bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 1969: Off-target autophagy inhibition by SHP2 allosteric inhibitors and therapeutic implications for aberrant RAS-driven cancers
Authors: Miao Yiming , Bai Yunpeng , Miao Jinmin , Murray Allison A. , Lin Jianping , Dong Jiajun , Qu Zihan , Zhang Ruo-Yu , Nguyen Quyen , Wang Shaomeng , Zhang Zhong-Yin
Published: March 2024

Aberrant activation of RAS-MAPK signaling is common in cancer, and efforts to inhibit pathway components have yielded drugs with promising clinical activities. Unfortunately, treatment-provoked adaptive resistance mechanisms inevitably develop, limiting their therapeutic potential. As a central node essential for receptor tyrosine kinase mediated RAS activation, SHP2 has emerged as an attractive cancer target. Consequently, many SHP2 allosteric inhibitors are now in clinical testing. Here we discovered a previously unrecognized off-target effect associated with SHP2 allosteric inhibitors. We found that these inhibitors accumulate in the lysosome and block autophagic flux in a SHP2-independent manner. We showed that off-target autophagy inhibition by SHP2 allosteric inhibitors contributes to their anti-tumor activity. We also demonstrated that SHP2 allosteric inhibitors harboring this off-target activity not only suppress oncogenic RAS signaling but also overcome drug resistance such as MAPK rebound and protective autophagy in response to RAS-MAPK pathway blockage. Finally, we exemplified a new therapeutic framework that harnesses both the on- and off-target activities of SHP2 allosteric inhibitors for improved treatment of mutant RAS driven and drug resistant malignancies such as pancreatic and colorectal cancers.

Citation Format: Yiming Miao, Yunpeng Bai, Jinmin Miao, Allison A. Murray, Jianping Lin, Jiajun Dong, Zihan Qu, Ruo-Yu Zhang, Quyen Nguyen, Shaomeng Wang, Zhong-Yin Zhang. Off-target autophagy inhibition by SHP2 allosteric inhibitors and therapeutic implications for aberrant RAS-driven cancers [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 1969.
Abstract 1996: Novel mechanism of temozolomide resistance in glioblastoma
Authors: Hung Yuet Yi Charmaine , Kiang Mei Yee Karrie , Leung Ka Kit Gilberto
Published: March 2024

Intrinsic expression of PD-1 has been discovered in different types of tumurs, exhibiting either oncogenic or tumor-suppressing function. In glioblastoma (GBM), intrinsic PD-1 has been found to play a role in promoting the proliferation and self-renewal of brain tumor-initiating cells through nuclear factor κB without involving PD-L1 ligation, with unknown factors activating this signalling pathway. Meanwhile, TMZ resistance significantly contributes to treatment failure and an extremely poor prognosis for GBM. This study investigated whether intrinsic PD-1 is also expressed in differentiated human GBM cell lines and its role in GBM proliferation and temozolomide (TMZ) resistance. In vitro studies demonstrated the presence of PD-1 in both U87 and U251 TMZ-sensitive and -resistant cell lines, with a higher expression on TMZ-resistant cell lines. PDCD1 knockdown led to decreased GBM progression, including cell proliferation, colony formation and cell migration, in TMZ-resistant U87 and U251 cell lines using cell viability assays. It also resensitizes these cell lines to TMZ. Overexpression of PDCD1 in the PDCD1-knockdown cell lines increases their proliferation and restores their resistance to TMZ. Treatment of U87 and U251 TMZ-resistant cell lines with TMZ upregulated PD-1 expression. An orthotopic xenograft mouse model is further deployed by injecting previously cultured U87 and U251 cell lines into the mouse brains. A smaller tumour size is observed in the model with PDCD1 knockdown model than the one without PDCD1 knockdown when treated with TMZ. This study reveals that intrinsic PD-1 expression contributes to TMZ resistance in GBM and TMZ may be a factor activating the PD-L1-independent PD-1 signalling. PD-1 and its downstream signalling pathway, such as SHP-2 and IKK, may be potential therapeutic targets for GBM patients with TMZ resistance. Co-administration of TMZ and agents inhibiting the intrinsic PD-1 signalling pathway can potentially produce synergistic therapeutic effects. The higher expression of PD-1 on TMZ-resistant GBM than on TMZ-sensitive GBM also suggests that the intrinsic PD-1 level can be a predictor of TMZ outcome.

Citation Format: Yuet Yi Charmaine Hung, Mei Yee Karrie Kiang, Ka Kit Gilberto Leung. Novel mechanism of temozolomide resistance in glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1996.
Abstract 1998: ABCB1 promotes uveal melanoma cell resistance to FR900359 and identifies a tumor cell subpopulation with a distinct gene expression signature
Authors: Murray Sarina Dion , Riordan Jesse D. , Anderson Eric R. , Onken Michael D. , Blumer Kendall J. , Dupuy Adam J. , Stipp Christopher S.
Published: March 2024

