Patient-derived Tumor Organoids Research Articles

Abstract B025: Luminal-to-basal phenotypic plasticity promotes invasive phenotypes in a live-imaging assay using patient-derived bladder tumor organoids

Abstract Lineage plasticity in cancer is characterized by changes in cell state that are often associated with tumor progression and treatment resistance. While nearly all non-muscle invasive bladder cancer (NMIBC) tumors have a luminal epithelial phenotype, many muscle invasive bladder cancers (MIBC) display a basal identity. NMIBC to MIBC progression may therefore be related to a phenotypic switch from luminal-to-basal subtypes, which in turn may be associated with poorer clinical outcomes. However, current understanding of the molecular processes linking cell plasticity and tumor invasion is limited, due in part to a lack of physiologically relevant in vitro models and assays. To address these questions, we are utilizing a living biobank of 82 patient-derived bladder tumor organoid lines that our group has established. These organoids represent a 3-dimensional, heterogeneous model system for studying bladder cancer, as they can be genetically manipulated and recapitulate the molecular and histopathological features of the parental tumor. Notably, in previous work, we described luminal-to-basal phenotypic plasticity in a subset of organoid lines derived from luminal tumors, which display a shift to basal/squamous identity in culture that is reversible by orthotopic xenografting. In current studies, we are investigating cell migration and invasiveness using a live-imaging assay that we have developed to examine bladder tumor organoid outgrowth in vitro. Importantly, this assay allows longitudinal visualization as well as quantitation of invasiveness over a four-day time span. Analysis of over 25 organoid lines with plastic, stable luminal, and stable basal properties has revealed a broad spectrum of organoid outgrowth phenotypes that do not correlate with cell proliferation or clinical parameters. Instead, the degree of outgrowth correlates precisely with luminal-to-basal phenotypic plasticity, as assessed by transcriptome analyses, immunofluorescence microscopy, and in vivo xenografting. Organoid lines with minimal outgrowth have stable luminal phenotypes, whereas lines that produce their own extracellular matrix to create a leading edge of migrating cells have plastic phenotypes. Furthermore, movies of the invading organoids reveal distinct cell migratory patterns, as several organoid lines display collective migration that generates an invasive front at the leading edge. This collective migration phenotype is distinct from phenotypic plasticity, is at least partially independent from organoid outgrowth, and is undergoing further analysis. Thus, our organoid outgrowth assay identifies two different parameters of invasive potential, one of which correlates with phenotypic plasticity. Our findings characterize bladder tumor invasion patterns for the first time and suggest that lineage plasticity in NMIBC represents a key mechanism that promotes tumor invasion in MIBC. Citation Format: Clementine Le Coz, John R. Christin, Talal Syed, Zejian Wang, Caroline J. Laplaca, Andrew T. Lenis, Michael M. Shen. Luminal-to-basal phenotypic plasticity promotes invasive phenotypes in a live-imaging assay using patient-derived bladder tumor organoids [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr B025.

Biomimetic hydrogels with mesoscale collagen architecture for patient-derived tumor organoids culture

Patient-derived tumor organoids (PDTOs) shows great potential as a preclinical model. However, the current methods for establishing PDTOs primarily focus on modulating local properties, such as sub-micrometer topographies. Nevertheless, they neglect to capture the global millimeter or intermediate mesoscale architecture that have been demonstrated to influence tumor response to therapeutic treatment and tumor progression. In this study, we present a rapid technique for generating collagen bundles with an average length of 90 ± 27 μm and a mean diameter of 5 ± 1.5 μm from tumor tissue debris that underwent mechanical agitation following enzymatic digestion. The collagen bundles were subsequently utilized for the fabrication of biomimetic hydrogels, incorporating microbial transglutaminase (mTG) crosslinked gelatin. These biomimetic hydrogels, referred to as MC-gel, were specifically designed for patient-derived tumor organoids. The lung cancer organoids cultured in MC-gel exhibited larger diameters and higher cell viability compared to those cultured in gels lacking the mesoscale collagen bundle; moreover, their irregular morphology more closely resembled that observed in vivo. The MC-gel-based lung cancer organoids effectively replicated the histology and mutational landscapes observed in the original donor patient’s tumor tissue. Additionally, these lung cancer organoids showed a remarkable similarity in their gene expression and drug response across different matrices. This recently developed model holds great potential for investigating the occurrence, progression, metastasis, and management of tumors, thereby offering opportunities for personalized medicine and customized treatment options.

