bluuebunny/crossref_metadata_2025 huggingface dataset:
Abstract 2006: Deciphering the interplay of β-catenin/YAP signaling and alveolar lineage plasticity during targeted therapy in non-small cell lung cancer
Authors: Chou Yu-Ting , Wu Wei , Kerr Daniel , Slota Macey , Bivona Trever
Published: March 2024

Molecularly targeted therapies have significantly enhanced clinical outcomes by directly addressing oncogenic driver mutations in genes such as EGFR. However, despite the success of treatments targeting these mutations, long-term patient survival remains limited. This study investigates the molecular mechanisms underlying drug-tolerance in response to targeted therapies in non-small cell lung cancer (NSCLC). Using single-cell RNA sequencing of oncogene-driven human NSCLCs at the residual disease (RD) state during active targeted therapy, our investigation reveals an increase of an alveolar type I/II (AT1/2) mixed lineage program in surviving cancer cells, resembling an alveolar cell-like state. We observed increased WNT3A/4 ligands, FZD2 receptors, β-catenin signaling, and AT1/2 signatures at the RD stage. Consistent with clinical results, AT1/2 signatures and target genes of β-catenin and YAP are increased in drug-tolerant persister (DTP) cells in preclinical models. Additionally, we discovered that β-catenin and YAP form a stable nuclear protein complex in DTP cells. Disrupting β-catenin/YAP protein expression and stability in DTP cells by knocking down FZD2 or interrupting the destruction complex of β-catenin/YAP leads to re-sensitization to the EGFR inhibitor Osimertinib, suggesting a potential therapeutic approach. Furthermore, this therapeutic strategy decreased AT1/2 gene signatures. Our results highlight an interdependence between β-catenin and YAP, with both proteins playing crucial roles in sustaining DTP cells and promoting the alveolar cell like lineage plasticity. These findings shed light on the complex interplay between β-catenin/YAP signaling and alveolar signatures in the residual cancer state, offering mechanistic insights and potential therapeutic strategies to address drug tolerance and improve clinical outcomes.

Citation Format: Yu-Ting Chou, Wei Wu, Daniel Kerr, Macey Slota, Trever Bivona. Deciphering the interplay of β-catenin/YAP signaling and alveolar lineage plasticity during targeted therapy in non-small cell lung 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 2006.
Abstract 2063: Using the edge wells in 96-well plates without increasing variability in cytotoxicity assays through thermal controls
Authors: Henn Alicia D. , Darou Shannon , Yerden Randy
Published: March 2024

There are very few things as fundamental to cancer research as the 96-well-plate, yet edge effect has continued to cause problems since its introduction. The most common remedy for edge effect is to avoid using edge wells altogether, which eliminates 37% of the plate from the assay. If all of those wells could be used, an estimated USD $119M could be saved in research costs annually across the globe. We have shown previously that maintaining constant thermal control of plating conditions reduces variability in stem cell toxicity assays. Here, we ask the question: can we use the edge wells in cancer screening assays if we control thermal changes that happen in the traditional lab as cells are plated at room temperature and incubated at 37 degrees C? We had the null hypothesis that including the edge wells would add variability to an A549 cytotoxicity assay, even if the cell handling and incubation temperatures were matched and held constant. We plated A549 cells at either room temperature (like a BSC) or at 37 degrees C using the Xvivo System, which maintains constant temperature, oxygen, CO2, and relative humidity levels around cell handling operations. The cells were treated with serial dilutions of peracetic acid/hydrogen peroxide solution. After incubation for 3 days, the plates were stained with Crystal Violet and assessed for cell density (n=3 separate experiments). The null hypothesis was disproven. We found that if the plates were maintained at 37 degrees C during cell handling as well as incubation, that cell distribution was random and even across all wells, even edge wells. We found that there was no statistical difference between edge well and center well results in cytotoxicity assays. Edge wells were usable without increasing variability in the assays. This is consistent with earlier findings showing that when temperature changes between cell plating and incubation were averted, stem cell distribution across the plate was random and the edge effect was eliminated.

Citation Format: Alicia D. Henn, Shannon Darou, Randy Yerden. Using the edge wells in 96-well plates without increasing variability in cytotoxicity assays through thermal controls [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 2063.
Abstract 2070: Engineered Inhalation nanoparticle formulation for lung cancer
Authors: Tiwari Rahul , Ghali Eswara N. , Chauhan Neeraj , Kashyap Vivek , Chauhan Subhash C. , Yallapu Murali M.
Published: March 2024

Background: Lung cancer is a predominant cause of cancer-related morbidity and mortality across the world including in the United States. Treatment modalities for lung cancer include surgery, chemotherapy, radiotherapy, and/or targeted therapies depending on the cancer stage. Despite the survival benefits of chemotherapy, its value is offset by severe systemic side effects such as renal and/or hepatic toxicity or insufficient amounts of drug reaching to the target site. Such pitfalls can be handled by inhalable therapy which avoids first-pass metabolism and increases patients' compliance. In this study, we have investigated the inhalable therapy of cross-linked tannic acid-based nanoparticles (CTA NPs) into cancer cells and determined the synergistic effect of gambogic acid (GA) and gemcitabine (Gem).