Uveal melanoma (UM) is the leading form of intraocular cancer in adults and the second most common form of melanoma. Although rare, UM has a median survival rate of ~1 year after metastasis occurs. Metastatic UM is largely refractory to treatment and there are no effective pharmacological therapies, resulting in poor overall survival. In >90% UM cases, the oncogenic initiator proteins are constitutively active mutant GNAQ or GNA11 proteins (GNAQ/11). FR900359 (FR) is a natural compound that inhibits GNAQ/11 and has anti-proliferative effects on UM cells. To identify key oncogenic mechanisms downstream of mutant GNAQ/11, we performed a Sleeping Beauty (SB) transposon forward genetic screen to identify drivers of FR resistance. The SB screen identified ATP-binding cassette sub-family B member 1 (ABCB1) as one of the top genes upregulated by SB in FR-resistant UM cell populations. We determined that although ABCB1 does not provide immediate resistance to FR, the overexpression of ABCB1 leads to emergence of resistant colonies at a much higher rate than spontaneous resistance, validating ABCB1 as contributors to FR resistance. Unexpectedly, immunofluorescence revealed that a relatively small fraction of UM cells strongly expresses the transgenes after stable transfection. Immunoblotting confirmed that ABCB1 expression was initially modest in ABCB1-transfected populations but increased in the cells that developed resistance to FR. To examine the kinetics of FR resistance, population doubling versus time (PDVT) assays were performed in UM cells expressing ABCB1 or empty vector control treated with FR or vehicle. FR potently suppressed the proliferation of vector control cells. Drug-naïve ABCB1-transfected cells developed resistance to FR over time but accomplished fewer population doublings than vehicle-treated cells in the same time interval. Once transgenic populations emerged as resistant populations in FR, they grew similarly in drug or vehicle. Ongoing RNA-sequencing analysis from PDVT samples has identified distinct gene expression signatures associated with FR treatment and ABCB1 expression. These findings are expected to illuminate tumor cell heterogeneity amongst UM cell populations that may be related to drug resistance and metastasis.

Citation Format: Sarina Dion Murray, Jesse D. Riordan, Eric R. Anderson, Michael D. Onken, Kendall J. Blumer, Adam J. Dupuy, Christopher S. Stipp. ABCB1 promotes uveal melanoma cell resistance to FR900359 and identifies a tumor cell subpopulation with a distinct gene expression signature [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 1998.
Abstract 2073: Human breast patient derived organoids: Development and characterization of a new tissue mimetic model
Authors: Bhowmick Rudra , Malla Sudarshan , Wani Sameena , Chatterjee Anirban
Published: March 2024

Worldwide, breast cancer (BC), is the most frequently diagnosed cancer among women. In the US, 1 out of 8 women may expect to be diagnosed with BC In their lifetime. Current models for studying BC tumor biology and BC drug discovery include 2D cultured cell lines and patient derived xenografts (PDX). As 2D cultured cells do not represent the 3D complexity of human tissue, and PDX models are time consuming and cost prohibitive, better tissue mimetic models are needed. Organoids are self-assembled 3D cultured cellular units that may mimic the corresponding human tissue structurally and functionally (1). Patient derived organoids (PDO) are developed from tissue of specific patients and may resemble the source tissue in molecular features, including recapitulation of patient specific responses to therapies (2). Here, we report development and characterization of novel breast PDO lines from fresh (≤24h post-surgery) and cryopreserved (≤7 days post-surgery) tissue. Breast tumor and normal, tumor adjacent (NTA) tissue were sourced from consented patients. Breast PDO were generated following modifications to a published protocol (3). Briefly, tissue samples were minced, digested with collagenase, and filtered. The filtrate was resuspended in Matrigel (Corning) and small drops were added on cell culture plates. Both tumor and NTA PDO were cultured using the same media and organoids were monitored using brightfield microscopy (Olympus CK40) and live cell imaging (Muvicyte, Perkin Elmer). PDO lines were analyzed for expression and distribution of important breast-specific biomarkers using confocal microscopy (ImagExpress, Molecular Devices). PDO lines displayed hormone receptors (ER, PR), cell surface (EpCAM, CD49f), cytoskeletal (cytokeratin 14, 19, E-cadherin, vimentin) and cell proliferation (Ki67) markers. Transcriptome profiles were analyzed using vendor services (Azenta). PDO were also tested for their susceptibility to breast cancer drugs, e.g., Tamoxifen, chlorambucil and Docetaxel. We have successfully generated one NTA ER+/PR+/HER2− PDO line and one tumor ER+/PR+/HER2− PDO line from different donors. Our breast PDO lines would be highly useful in understanding tumor biology, BC progression, signal transduction, and drug discovery/testing. Future efforts would include process scaling up and development of BC specific assays. References:1.Zhao et al., 2022. STAR Protocols 2.Bleijs, M. et al., 2019. EMBO J3.Dekkers et al., 2021. Nature Protocols

Citation Format: Rudra Bhowmick, Sudarshan Malla, Sameena Wani, Anirban Chatterjee. Human breast patient derived organoids: Development and characterization of a new tissue mimetic model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2073.
Abstract 2177: Postbiotic metabolites secreted by L. acidophilus reduce DNA damage in an experimental model of Barrett’s tumorigenesis
Authors: Joshi Divya , Andl Claudia
Published: March 2024

