bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 2884: Cancer-associated fibroblasts potentiate subcutaneous tumor growth in a novel bladder cancer mouse model with a genotype dependency
Authors: Valentine Henkel Lee , Satyal Uttam , Metz Alexander , Bukavina Laura , Abbosh Philip H. 
Published: April 2023

Abstract
Introduction Interrogation of the relationship of genotype (mutation in relevant gene) and phenotype (sensitivity to therapy) in targeted therapy would be facilitated by the use of isogenic in vitro and in vivo models. The PI3K/AKT/mTOR pathway is widely activated but heretofore untargeted in bladder cancer. We sought to develop an immunocompetent CRISPR-edited bladder cancer mouse model that recapitulates common PI3K/AKT/mTOR mutations to study a genotype-phenotype relationship. Our in vitro CRISPR-edited organoids are immunogenic in vivo, as such, we explored utilizing Cancer-Associated Fibroblasts (CAFs) to mediate immunosuppression and promote a pro-tumorigenic environment.
Methods and Results We isolated bladder urothelial cells from Rosa26 LSL-Cas9/GFP transgenic mice and grew them as organoids. Trp53 and Rb1 were co-edited to establish ‘base organoids’. As proof of concept, Pten was edited in base organoids in anticipation of developing a series of organoids with different mTOR pathway genotypes. We found that Pten-KO base organoids were 9x more sensitive to ipatasertib than Pten WT organoids. The edited urothelial cells were engrafted into mouse bladder to further test kinase inhibitor susceptibility as preclinical evidence to support human clinical trials. However, the cells successfully engrafted but disappeared after 3-4 weeks before tumors formed. Subcutaneous allografts were also rejected after 3-4 weeks and showed CD45+ immune infiltration during rejection. When cells were injected subcutaneously with CAFs, tumors persisted for 12 weeks, but only in organoids with both Trp53 loss and loss of murine chromosome 4qC4 (which is homologous to 9p21 loss in humans). 9p21 contains 3 genes which are co-deleted in ~40% of bladder cancers: MTAP, CDKN2A, and CDKN2B. Histopathological analysis of these masses confirmed their malignant nature and revealed an immune-excluded architecture. IHC staining of 9p21/Trp53 KO tumors for CD206 and CD11c revealed greater recruitment of M2 macrophages than M1 macrophages.
Conclusions CAFs remodel the tumor-microenvironment in bladder cancer via the recruitment of pro-tumorigenic M2 macrophages. This may occur in a genotype-specific manner and 9p21 loss may be a requirement for some genotypes to be tumorigenic.
Citation Format: Henkel Lee Valentine, Uttam Satyal, Alexander Metz, Laura Bukavina, Philip H. Abbosh. Cancer-associated fibroblasts potentiate subcutaneous tumor growth in a novel bladder cancer mouse model with a genotype dependency [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2884.
Abstract 2925: In vitro characterization of next generation therapeutic antibodies
Authors: Quist Benita , Janbazacyabar Hamed , Lopez David Cobeta , Jayanth Namrata , Moiset Gemma 
Published: April 2023