Methods: The CTA NPs formulations were characterized for particle size, chemical composition, and drug loading efficiency using various physicochemical methods (FT-IR, DSC, SEM, and TGA). Cellular uptake of CTA NPs was evaluated in lung cancer cell lines (A549 and NCI-H1299) using fluorescence microscopy and flow cytometry analysis. Further, the therapeutic efficacy of GA-Gem encapsulated CTA NPs (G-G CTA NPs) formulation was determined by various in vitro assays (CCK-8, mucoadhesion Boyden chamber, and apoptosis assays). The molecular effects of G-G CTA NPs formulation were also observed in lung cancer cell lines.

Results: Our novel CTA NPs formulation provided an average size of 110 nm in dynamic light scattering with a sustained release of the drug(s). CTA NPs formulation showed a remarkable mucoadhesion and mucopenetration penetration potential in-vitro model(s). Cellular uptake studies show that CTA NPs formulation allows for effective endosomal release into the cytosol. Additionally, the G-G CTA NPs formulation showed superior in vitro anti-cancer activity in lung cancer cells (A549 and NCI-H1299) compared to free drugs.

Conclusions: Taken together, our results demonstrate that G-G CTA NPs formulation exhibits superior anti-cancer potential than free drug against lung cancer and could be a novel therapeutic modality for the management of lung cancer.

Citation Format: Rahul Tiwari, Eswara N. Ghali, Neeraj Chauhan, Vivek Kashyap, Subhash C. Chauhan, Murali M. Yallapu. Engineered Inhalation nanoparticle formulation for lung 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 2070.
Abstract 2103: Small extracellular vesicles derived from macrophages show anti-tumor effects in MDA-MB-231 cells
Authors: Desai Parth , Kumari Anjali , Abdullah Saqer Al , Dellinger Kristen
Published: March 2024

Triple-negative breast cancer is the primary cause of death in women globally due to the absence of targeted receptors on the tumor, making it hard to treat. In addition, the rapid spread of triple-negative breast cancer makes it difficult to manage using current treatment options such as lumpectomies, mastectomies, radiation, and chemotherapy. The survival rate for patients with triple-negative breast cancer is only 8-16%. Therefore, there is a critical need to develop new and effective treatment options. The objective of this study was to investigate the potential of M1 macrophage-derived exosomes to induce cancer cell apoptosis. To test this, we isolated M1 macrophage-derived exosomes to see their effects on triple-negative breast cancer MDA-MB-231 cells. We induce polarization in RAW 264.7 macrophage cells via lipopolysaccharide (LPS). Macrophage polarization was characterized using an enzyme-linked immunosorbent assay (ELISA), real-time PCR, nitric oxide production, and bright field microscopy. We characterized exosomes using nanoparticle tracking analysis (NTA) and scanning electron microscopy (SEM). The apoptosis marker, caspase 3/7 activation, was assessed using confocal microscopy in MDA-MB-231 cells. M1 macrophage-derived exosomes were isolated, characterized, and incubated with breast cancer cells to see their anticancer effects. Data showed the induction of apoptosis in 48 hours in triple-negative breast cancer cells. We conclude that exosomes derived from M1 macrophages may have the capability to induce apoptosis in triple-negative breast cancer.

Citation Format: Parth Desai, Anjali Kumari, Saqer Al Abdullah, Kristen Dellinger. Small extracellular vesicles derived from macrophages show anti-tumor effects in MDA-MB-231 cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2103.
Abstract 2106: Creating a living public oncology drug resource using PRISM cell line viability screening
Authors: Rees Matthew G. , Kocak Mustafa , Mapa Claudine , Frederick Dennie , Nguyen Ellen , Kalathungal Alvin , Fazio Anthony , Davis John F. , Reeves Emily , Tucci Ariah , Barry Rachael , Harrington Colleen , Eskra Jillian , Ronan Melissa M. , Sellers William R. , Roth Jennifer A.
Published: March 2024