The origins of esophageal adenocarcinoma (EAC) are commonly attributed to the progression from gastroesophageal reflux disease (GERD) to Barrett’s Esophagus (BE) and finally to esophageal adenocarcinoma. During GERD, various types of bile induce oxidative stress and generate reactive oxygen species (ROS), resulting in DNA damage and inflammation in cells. Although there has been much research documenting the shift in the esophageal microbiome from gram-positive to gram-negative bacteria during this progression, there has also been an observed increase in the presence of Lactobacillus, a gram-positive commensal bacterium with probiotic qualities, in the esophagus during the progression from GERD to BE and eventually to EAC. Our previous research has demonstrated the ability of Lactobacillus spp. to not only colonize the esophagus under in vitro conditions of GERD, but also their anti-inflammatory and anti-genotoxic properties on esophageal cells exposed to bile. To assess the extent of reflux-induced DNA damage and oxidative stress during the progression of BE, we exposed two BE cell lines, CP-B and BAR-T, and the EAC cell line FLO-1 to ox bile or deoxycholic acid. Both bile types demonstrated significant increases in phosphorylated H2AX, as a marker for pronounced DNA damage repair. Next, we supplemented both live L. acidophilus and its postbiotic metabolites to cells exposed to ox bile and deoxycholic acid. We show a significant reduction in DNA damage as measured by pH2AX with both the live treatment and the treatment with postbiotic metabolites when compared to untreated, bile-exposed cells at various stages of BE and EAC. Ongoing experiments include assessing anti-genotoxic effects of postbiotic metabolites through DNA repair protein RAD51, reductions in oxidative stress though ROS marker 8-oxo-guanine, and anti-inflammatory effects through NFkB-associated inflammation. BE and EAC cell viability and proliferation upon bile exposure and postbiotic metabolite administration will also be assessed. This study aims to determine the supplementation with Lactobacillus postbiotic metabolites in the prevention and intervention of esophageal adenocarcinoma development.

Citation Format: Divya Joshi, Claudia Andl. Postbiotic metabolites secreted by L. acidophilus reduce DNA damage in an experimental model of Barrett’s 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 2177.
Abstract 2270: UALCAN Mobile, An app for cancer gene expression data analysis
Authors: Varambally Sooryanarayana , Chandrashekar Darshan Shimoga , Puli Gopi Chand , Karthikeyan Santhosh Kumar , Manne Upender , Creighton Chad J. , Kumar Sidarth
Published: March 2024

Cancer is a complex disease effecting different organs and a major cause of death and a burden on the society. Multiple molecular alteration occur during cancer initiation and disease progression and metastasis. Recent advances in technology led to generation of large amount of molecular data including transcriptome. These large datasets can be used to analyze and identify sub-class specific cancer biomarkers and targets. However, there is a need for the development user friendly tools for its analysis and dissemination of the large scale cancer molecular data. Earlier, we had developed and upgraded web based comprehensive proteogenomic platform UALCAN (ualcan.path.uab.edu), which allows users to analyze and integrate the disparate data to better understand the gene, proteins, and pathways perturbed in cancer and make discoveries. UALCAN web platform enables intuitive analysis and discovery by cancer research community. In the current study, we describe the development of UALCAN Mobile application (App) that will provide cancer transcriptomic data obtained from The Cancer Genome Atlas (TCGA) project, to evaluate protein-coding gene expression based on various stratification including stage, grade, race, gender and molecular-subtypes across over 30 types of cancers. The UALCAN Mobile app aims at providing large cancer dataset on the go. In order to find causative gene expression changes, identify biomarkers and therapeutic targets, UALCAN Mobile will assist as the data will be easily mobile and transportable with this App. Here, we describe the development of UALCAN Mobile and its utility to the cancer research community. UALCAN Mobile App can be found at both iOS/Apple and Android play store and is free to download and use.

Citation Format: Sooryanarayana Varambally, Darshan Shimoga Chandrashekar, Gopi Chand Puli, Santhosh Kumar Karthikeyan, Upender Manne, Chad J. Creighton, Sidarth Kumar. UALCAN Mobile, An app for cancer gene expression data analysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2270.
Abstract 2274: Genomic and transcriptomic analyses of chemical hepatocarcinogenesis aggravated by loss of oncoproteins in hepatocytes
Authors: Wang Xinyi , Zhang Jiemeng , Liu Yingluo , Zhang Shuo , Liang Yan , Zong Min , Lin Xiaoxue , Karin Michael , Feng Gensheng
Published: March 2024

Hepatocellular carcinoma (HCC) is one of the most common causes of cancer-related death without effective treatment. Oncogenic drivers, including PTPN11/Shp2, Ikkβ kinase (IKK), c-Met and β-catenin, as well as tumor microenvironment as illustrated by a carcinogen or diethylnitrosamine (DEN)-treated models, have combined contribution to cancer progression that have distinct prevalence in human HCC progression. We previously found that disruption of Ras/Erk by Shp2 deletion combined with deletion of NF-κB unexpectedly dysregulated circadian clock genes which leads to further cancer progression. Except for this, limited reports investigated how various other oncogenic genes aberration would incorporate with DEN to induce HCC. Further, no reports investigated the dynamic evolution of transcriptomic aberration incorporating genetic changes and the differential functional pathways involved in DEN plus oncogene triggered-HCC progression. Thus, we here sought to investigate the context-dependent contribution of PTPN11/Shp2, IKK, c-Met and β-catenin to HCC using hepatocyte-specific deletion models (SKO, IKO, MKO, BKO) combined with DEN treatment. Exome sequencing and RNAseq were used to identify dynamic changes of the genomic and transcriptomic variations of HCC development under the influence of both genetic deletion and DEN-treatment. We found that upregulated epithelial-mesenchymal transition (EMT), cancer metastasis/migration and downregulated fatty-acid and cholesterol metabolism were highly involved across models. Macrophages together with genes including Spi1, Clec7a, and microRNA networks including miR-122 and miR-155 etc. were also deregulated. Specifically, upregulated IL2-STAT5 signaling in DEN-SKO liver tissues, upregulated myogenesis, KRAS signaling and EMT as well as apoptosis in DEN-MKO, downregulated xenobiotic metabolism and bile acid metabolism in DEN-IKO and -BKO were identified to be distinct to oncogenic deletion in relation with HCC development.

