youngsoo Han, Aidan Shen, Zhaohui Wang, Aliesha Garrett, Chongming Jiang. Distinct signatures of tumor-associated macrophage subpopulations predict survival in renal cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3457.
Abstract 3501: Concurrent amplification of TBXT and highly activated enhancers in extrachromosomal DNA (ecDNA) drives chordoma tumorigenesis
Authors: Zhao Bo , Ines Martin Barrio , Ye Lingqun , Wu Xizi , Soragni Alice , Futreal Andrew , Akdemir Kadir
Published: March 2024

Chordoma, a rare bone cancer characterized by limited actionable clinical targets, exhibits a pivotal hallmark in the activation of the developmental transcription factor gene TBXT (Brachyury) through its association with highly active enhancers. TBXT amplification emerges as a major causative factor in familial chordomas, yet the amplification mechanism and its consequential impact on genomic instability remain inadequately elucidated. In this study, we conducted a comprehensive analysis of multiple genomic and epigenomic sequencing datasets, including WGS-seq, H3K27ac ChIP-seq, and ATAC-seq in six chordoma cell lines, and HiC data in two of them, to unravel the mechanisms of structural variations and their biological implications. Notably, our focus extends to JHC7 cells, which exhibit extrachromosomal amplification of a 2.4M region encompassing TBXT and the associated enhancers. The existence of such extrachromosomal DNA (ecDNA) in JHC7 was further validated through DNA FISH and Sanger sequencing. Comparing JHC7 with CH22, a chordoma cell line lacking TBXT amplification, revealed heightened chromatin relaxation and increased DNA rearrangements in JHC7. Interestingly, FISH results showed significant genomic ploidy heterogeneity within JHC7 cells, a finding demonstrated by nucleus FACS sorting. Single-cell multiomic analysis, combining snRNA-seq and snATAC-seq, demonstrated heterogeneous gene expression and distinct copy number variations among JHC7 cells. However, the amplification of the TBXT locus was observed in nearly all cells examined, indicating the rapid genomic evolution in the cultured JHC7 cells. These results collectively show that TBXT is extensively amplified through the formation of ecDNA, providing a fitness advantage to chordoma cells and concurrently exacerbating genomic instability. The findings in this study provide an insight for understanding the pathogenesis of chordoma and may inform the development of targeted therapeutic strategies.

Citation Format: Bo Zhao, Martin Barrio Ines, Lingqun Ye, Xizi Wu, Alice Soragni, Andrew Futreal, Kadir Akdemir. Concurrent amplification of TBXT and highly activated enhancers in extrachromosomal DNA (ecDNA) drives chordoma tumorigenesis [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 3501.
Abstract 3521: Robust inference of PTEN deletion in prostate cancer from routine histopathology whole slide images using attention-based deep learning
Authors: Scarfò Federico , Omar Mohamed , Marchionni Luigi
Published: March 2024

The diagnostic workup of prostate cancer (PCa) requires a thorough manual histopathological inspection of prostate tissue specimens stained with hematoxylin and eosin (H&E). While immunohistochemistry and advanced molecular tests like FISH could uncover key genetic alterations, they are not cost-effective and often require special training, necessitating the development of more effective tools that can accurately infer the status of such alterations directly from the tissue morphology depicted in routine H&E-stained glass slides. PTEN deletion, which is present in 15-20% of PCa, is significantly associated with tumor aggressiveness and negative prognostic impact. Deep learning (DL) models can be trained to predict the presence of PTEN deletion on routine whole slide images (WSIs) and select patients that could benefit from further treatment. In this study, we trained and tested the performance of a weakly supervised, multiple-instance learning network on a cohort of 449 WSIs radical prostatectomy specimens stained with hematoxylin & eosin. Our model demonstrated robust performance in predicting PTEN loss based on tumor morphology alone. Through the model, we also generated attention heatmaps of the most informative tiles of each slide, allowing us to quantify the different cellular components, thus inferring the morphological features associated with PTEN loss. This study shows that DL is a potential tool that can assist the pathologist in accurately inferring the molecular status of key genetic alterations using the tissue morphology depicted in histopathology slides. Moreover, the morphological information that can be obtained by attention-based models can be leveraged to close the gap between the pathologist’s morphological analysis and the interpretability of artificial intelligence models.