Cancer treatment options are rapidly expanding, with many new targeted agents and therapeutic modalities under development. However, systematic characterization of the cellular effects of emerging drug candidates is limited. Screening such agents against the approximately 900 diverse cancer cell lines in the PRISM assay can provide insights into drug specificity and cancer subtype selectivity and, leveraging the rich genomic and functional characterization of PRISM cell lines, support for annotated mechanisms of action. Our goal was to generate a large, high-quality, oncology-focused dataset that can benefit the cancer research community by characterizing new test agents of high clinical relevance. In the past year, this effort has been utilized to screen a total of 180 test agents with plans to extend testing to an additional 140 over the next year. The collection includes biologics (e.g., cytokines, antibodies, antibody-drug conjugates), targeted protein degraders, and small molecules. Supporting the quality of the screening collection and the robustness of the PRISM assay, the majority of inhibitors (including mutant-selective KRAS inhibitors, and inhibitors targeting the WRN helicase, a preferential vulnerability in cancers with microsatellite instability) tested to date closely mimic the effects of genetic knockout and/or knockdown of their annotated target, as measured by CRISPR and shRNA data available through the Dependency Map Portal (depmap.org). Further, while we observe strong modality-independent co-clustering of test agents annotated to act on the same target(s) (e.g., tucatinib with the antibody-drug conjugates T-DM1 and T-DXd for HER2), intriguing differences in efficacy and selectivity emerge in individual cell line models. All PRISM reference screening data and analyses will be made publicly available through depmap.org to serve as a benchmark for new drug development candidates and to further the efforts of researchers worldwide to match emerging cancer therapies to the patients most likely to benefit.

Citation Format: Matthew G. Rees, Mustafa Kocak, Claudine Mapa, Dennie Frederick, Ellen Nguyen, Alvin Kalathungal, Anthony Fazio, John F. Davis, Emily Reeves, Ariah Tucci, Rachael Barry, Colleen Harrington, Jillian Eskra, Melissa M. Ronan, William R. Sellers, Jennifer A. Roth. Creating a living public oncology drug resource using PRISM cell line viability screening [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 2106.
Abstract 2112: Identification of biomarkers associated with sensitivity to a novel PCNA inhibitor (AOH1996) by CRISPRi screening
Authors: Gu Long , li Ming , Chen Chun-Wei , Hickey Robert J. , Malkas Linda H.
Published: March 2024

Proliferating cell nuclear antigen (PCNA) plays an essential role in regulating DNA synthesis and repair and is essential for cancer cell growth and survival. We discovered a cancer-associated isoform of PCNA (caPCNA), which is ubiquitously and highly expressed in a broad range of cancer cells and tumor tissues but is not significantly expressed in non-malignant cells. Further studies of this novel caPCNA isoform as an anti-cancer drug target led to the identification of a cancer distinct region of PCNA which is partly delineated by the L126-Y133 peptide sequence and the discovery of a small molecule (AOH1996), which binds to this cancer distinct region as shown by crystallization studies. By targeting caPCNA, AOH1996 selectively kills cancer cells by interfering with the resolution of transcription-replication conflicts (TRC). Importantly, it causes no discernable toxicity at 6 times of its effective dose in mice. AOH1996 is currently in a phase 1 clinical trial for adult solid tumors at City of Hope (IND 138273). To identify genes that may be used as biomarkers for patient selection or potential targets for combination therapies, we screened a CRISPR interference (CRISPRi) library, which targets genes that are involved in cell signaling and cell cycle regulation. After culturing transduced cells in the presence of DMSO or 250 nM AOH1996 (corresponding to IC20) in triplicates for 14 generations, we measured the relative abundance of each guide RNA (gRNA) construct. Significant changes in the abundance of the gRNA constructs in AOH1996-treated cells relative to that in DMSO-treated cells were determined by the MAGeCK method. The target genes of the depleted or enriched gRNAs are predominantly involved in DNA repair, cell cycle regulation, and transcription regulation, which is consistent with the action mechanism of AOH1996. We validated the effect of these genes on sensitivity to AOH1996 and identified a panel of target proteins whose up or down-regulation is associated with sensitivity to AOH1996. Some of these proteins are targets of known chemotherapeutic drugs, which may be used in combination with AOH1996 in the clinic.

Citation Format: Long Gu, Ming li, Chun-Wei Chen, Robert J. Hickey, Linda H. Malkas. Identification of biomarkers associated with sensitivity to a novel PCNA inhibitor (AOH1996) by CRISPRi screening [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 2112.
Abstract 2187: Influences of high-fat diet on tumor biology in a mouse model of colorectal cancer
Authors: Mahanty Anindita , Wallingford Cara , Hammontree Revan , Njoka Muturi , Clark Zachary , Rekowski Michaella , Washburn Michael , Davis Jennifer S.
Published: March 2024

Purpose: To test the influence of high-fat diet on tumor biology in the inducible Kras, Apc and p53 (iKAP) model (Boutin, et al Genes & Development 2017, 31:370).

Methods: At weening, both male and female mice were fed either a high-fat (60%) or low-fat (10%) diet for 5-6 weeks prior to tumor induction. Mutant Kras expression was controlled using a tet-on system. Expression of mutant Kras was activated by the addition of doxycycline hyclate in the drinking water. Tumor growth was monitored by bi-weekly endoscopy and calculated as percent luminal occlusion. Tumor biology was assessed with proteomics and phospho-proteomics with comparisons by sex and diet.

Results: In the absence of mutant Kras expression (no doxycycline in drinking water), tumors were larger in females on high-fat diet compared to low-fat diet. Tumor sizes were not significantly different in males or in the presence of mutant Kras expression. Proteomics analyses of tumor tissue identified significantly different patterns by diet in female mice, including altered levels of KIF4, DAB2iP, JNK cascade and JUN kinase activity (Table).