Citation Format: Xinyi Wang, Jiemeng Zhang, Yingluo Liu, Shuo Zhang, Yan Liang, Min Zong, Xiaoxue Lin, Michael Karin, Gensheng Feng. Genomic and transcriptomic analyses of chemical hepatocarcinogenesis aggravated by loss of oncoproteins in hepatocytes [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 2274.
Abstract 2291: Bravo automation of Agilent Avida targeted enrichment for high-throughput detection of genomic alteration and DNA methylation
Authors: Wahba Ashraf , Ho Tony , Johns Sarah , Aravind Aswati , Wang Heng , Mehendale Neelima V. , Amparo Gilbert P. , Win Khine , Gomez Manuel , Zhao Grace , Roberts Douglas N.
Published: March 2024

Background: Current genomic and epigenomic profiling of cancer tissue DNA or cfDNA (cell-free DNA) in liquid biopsy relies upon separate, time- and sample-consuming technologies for somatic variant detection or methylation analysis. Here we describe workflow and performance of the Agilent Bravo automated liquid handling platform with the Agilent Avida targeted enrichment solution for next generation sequencing of somatic variants and methylation profiling. This solution can effectively analyze low-input tumor DNA or cfDNA samples. The Avida Duo workflow enables highly sensitive detection of single nucleotide variant (SNV), insertions and deletions (INDEL), copy number variation (CNV) and DNA methylation profiles from a single sample, without any sample splitting. Methods and Results: Panels, reagents, and automated workflows for Avida DNA, Avida Methyl, and Avida Duo Methyl (combined DNA & methylation) kits were developed to accommodate up to 96 samples on the Bravo NGS workstation. The automated solution supports independent single-day workflows for somatic variants or methylation sample preparation. The Avida Duo analysis combines both workflows without sample splitting, streamlining the process and reducing sample consumption. Leveraging a focused cancer hotspot panel, we demonstrate excellent reproducibility and low allele frequency (SNV at sub 1%) variant detection in cfDNA samples and reference standards with as little as 10ng DNA input. We exhibit similar performance with a larger ~300 kb target region tumor profiling panel. Finally, we demonstrate DNA methylation detection in the standalone or combined (“Duo”) workflows across differentially methylated regions (DMRs) with a panel of ~3400 targets. Conclusions: Automation of the Avida targeted enrichment solution with the Bravo NGS workstation enables a sensitive, high-throughput, end-to-end analysis for detection of genomic alterations and DNA methylation changes from a single low-input cfDNA or tumor DNA sample.

Citation Format: Ashraf Wahba, Tony Ho, Sarah Johns, Aswati Aravind, Heng Wang, Neelima V. Mehendale, Gilbert P. Amparo, Khine Win, Manuel Gomez, Grace Zhao, Douglas N. Roberts. Bravo automation of Agilent Avida targeted enrichment for high-throughput detection of genomic alteration and DNA methylation [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 2291.
Abstract 2340: STRUMP-I: Structure-based binding prediction of MHC class I
Authors: Voshall Adam , Park Woongyang , Lee Eunjung Alice , Choi Yoonjoo
Published: March 2024

The presentation of short peptides derived from endogenously expressed proteins within the Major Histocompatability Complex-I (MHC-I), together known as the pMHC, allows the adaptive immune system to monitor the internal functioning of a cell and surveil for foreign or mutated self-proteins. With the rising importance of immunotherapies targeting neoantigens in cancers, the ability to accurately predict which peptides will bind to the diverse population of MHC alleles is critically important. Computational methods for predicting MHC/peptide interactions fall into two broad categories: sequence-based methods that utilize machine learning or deep learning to predict binding from information about the MHC and peptide sequence alone, and structure-based methods that leverage the computed structure and energetics of the pMHC to predict binding. While sequence-based methods have outperformed structure-based methods, their performance varies with the quantity and quality of training data for each MHC allele. The pMHC structure also provides additional insights into downstream analyses, such as predicting the immunogenicity of cancer neoantigens, that cannot be determined from the sequence alone. We developed a STRUMP-I (STRUcture-based pMHC Prediction (for class I)), a novel pMHC binding prediction tool that combines structural modelling with a machine learning-based classifier to discriminate binders from non-binders. STRUMP-I has comparable performance to the state-of-the-art sequence-based methods on data taken from IEDB, the HLAthena training set, TESLA, PRIME, and an in-house cancer neoantigen dataset. However, it generalizes better to alleles with low representation or a lower proportion of positive examples in the training data than the sequence-based methods. Additionally, we demonstrate how STRUMP-I can be used in conjunction with PRIME, a sequence-based immunogenicity prediction method, to use structural information about the peptide to filter out false positive predictions and increase the precision of immunogenicity predictions, increasing the precision by up to 2-fold. Further, on a set of 10 experimentally validated peptides from the in-house cancer neoantigen dataset containing only a single immunogenic peptide, STRUMP-I filtered all false positive predictions and retained only the true positive prediction. By leveraging structural information about the pMHC, STRUMP-I provides robust binding predicting performance across MHC alleles and increases the precision of immunogenicity prediction for neoantigen screening.