Citation Format: Federico Scarfò, Mohamed Omar, Luigi Marchionni. Robust inference of PTEN deletion in prostate cancer from routine histopathology whole slide images using attention-based deep learning [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 3521.
Abstract 3533: Spatially Resolved Laser-Activated Cell Sorting (SLACS) and AI integration for enhanced pathological analysis and biomarker discovery
Authors: Jang Haewook , Lee Amos Chungwon , Lee Sumin , Kwon Sunghoon
Published: March 2024

This study focuses on the integration of Artificial Intelligence (AI) with Spatially Resolved Laser-Activated Cell Sorting (SLACS) for enhanced pathological analysis and biomarker discovery. The primary approach involves using AI to automatically analyze slide images, identifying critical areas associated with diseases such as cancer or cells emitting specific signals. AI algorithms efficiently segment these significant regions or cellular groups, facilitating targeted analysis.

Following the AI-driven segmentation, SLACS comes into play, isolating the identified cells from the slide for further examination. This precise sorting allows for the focused study of cells relevant to disease processes, enhancing the efficiency and accuracy of pathological analysis.

The separated samples obtained through SLACS are then subjected to detailed analysis. This step is crucial for understanding the cellular mechanisms at play in disease states and for the identification of potential biomarkers. These biomarkers are vital for developing targeted therapeutic strategies and advancing personalized medicine.

By combining AI's advanced image processing and pattern recognition capabilities with the precision of SLACS, this integrated approach significantly improves the identification and analysis of disease-related cellular characteristics. It streamlines the process of isolating and studying specific cell populations, contributing to a deeper understanding of disease mechanisms and progression.

In conclusion, the synergistic application of AI and SLACS represents a significant advancement in pathological research and biomarker discovery. This methodology not only enhances the accuracy of disease marker identification but also opens new avenues for research and clinical application.

Citation Format: Haewook Jang, Amos Chungwon Lee, Sumin Lee, Sunghoon Kwon. Spatially Resolved Laser-Activated Cell Sorting (SLACS) and AI integration for enhanced pathological analysis and biomarker discovery [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 3533.
Abstract 3545: Atlas of therapeutic targets: Evolution of druggable proteome
Authors: Babic Ivan , Nurmemmedov Elmar
Published: March 2024

Selection of therapeutic targets and modalities is of fundamental importance in drug discovery, as it can have a direct impact on the economics of drug discovery as well as its success rate. With the advancement of chem-bio and proteomics methods together with advent of artificial intelligence, the scope of the druggable proteome is expanding. The choice of drug targets gains further importance as we link it to potential clinical efficacy and safety, genetic variation and patient populations. Drug targets are often selected based on inadequate understanding of target biology, tractability by existing toolbox of therapeutic modalities and insufficient insight into possible clinical outcome. We have developed an “Atlas of Therapeutic Targets”, an interactive resource that provides classification of drug target families with linked information on clinical and investigational drugs. The atlas also provides key insights and score for tractability of targets with various therapeutic modalities. Particularly, our scoring system grades the targets on dimensions such as ligandability, involvement in protein-protein complexes, structural disorder, hotspot analysis and cross-referencing with known targets, thus yielding a total tractability score of 1-10. Dissection of targets based on such dimensions, enables critical evaluation therapeutic modalities as well tools and methodologies needed for their conversion into successful drug discovery programs. We curate 900+ human drug targets, analysis of which indicates the continued dominance of privileged target families across disease areas, but also the growth of novel first-in-class mechanisms. This atlas will be available as a resource for the wide drug discovery community.

