bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 7323: Tissue resident memory T cell abundances impact non-small-cell lung cancer immune microenvironment and patient prognosis
Authors: Shen Aidan , Garrett Aliesha , Mai Junhua , Zhu Yangzhi , Jiang Chongming
Published: March 2024

Tissue resident memory T cells (TRM) are a specialized subset of long-lived memory T cells that reside in peripheral tissues. However, whether TRM exerts any immunosurveillance role in the tumor immune microenvironment (TIME) and progression of non-small-cell lung cancer (NSCLC), which accounts for 85% of all lung cancers, remains unclear. Our comprehensive analysis of multiple independent single-cell and bulk RNA-seq datasets of patient NSCLC samples generated reliable, unique TRM signatures, through which we could infer the abundance of TRM in NSCLC. We discovered that TRM abundance is consistently positively correlated with CD4+ T helper 1 cells, M1 macrophages, and resting dendritic cells in TIME and significantly impacts the prognosis of NSCLC patients. In addition, TRM signatures are strongly associated with immune checkpoint genes and the prognosis of NSCLC patients, suggesting that TRM signatures are promising prognostic markers for immunotherapy in NSCLC. We then built a machine learning model to predict patient survival based on the TRM signatures and immune related genes. The accuracy of the model was validated by Kaplan-Meyer survival analysis, receiver operating characteristic curves, principal component analysis, and t-distributed random neighbor embedding. We developed a 4-gene risk score that effectively stratified patients into low-risk and high-risk categories. The patients with high-risk scores had significantly lower overall survival than patients with low-risk. The prognostic value of the risk score was independently validated by the Cancer Genome Atlas Program (TCGA) dataset and multiple independent NSCLC patient datasets. Notably, low-risk NSCLC patients with higher TRM infiltration exhibited enhanced T-cell activation, macrophage regulation, and other TIME immune responses related pathways, indicating a more active immune profile benefitting from immunotherapy. Altogether, this study provides valuable insights into the complex interactions between NSCLC TRM and TIME and their impact on patient prognosis, highlighting the importance of TRM in shaping the NSCLC microenvironment. The development of a simplified 4-gene risk score provides a practical prognostic marker for risk stratification.

Keywords: Tissue resident memory T cell, non-small-cell lung cancer, prognosis, tumor immune microenvironment, machine learning

Citation Format: Aidan Shen, Aliesha Garrett, Junhua Mai, Yangzhi Zhu, Chongming Jiang. Tissue resident memory T cell abundances impact non-small-cell lung cancer immune microenvironment and patient prognosis [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 7323.
Abstract 7348: CytoCellDB: A gold standard database for classification and analysis of extrachromosomal DNA in cancer
Authors: Brunk Liz
Published: March 2024

Extrachromosomal DNA (ecDNA), or double minute chromosomes, are established cytogenetic markers for malignancy and genome instability. More recently, the cancer community has gained a heightened awareness of the roles of ecDNA in cancer proliferation, drug resistance and epigenetic remodeling. A current hindrance to understanding the biological roles of ecDNA is the lack of available cell line model systems with experimental cytogenetic data that confirm ecDNA status. Although several recent landmark studies have identified numerous cell lines and tumor models with ecDNA, the current sample size limits our ability to detect ecDNA-driven molecular differences due to limitations in power. Increasing the number of model systems that are known to express ecDNA would provide new avenues for understanding the fundamental underpinnings of ecDNA biology and would unlock a wealth of potential targeting strategies for ecDNA-driven cancers. To bridge this gap, we created CytoCellDB, a resource that provides karyotype annotations, including ecDNA status, and leverages publicly available global cell line data from the Cancer Dependency Map (DepMap) and the Cancer Cell Line Encyclopedia (CCLE). We expanded the total number of cancer cell lines with ecDNA annotations to 632, or 34% of the cell lines in CCLE/DepMap. Of these, 154 cell lines express ecDNA, which is a 240% increase from the current sample size. We demonstrate that a strength of our framework is the ability to interrogate ecDNA, and the compendium of other chromosomal aberrations, in the context of cancer-specific vulnerabilities, drug sensitivities, and other multi-omic features (genomics, transcriptomics, methylation, proteomics). We anticipate that this resource will lower the barrier to systematic, population-scale discoveries related to ecDNA and will provide insights into strategies and best practices for determining novel therapeutics that overcome ecDNA-mediated drug resistance.