Citation Format: Adam Voshall, Woongyang Park, Eunjung Alice Lee, Yoonjoo Choi. STRUMP-I: Structure-based binding prediction of MHC class I [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 2340.
Abstract 2356: NAV-006: A next-generation rituximab targeting CD20 for the treatment of B-cell lymphomas immunosuppressed by MUC16/CA125
Authors: Grasso Luigi , Kline J. Bradford , Nicolaides Nicholas C.
Published: March 2024

Rituximab is a CD20-targeting antibody that is the standard-of-care for patients with Non-Hodgkin Lymphoma (NHL) cases. Rituximab’s mechanism of action includes complement-dependent cytotoxicity (CDC) and antibody-dependent cellular cytotoxicity (ADCC), herein referred to as Humoral Immuno-Oncology (HIO) mechanisms. Recent clinical evidence suggest that high serum levels of the MUC16 (CA125) protein inversely correlate with the effectiveness of rituximab clinical activity in 40-50% of follicular lymphoma (FL) as well as diffuse large B-cell lymphoma patients with newly diagnosed or relapsed/refractory (R/R) disease. In this study we demonstrated that CA125 binds to and suppresses the activity of rituximab, tafasitamab as well as the bispecific mosunetuzumab and glofitamab antibodies, which are approved for treating cases with indolent disease. These therapies have an overall response rate around 50-60%, suggesting the presence of a mechanism that allows lymphoma cells to escape these agents’ immune-mediated killing effects. CA125 may facilitate this immunosuppressive mechanism, and in fact, upon binding rituximab, CA125 reduces its affinity for the Fc receptor, CD16a, thus suppressing ADCC. Using a proprietary technology called Block-Removed Immunoglobulin Technology (BRITE) that employs randomized amino acid substitution and HIO effector function screening, we have identified a rituximab variant named NAV-006. NAV-006 is refractory to the immunosuppressive effects mediated by CA125 via its reduced CA125 interaction and increased HIO activity as compared to parent rituximab as well as the other antibodies used to treat R/R FL. In an in vivo model of human B-cell lymphoma, NAV-006 showed superior efficacy compared to parent rituximab. These data warrant further investigation of NAV-006 as a next generation anti-CD20 antibody that could improve upon the efficacy of antibody-mediated therapies used to treat NHL patients with high levels of CA125.

Citation Format: Luigi Grasso, J. Bradford Kline, Nicholas C. Nicolaides. NAV-006: A next-generation rituximab targeting CD20 for the treatment of B-cell lymphomas immunosuppressed by MUC16/CA125 [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 2356.
Abstract 2431: Identification of highly expressed exosomal RNAs derived from pancreatic cancer cell lines and exploration of their potential as biomarkers
Authors: Rong Yuhan , Okubo Naoki , Kobayashi Noritoshi , Katsuta Eriko , Ichikawa Yasushi
Published: March 2024

Background: Not all exosomes in the blood of cancer patients originate from cancer cells. This study evaluated the relationships between mRNAs and miRNAs in pancreatic cancer (PC) cell lines and those in exosomes secreted into the supernatant. We aimed to identify candidates for PC biomarkers from cancer-specific exosomal mRNAs and miRNAs.

Materials and Methods: Three PC cell lines were utilized. Exosomes were isolated from the supernatant, and cellular and exosomal mRNAs and miRNAs were extracted. Subsequently, RNA sequencing (RNA-seq) was performed, and the data were analyzed using R software.

Results: In the MIAPaCa-2 cell line, the expression of cellular mRNAs and corresponding exosomal mRNAs showed a strong correlation. In the other two cell lines, a moderate correlation was observed. Across all three cell lines, cellular miRNAs and corresponding exosomal miRNAs exhibited moderate correlation. We focused on RNAs that were lowly expressed in cells but highly expressed in exosomes and conducted differential expression analysis using R. Compared with healthy volunteers in the GEO database, some RNAs showed high expression in the supernatant and low expression in the plasma of healthy volunteers.

Conclusion: We identified three mRNAs and three miRNAs that may serve as promising biomarker candidates for PC.

Citation Format: Yuhan Rong, Naoki Okubo, Noritoshi Kobayashi, Eriko Katsuta, Yasushi Ichikawa. Identification of highly expressed exosomal RNAs derived from pancreatic cancer cell lines and exploration of their potential as biomarkers [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 2431.
Abstract 2449: Case report: DETECT-A participants with pre-malignant conditions
Authors: Choudhry Omair A. , Kharge Angana , Rego Seema P. , Elias Paul Z. , Buchanan Adam H. , Lennon Anne Marie , Papadopoulos Nickolas , Diehl Frank , Beer Tomasz M.
Published: March 2024

Background: Blood based tests for multi-cancer early detection (MCED) are being developed to facilitate the earlier detection of various cancer types. The Detecting cancers Earlier Through Elective mutation-based blood Collection and Testing (DETECT-A) study evaluated the CancerSEEK MCED test, an early version of the Exact Sciences MCED test in development, in 9,911 women, age 65-75, without previous history of cancer (Lennon et al., Science 2020). The degree to which MCED testing will facilitate detection of precancerous conditions or incidental findings is unclear. Here we focus on DETECT-A participants who had pre-cancerous conditions diagnosed during a diagnostic work-up for a positive CancerSEEK MCED test.