Citation Format: Ivan Babic, Elmar Nurmemmedov. Atlas of therapeutic targets: Evolution of druggable proteome [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 3545.
Abstract 3549: PMed-TRIAL PDX database: Integrated multidimensional information to facilitate new drug development
Authors: Chen Xinlei , Guo Youbin , Van Loc , Caggiula Josh , Gu Xiaorong , Wen Danyi
Published: March 2024

PDX models play a crucial role in pre-clinical research for new drugs. In recent years, research based on PDX models has entered the 'Big Data Era.' On the one hand, there are numerous factors influencing drug responses, such as cancer types, genetic backgrounds, clinical treatment histories, and more. Therefore, selecting the appropriate PDX models for drug efficacy testing based on relevant information has become increasingly important. On the other hand, conducting in-depth genomics and transcriptomics analyses on PDX models allows us to gain a deeper understanding of the mechanisms of drug efficacy and drug sensitivity. After years of effort, LIDE have successfully built and maintained over 1800 PDX models from 40 different cancer types. And in this year (2023), we launched LIDE’s PMed-TRIAL PDX database website. As a comprehensive database of PDX models, it includes fundamental PDX clinical information, medication history, growth curves, and standard of care (SOC) data. It also contains whole exome sequencing data and RNA-seq data. Cancer is a complex and heterogeneous disease characterized by tumor heterogeneity, encompassing both inter-tumor diversity (between patients) and intra-tumor variability (within a single patient), thereby complicating drug responsiveness. PDX models preserve heterogeneity of individual patients, and a robust PDX cohort is essential for accurately representing inter-tumor heterogeneity. LIDE’s PDX cohorts effectively capture representative molecular subtypes across various major cancer types, highlighting their potential as a valuable resource for pre-clinical trials. LIDE’s PMed-TRIAL PDX database comes with a concise and efficient web user interface. Users can search and filter models using keywords, such as drug names, gene symbols, and other information. The website can now be accessed via the following URL (https://pmed.lidebiotech.com:8000/).

Citation Format: Xinlei Chen, Youbin Guo, Loc Van, Josh Caggiula, Xiaorong Gu, Danyi Wen. PMed-TRIAL PDX database: Integrated multidimensional information to facilitate new drug development [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 3549.
Abstract 3553: OralDB, A integrative data portal for oral and oropharyngeal cancer omics and clinical research
Authors: Wang Junlin , Lam Pui Ying , Su Yuxiong , Wang Junwen
Published: March 2024

Oral and oropharyngeal cancer is one of the more common cancers worldwide, with a poor prognosis in advanced stages and a higher incidence in Asian populations than in other regions. Its affected Affected areas include the lips, gums, tongue, the inside of the cheeks, the roof of the mouth, the floor of the mouth, the tonsils, and the oropharynx. Currently, the distribution of RNA expression data and clinical data in oral and oropharyngeal cancer is fragmented, impeding effective data mining for the discovery of novel biological markers and testing of new hypotheses. We constructed an oral and oropharyngeal cancer-specific database with expression dataRNA expression and clinical data from more than 4,356 patients in 41 studies. The RNA Expression data from 23 genome-wide platforms are carefully processed and quality-controlled, while clinical data is standardized and tightly managed. With the support of this oral and oropharyngeal cancer-specific database oral cancer-specific database, we have created an open-access web resource, the Oral and Oropharyngeal Cancer Browser, to facilitate researchers interested in oral and Oropharyngeal cancer to quickly access and analyze all currently published RNAoral cancer expression data and clinical data. Users can perform a meta-analysis of Oral and oropharyngeal oropharyngeal cancer to quickly understand the results of tumor versus non-malignant tissue (normal), differential gene expression, and expression-survival associations. Flexible options for survival analysis, comparative analysis, and correlation analysis based on a single dataset are also available. At the same time, the database also accepts the user's own input data and allows the user to do theircarry out their own analysis by combining the input data with the existing data in the database.