Citation Format: Liz Brunk. CytoCellDB: A gold standard database for classification and analysis of extrachromosomal DNA in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7348.
Abstract 7367: Dissecting cellular and molecular alterations in pre-invasive to invasive lung cancer progression at single-cell resolution
Authors: Yoffe Liron
Published: March 2024

Non-small cell lung cancer (NSCLC) accounts for most cancer-related deaths worldwide, largely due to diagnosis at advanced metastatic stages. Increased implementation of low-dose computed tomography (CT)-guided screening has led to the identification of non-solid lesions or ground-glass opacities (GGOs) that are not visible on plain chest radiography and can harbor very early-stage tumors. Growth of the lesions and/or development of a solid component can indicate more aggressive behavior. Using the low-dose CT reduced lung cancer mortality by >20%, underscoring the need for early detection and intervention. However, the cellular and molecular determinants contributing to the malignant progression of those early preinvasive lesions remain poorly understood. To assess intratumoral heterogeneity and associated dynamic changes in the immune contexture during early lung carcinogenesis, we performed single-cell RNA-seq and Hyperion imaging on surgically resected freshly harvested tissues from 37 patients (matched solid and non-solid components of lesions and adjacent non-involved lungs), representing a spectrum from preneoplasia to invasive disease. Analysis of >300K cells identified cellular, transcriptomic, and metabolic alterations as well as tumor-stroma cross-talk pathways. Specifically, preinvasive to invasive disease progression was associated with significant changes in the immune landscape determined by an increase in exhausted CD4/CD8 T-cells, suppressive T-regs, polymorphonuclear myeloid-derived suppressor cells, and M2-like macrophages; and a decrease in cytotoxic CD8 T-cells, NK cells, and inflammatory cDC2 cells, suggesting that activation of immunosuppressive/anti-inflammatory microenvironment and suppression of immune activation microenvironment may enable tumor progression.

Citation Format: Liron Yoffe. Dissecting cellular and molecular alterations in pre-invasive to invasive lung cancer progression at single-cell resolution [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 7367.
Abstract 739: AMT-253, a first-in-class MUC18-targeting antibody-drug conjugate, for the treatment of MUC18-positive solid tumors
Authors: Shi Jing , Yan Jiaqing , Huang Yaling , Guo Jun , Kong Yan , Meng Xun , Liu Shu-Hui
Published: March 2024

MUC18, also known as MCAM (melanoma cell adhesion molecule) or CD146, is a type I transmembrane glycoprotein originally identified as a cell adhesion molecule of melanoma that plays important roles in tumor growth and progression including tumor angiogenesis, epithelial-mesenchymal transition (EMT), and metastasis. MUC18 is overexpressed in a variety of solid tumors including (but not limited to) melanoma, osteosarcoma, head and neck, lung, esophagus, breast, ovarian, and cervical cancer and hepatocellular carcinoma, with restricted presence on normal healthy tissues, mainly on blood vessels and a minor subset of T helper cells. Limited expression in normal tissues and high expression in tumors makes MUC18 a promising target for the development of antibody drug conjugate (ADC). AMT-253 is a novel ADC targeting MUC18. It is composed of a humanized MUC18-targeting IgG1 antibody conjugated with Exatecan, a topoisomerase I inhibitor, attached to a proprietary self immolative T moiety linker through reduced interchain disulfide bonds with a drug-to-antibody ratio (DAR) of 8. AMT-253 was stable in vitro with less than 0.5% of payload releasing when incubated with human, monkey, mouse or rat plasma for 21 days at 37°C. AMT-253 selectively bound to cell surface MUC18 and was efficiently internalized into MUC18-positive cancer cells. AMT-253 exhibited antiproliferative activity against several MUC18-positive cancer cell lines and demonstrated potent bystander killing effect in vitro. Treatment with AMT-253 resulted in tumor growth inhibition or regression in a panel of MUC18 positive cell line derived xenograft (CDX) or patient derived xenograft (PDX) models. In addition, AMT-253 was well tolerated in a GLP compliant toxicity study in cynomolgus monkeys at dose levels ≤45 mg/kg. Taken together, our preclinical in vivo efficacy and toxicity studies demonstrated that AMT-253 has a wide therapeutic window and could potentially provide benefits for cancer patients with highly unmet medical needs. AMT-253 is currently being evaluated in a Phase I first-in-human clinical trial (NCT05906862).

Citation Format: Jing Shi, Jiaqing Yan, Yaling Huang, Jun Guo, Yan Kong, Xun Meng, Shu-Hui Liu. AMT-253, a first-in-class MUC18-targeting antibody-drug conjugate, for the treatment of MUC18-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 739.
Abstract 740: CNTN4 as a novel target for solid cancer with antibody-drug conjugate
Authors: Cha Mi Young , Kim Hyunuk , Byun Seungmin , Ha Youngeun , Park Kitae , Yu Hyunkyung , Jeon Bu-Nam , Kim Mira , Moon Soojung , Park Kyung Mi , Park Hansoo
Published: March 2024