Abstract
Therapeutic antibodies are an established drug class. Checkpoint inhibitors, such as anti-PD-1/PD-L1 and anti-CTLA-4 antibodies for cancer indications, and anti-TNF-α monoclonal antibody against autoimmune disorders represent some of most successful therapeutics in the past decade. Over 100 therapeutic targets suitable for antibody therapy have been identified for various disease indications, with several currently in late-stage clinical trials. In addition, there has been an explosion in the various types of therapeutic antibody modalities due to the increasing number of antibody engineering platforms. The new emerging bi-specific T-cell engaging antibodies (BiTEs) along with antibody-drug conjugates (ADCs) have demonstrated superior therapeutic qualities over the traditional monoclonal antibodies.
Here, we describe a pipeline to extensively characterize the various antibody therapeutics in vitro utilizing multiple innovative technologies. Assays to determine target expression and binding potency provide a thorough understanding of the target engagement. Furthermore, we present data from an innovative technology platform, the z-Movi, which measures cell avidity to predict invitro effector functions of T-cell engaging therapies, enabling more robust read-outs and could drive the lead selection of said therapies. Several mechanisms of action of different antibodies were investigated and relevant case studies describing the innate immune effector functions and the signaling pathway modulation are presented. Using a unique label-free approach, the xCELLigence, we report on the kinetics of target cell killing mediated by lymphocytes upon recognition of antigen-antibody complexes. Finally, safety assessment studies focusing on on-target/off-tumor effects of antibodies on primary cells were conducted. The cytokine profiling and cell viability assays to assess potential risk due to exaggerated levels of cytokine, reiterate the specificity and safety of the next generation of antibody therapeutics and support Investigational New Drug (IND) applications. In conclusion, we provide a comprehensive report on the in vitro characterization of the advanced antibody therapeutics, showcasing a pipeline for development and functional characterization of various antibody modalities, including bispecific T-cell engagers. This workflow can be used to progress a wide range of engineered antibodies from pre-clinical to the clinical phase of the drug discovery process. NJ and GM contributed equally to the work.
Citation Format: Benita Quist, Hamed Janbazacyabar, David Cobeta Lopez, Namrata Jayanth, Gemma Moiset. In vitro characterization of next generation therapeutic antibodies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2925.
Abstract 3154: Integrating DNA damage and mutation enrichment to understand mutagenesis at transcription factor binding sites
Authors: Chi Bo , Gordan Raluca 
Published: April 2023

Abstract
The buildup of ultraviolet (UV) light-induced DNA damage, such as Cyclobutane Pyrimidine Dimers (CPDs), is a crucial precursor to genetic mutations and the development of skin melanoma. These damaged sites and mutations are known to not be randomly distributed; in fact, previous research suggests potential relationships between damaged/mutated sites and transcription factors (TFs), proteins that regulate gene expression by binding to target sequences across the genome. To examine relationships between UV damages and TF binding sites on a genomic level, we integrated data from the Duke iMADS database of TF binding sites, CPD damage maps across the human genome, ATAC-seq accessibility data from the Cistrome database, and mutation data from Australian melanoma patients (from the ICGC consortium). We developed a computational workflow to measure the spatial distribution of damage/mutations at TF binding sites. Our analysis showed a strong association between the positions of CPD damages and mutations within the binding sites of ETS1, but not E2F or c-Myc, with the peaks in damage/mutations primarily residing at the central core of the ETS1 binding sites. The creation of such an analytic pipeline will enable the further quantitative genome-wide study of the relationships between the degrees of damages/mutations within TF binding sites, chromatin accessibility, and other genomic contexts. With these results, we can better understand the mechanisms involved in accumulating damages and mutations and how they progress to cancer, aging, and senescence.
Citation Format: Bo Chi, Raluca Gordan. Integrating DNA damage and mutation enrichment to understand mutagenesis at transcription factor binding sites [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3154.
Abstract 3169: Decoupling the correlation between cytotoxic and exhausted T lymphocyte transcriptomic signatures in melanoma enhances immunotherapy response prediction
Authors: Wang Binbin , Wang Kun , Jiang Peng , Ruppin Eytan 
Published: April 2023