Conclusion: Based on our preliminary data, high-fat diet may alter tumor kinase activities, even in a genetically engineered mouse model. Replication and validation studies are ongoing.

Table of significantly upregulated biologic processes in female mice on high-fat diet compared to lo XXXXXXXXXXXXXXXX XXXXXXXXXXXXXXX

Citation Format: Anindita Mahanty, Cara Wallingford, Revan Hammontree, Muturi Njoka, Zachary Clark, Michaella Rekowski, Michael Washburn, Jennifer S. Davis. Influences of high-fat diet on tumor biology in a mouse model of colorectal 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 2187.
Abstract 2228: Long-term trajectories of functional disability in older adults with cancer
Authors: Nam Gina E. , Mayeda Elizabeth Rose , Zhang Zuo-Feng
Published: March 2024

Background: Older individuals with cancer history have lower risk of developing Alzheimer’s disease (AD). Cognitive impairment is associated with lower functioning in Instrumental Activities of Daily Living (IADL) and Activities of Daily Living (ADL). However, little is known about long-term IADL and ADL trajectories among individuals with cancer, hindering understanding of the underlying biological mechanisms between cancer and AD. We investigated the long-term functional disability trajectories of adults with cancer, comparing them with similarly aged individuals without a cancer diagnosis.

Methods: Our study included 16,006 individuals aged 50 and older without a cancer history at baseline from the Health and Retirement Study. Biennial assessments were conducted from 1998 to 2020, including self-reported cancer status, IADL, and ADL. Linear probability models with repeated measures were used to assess IADL and ADL independence probabilities, adjusting for demographic and socioeconomic covariates.

Results: Among 16,006 participants (mean [SD] baseline age, 66.1 [9.9] years; 9,169 [57.3%] female), 3,723 (23.3%) reported a cancer diagnosis during follow-up. Before cancer diagnosis, individuals who later developed cancer had a higher probability of IADL independence and experienced a slower decline in independence compared to their similarly aged counterparts who remained cancer-free. Probability of IADL independence was 0.05 lower immediately after cancer diagnosis compared to the pre-cancer phase, followed by accelerated independence losses relative to the pre-cancer period. After diagnosis, the rate of decline in probability of IADL independence remained slower for individuals with cancer than their cancer-free counterparts, but differences in the rate of decline were smaller than prior to cancer diagnosis. Similar trends were observed for ADL independence.

Conclusions: We observed a decline in both IADL and ADL independence around the time of cancer diagnosis, possibly attributed to treatments. Overall, individuals with cancer experienced a more gradual loss in functional independence compared to individuals who remained cancer-free, consistent with the documented inverse association between cancer and AD.

Funding information: The current research was supported by the National Cancer Institute of the National Institutes of Health (T32CA009142), T32 Training Grants from the NCI/NIH, and the National Institute on Aging (RF1AG059872).

Citation Format: Gina E. Nam, Elizabeth Rose Mayeda, Zuo-Feng Zhang. Long-term trajectories of functional disability in older adults with 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 2228.
Abstract 2334: Computational methods for optimizing marker selection, clonal lineage reconstruction, and longitudinal tracking of clonal dynamics via circulating tumor DNA (ctDNA)
Authors: Fu Xuecong , Deng Yueqian , Luo Zhicheng , Laframboise William , Bartlett David , Schwartz Russell
Published: March 2024

Background: Technologies for blood-based profiling of tumor DNA (“liquid biopsy”) have offered great prospects for non-invasive early cancer diagnosis, treatment monitoring, and clinical guidance, but further advances in computational models and data analysis to optimize monitoring protocols and develop liquid biopsy as a robust quantitative assay of tumor clonal evolution.

Methods: We propose new computational methods to improve our ability to characterize tumor clonal dynamics from circulating tumor DNA (ctDNA). Our methods address how to apply ctDNA assays most effectively to two distinct questions in profiling tumor clonal dynamics: 1) How to apply longitudinal ctDNA data to refine phylogenetic tree models of clonal evolution, and 2) how to most effectively characterize changes in clonal frequencies that may be indicative of treatment response or tumor progression. We pose these questions computationally in terms of a probabilistic framework for optimally identifying maximum likelihood markers for the preceding tasks and applying measured marker concentrations to their solution. We apply this framework by first evaluating the distribution of plausible clonal lineage models using bootstrap samples over pre-treatment tissue-based genetic variation data, then refining these lineage models and the clonal frequencies we can infer from them over successive longitudinal samples of selected markers.

Results: We tested our method on synthetic data under various model assumptions and showed the method to be effective at refining distribution tree models and clonal frequencies over longitudinal samples so as to minimize measures of tree distance relative to the ground truth. We further apply the methods to a real ovarian cancer case and show their ability to develop and refine a clonal lineage model and assess clonal frequencies.