As a novel immune checkpoint, we previously confirmed that contactin 4 (CNTN4) regulates T cell activity negatively by binding to amyloid precursor protein (APP) on T cells. CNTN4 is highly expressed in various types of tumors, including gallbladder, pancreas, stomach, endometrium, liver, prostate, bladder cancer, melanoma, and other tumors, with positive rates over 70% through immunohistochemistry analysis in contrast to low-level expression in normal tissues. Based on the tumor-specific expression profile of CNTN4, we evaluated the potential of CNTN4 as a novel target for antibody-drug conjugate (ADC). First, the internalization of the anti-CNTN4 antibody in the IND submission stage, GENA-104A16, into CNTN4-positive cancer cells was confirmed. For investigation of the potential of targeting CNTN4 using ADC, clinically validated various linker-payloads (MMAE, MMAF, SN-38, and exatecan derivate) were conjugated to GENA-104A16 using thiol maleimide conjugation with average drug-to-antibody ratio (DAR) in the range of 4.0 to 4.8. After preparing ADCs, we confirmed the binding affinity for CNTN4 was maintained as high even after the payload conjugation through an ELISA. In vitro studies have demonstrated the highly cytotoxic effect of MMAF conjugate among the conjugates of GENA-104A16 on CNTN4-positive cancer cells compared to negative cancer cells. And there was no cytotoxic effect on normal cells. Furthermore, treating MMAF conjugate of GENA-104A16 showed promising efficacy in the Pan02 pancreatic orthotopic mouse model and the patient-derived xenograft model. These results suggest that CNTN4 could be a highly potential ADC target that could expand the options for cancer treatment strategies.

Citation Format: Mi Young Cha, Hyunuk Kim, Seungmin Byun, Youngeun Ha, Kitae Park, Hyunkyung Yu, Bu-Nam Jeon, Mira Kim, Soojung Moon, Kyung Mi Park, Hansoo Park. CNTN4 as a novel target for solid cancer with antibody-drug conjugate [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 740.
Abstract 7411: CAMStool: Cancer-associated somatic mutation selection tool for cancer risk prediction in whole-genome data
Authors: Kim Jae-Yoon , Park Seung-Jin , Park Seong-Hwan , Kim Seon-Kyu
Published: March 2024

Predicting cancer risk plays a useful role in presenting guidelines to prevent and manage cancers of individuals. Genomic variants have recently been widely used as a genetic factor, and the utilization of the genetic factor consisting of somatic mutations has shown remarkable predictive performance in many cancer prediction studies. Typically, the accuracy of such prediction studies is significantly affected by the composition of somatic mutations used as the genetic factor; however, in practice, choosing the optimal set of mutations with high prediction accuracy is a challenging task in cancer prediction research. From this perspective, we present a new analysis tool for selecting an optimal set of somatic mutations associated with cancers of interest, named CAMStool. The CAMStool is based on the statistical values, which are the effect size and its p-value of each somatic mutation for the cancers of interest. It heuristically searches for the only somatic mutations that directly increase the prediction accuracy of cancer, through statistical and machine-learning models. Then, our tool presents the finally selected somatic mutations as the final optimal mutation set, and additionally presents an optimal cancer risk prediction model through various machine/deep learning modeling using the optimal set as a genetic factor. For the evaluation, the CAMStool was applied to our real whole-genome dataset which are sequenced from normal-tumor tissues of 459 individuals with thyroid cancer. The CAMStool selected 36 and 55 optimal somatic mutations associated with the benign thyroid and non-invasive follicular thyroid cancer, and presented risk prediction models with sensitivity of 88.04% and 90.32%, respectively. Although the CAMStools has some limitations, it is expected to contribute to various cancer prediction studies that require selecting optimal mutation sets in the future. The CAMStools is written in R and will be released soon on our github (https://github.com/JaeYoonKim72).

Citation Format: Jae-Yoon Kim, Seung-Jin Park, Seong-Hwan Park, Seon-Kyu Kim. CAMStool: Cancer-associated somatic mutation selection tool for cancer risk prediction in whole-genome data [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 7411.
Abstract 7460: Characterizing the role of PCBP1 in the activation of the cGAS-STING/type I Interferon axis to promote anti-tumor immunity
Authors: Fréreux Cécile , Chakraborty Paramita , Dalton Annamarie C. , Howley Breege V. , Granger Bryan , Karam Joseph A. , Vaena Silvia G. , Romeo Martin J. , Howe Philip H.
Published: March 2024

The emergence of immunotherapies has encouraged the need to better understand the molecular mechanisms that modulate the tumor immune microenvironment to kill cancer cells as well as the strategies used by cancer cells to evade the immune system. In several cancer types, the Poly(rC) Binding Protein 1 (PCBP1) has shown to have tumor suppressive effects, however its function in regulating the tumor immune environment remains unclear. To investigate this in the context of breast cancer, we established a CRISPR-Cas9-medited knock-out of PCBP1 in a Py8119 murine breast cancer cell line. PCBP1−/− cells revealed a decrease in the activation of the cGAS-STING pathway and is associated with lower levels of type I interferons (IFNs) and Interferon Stimulated Genes’ (ISGs) expression. The cGAS-STING pathway plays an important role in innate immunity as it fights pathogenic infections and tumorigenesis through the production of type I IFN and ISGs. It also promotes the priming and infiltration of T cells at the tumor site to fight cancer cells. Our results suggested that PCBP1 is acting on the activation of the cGAS-STING pathway and could further modulate the tumor immune microenvironment. We then confirmed our results in vivo by establishing a tumorigenic C57BL/6 PyMT transgenic mouse model with conditional knockout for PCBP1 in mammary cells. Our data demonstrate that PCBP1−/− PyMT mice have higher tumor burdens compared to PCBP1+/+ PyMT mice and also show a decreased ISGs’ signature by RNA-sequencing, qPCR and western blot, as previously observed in vitro in the Py8119 PCBP1−/− cell line. Additional single nuclei RNA-sequencing analyses confirmed that this downregulation of ISGs is observed in mammary cancer cells where PCBP1 is knocked-out. Strikingly, IHC and flow cytometry analyses of PCBP1−/− tumors isolated from these mice also revealed a decrease in CD8+ T-cells. Therefore, PCBP1 silencing may promote tumor growth by impairing the activation of the cGAS-STING/IFN-I/ISGs axis, which may contribute to the decrease in CD8+ T-cells’ infiltration at the tumor site. Additionally, we are further investigating the molecular mechanisms mediated by PCBP1 that trigger this activation of the cGAS-STING pathway.