Citation Format: Junlin Wang, Pui Ying Lam, Yuxiong Su, Junwen Wang. OralDB, A integrative data portal for oral and oropharyngeal cancer omics and clinical research [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 3553.
Abstract 3563: Multi-modal mutational signatures elucidate the comprehensive consequences of mutational processes
Authors: Steele Christopher D. , Alexandrov Ludmil , Khandekar Azhar
Published: March 2024

The development of mutational signatures defined individually in the contexts of single/double base substitutions, insertions and deletions, structural variants and copy number variation have led to improved understanding of cancer mutagenesis and potential for improved patient stratification. We hypothesized that combining these contexts into a multi-modal mutational signature framework may improve the accuracy of assigning mutational processes to samples, and provide a holistic view of the full repertoire of mutations conferred from such processes. In order to develop multi-modal signatures, bespoke feature engineering was required for each mutational modality to enhance signal, in addition to individual modality matrix normalization so that the data could be harmonized and analyzed as a whole. These methods, and subsequent signature extraction were developed on 2,438 whole genome sequenced cancers from 21 distinct cancer types from the PCAWG consortium for which all modalities of data were available, incorporating a 348 channel signature definition. Deployment of these methods identified multi-modal signatures that encompass multiple mutation types known to associate with specific processes, for example SBS, indel and rearrangement channels defining a signature of homologous recombination deficiency. In contrast, some signatures remain defined by a single mutational modality, highlighting the distinction between broadly mutational processes, and more focused mutation processes. Multi-modal signatures show promise in increasing accuracy for difficult to assign signatures, such as those for homologous recombination deficiency, and therefore in improving patient stratification for life-saving treatment.

Citation Format: Christopher D. Steele, Ludmil Alexandrov, Azhar Khandekar. Multi-modal mutational signatures elucidate the comprehensive consequences of mutational processes [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 3563.
Abstract 357: Reducing reagent-resistant transferrin receptor 1 dimer is a specific marker for ferroptosis
Authors: He Jianping , Kelleher Mackenzie , Reynolds Lucas , Tanczos Hannah , Huang Zhengrong , McLaughlin Brett , Huang Wesley , Pope Lauren , Veeckmans Geraldine , Berghe Tom Vanden , Dixon Scott J. , Shah Yatrik , Schafer Zachary T.
Published: March 2024

Ferroptosis is an iron-dependent cell death caused by the catastrophic accumulation of lipid peroxidation. Despite the burgeoning ferroptosis research, there remains a void for an intrinsic and comprehensive ferroptosis indicator. Here we reported a simple and cost-effective way to detect ferroptotic cell death using reducing reagent-resistant (RRR) transferrin receptor 1 (TfR1). The TfR1 RRR dimer strongly correlates with ferroptosis induced by various ferroptosis-inducing conditions and relies on lipid peroxidation, which is not observed in other types of cell death. Through iron-overloading and tumor xenograft mouse models, we validate the in vivo ferroptosis detection using this technique. Furthermore, we identify the presence of TfR1 RRR dimers in extracellular vesicles isolated from the plasma of mice with ferroptosis-related diseases. Since TfR1 is a ubiquitously expressed protein, the increase of TfR1 RRR dimer can be used as a specific and endogenous ferroptosis marker with potential clinical applications.

Citation Format: Jianping He, Mackenzie Kelleher, Lucas Reynolds, Hannah Tanczos, Zhengrong Huang, Brett McLaughlin, Wesley Huang, Lauren Pope, Geraldine Veeckmans, Tom Vanden Berghe, Scott J. Dixon, Yatrik Shah, Zachary T. Schafer. Reducing reagent-resistant transferrin receptor 1 dimer is a specific marker for ferroptosis [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 357.
Abstract 3598: A new strategy for T cell therapy: T cells secreting TCR anti-CD3 bispecific T-cell engager
Authors: Sun Hanli , Huang Jiao , Zhan Kai , Wu Wanli , Tang Xianqing , Liu Min , Guo Shanshan , Zheng Hongjun , Huang Yingjie , Zhong Shi
Published: March 2024