Conclusion: Our methods show the power of ctDNA assays in conjunction with computational optimization to lead to improved marker selection, clonal lineage reconstruction, and tracking of clonal dynamics, with potential for more precise and quantitative profiling of tumor progression enabling improved clinical decision-making.

Citation Format: Xuecong Fu, Yueqian Deng, Zhicheng Luo, William Laframboise, David Bartlett, Russell Schwartz. Computational methods for optimizing marker selection, clonal lineage reconstruction, and longitudinal tracking of clonal dynamics via circulating tumor DNA (ctDNA) [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 2334.
Abstract 234: Microfluidic chip for drug response studies in non-small cell lung carcinoma patient-derived organoids
Authors: Luan Qiyue , Pulido Ines , Isagirre Angelique , Zhou Jian , Shimamura Takeshi , Papautsky Ian
Published: March 2024

Background. Organoids have been widely accepted as 3D tumor models for patient-specific drug response. However, research involving non-small cell lung cancer (NSCLC) organoids is hampered by the lack of appropriate platforms. Although dome cultures show promising results, the relatively large size variability of patient-derived organoids (PDOs) hinders their application in drug response studies. Here, we report a microfluidic chip for maintaining high uniformity and requiring miniscule sample volume for PDO drug screening.

Methods. The microfluidic chip includes a bottom microwell layer and a top microchannel layer. Each chip has 5 channels for parallel treatment conditions, with 30 U-shaped microwells (400μm dia x 250μm deep) per channel. PDOs were loaded from side channels and trapped by filters adjacent to microwells. NSCLC PDOs F231/F671 (NCI PDMR) were cultured and treated by KRASG12C inhibitor adagrasib (0-2000nM, 72h). PDO drug response was assessed via viability using fluorescent dyes.

Results. On-chip PDO size after one-week incubation exhibited the coefficient of variation (CV) of 28% for F231 and 36% for F671, which was notably lower than measurements obtained using Matrigel dome (126%, n=3) and low attachment plate (80%, n=4). The F231/F671 showed viability >81% after 1wk (n=20). On-chip cytotoxicity results showed that both KRASG12C PDOs exhibited sensitivity to adagrasib, matching the clinical response, with IC50 values of 830 nM (F231) and 1324nM (F671). When cultured with fibroblast (WI-38) supernatant, the cytotoxic effect was mitigated due to the fibroblast-induced resistance, with IC50 increasing ≥2 ×. No statistical difference was observed for the fibroblast effect in the open-format microwells and our microfluidic chip (69.6±16.9% to 80.2±9.0% vs. 69.0±12.2% to 82.2±4.1%, respectively, following 500nM adagrasib for 72h), further underscoring the reliability of our chip for PDOs’ drug response studies. Application of continuous perfusion at 70nL/min yielded no statistical difference in viability from static conditions.

Conclusions. Our microfluidic chip offers uniform PDO growth with perfusion allowing drug screening in almost real time. The on-chip response to adagrasib was clinically relevant. Resistance due to tumor microenvironment (TME) can be readily assessed using fibroblast supernatant, and could be expanded to other TME components in future studies to investigate their impact on treatment resistance.

Citation Format: Qiyue Luan, Ines Pulido, Angelique Isagirre, Jian Zhou, Takeshi Shimamura, Ian Papautsky. Microfluidic chip for drug response studies in non-small cell lung carcinoma patient-derived organoids [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 234.
Abstract 2343: Adapting gene set enrichment analysis to single cell data
Authors: Wenzel Alexander T. , Jun John , Mesirov Jill P.
Published: March 2024

Gene Set Enrichment Analysis (GSEA) is a method for quantifying the activation of pathways and processes in gene expression data. GSEA works by ranking genes and testing if genes in annotated gene sets representing molecular pathways are overrepresented at the top or bottom of the ranked list. Standard GSEA assumes a gene-by-sample matrix with samples falling in two phenotype class labels and ranks genes based on correlation of expression and sample class labels. Single sample (ssGSEA) uses a similar approach to enrichment scoring but ranks genes in a single sample based on their expression. There has been recent interest in using the ssGSEA modality to measure pathway activity in individual cells from single cell RNA-sequencing (scRNA-seq) data. However, we have observed that ssGSEA scores in scRNA-seq cells are prone to uncertainty due to the characteristic sparsity of scRNA-seq data. This is because sparse data leads to large groups of tied genes, that is, genes with equal expression and subsequently equivalent positions in the ranked list. Because ssGSEA, which was designed for bulk gene expression technologies which yield much less sparse data, breaks ties arbitrarily, these ties can lead to variability in enrichment scores that is purely algorithmic and not a result of the underlying biology. To address this issue, we performed benchmarking to characterize the stability of scores using different enrichment scoring statistics, normalization methods, and aggregation of similar single cells. We have implemented the best practices identified using this analysis as Single Cell GSEA (scGSEA), a software tool which we will make freely available to researchers as open-source software to enable robust gene set enrichment scoring in scRNA-seq data.