Citation Format: Cécile Fréreux, Paramita Chakraborty, Annamarie C. Dalton, Breege V. Howley, Bryan Granger, Joseph A. Karam, Silvia G. Vaena, Martin J. Romeo, Philip H. Howe. Characterizing the role of PCBP1 in the activation of the cGAS-STING/type I Interferon axis to promote 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 7460.
Abstract 7468: Development of a high complexity flow cytometry panel to assess minimum residual disease in acute myeloid leukemia
Authors: Pearl Jessica , Bruni Elena , Hsu Haoting , Walling Brandon , Abarca-Heidemann Karin
Published: March 2024

Acute Myeloid Leukemia (AML) is a highly heterogeneous disease with a diverse range of abnormal myeloid subpopulations resulting in challenges in clinical diagnosis and treatment. Many methods such as flow cytometry are used to provide precise information for risk stratification and treatment methods. Flow cytometry utilizes the expression patterns of cellular markers to characterize the high diversity in AML subpopulations with high sensitivity and specificity. This coupled with rapid analysis timelines allows for flow cytometry to be an excellent tool for the identification of AML lineage and progression through both phenotypic analysis and difference from normal. As AML lineage and disease progression are predictors of residual disease and relapse; the need for effective and accurate characterization of AML populations is critical. Here, Champions Oncology has developed a high-complexity 18-color flow cytometry panel to identify AML subpopulations at high resolution. We have characterized AML samples to evaluate the expression of phenotypic markers and their heterogeneity. Utilizing primary AML samples, we have evaluated the stability of AML subpopulations to understand how delayed analysis, such as what is seen in clinical trials, may impact marker expression and observed key populations were stable for up to 72 hours after collection. In addition to stability, understanding the lower limits of detection is critical for AML patients, particularly for minimum residual disease and relapse screening. The use of a flow cytometric panel again provides an excellent tool for these tests due to the single cell nature that allows for the interrogation of individual populations with primary AML subpopulations detected at a range of 10−3 to 10−4. Finally, with hundreds of never-passaged AML models characterized and cryopreserved by both flow cytometry and sequencing at Champions Oncology, we investigated how the cryopreservation processes impacted the expression of AML subpopulations. We have observed similar expression and detection of AML populations following cryopreservation indicating that these models can be utilized as an excellent tool for further studies. Collectively, our data indicates that the panel developed at Champions Oncology provides robust data analysis of AML subpopulations and can be an excellent tool for the tracking of AML disease progression in the clinic.

Citation Format: Jessica Pearl, Elena Bruni, Haoting Hsu, Brandon Walling, Karin Abarca-Heidemann. Development of a high complexity flow cytometry panel to assess minimum residual disease in acute myeloid leukemia [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 7468.
Abstract 7486: Development and analytic validation of an ARv7/PSMA dual biomarker circulating tumor cell assay
Authors: Ladd Jon , Bayer Erin , Bartels Brock , Kaldjian Eric , Ramirez Arturo
Published: March 2024

Background Prostate cancer drug targets and biomarkers may be investigated non-invasively on circulating tumor cells (CTCs) obtained via liquid biopsies. PSMA is an important drug target in prostate cancer, and ARv7 is a splice variant that confers resistance to second-generation androgen receptor inhibitors. In this study, we describe the development and analytic validation of a novel assay to quantify ARv7 and PSMA protein expression on CTCs. The assay was validated with blood samples from patients with Stage IV prostate cancer to demonstrate clinical feasibility. To our knowledge, a PSMA/ARv7 dual protein assay for CTCs has not previously been reported.

Methods LNCaP (PSMA positive), PC3 (PSMA negative), 22Rv1 (ARv7 positive), and BT474 (ARv7 negative) cells were spiked into healthy donor blood to generate model CTCs. Nucleated cells were collected from these spike-in samples using the AccuCyte® sample preparation kit and spread onto microscope slides. Slides were fixed and stained with antibodies to cytokeratin, EpCAM, and CD45 to detect CTCs and exclude white blood cells (WBCs), and with PSMA and ARv7 to evaluate protein expression on identified CTCs. The slides were imaged with the CyteFinder® automated immunofluorescence scanning microscope that identifies CTCs for confirmation by trained reviewers based on machine learning algorithms and quantitatively measures biomarker signal mean fluorescence intensity (MFI).