TCR-engineered T (TCR-T) cells and TCR-anti-CD3 bispecific T-cell engagers (TCEs) are potent TCR-based therapeutic agents with distinct advantages and limitations in tumor treatment. TCR-T cells offer durable persistence within patients but necessitate personalized manufacturing and lack the capacity to harness bystander T cells. Conversely, TCEs are readily available as "off-the-shelf" products and can recruit bystander T cells, yet they exhibit a shorter lifespan. In our study, we sought to merge the merits of both approaches by engineering T cells to secrete a TCR-anti-CD3 TCE specific for alpha fetoprotein (AFP), a tumor-associated antigen abundantly expressed in hepatocellular carcinoma (HCC). We initially identified a TCR with specificity for the AFP158-166 peptide bound to HLA-A*02:01 and enhanced its affinity to picomolar via phage display. To facilitate efficient secretion by T cells, we adapted the high-affinity TCR to a single-chain format (scTCR) and fused it with a CD3-specific single-chain antibody fragment (scAFP-TCE). Our findings demonstrated that scAFP-TCE effectively redirected bystander T cells to engage in the lysis of HCC cells. Moreover, scAFP-TCE could be secreted by T cells transduced with lentiviral particles encoding the TCE gene. These transduced T cells exhibited potent antitumor activity both independently and by enlisting bystander T cells. This innovative T cell strategy, combining the bystander-recruiting ability of fusion proteins with the durable persistence seen in T cell therapy after a single infusion, presents a promising alternative to conventional TCR-based therapeutic agents. We anticipate that this novel approach may hold substantial potential for enhancing HCC treatment and expanding the scope of TCR-based immunotherapies.

Citation Format: Hanli Sun, Jiao Huang, Kai Zhan, Wanli Wu, Xianqing Tang, Min Liu, Shanshan Guo, Hongjun Zheng, Yingjie Huang, Shi Zhong. A new strategy for T cell therapy: T cells secreting TCR anti-CD3 bispecific T-cell engager [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 3598.
Abstract 3599: Recombinant chimeric antibody-based gamma-delta TCR targeting GPC3 induces potent antitumor response against hepatocellular carcinoma
Authors: Li Dan , Liang Tianyuzhou , Duan Zhijian , Zhang Hongbing , Liu Cheng , Ho Mitchell
Published: March 2024

Background and Significance: Hepatocellular carcinoma (HCC), a major type of primary liver cancer, is the third leading cause of cancer-related death worldwide. While Glypican-3 (GPC3) is highly upregulated in HCC, it is minimally expressed in normal tissues. The research in our laboratory has been focused on the development of GPC3 as an immunotherapeutic target for liver cancer. Despite many clinical trials, there has not been any approved therapy targeting GPC3 largely due to the combination of antigen heterogeneity, poor tumor penetration, and the inability to induce a durable, potent immune response in the tumor microenvironment (TME). Here, we made a recombinant chimeric antibody-based T cell receptors (named AbTCR) targeting GPC3 and explored its anti-tumor efficacy in xenograft mouse models.

Methods: The AbTCR constructs were built by fusing an antigen recognition domain (hYP7 scFv or HN3 VH) specific for GPC3 to the gamma-delta TCR constant region along with a secondary T cell signaling activation motif. The NFAT-tdTomato reporter cell line was established and used to measure the AbTCR-triggered T cell signaling upon stimulation with tumor cells. Anti-tumor efficacy of AbTCR-T cells was determined via luciferase-based cell killing assay as well as multiple HCC xenograft mouse models.

Results: The hYP7 GPC3 AbTCR-T cell not only enhances antigen-binding capacity and T cell activity, but also induces infiltration and expansion of T cells in the TME, thereby causing robust liver tumor regression in mice.

Conclusion: Our data show that new hYP7-directed GPC3 AbTCR is a promising strategy for treating liver cancer. This work provides a rationale for the use of hYP7 GPC3 AbTCR in clinical studies for treating HCC and other GPC3-positive solid tumors.