Citation Format: Alexander T. Wenzel, John Jun, Jill P. Mesirov. Adapting gene set enrichment analysis to single cell 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 2343.
Abstract 2364: Anti-CADM1 chimeric antigen receptor (CAR) is a novel therapeutic strategy against small cell lung cancer
Authors: Katkam Shiva Krishna , Zolov Sergei , Shield Delaney , Chuikov Sergei , Keshamouni Venkateshwar G
Published: March 2024

Small cell lung cancer (SCLC) is a highly aggressive form accounting for 15% of all lung cancers. SCLC is characterized by high proliferative rates, early metastasis, and poor prognosis. The median survival is less than 2 years even in patients with early-stage disease and less than a year in patients with metastatic disease which highlights the need for new therapeutic strategies. Cell Adhesion Molecule (CADM) 1 encodes a glycoprotein which belongs to an immunoglobulin superfamily of cell adhesion molecules responsible for epithelial cell adhesion through its homophilic trans-interaction between the adjacent cells. CADM1 is highly expressed on the cell surface of 80% of the SCLC cells, associated with its neuroendocrine features, along with the expression of Neural Cell Adhesion Molecule (NCAM). CADM1 is known to act as tumor promoter through its interactions with actin binding proteins. Consistently, we observed CADM1 expression in H69, H82, and H510 SCLC cell lines as assessed by western immuno blot. More importantly they were all susceptible to NK mediated cytotoxicity when assessed against NK cell line, NK92. We previously demonstrated that CADM1 mediates NK-mediated immune surveillance in non-small cell lung cancer, suggesting that CADM1 could be a potential immunotherapeutic target for SCLC. Here we report the development of an anti-CADM1 chimeric antigen receptor (CAR) specific for T and NK cells engineered with T and NK cell specific adaptor domains. Assessed the specificity of CARs by expressing them in NK92 cells and testing them against CADM1 expressing and CADM1-null A549 cells as targets. Finally, we evaluated the efficacy of anti-CADM1 CAR-T and CAR-NK cells against SCLC targets and observed a robust killing, largely proportionate to the levels of CADM1 expression in them. We are further assessing the efficacy of anti-CADM1 CAR-T and CAR-NK products in inhibiting tumor growth in NSG mice against SCLC xenografts. Together, these observations demonstrate that targeting CADM1 with CAR-T and CAR-NK cells is a potential new therapeutic strategy for SCLC.

Citation Format: Shiva Krishna Katkam, Sergei Zolov, Delaney Shield, Sergei Chuikov, Venkateshwar G Keshamouni. Anti-CADM1 chimeric antigen receptor (CAR) is a novel therapeutic strategy against small cell lung 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 2364.
Abstract 2382: KY-CLC-mouse: a common light chain bispecific antibody discovery platform
Authors: Peng Hao , Wu Guojin , Hao Feng , He Feng , Gu Yi , Ning Jinying
Published: March 2024

Bispecific antibodies (BsAbs) have emerged as a potent therapeutic tool in cancer treatment, gaining increasing centrality in therapeutic applications. However, the development of bispecific antibodies is hindered by the mispairing of light and heavy chains. In response to this challenge, our company developed the KY-CLC-mouse, featuring an identical κ light chain without the expression of the λ light chain. This mouse shows great promise in bispecific antibody development, as the identical κ light chain, modified from a frequently occurring light chain in mice, pairs with multiple heavy chains. The advantages of such a light chain include good solubility and stability, as well as ease of humanization without post-translational modifications in the complementary-determining regions (CDRs). Furthermore, the CDRs were modified to reduce immunogenicity. This KY-CLC-mouse platform has facilitated the identification of antibodies that specifically target over a dozen antigens, such as PD-1, LAG33, MET, PSMA, and CD28, with KD ranging from 0.1 nM to 10 nM. We apply the knob-in-hole technology to assemble bispecific antibodies, targeting two antigens or different epitopes of the same antigen, following their humanization. Prime examples include fully humanized BsAbs PD1xLAG-3, PDL1xEGFR, PSMAxCD28, and EGFRxB7H3. These bispecific antibodies have an identical light chain and were developed with knob-into-hole technology. With different treatments such as high concentration, low pH, repeated freezing and thawing, and high temperature, the BsAbs show neither aggregation nor degradation, suggesting good developability of these antibodies. Additionally, these BsAbs have a half-life of more than five days in the blood of both mice and monkeys. In conclusion, our common light chain KY-CLC-mouse is a powerful bispecific antibody discovery platform.