Results For ARv7/PSMA expression classification of the model CTCs, the dual biomarker assay showed analytic sensitivity of 83%/97% and specificity 98%/99%, yielding accuracy of 90.2%/97.9%, respectively. The dynamic range of MFI for both biomarkers was approximately three orders of magnitude. Inter-run reproducibility CV was 13.6% (ARv7) and 6.9% (PSMA). Slide repeatability mean CV was 11.1% (ARv7) and 12.0% (PSMA). Clinical feasibility of the assay was investigated in 9 progressing Stage IV prostate cancer patient blood samples. CTCs were identified in all clinical samples (median 4, range 1 - 384). Thresholds for biomarker positivity were established based on MFI measurements of positive and negative control cell lines. ARv7 positivity in clinical samples ranged from 33% to 100%, and PSMA positivity ranged from 0% to 75%.

Conclusions We have developed a dual ARv7/PSMA assay that simultaneously measures protein expression of both biomarkers on individual CTCs. The assay is accurate and reproducible for the assessment of ARv7 and PSMA expression by liquid biopsy in clinical studies.

Citation Format: Jon Ladd, Erin Bayer, Brock Bartels, Eric Kaldjian, Arturo Ramirez. Development and analytic validation of an ARv7/PSMA dual biomarker circulating tumor cell assay [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 7486.
Abstract 7574: Exploring the therapeutic potential of proteasome inhibitors in targeting SOX2-driven LUSC and SCLC
Authors: Mohanty Atish , Guo Linlin , Ramisetty Sravani , Singhal Sharad , Massarelli Erminia , Kulkarni Prakash , Salgia Ravi
Published: March 2024

This study addresses the current lack of small molecules targeting SOX2, a pivotal protein in cancer, through an examination of the effectiveness of FDA-approved drugs and proteasome inhibitors. Building on prior research demonstrating the proteasome inhibitor CFZ's capacity to diminish the expression of ITGB4 and PXN in LUAD effectively, our investigation highlights CFZ and IXA as potent inhibitors at nanomolar concentrations. Notably, CFZ treatment enhances sensitivity to cisplatin by suppressing the expression of ITGB4 and the stemness-associated gene SOX2.At a mechanistic level, CFZ hinders histone acetylation at the SOX2 promoter site, leading to rapid and specific downregulation. RNA-seq analysis of COH2 cells treated with CFZ unveils substantial downregulation of genes related to transcription and DNA binding. Z score analysis further reveals a noteworthy inhibition of key transcription factors (TFs), including SOX2, NANOG, POU5F1, SALL4, and KLF4. This TF inhibition extends to neuroendocrine cell lines, identifying 16 overlapping targets of SOX2 associated with stemness. These findings suggest a potential therapeutic approach for targeting cisplatin-resistant cancer stem cells across various cancer types. Moreover, the study proposes a synergistic effect of cisplatin and CFZ in mitigating the growth of neuroendocrine phenotype, SCLC. Given the limited medical options currently available for this phenotype, this insight holds particular significance. In conclusion, our study unveils CFZ as a potent transcriptional suppressor of SOX2, providing a novel strategy to sensitize cisplatin-resistant cancer stem cells. The results underscore the interplay of genetic and non-genetic mechanisms in drug resistance, emphasizing the significance of repurposing drugs for other indications.

Citation Format: Atish Mohanty, Linlin Guo, Sravani Ramisetty, Sharad Singhal, Erminia Massarelli, Prakash Kulkarni, Ravi Salgia. Exploring the therapeutic potential of proteasome inhibitors in targeting SOX2-driven LUSC and SCLC [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 7574.
Abstract 7575: BPI-460372, a covalent, irreversible TEAD inhibitor in Phase I clinical development
Authors: Han Xiaohong , Guo Jing , Jin Xiangyu , Zhu Lingyin , Shen Hongling , Xu Xiaofeng , Zhang Mengjie , Liu Xiaoyun , Liu Yanju , Cheng Hongke , Guo Shunna , Ding Lieming , Wang Jiabing , Lan Hong , Wang Mengzhao
Published: March 2024

The Hippo signaling pathway is critical for the regulation of organ development, tissue homeostasis, and tumorigenesis by controlling the activation status of yes-associated protein (YAP) or its homolog PDZ-binding motif (TAZ). As a major downstream effector, the transcription factor TEAD is activated by forming a complex with YAP/TAZ. Hippo pathway aberrations leading to TEAD activation have been reported in many cancers. Inhibiting TEAD function by directly blocking the palmitoylation pocket of TEAD is a potential therapeutic approach for cancer treatment. Betta Pharma has discovered a selective, covalent and irreversible TEAD inhibitor known as BPI-460372. The discovery of BPI-460372 was first reported in AACR 2023. Here we present additional preclinical and clinical data characterizing BPI-460372 as a promising candidate drug. In the dose-escalating part of the Phase Ι study, the exposure of BPI-460372 increased proportionally over 10 to 80 mg dose range after oral administration and exhibited linear pharmacokinetics, with a clearance rate suitable for once-daily dosing. The compound is generally well tolerated, with no drug-related Grade ≥3 adverse event observed. Remarkably, we have not seen renal toxicities that was perceived as a potential risk associated with certain TEAD inhibitors. Preliminary efficacy was observed in a few subjects. In preclinical studies, we found that intermittent dosing schedule of 3 days on/4 days off, compared with continuous dosing at equivalent weekly exposure, can ameliorate kidney damage and improve early renal injury biomarkers while maintaining anti-

tumor activity. Thus, alternative dosing schedule could further improve the therapeutic window and enable combination studies in clinical development. Collectively, these results support further development of BPI-460372 for the treatment of cancers harboring Hippo pathway alterations.