Citation Format: Dan Li, Tianyuzhou Liang, Zhijian Duan, Hongbing Zhang, Cheng Liu, Mitchell Ho. Recombinant chimeric antibody-based gamma-delta TCR targeting GPC3 induces potent antitumor response against hepatocellular 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 3599.
Abstract 3610: Utilizing fructose metabolism to fuel anti-tumor immunity
Authors: Schild Tanya , Chirayil Rachel , Haughton Lyric , Wallisch Patrick , Berishaj Marjan , Scheinberg David A. , Keshari Kayvan R.
Published: March 2024

Consumption of fructose in the form of high fructose corn syrup is elevated in the western diet, but it is not fully understood how fructose metabolism influences anti-tumor immunity. Fructose is canonically metabolized in the intestine and the liver and can shunt into glycolysis. In certain tumor types, fructose metabolism becomes deregulated, allowing tumor cells to metabolize fructose to power their biosynthetic processes. Similarly, reprogramming immune cells to be able to efficiently metabolize fructose may help us power immunotherapy to work in difficult to treat cancers, especially in individuals who have high fructose in their blood or in the tumor microenvironment (TME). Imparting effector T cells with the ability to use fructose for fuel can overcome one of the major metabolic limitations of the TME: limited nutrient supply. As T cells become activated, they alter their metabolism to support growth and proliferation. Activated CD8+ T cells upregulate their glycolysis which results in increased biosynthetic processes, such as synthesis of macromolecules and effector cytokines. However, tumor cells also consume substantial amounts of glucose, resulting in a glucose-depleted microenvironment, which could be one of the major barriers to immunotherapy working in solid tumors. Therefore, we engineered T cells to overexpress a fructose transporter, GLUT5, which is normally not expressed in the immune compartment at high levels. We hypothesized that increased fructose uptake by CD8+ T cells will ameliorate exhaustion caused by the glucose-low tumor microenvironment. Indeed, we determined that GLUT5 T cells are more efficient in killing in low glucose supplemented with fructose. We also observed that GLUT5 expression restores T cell glycolytic capacity under fructose to that of unexhausted T cells under glucose replete conditions. Similarly, GLUT5-expressing T cells proliferate faster in vitro and exhibit an improved ability to control B16 tumor growth in vivo. Additionally, combining GLUT5 cell infusion with checkpoint inhibition resulted in durable tumor control and prolonged mouse survival. Further, engineered CD19-targeted CAR T cells with expression of GLUT5 were more metabolically active and cytotoxic in low glucose conditions, mimicking the TME. In conclusion, GLUT5 expression in effector CD8+ and CAR T cells may allow immunotherapy to function in solid tumors under low glucose conditions.

Citation Format: Tanya Schild, Rachel Chirayil, Lyric Haughton, Patrick Wallisch, Marjan Berishaj, David A. Scheinberg, Kayvan R. Keshari. Utilizing fructose metabolism to fuel anti-tumor 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 3610.
Abstract 3681: Transcribed ultraconserved regions are associated with survival in multiple tumor types
Authors: Rodrigues Ana Carolina , Adamoski Douglas , Gradia Daniela F. , de Oliveira Jaqueline Carvalho
Published: March 2024