Abstract
Background: Cytotoxic T lymphocytes (CTL) play a crucial role in anti-cancer immunity. Progression of CTL to exhausted T lymphocytes (ETL) that overexpress inhibitory receptors can substantially decrease effector cytokines production and diminish cytolytic activity in tumor microenvironment (TME). However, while the activity levels of CTL and ETL are considered important determinants of immune checkpoint inhibitors (ICIs) response, it has been repeatedly observed that their predictive power is quite limited. Studying this conundrum on a large scale across the TCGA cohort, we find that ETL and CTL activity (estimated based on conventional gene signatures in the bulk tumor expression) is strongly positively correlated in most cancer types. We thus hypothesized that their limited predictive power may arise due to this high expression concordance, such that their opposing associations with response effectively cancel each other.
Methods and Results: Aiming to find conditions where the association between these CD8+ T cell states and ICIs response is enhanced, we analyzed TCGA melanoma bulk gene expression via an interaction linear regression model to identify a set of genes whose expression diminishes the CTL and ETL correlation as much as possible. We further tested this decoupling signature (DS) in several independent melanoma bulk expression ICIs cohorts, showing that in high-DS patients, the correlation between ETL and CTL activities is indeed markedly lower than in the low-DS patient groups. Second, this successful decoupling now increases the power of CTL activity in predicting ICIs response in high DS patients, making it superior to other state-of-art ICIs prediction transcriptomic signatures.
Significance: These results demonstrate the utility of a new decoupling score for boosting the power of CTL activity in predicting ICIs response in melanoma.
Citation Format: Binbin Wang, Kun Wang, Peng Jiang, Eytan Ruppin. Decoupling the correlation between cytotoxic and exhausted T lymphocyte transcriptomic signatures in melanoma enhances immunotherapy response prediction [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3169.
Abstract 3213: Association of Tumor Treating Fields (TTFields) with survival in newly diagnosed glioblastoma: A systematic review and meta-analysis
Authors: Conlon Patrick , Lavy-Shahaf Gitit , Urman Noa , Ballo Matthew T. 
Published: April 2023

Abstract
Background: Tumor Treating Fields (TTFields) became an FDA-approved treatment option for patients with newly diagnosed GBM in 2015 on the basis of the randomized controlled EF-14 trial. Subsequent approvals worldwide and increased adoption of TTFields has led to the question of whether or not a consistent survival benefit has been observed in the real world setting, and whether device usage has played a role.
Methods: We conducted a literature search using PubMed, Embase, and Google Scholar to identify clinical studies evaluating overall survival in adult patients with GBM treated with TTFields. Comparative studies and single-cohort studies reporting on survival outcomes were included in the analysis. Inter-study heterogeneity was assessed using the Cochran Q test and quantified using the Higgins I2 statistic.
Results: Of 7 studies evaluating the clinical efficacy of TTFields in newly diagnosed patients, 5 studies (reporting on a total of 1,228 patients) compared the addition of TTFields to standard of care (SoC) vs SoC alone, and were included in a pooled analysis for overall survival. Meta-analysis of comparative studies indicated a significant improvement in overall survival for patients treated with TTFields vs those not receiving treatment. Inter-study heterogeneity was examined, and a sensitivity analysis indicated the pooled effect was robust and not dependent on any individual study. Furthermore, among studies reporting data on TTFields device usage, an average device usage rate of 75% or higher was found to consistently associate with prolonged survival when compared to an average usage rate below 75% (P = 0.001).
Conclusions: Pooled analysis of comparative TTFields studies suggests survival may be improved with the addition of TTFields to standard chemoradiotherapy treatment for patients with newly diagnosed GBM, and that a 75% usage rate may be meaningful in the real-world setting.
Citation Format: Patrick Conlon, Gitit Lavy-Shahaf, Noa Urman, Matthew T. Ballo. Association of Tumor Treating Fields (TTFields) with survival in newly diagnosed glioblastoma: A systematic review and meta-analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3213.
Abstract 3280: Vrd induction therapy drives memory like NK cell development in newly diagnosed multiple myeloma patients
Authors: Peng Tao , Kuan Emma , Cicalo Anthony , Gong Qiuyu , Torgerson Troy , Li Xiaojun 
Published: April 2023