Citation Format: Hao Peng, Guojin Wu, Feng Hao, Feng He, Yi Gu, Jinying Ning. KY-CLC-mouse: a common light chain bispecific antibody discovery platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2382.
Abstract 2391: Towards better prediction of treatment resistance: Directly modeling progression from multiple lesions
Authors: Protich Samuel , Stoddard Madison , Yuan Lin , White Douglas , Bottino Dean , Chakravarty Arijit
Published: March 2024

Late-stage cancers in the clinic present as a set of dispersed tumors, each with distinct growth kinetics. As most patients enrolled in trials of experimental anticancer therapeutics have late-stage malignancies, it is important to understand the impact of data analysis methodologies on the ability to detect treatment effect. In particular, we are interested in the potential risk posed by aggregating individual tumor measurements from multiple-lesion clinical data into a single tumor burden measurement, as this may cause a loss of information. In this work, we use quantitative modeling to assess how analyzing multiple lesions separately versus using an aggregated readout affects tumor response and detection of progression free survival and relapse. To assess the impact of data aggregation, we built a two-population clonal dynamics model consisting of sensitive and resistant tumor cells undergoing growth in the presence or absence of treatment. We performed parameter sweeps to assess the impact of individual model parameters on progression free survival and relapse. We then extended these sweeps to the multi-lesion situation, using nonlinear regression to compare parameter values of aggregated models and the parameter values of the individual models that comprised it. From our simulations, the most influential parameters in determining rebound are the growth rate of the resistant cells and the fraction of these cells, while growth rate of sensitive cells and growth rate inhibition affect effectiveness of treatment. In analyzing the multiple lesion model in different situations, we found that estimates for progression free survival were significantly more sensitive when the lesions were analyzed separately, rather than being aggregated. Our work suggests that aggregating the lesions into a single readout loses impact of individual lesion growth rate inhibitions, impairing early detection as the ability to detect fast growing, small, resistant lesions (despite overall tumor burden decreasing) is lost. Taken together, our findings suggest that data aggregation causes a loss of information. Relapse can be predicted at earlier times when using the multiple lesion model compared to an aggregated model.

Citation Format: Samuel Protich, Madison Stoddard, Lin Yuan, Douglas White, Dean Bottino, Arijit Chakravarty. Towards better prediction of treatment resistance: Directly modeling progression from multiple lesions [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 2391.
Abstract 2394: Significance of regional lymph node dissection in patients with clear cell sarcoma and epithelioid sarcoma
Authors: Takemori Toshiyuki , Kobayashi Eisuke , Iwata Shintaro , Ogura Koichi , Osaki Shuhei , Fukushima Suguru , Kawai Akira
Published: March 2024

Objective Clear cell sarcoma (CCS) and epithelioid sarcoma (ES) are common as soft-tissue sarcoma subtypes causing lymph node metastasis (LNM), but the role of regional lymph node dissection is still unclear especially in these patients without imaging evidence of LNM. Here we retrospectively investigated the significance of lymph node dissection for patients with CCS and ES. Methods Forty-one patients (CCS: 13, ES: 28) with no distant metastasis other than in the regional lymph nodes were enrolled in this study. Of these 41 patients, those without LNM on imaging findings were categorized into two groups: "with dissection (WD)" group and "no dissection (ND)" group, respectively. Overall survival (OS), lymph node metastatic-free survival (LNMFS), progression-free survival (PFS), and post-operative LNM rate were compared between two groups. Results There were 26 patients who had undergone regional lymph node dissection and 15 patients who had not undergone regional lymph node dissection (ND group). Histopathological examination revealed metastasis to the lymph nodes in 9 of the 26 patients (38.5%). 9 patients were suspected of having LNM based on preoperative imaging findings such as CT or FDG PET/CT. Among the remaining 17 patients (WD group) in whom LNM was not suspected based on preoperative imaging findings, 6 patients (35.3%) had LNM. OS (p=0.03), LNMFS (p<0.01), and PFS (p<0.01) were all significantly better in the WD group. The postoperative LNM rate was significantly lower in the WD group than in the ND group (p=0.03), and there were no significant differences in OS, LNMFS, or PFS between the CCS and ES groups in terms of histological type. Discussion Even in cases where LNM was not suspected on preoperative imaging, LNM was present in more than 30% of cases. The possibility of regional LNM should be borne in mind in soft-tissue sarcomas, which frequently present with LNM, regardless of imaging findings. We also suggested that simultaneous dissection of the regional lymph nodes at the time of resection of the primary tumor improves the prognosis. Although ES and CCS are ultra-rare sarcomas, further validation with the accumulation of case series is desirable.

Citation Format: Toshiyuki Takemori, Eisuke Kobayashi, Shintaro Iwata, Koichi Ogura, Shuhei Osaki, Suguru Fukushima, Akira Kawai. Significance of regional lymph node dissection in patients with clear cell sarcoma and epithelioid sarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2394.
Abstract 2437: Distinct DNA methylation patterns in male urogenital cancers
Authors: Yu Guopeng , Wang Jiangyi , Li Long , Xie Wenchuan , Liu Yushan , Yang Qing , Xu Bin
Published: March 2024

Background: Male urogenital cancers including prostate cancer (PCa), bladder cancer (BLCA) and kidney renal cancer (KIRC), account for 38% of the total number of new male cancers. Previous studies have shown that changes in DNA methylation patterns are associated with the occurrence and progression of these cancers. Here, we performed whole-genome bisulfite methylation sequencing (WGBS) on tissue samples from these cancers to comprehensively characterize the methylation patterns to provide insights into the potential biological functions of methylation and to identify possible early detection biomarkers.