Methods: In a post-hoc analysis, we report on the detection of precancerous conditions consequent to CancerSEEK MCED testing and follow-up. Electronic health records were reviewed for diagnostic procedures performed, details of premalignant and cancer diagnoses, and vital status.

Results: In three individuals, mutations in PIK3CA, TP53, or KRAS genes led to a positive CancerSEEK MCED test result. The prescribed imaging protocol using 2-deoxy-2[fluorine-18] fluoro-D-glucose positron emission tomography-computed tomography (18-FDG PET-CT), revealed a 10.3 × 9.8 × 7.8(cm) ovarian mucinous cystadenoma, a 0.8 cm appendiceal mucinous neoplasm, and 3 colonic polyps displaying high-grade dysplasia. All three participants were diagnosed with clinically significant pre-cancerous lesions, subsequently underwent surgical treatment, and remain alive and cancer-free as of February 2023 (Table 1).

Conclusion: The diagnostic evaluation of a positive MCED test may occasionally reveal clinically significant pre-cancerous conditions amenable to interventions. The frequency of such findings and their clinical impact warrants further study.

Citation Format: Omair A. Choudhry, Angana Kharge, Seema P. Rego, Paul Z. Elias, Adam H. Buchanan, Anne Marie Lennon, Nickolas Papadopoulos, Frank Diehl, Tomasz M. Beer. Case report: DETECT-A participants with pre-malignant conditions [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 2449.
Abstract 2460: Receptor antibody conjugated engager (RACE): A novel bispecific 4-1BB engager platform for enhanced immuno-oncology therapy
Authors: Lee DaeHee , Yoon Jihye , Jeong Jonggwan , Bak Jeonghyeon , Son KkaBi , Kim Heechan , Jang Seil , Kim Minseok S.
Published: March 2024

Background: Traditional immuno-oncology strategies, such as checkpoint blockade therapy, are evolving to immune cell engagers as a smarter strategy. The early successes of Blincyto, a CD3 engager, demonstrated its capacity to activate host pan-T cells irrespective of their TCR-pMHC restriction status. However, this broad activation has been linked to off-target immunotoxicities, thus limiting its therapeutic applicability. In response, targeting immune co-stimulatory receptors like CD28 or 4-1BB has gained attention by their expression being induced on activated immune effector cells, presenting a more targeted approach to cancer therapy.

Methods: We developed RACE, a novel bispecific 4-1BB engager. This platform fuses a 4-1BB ligand (4-1BBL) trimer with antibody F(ab’)2 fragments, excluding Fc domains. A Key and lock design on the 4-1BBL trimer interface facilitates asymmetric assembly of 4-1BBL dimer and monomer in the endoplasmic reticulum, achieving over 95% assembly efficiency in mammalian systems.

Results: RACE differs from conventional 4-1BB agonistic antibodies in its ability to form natural hexagonal hyper-clusters of 4-1BB receptors, enhancing NF-κB signal transduction. Unlike first-generation 4-1BB antibodies, which incurred off-tumor hepatotoxicity, RACE selectively activates 4-1BB receptors only in the presence of tumor antigens. Enhanced cytotoxicity requires successful TCR signaling complex formation between T cells and cancer cells. In CT26 and MC38 tumor models, RACE not only induced strong anti-tumor effects without hepatic or systemic toxicities but showed synergistic efficacy with anti-PD-1 antibodies as well.

Conclusion: The novel RACE platform represents a potent as well as safe immuno-oncology strategy, demonstrating significant potential for clinical application.

Citation Format: DaeHee Lee, Jihye Yoon, Jonggwan Jeong, Jeonghyeon Bak, KkaBi Son, Heechan Kim, Seil Jang, Minseok S. Kim. Receptor antibody conjugated engager (RACE): A novel bispecific 4-1BB engager platform for enhanced immuno-oncology 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 2460.
Abstract 2474: Antitumoral efficacy of ASKG812, a Smartkine® based bifunctional PD-1-eIL-2 molecule, through enhancing T effector cis agonism
Authors: Yu Chunxiao , Shanebeck Kurt , Yu Shiguang , Ruiz Jeanine , Li Shichang , Shi Stone D.-H , Ma Hong , Lu Yuefeng
Published: March 2024