Ultraconserved regions (UCRs), encompassing 481 genomic segments identical across humans, mice, and rats, and conserved in other species, are distributed across all human chromosomes except 21 and Y. Over 90% of these regions, termed transcribed ultraconserved regions (T-UCRs) are expressed in at least one human tissue. Although extensively studied in the context of cancer since their discovery, the prognostic significance of T-UCRs in a pan-cancer context has not been explored. For this, TCGA data extracted from the TANRIC platform was utilized, differential expression and survival analysis was performed on different tumor types. Our analysis revealed that approximately 300 UCRs were expressed in the majority of the 20 tumor tissues. Additionally, it was noted that all examined tumor tissues expressed a higher number of UCRs compared to their non-tumor counterparts. Through t-distributed stochastic neighbor embedding (t-SNE) analysis, UCR expression patterns could distinguish primary tumor origins and types. Regarding the prognostic value, we identified 100 (20,8%) T-UCRs associated with disease-specific survival (DSS) and 102 (21.2%) T-UCRs associated with progression-free interval (PFI). Those T-UCRs are particularly important in the survival outcomes of kidney renal clear cell carcinoma (KIRC) and low-grade gliomas (LGC). In addition, we verified that uc.44, uc.48, uc.135, uc.144, uc.153, uc.217, uc.255, uc.256, uc.344, uc.357, uc.390, uc.427 and uc.436 were associated with survival of more than one tumor. Particularly, uc.135 high expression was associated with poor prognosis in Kidney Renal Papillary Cell Carcinoma (KIRP) and LGC, and good prognosis in KIRC. Uc.135 are mapped on MECOM gene, coding an oncoprotein acting as transcriptional regulator and involved in apoptosis, proliferation, and cell differentiation. Our findings suggest that analysis of T-UCRs expression have the potential to be used as predictive biomarkers and can help in studying the mechanisms and specific roles of the highlighted T-UCRs in cancer.

Citation Format: Ana Carolina Rodrigues, Douglas Adamoski, Daniela F. Gradia, Jaqueline Carvalho de Oliveira. Transcribed ultraconserved regions are associated with survival in multiple tumor types [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 3681.
Abstract 3704: Whole genome and targeted proteome analysis of single cancer cells
Authors: Alyasin Atieh , Weidele Kathrin , Botteron Catherine , Klein Christoph A. , Czyż Zbigniew T.
Published: March 2024

The simultaneous genome and proteome analysis of very rare single cells would enable addressing important biological and diagnostic questions particularly in cancer. Here, we introduce a novel genome and proteome (G&P) analytic workflow, a method allowing comprehensive analysis of single-cell DNA and targeted profiling of protein expression in single cells. As a proof of concept, we demonstrate the capability of the method by quantifying copy number of the ERBB2 gene alongside with protein expression levels of HER2 and phospho-HER2 in single cells. The G&P workflow utilizes antibodies conjugated with DNA oligonucleotides designed to enable their amplification alongside the single-cell genome facilitating parallel genome and proteome profiling by either quantitative PCR (qPCR) or sequencing. We utilized antibodies targeting cytokeratin 8/18/19, HER2 and phospho-HER (Tyr1248). Performance of each DNA-conjugated antibody was assessed by immunofluorescence staining in a variety of breast cancer cell lines (MDA-MB231, MDA-MB453, BT474 and MCF7) and sample types. Stained cells were isolated by manual micromanipulation and subjected to whole genome amplification (WGA). Protein expression levels, derived from quantification of the amplified DNA tags, were measured by qPCR. Shallow whole genome sequencing was employed to facilitate genome-wide profiling of copy number variations (CNVs), including the ERBB2 locus. We successfully developed and tested a G&P workflow allowing parallel genome-wide CNV profiling and quantification of three target proteins. G&P measurement yielded concordant results to immunofluorescence quantification for all tested markers. Furthermore, the workflow allowed direct correlation of copy numbers of the ERBB2 gene with HER2 expression in single cancer cells. Notably, the method enabled measurements of cellular and molecular responses at the single-cell level to lapatinib treatment, i.e. monitoring of the HER2 pathway activation level. Our novel multiplex G&P technique is capable of generating multiparametric measurements linking DNA copy numbers and expression levels of selected genes of interest. The method is optimized for analysis of single cells from rare cell populations and is readily translatable to study circulating tumor cells (CTCs) and disseminated cancer cells (DCCs), enabling for the first time pathway analysis via phosphoprotein analyses of these cells.

Citation Format: Atieh Alyasin, Kathrin Weidele, Catherine Botteron, Christoph A. Klein, Zbigniew T. Czyż. Whole genome and targeted proteome analysis of single 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 3704.