Methods: Tissue samples were collected from patients with PCa, BLCA and KIRC who had not received any treatment prior to surgery from Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine. Samples with the cancer cells content ≥30% in cancer tissues and no cancer cells in the adjacent tissues was deemed qualified. A total of 43 samples were sequenced by whole-genome bisulfite methylation sequencing (WGBS) with a depth of 30X, including PCa, BLCA, KIRC cancer tissues, and their adjacent cancer tissues.

Results: Distinct methylation patterns were observed in the 3 cancers. By comparing cancer and adjacent tissues, the numbers of differentially methylated sites (DMSs) were 21,195 (31% hyperDMSs and 69% hypoDMSs), 587,010 (23% hyperDMSs and 77% hypoDMSs) and 7,855,162 (5% hyperDMSs and 95% hypoDMSs) in PCa, BLCA and KIRC, respectively. The distribution of hyperDMSs and hypoDMSs across various chromosomes was relatively consistent in KIRC and BLCA. However, in PCa, the hypoDMSs were mainly located on chromosome 8 (5265/14666, 36%). Among the three cancers, only 2-3% of hypoDMSs were located in gene promoter regions, while the proportions of hyperDMSs in gene promoter regions were higher with 4%, 8% and 17% for PCa, BLCA and KIRC, respectively. Among the above DMSs, 1901 DMSs-related genes were shared by PCa, BLCA and KIRC and 251, 4252, 2475 DMSs-related genes were unique in PCa, BLCA and KIRC, respectively. Gene Ontology analysis revealed that the shared DMSs-related genes were enriched in Wnt signaling pathway and positive regulation of MAPK cascade.

Conclusions: Our present study demonstrated the differential methylation patterns in male urogenital cancers, which may provide insights into the potential biological functions of methylation and to identify possible early detection biomarkers.

Citation Format: Guopeng Yu, Jiangyi Wang, Long Li, Wenchuan Xie, Yushan Liu, Qing Yang, Bin Xu. Distinct DNA methylation patterns in male urogenital 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 2437.
Abstract 2445: Peripheral blood immune phenotypes in pancreatic ductal adenocarcinoma
Authors: Pavelko Kevin D. , Villasboas Jose C. , Taylor William R. , Doering Karen A. , Kisiel John B. , Majumder Shounak
Published: March 2024

Introduction: Pancreatic ductal adenocarcinoma (PDAC) is a major cancer killer with a low 5-year survival rate of 12%. Diagnosing PDAC at an early stage is one of the strongest predictors of long-term survival. Therefore, novel methods for early detection of PDAC must be explored. In this pilot study we aimed to compare the peripheral blood immune cell phenotypes in PDAC cases and cancer-free controls.

Method: CyTOF (cytometry by time-of-flight) was used to evaluate peripheral blood mononuclear cells (PBMC) from newly diagnosed treatment naïve patients with PDAC and sex and age matched cancer-free controls using a 29-marker immune phenotyping panel. Multiple analysis approaches including dimensionality reduction using tSNE and clustering using Phenograph were used to evaluate the results. Immune subsets having differential abundance differences were verified by manual gating.

Results: Twenty patients were included in this pilot study (15 PDAC cases; 5 Cancer-free controls). Among the 15 PDAC cases, 5 were early stage (Stage 1-2). Thirty-two unique immune cell clusters were identified using the Phenograph algorithm: 10 unique clusters with properties consistent with monocytes/macrophages, 9 CD4 T cell clusters, 6 CD8 T cell clusters and 4 NK cells clusters. When comparing the case and control groups we noted lower percentages of CD8+CD27+ T-cells in cases. This was further verified by manual gating that confirmed the distribution of CD8+CD27+ T-cells relative to all T-cells were decreased in PDAC patients. In addition, a 57% increase in naïve CD4 T cells was found in case samples compared to controls. A principal component analysis of the clustering results identified two unique clusters of immune profiles that emerged providing a potential peripheral blood immune cell signature that could stratify and differentiate PDAC cases from controls. A CD14+CD16+CD4LoCD38+CD45RO+ population of monocytes was the primary cell population driving this difference.

Conclusion: This study provides early evidence to indicate that a distinct PBMC immune phenotype may differentiate PDAC patients from control subjects. Further analysis in larger sample sets is warranted for in-depth characterization and identification of unique immune based biomarkers for PDAC detection.

Citation Format: Kevin D. Pavelko, Jose C. Villasboas, William R. Taylor, Karen A. Doering, John B. Kisiel, Shounak Majumder. Peripheral blood immune phenotypes in 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 2445.