Citation Format: Xiaohong Han, Jing Guo, Xiangyu Jin, Lingyin Zhu, Hongling Shen, Xiaofeng Xu, Mengjie Zhang, Xiaoyun Liu, Yanju Liu, Hongke Cheng, Shunna Guo, Lieming Ding, Jiabing Wang, Hong Lan, Mengzhao Wang. BPI-460372, a covalent, irreversible TEAD inhibitor in Phase I clinical 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 7575.
Abstract 7577: A new cancer therapy strategy: Synthetic lethality induced by inhibition of mTOR and cMYC and JNK activation
Authors: Chen Hui , Rivera Jason , Paradise Marc , Xu Zihan , Mognol Giuliana , Varner Judith
Published: March 2024

Cancer cells are characterized by aberrant signal transduction and cell cycle control pathways that lead to unchecked cell proliferation. Uncontrolled cancer cell proliferation, as well as immune suppressive macrophage proliferation, contribute to tumor growth and spread. Effort to suppress tumor cell growth using Inhibitors of PI3K or MEK signaling pathways can initially inhibit tumor growth, but resistance develops due to upregulation of the alternative pathway. We identified a novel series of allosteric tyrosine kinase receptor inhibitors that induce synthetic lethality in AML, lung carcinoma, pancreatic carcinoma, and other tumor cells and in proliferating macrophages in vitro and in vivo by simultaneously inhibiting cMyc and Tor and activating the stress activated kinase JNK, leading to p53 mediated cell cycle arrest. Select kinase inhibitors with a unique positioning of a single side chain inhibited CDK8/19 and thereby Myc while stimulating phosphorylation and activation of JNK and p38. JNK activation promoted sustained ATF-2 and cJun-mediated p53 and Chk1/Chk2 activation, thereby promoting cell cycle arrest in G2/M and ultimately, apoptosis. These inhibitors potently suppressed tumor growth in vivo by halting both tumor cell and macrophage proliferation in G2/M. They synergized with anti-PD-1 and anti-CTLA-4 and led to tumor eradication and immunological memory formation. These studies identify novel allosteric inhibitors with potent synthetically lethal anti-tumor activity.

Citation Format: Hui Chen, Jason Rivera, Marc Paradise, Zihan Xu, Giuliana Mognol, Judith Varner. A new cancer therapy strategy: Synthetic lethality induced by inhibition of mTOR and cMYC and JNK activation [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 7577.
Abstract 760: Alteration to transcriptional rhythmicity in mammary glands from pubertal MMTV-PyMT mice fed a high-fat diet
Authors: Yan Lin , Palmer Daniel G. , Zeng Huawei
Published: March 2024

Biological clocks, existing in all human organ systems, cycle every 24 hours in a diurnal pattern and control the daily rhythms of human life (e.g., eating vs. fasting, sleep vs. wakefulness), which is essential for health and wellbeing. Disruption of the biological clocks, either by genetic or environmental alteration, disturbs circadian rhythms, which may lead to chronic diseases. Childhood obesity is a risk factor for breast cancer in adult women. Lifestyle changes in the modern world (e.g., energy-dense diets) serve as environmental factors that contribute to alterations in biological clocks and obesity. The present study examined transcriptional rhythmic changes in mammary glands from pubertal MMTV-PyMT mice fed a high-fat diet (HFD). Three-week-old female mice (FVB background) were randomly assigned into three groups - wild-type (WT) mice fed the AIN93G diet and MMTV-PyMT mice fed the AIN93G diet or an HFD for three weeks. At the end of the study, mammary glands were collected every 4 hours over a period of 24 hours (Zeitgeber time 0-24 hours) for RNA-sequencing analysis. The mammary weight was 0.45±0.02, 0.59±0.02, and 0.67±0.02 g for WT mice fed the AIN93G diet and MMTV-PyMT mice fed the AIN93G and HFD, respectively (means ± SEM, all p<0.05 when three groups were compared each other). The rhythmicity analysis using R showed that greater than 1,000 transcripts were classified as “loss of rhythm” when MMTV-PyMT mice (both AIN93G-fed and HFD-fed groups) were compared to WT mice fed the AIN93G diet. Eighteen transcripts were classified as “loss of rhythm” in MMTV-PyMT mice when the HFD was compared to AIN93G diet. Hierarchical clustering analysis showed differentially expressed genes that were significantly altered and KEGG enrichment analysis showed the most upregulated and downregulated metabolic pathways in treatment groups than in the control group at each time point over the 24-hour period. These findings indicates that genetic alterations may have a greater effect than dietary effects on transcriptional rhythmicity in mammary glands from pubertal mice.