Abstract
VRd induction therapy is a common approach to treat newly diagnosed multiple myeloma (MM) patients. Although in vitro studies of bortezomib (Velcade, V), lenalidomide (Revlimid, R), and dexamethasone (d) reveal mechanisms of these individual drugs, VRd therapy induced immune cell phenotype changes in vivo are unknown. We have utilized multimodal single cell methods to elucidate novel mechanisms of induction therapy response in human immune cells over time as a longitudinal study: pre-treatment (pretrt), after 2-cycles of VRd therapy (post-induction; pi) and after the end of 4-6 additional cycles of VRd therapy (end induction; ei). Protein measurements in plasma demonstrate significantly increased levels of IL-15 and IL-18 only at pi compared to pretrt but IL-2 and IFN-γ are progressively reduced from pretrt to ei. Both flow cytometry and single cell RNA -seq reveal that the proportion of NK cells (NK) significantly increased in PBMC only at pi compared to pretrt. NK subsets with strong dexamethasone effect emerge at pi; In contrast, memory like NK subsets (CD56dimCD16+NKG2A+CD94+) become the major NK in PBMC and bone marrow (BM) at ei. In addition, single cell ATAC-seq suggests that RUNX-family transcription factors may mediate lenalidomide to up-regulate NK cytotoxic gene expression during VRd therapy. In summary, comprehensive immune profiling of newly diagnosed MM patients suggests that transient increase of IL-15 and IL-18 may mediate the generation of memory like NK cells, which may play important roles in controlling MM growth and/or reducing risk of infection during VRd induction therapy.
Citation Format: Tao Peng, Emma Kuan, Anthony Cicalo, Qiuyu Gong, Troy Torgerson, Xiaojun Li. Vrd induction therapy drives memory like NK cell development in newly diagnosed multiple myeloma patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3280.
Abstract 3298: Two detection methods of clinical KRAS G12C mutation detection for companion diagnostics
Authors: Brown Robert William , Liu Wei , Sun Qing , Ren Hui , Li Jonathan , Pastor Larry , Kim Daniel , Sha Michael , Zhang Aiguo 
Published: April 2023

Abstract
KRAS G12C is a common mutation in approximately 13% of lung adenocarcinoma, 3% of colorectal cancer and 2% of other solid tumors. The FDA approved sotorasib, a KRAS G12C inhibitor, for targeted treatment of patients with KRAS G12C-mutated locally or metastatic non-small cell lung cancer (NSCLC). It is essential to detect the KRAS G12C mutation with a companion diagnostic before the drug is administered. We have developed two KRAS G12C mutation detection assays for qPCR or Sanger sequencing. Both QClamp® assays use our proprietary xeno nucleic acid (XNA) technology which specifically enhances the amplification of the target mutant DNA sequence while blocking amplification of the wildtype sequence, thus significantly improving the sensitivity of the assays for qPCR (~1%) and Sanger sequencing (~15 to 20%) to 0.1% variant allele frequency. These simple and sensitive assays can be used for clinical research or validated in CLIA labs for KRAS G12C mutation detection for the purpose of companion diagnostic use. Although NGS methods are gaining traction in clinical settings, our methods are suitable for standard molecular diagnostics laboratory settings and do not add any additional steps to the qPCR or Sanger sequencing protocols. Our methods are especially valuable for labs that appreciate simple, economical, yet sensitive companion diagnostics assays for KRAS G12C mutation. QClamp® assays can be easily adapted to detect other single gene mutations with high sensitivity for companion diagnostics use or other mutation detection applications.
Citation Format: Robert William Brown, Wei Liu, Qing Sun, Hui Ren, Jonathan Li, Larry Pastor, Daniel Kim, Michael Sha, Aiguo Zhang. Two detection methods of clinical KRAS G12C mutation detection for companion diagnostics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3298.
Abstract 3299: Usefulness of protocadherin GA12 and cysteine ​​dioxygenase type 1 methylation biomarkers in the diagnosis of lung cancer
Authors: Son Ji Woong , Lee Minhyeok , Jeong In Beom , Kwon Sun Jung , Kang Daeun , Na Moon Jun 
Published: April 2023