Cytokines are potent molecules, yet their broad application as therapeutics has been significantly hampered due to short PK, severe systemic toxicity, and narrow therapeutic window. To improve the developability of cytokines, AskGene has invented a proprietary cytokine platform (Smartkine®) to achieve its overarching objective of modulating immune reactions at a disease site in a selective and controlled manner. Several antibody-cytokine fusion molecules using the SmartKine® platform have been moving into preclinical and clinical development. ASKG812 is a unique fusion molecule composed of anti-PD-1 antibody and engineered IL-2 (eIL-2). The eIL-2 moiety also comprises a specific mask such that the eIL-2 molecule binding biases towards PD-1+ T effector cells in a cis agonism manner for improved efficacy and therapeutic window. In ex vivo human PBMC assays, we demonstrated that ASKG812 significantly reduced activity in PD-1− T and NK cells, and enhanced activity in PD-1+ T cells judged by levels of pSTAT5, Ki67 and Granzyme B. In a cytotoxicity assay, ASKG812 can efficiently induce PBMC-mediated killing of MDA-MB-231 tumor cells in a dose-dependent manner. Moreover, in both anti-PD-1 therapy responsive and non-responsive syngeneic mouse tumor models, ASKG812 showed robust efficacy; without noticeable toxicity compared to a reference anti-PD-1-IL-2v fusion molecule. In conclusion, these findings provide the basis for the development of this new generation of PD-1 cis-targeted IL-2R agonists with enhanced therapeutic potential for the clinical treatment of cancer.

Citation Format: Chunxiao Yu, Kurt Shanebeck, Shiguang Yu, Jeanine Ruiz, Shichang Li, Stone D.-H Shi, Hong Ma, Yuefeng Lu. Antitumoral efficacy of ASKG812, a Smartkine® based bifunctional PD-1-eIL-2 molecule, through enhancing T effector cis agonism [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 2474.
Abstract 2487: KRAS and TP53 co-mutation predicts benefit of immune checkpoint blockade in lung adenocarcinoma
Authors: Budczies Jan , Romanovsky Eva , Kirchner Martina , Neumann Olaf , Blasi Miriam , Schnorbach Johannes , Shah Rajiv , Bozorgmehr Farastuk , Savai Rajkumar , Stiewe Thorsten , Peters Solange , Schirmacher Peter , Michael Thomas , Kazdal Daniel , Christopoulos Petros , Stenzinger Albrecht
Published: March 2024

PD-L1 protein expression is the most important predictive biomarker for immune checkpoint inhibition (ICI) in advanced non-small cell lung cancer (NSCLC), but has limited sensitivity and specificity. We analyzed the potential of activating KRAS and pathogenic TP53 mutations to provide additional predictive information. The study cohort included 713 consecutive immunotherapy patients with advanced lung adenocarcinomas of the Thoraxklinik Heidelberg who were negative for actionable EGFR and ALK/RET/ROS1 alterations. Two external cohorts of patients treated with immunotherapy (SU2C-ICI: n=247, MSK-ICI: n=135) and two external cohorts of surgical early stage patients were additionally analyzed (TCGA-LUAD: n=417, MSK-LUAD: n=394). Therapy benefit was assessed stratified by KRAS and TP53 mutations. RNA-Seq data of TCGA were analyzed to reveal the molecular characteristics of KRASmut/TP53mut tumors. Analyzing overall survival, an interaction between KRAS and TP53 mutations was observed in univariate and multivariate analyses (HR=0.56, p=0.0044 and HR=0.53, p=0.0021). KRASmut/TP53muts tumors performed better than tumors not harboring the dual mutation configuration (HR=0.71, CI 0.55-0.92). This observation could be confirmed in the external cohorts of immunotherapy patients (SU2C-ICI: HR=0.54, CI 0.28-1.03 and MSK-ICI: HR=0.35, CI 0.14-0.88), whereas KRASmut/TP53mut was not associated with prolonged survival in the surgical cohorts. Tumor mutational burden, proliferation (measured by TOP2A mRNA expression), and PD-L1 mRNA were significantly higher in TP53mut compared with TP53wt tumors, regardless of KRAS status. Genome-wide mRNA expression analysis revealed 64 genes including the chemokine CX3CL1 (fractalkine) as specific transcriptomic characteristic of KRASmut/TP53mut tumors. In summary, KRAS/TP53 co-mutation predicts ICI benefit in univariate and multivariate survival analyses and is associated with unique molecular tumor features. Further validation studies are warranted. Mutation testing of the two genes can be easily implemented using small gene panels or even single gene analyses.

Citation Format: Jan Budczies, Eva Romanovsky, Martina Kirchner, Olaf Neumann, Miriam Blasi, Johannes Schnorbach, Rajiv Shah, Farastuk Bozorgmehr, Rajkumar Savai, Thorsten Stiewe, Solange Peters, Peter Schirmacher, Thomas Michael, Daniel Kazdal, Petros Christopoulos, Albrecht Stenzinger. KRAS and TP53 co-mutation predicts benefit of immune checkpoint blockade in lung adenocarcinoma [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 2487.
Abstract 2497: Extracellular vesicle based ALPPL2 and THBS2 as biomarkers for disease monitoring in patients with pancreatic ductal adenocarcinoma
Authors: Halder Kuntal , Jameson Gayle , Borazanci Erkut , Lin Wei , Cridebring Dereck , Von Hoff Daniel , Han Haiyong
Published: March 2024