Citation Format: Lin Yan, Daniel G. Palmer, Huawei Zeng. Alteration to transcriptional rhythmicity in mammary glands from pubertal MMTV-PyMT mice fed a high-fat diet [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 760.
Abstract 7619: Tissue-derived peripheral biomarkers that reflect activity of T-cells, macrophages, and neutrophils in patients with solid tumors
Authors: Willumsen Nicholas , Nissen Neel I. , Karsdal Morten A.
Published: March 2024

Background: A toolbox of tissue-derived peripheral biomarkers that reflect the activity of T-cells, macrophages and neutrophils is a medical need for immuno-oncology drug development allowing non-invasive quantification of immune cell activity before - and during - treatment, both for predictive and pharmacodynamic purposes. By identifying and quantifying specific extracellular matrix fragments with neo-epitopes that are generated by proteases specific for T-cells, macrophages, and neutrophils, respectively, it is possible to develop peripheral biomarkers that reflect the activity of these immune cells. Such biomarkers have previously shown associations with outcome of patients treated with immune checkpoint inhibitors. Here we investigated the distribution of 3 such biomarkers in different cancer indications. Moreover, these data were compared to data from melanoma patients showing associations with response to cancer immunotherapy.

Methods: Tissue-derived biomarkers related to activity of T-cells (C4G: Collagen-4 degraded by Granzyme B), Neutrophils (CPA9-HNE: Calprotectin degraded by neutrophil elastase), Macrophages (VICM: citrullinated and MMP-degraded vimentin) were measured by validated ELISA/ECLIA in serum from patients with various solid tumor types (bladder-, breast- colorectal-, head and neck-, kidney-, lung-, ovarian-, pancreatic, stomach-, prostate- cancer, and melanoma, n=220) and compared to age-matched healthy controls (n=33) by ANOVA. The biomarker levels were compared to historical data.

Results: Median biomarker levels of CPA9HNE (neutrophil activity/NETosis) and VICM (macrophage activity) were significantly increased in all solid tumor types (p<0.001), respectively and with a ~5-fold inter-patient variation as well. Median C4G levels was only slightly elevated in a few indications (p<0.05) and with a 5-10-fold inter-patient variation across tumor types. All biomarker levels were independent of disease stage. Similar biomarkers levels were seen to those found to be associated with objective response rate and overall survival of melanoma patients treated with cancer immunotherapy.

Conclusion: Tissue-derived peripheral biomarkers that reflect the activity of T-cells (C4G), macrophages (VICM) and neutrophils (CPA9HNE) has biomarker potential in solid tumors and may serve as prognostic, predictive and pharmacodynamic biomarkers in clinical trials investigating cancer immunotherapy.

Citation Format: Nicholas Willumsen, Neel I. Nissen, Morten A. Karsdal. Tissue-derived peripheral biomarkers that reflect activity of T-cells, macrophages, and neutrophils in patients with 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 7619.
Abstract 7624: DNA checkpoint gene mutation as a biomarker of immune checkpoint inhibitor in advanced biliary tract cancer
Authors: Shin Ji Eun , Kim Seung Tae , Choi Dae-Ho , Lee Junho , Hyeon Jiyeon
Published: March 2024

Introduction: The DNA checkpoint (DNACHK) pathway is engaged in signaling the need for cell cycle arrest. The G1 and S phase checkpoint allows for repair of damaged DNA, preventing damaged DNA from being copied. The G2 and M phase checkpoint prevents transmission of mutated DNA to the next generation. This pathway, along with mismatch repair (MMR), homologous recombination (HR), and base excision repair (BER), is being actively researched to assess its role in cancer immunotherapy.

Methods: Sixty-two patients participated in this study. These patients were treated with immune checkpoint inhibitors (ICIs) for advanced biliary tract cancers (BTCs) from Mar. 2020 to Aug. 2022 at Samsung Medical Center. DNACHK mutations were defined as genomic alterations such as SNVs, MNVs, and short insertion and deletions in seven genes These genes include checkpoint kinase 1 (CHEK1), checkpoint kinase 2 (CHEK2), BRCA1, DNA repair associated (BRCA1), the serine/threonine kinase ATM, the serine/threonine kinase ATR, and mediator of DNA damage checkpoint 1 (MDC1). We analyzed the effect of DNACHK mutations on the efficacy of ICIs in advanced BTCs.