Abstract
Rationale: The use of bronchoscopy is key to the diagnosis of lung cancer. However, the sensitivity of bronchoscopy is low. In addition, bronchial washing cytology, a routine auxiliary test, does not significantly improve the performance of bronchoscopy due to its low sensitivity. To improve the diagnostic performance of bronchoscopy, protocadherin GA12 (PCDHGA12) and Cysteine ​​Dioxygenase Type 1 (CDO1) methylation biomarkers in bronchial washing fluid have been introduced as novel adjunctive diagnostic tests.
Methods: A total of 161 patients with suspected lung cancer who underwent bronchoscopy were analyzed. Cytological examination of bronchial washing fluid and testing for PCDHGA12 and CDO1 methylation biomarkers were performed.
Results: The final diagnosis was lung cancer in 114 patients, and benign disease in 49 patients. PCDHGA12 methylation biomarker showed sensitivity of 80.4% and specificity of 87.8%. CDO1 methylation biomarker showed sensitivity of 66.1% and specificity of 98.0%, whereas cytological evaluation showed sensitivity of 43.8% and specificity of 100%. The combined analysis of PCDHGA12 and CDO1 methylation showed sensitivity of 84.8% and specificity of 85.7%. The combined analysis of the methylation biomarkers and cytology tests resulted in a slightly increased sensitivity of 86.6% and specificity of 85.7%. The specificity and sensitivity of the methylation biomarkers were also high in peripheral lung cancer.
Conclusion: The results of this study demonstrated that PCDHGA12 and CDO1 methylation as lung cancer biomarkers of bronchial washing may be used as adjunctive tests for bronchoscopy. Keywords: biomarker; bronchoscopy; lung cancer; protocadherin GA12: CDO1, methylation
Citation Format: Ji Woong Son, Minhyeok Lee, In Beom Jeong, Sun Jung Kwon, Daeun Kang, Moon Jun Na. Usefulness of protocadherin GA12 and cysteine ​​dioxygenase type 1 methylation biomarkers in the diagnosis of lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3299.
Abstract 3300: Development of a diagnostic antibody for anti-BTN1A1 therapy, a novel immune checkpoint inhibitor mutually exclusive of PD-L1/PD-1
Authors: Yoo Stephen S. 
Published: April 2023

Abstract
Butyrophilin 1A1 (BTN1A1) is currently undergoing investigation in Phase 1 clinical trials as a novel immune checkpoint protein for the treatment of solid tumors. BTN1A1 exhibits a mutually exclusive expression pattern to that of PD-1/PD-L1, making anti-BTN1A1 antibody therapy an attractive option for cancer patients with PD-L1 refractory or relapsed disease. While current cancer immunotherapies have shown some efficacy against late-stage disease, there remains a major unmet medical need as a large number of patients fail to respond to current treatments. BTN1A1 has been studied at length in preclinical models to characterize its immunomodulatory functions, revealing its ability to inhibit the proliferation of activated T cells and the ability of these cells to kill tumor cells in vitro. In vivo, BTN1A1-overexpressing tumor models exhibit accelerated growth, whereas the growth of BTN1A1-deficient tumors is impaired in immunocompetent settings, supporting a role for this protein in the regulation of immune evasion. Here in, we present the development of a diagnostic antibody for use in the anti-BTN1A1 therapy clinical trials to enable the immunohistochemical (IHC) detection of human BTN1A1. A high-quality BTN1A1 antibody may help predict which patients are more likely to respond to BTN1A1 antibody-based cancer therapy, similar to the PD-L1 companion diagnostic test for anti-PD-L1/PD-1 therapy. The characterization of the developed BTN1A1 antibody was conducted via ELISA, Western blotting, confocal microscopy, and flow cytometry to demonstrate its overall performance. Validation was performed using formalin-fixed paraffin-embedded human tumor tissue samples to determine the analytical sensitivity and specificity of the IHC assay. This antibody was also found to be of value for imaging mass cytometry and flow cytometry experiments elucidating applicable clinical features of both human tumor tissues and immune cells. Specifically, the developed antibody can detect the robust expression of BTN1A1 on both cancer cells and immune cells, while also revealing the mutually exclusive expression of BTN1A1 and PD-L1. Finally, we demonstrate the capability of a BTN1A1 antibody that can be used to identify BTN1A1-positive patients with a high degree of analytical sensitivity and specificity.
Citation Format: Stephen S. Yoo. Development of a diagnostic antibody for anti-BTN1A1 therapy, a novel immune checkpoint inhibitor mutually exclusive of PD-L1/PD-1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3300.