Pancreatic ductal adenocarcinoma (PDAC) remains a formidable challenge in the realm of oncology, characterized by its aggressive nature and resistance to treatment. Several therapeutic regimens have been shown to extend patient survival, but the majority of the patients become refractory to the treatments in a short period of time. Hence, it is critical to monitor a patient’s response to treatment in a timely manner so that different treatment regimens can be considered promptly. Currently, CA19-9 is the most common blood-based marker being used to monitor disease burden in patients with PDAC. However, 15-20% of patients with PDAC do not have elevated blood CA19-9 levels. In this study, we sought to determine the utility of two circulating extracellular vesicle (EV) based protein biomarkers, ALPPL2 (Alkaline phosphatase, placental-like 2) and THBS2 (Thrombospondin 2), for disease monitoring in patients with PDAC. We first established and optimized EV assays using the ExoViewTM platform for detecting and quantifying the number of ALPPL2+ or THBS2+ EVs in serum samples. We then determined the concentrations of ALPPL2+ or THBS2+ EVs in samples from healthy individuals and longitudinal samples from patients with Stage IV PDAC undergone treatment. The longitudinal samples were from 26 patients of which 16 were CA19-9 secretors (defined as >35 U/ml) and 10 were CA19-9 non-secretors (defined as <35 U/ml) that were treated with various regimens for 4-24 months with monthly blood sample collection and CT scans (a total of 305 samples). We found that the concentrations of ALPPL2+ and THBS2+ EVs are on average 1,737 and 1,113 times higher in PDAC patients than in the healthy controls, respectively. Correlation analysis using the mixed linear model showed that the concentrations of both ALPPL2+ and THBS2+ EVs significantly correlate with changes in tumor size (based on RECIST measurements) in the longitudinal samples of CA19-9 non-secretors or secretors. In CA19-9 non-secretors the correlation p values are 0.003 and 0.006 for ALPPL2+ and THBS2+ EVs, respectively, whereas in CA19-9 secretors, the p values are 0.014 and 0.016 for ALPPL2+ and THBS2+ EVs, respectively. Our data indicates that EV based ALPPL2 and THBS2 could potentially serve as biomarkers for disease monitoring in patients with PDAC. (This work was supported in part by the Dorrance Family Fund and the Flinn Foundation)

Citation Format: Kuntal Halder, Gayle Jameson, Erkut Borazanci, Wei Lin, Dereck Cridebring, Daniel Von Hoff, Haiyong Han. Extracellular vesicle based ALPPL2 and THBS2 as biomarkers for disease monitoring in patients with pancreatic ductal adenocarcinoma [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 2497.
Abstract 2601: Potent antitumor activity of anti-HER2 antibody-topoisomerase I inhibitor conjugate based on self-immolative dendritic dimeric-linker
Authors: Liubomirski Yulia , Tiram Galia , Scomparin Anna , Gnaim Samer , Das Sayantan , Gholap Sachin , Ge Liang , Yeini Eilam , Shelef Omri , Zauberman Arie , Berger Nir , Kalimi Doron , Toister-Achituv Mira , Schröter Christian , Dickgiesser Stephan , Tonillo Jason , Shan Min , Deutsch Carl , Sweeney-Lasch Stanley , Shabat Doron , Satchi-Fainaro Ronit
Published: March 2024

Antibody-drug conjugates (ADCs) are a rapidly expanding class of anticancer therapeutics, with 14 ADCs already approved worldwide. We developed unique linker technologies for the bioconjugation of drug molecules with controlled-release applications. We synthesized cathepsin-cleavable ADCs using a dimeric prodrug system based on a self-immolative dendritic scaffold, resulting in a high drug-antibody ratio (DAR) with the potential to reach 16 payloads due to its dendritic structure, increased stability in the circulation and efficient release profile of a highly cytotoxic payload at the targeted site. Using our novel cleavable linker technologies, we conjugated the anti-human epidermal growth factor receptor 2 (anti-HER2) antibody, trastuzumab, with topoisomerase I inhibitors, exatecan or belotecan. The newly synthesized ADCs were tested in vitro on mammary carcinoma cells overexpressing human HER2, demonstrating a substantial inhibitory effect on the proliferation of HER2-positive cells. Importantly, a single dose of our trastuzumab-based ADCs administered in vivo to mice bearing HER2-positive tumors, showed a dose-dependent inhibition of tumor growth and survival benefit, with the most potent antitumor effects observed at 10 mg/kg, which resulted in complete tumor regression and survival of 100% of the mice. Overall, our novel dendritic technologies using the protease-cleavable Val-Cit linker present an opportunity for the development of highly selective and potent controlled-released therapeutic payloads. This strategy could potentially lead to the development of novel and effective ADC technologies for patients diagnosed with HER2-positive cancers. Moreover, our proposed ADC linker technology can be implemented in additional medical conditions such as other malignancies as well as autoimmune diseases that overexpress targets, other than HER2.

Citation Format: Yulia Liubomirski, Galia Tiram, Anna Scomparin, Samer Gnaim, Sayantan Das, Sachin Gholap, Liang Ge, Eilam Yeini, Omri Shelef, Arie Zauberman, Nir Berger, Doron Kalimi, Mira Toister-Achituv, Christian Schröter, Stephan Dickgiesser, Jason Tonillo, Min Shan, Carl Deutsch, Stanley Sweeney-Lasch, Doron Shabat, Ronit Satchi-Fainaro. Potent antitumor activity of anti-HER2 antibody-topoisomerase I inhibitor conjugate based on self-immolative dendritic dimeric-linker [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 2601.