Results: Patient median age at diagnosis was 68.0 years. Ten patients (16.1%) had gall bladder (GB) cancer; the remaining patients (n = 52, 83.9%) were diagnosed with cholangiocarcinoma. Among the 62 patients with advanced BTCs treated with ICIs, 37 (59.7%) were categorized into the DNACHK wild-type (WT) group and 25 (40.3%) into the DNACHK mutated (MT) group. The most observed DNA checkpoint mutations were ATM mutations (n=14). MDC1 mutations were found in seven patients, ATR mutations in three, BRCA1 mutations in four, and CHEK2 mutations in three. Patients in the DNACHK MT group had better disease control rates than patients in the DNACHK WT group (60.0% vs. 48.6%, p=0.53). Median overall survival (OS) was 8.1 months (95% CI, 5.1, 22.8) in the MT group and 5.6 months (95% CI, 3.1, 11.0) in the WT group (p=0.33).

Conclusions: The results of this study suggest that the DNACHK pathway may be a valuable source of biomarkers for ICI and worthy of further study.

Citation Format: Ji Eun Shin, Seung Tae Kim, Dae-Ho Choi, Junho Lee, Jiyeon Hyeon. DNA checkpoint gene mutation as a biomarker of immune checkpoint inhibitor in advanced biliary tract 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 7624.
Abstract 7656: Clinicogenomic anlaysis reveals a role for TP53 mutations in distant progression of high-grade glioma
Authors: Kang Byung-Hee , Lee Seungbok , Lee Joo Ho
Published: March 2024

Purpose: High-grade glioma (HGG), the most common form of primary brain tumor, is highly lethal and treatment options remain limited. Despite advances in genomic technologies, there are few molecular biomarkers to guide precision medicine for HGG. Here, we aimed to identify the clinicogenomic features associated with HGG prognosis and recurrence patterns.

Methods: Our single-institution retrospective analysis included 220 patients initially diagnosed with adult HGG (grade 3 or 4) who underwent next-generation sequencing targeting 82 brain tumor-relevant genes. The patients were categorized according to the 2021 WHO classification and their clinical status, survival, genomic profile, and recurrence patterns were analyzed.

Results: At a median follow-up of 23 months (ranges, 2-59 months), 180 patients (82%) showed either progression or recurrence. A total of 15% of patients were reclassified under the 2021 WHO classification, revealing a clear separation of progression-free survival (PFS) and overall survival (OS) curves between grades 3 and 4 gliomas. We found that TP53 mutations were significantly associated with the occurrence of distant progression, especially in grade 4 gliomas. Additionally, TP53 mutations were more common in patients with higher Ki67 index and subependymal/leptomeningeal seeding, indicating an increased risk of distant progression in TP53-mutated grade 4 glioma patients. Following multivariate Cox regression analysis, TP53 mutations were independent predictors of OS (hazard ratio [HR]=1.47, P=0.039) and distant PFS (HR=1.71, P=0.005).

Conclusion: Considering the elevated risk of distant progression in grade 4 gliomas with TP53 mutations, our results underscore the necessity for additional research into the most effective treatment approaches for these patients.

Keywords: high-grade glioma, TP53, pattern of failure, distant progression, next-generation sequencing

Citation Format: Byung-Hee Kang, Seungbok Lee, Joo Ho Lee. Clinicogenomic anlaysis reveals a role for TP53 mutations in distant progression of high-grade glioma [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 7656.
Abstract 7668: Novel pretreatment nomograms based on pan-Immune-inflammation value for predicting clinical outcome in patients with head and neck squamous cell carcinoma
Authors: Chen Qian , Li Xiang , Bai Yanxia , Chen Yue
Published: March 2024

Background: The prognostic value of an effective biomarker, Pan-Immune-Inflammation Value (PIV), for head and neck squamous cell carcinoma (HNSCC) patients after radical surgery or chemoradiotherapy has not been well explored. This study aimed to construct and validate nomograms based on PIV to predict survival outcomes of HNSCC patients.

Methods: 161 HNSCC patients underwent radical surgery and 50 patients received chemoradiotherapy were enrolled retrospectively for development and external validation cohort, respectively. The cut-off of PIV was determined using the maximally selected rank statistics method. Multivariable Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses were performed to develop two nomograms (Model A and Model B) that predict disease-free survival (DFS).

Results: Patients with higher PIV (≥123.3) experienced a worse DFS (HR: 5.01, 95% CI: 3.25-7.72, p<0.0001) and overall survival (OS) (HR: 5.23, 95% CI: 3.34-8.18, p<0.0001) compared to patients with lower PIV (<123.3), which was also consistent in the external cohort. Predictors of Model A included age, TNM stage, neutrophil-to-lymphocyte ratio (NLR) and PIV, and that of Model B included TNM stage, lymphocyte-to-monocyte ratio (LMR) and PIV. In comparison with TNM stage alone, the concordance index (C-index), receiver operating characteristic (ROC) curves and calibration curves of the nomograms demonstrated good calibration and discrimination, and the decision curve analysis (DCA) also showed satisfactory clinical utility in both internal and external validation.

Conclusions: The nomograms based on PIV, a simple but forceful indicator, can provide intuitive and precise prognosis prediction of individual HNSCC patients after radical surgery or chemoradiotherapy.

Citation Format: Qian Chen, Xiang Li, Yanxia Bai, Yue Chen. Novel pretreatment nomograms based on pan-Immune-inflammation value for predicting clinical outcome in patients with head and neck squamous 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 7668.