Enhancing the Efficacy of HIPEC Through Bromelain: A Preclinical Investigation in Appendiceal Cancer.

Appendiceal cancer (AC) excessive mucin production is a barrier to heated intraperitoneal chemotherapy (HIPEC) drug delivery. Bromelain is a pineapple stem extract with mucolytic properties. We explored bromelain treatment effects against mucinous AC in a patient-derived tumor organoid (PTO) model and an AC cell line. PTOs were fabricated from tumor specimens obtained from patients with AC undergoing cytoreductive surgery with HIPEC. PTOs underwent HIPEC treatment with bromelain, cisplatin, and mitomycin C (MMC) at 37°C and 42°C with and without bromelain pretreatment. From October 2020 to May 2023, 16 specimens were collected from 13 patients with low-grade (12/16, 75%) and high-grade AC (4/16, 25%). The mucin-depleting effects of bromelain were most significant in combination with N-acetylcysteine (NAC) compared with bromelain (47% versus 10%, p = 0.0009) or NAC alone (47% versus 12.8%, p = 0.0027). Bromelain demonstrated > 31% organoid viability reduction at 60 min (p < 0.001) and > 66% in 48 h (p < 0.0001). Pretreatment with bromelain increased cytotoxicity of both cisplatin and MMC HIPEC conditions by 31.6% (p = 0.0001) and 35.5% (p = 0.0001), respectively. Ki67, CK20, and MUC2 expression decreased after bromelain treatment; while increased caspase 3/7 activity and decreased Bcl-2 (p = 0.009) and Bcl-xL (p = 0.01) suggest induction of apoptosis pathways. Furthermore, autophagy proteins LC3A/B I (p < 0.03) and II (p < 0.031) were increased; while ATG7 (p < 0.01), ATG 12 (p < 0.04), and Becline 1(p < 0.03), expression decreased in bromelain-treated PTOs. Bromelain demonstrates cytotoxicity and mucolytic activity against appendiceal cancer organoids. As a pretreatment agent, it potentiates the cytotoxicity of multiple HIPEC regimens, potentially mediated through programmed cell death and autophagy.

Bortezomib promotes the TRAIL-mediated killing of resistant rhabdomyosarcoma by ErbB2/Her2-targeted CAR-NK-92 cells via DR5 upregulation

Treatment resistance and immune escape are hallmarks of metastatic rhabdomyosarcoma (RMS), underscoring the urgent medical need for therapeutic agents against this disease entity as a key challenge in pediatric oncology. Chimeric antigen receptor (CAR)-based immunotherapies, such as the ErbB2 (Her2)-CAR-engineered natural killer (NK) cell line NK-92/5.28.z, provide antitumor cytotoxicity primarily through CAR-mediated cytotoxic granule release and thereafter - even in cases with low surface antigen expression or tumor escape - by triggering intrinsic NK cell-mediated apoptosis induction via additional ligand/receptors. In this study, we showed that bortezomib increased susceptibility towards apoptosis in clinically relevant RMS cell lines RH30 and RH41, and patient-derived RMS tumor organoid RMS335, by upregulation of the TRAIL receptor DR5 in these metastatic, relapsed/refractory (r/r) RMS tumors. Subsequent administration of NK-92/5.28.z cells significantly enhanced antitumor activity in vitro. Applying recombinant TRAIL instead of NK-92/5.28.z cells confirmed that the synergistic antitumor effects of the combination treatment were mediated via TRAIL. Western blot analyses indicated, that the combination treatment with bortezomib and NK-92/5.28.z cells increased apoptosis by interacting with the NF-κB, JNK and caspase pathways. Overall, bortezomib pretreatment can sensitize r/r RMS tumors to CAR- and by upregulating DR5, to TRAIL-mediated cytotoxicity of NK-92/5.28.z cells.

Live Imaging to Quantify Cellular Radiosensitivity in Patient-Derived Tumor Organoids.

Radiation therapy (RT) is one of the mainstays of modern clinical cancer management. However, not all cancer types are equally sensitive to irradiation, often (but not always) because of differences in the ability of malignant cells to repair oxidative DNA damage as elicited by ionizing rays. Clonogenic assays have been employed for decades to assess the sensitivity of cultured cancer cells to ionizing irradiation, largely because irradiated cancer cells often die in a delayed manner that is difficult to quantify with short-term flow cytometry- or microscopy-assisted techniques. Unfortunately, clonogenic assays cannot be employed as such for more complex tumor models, such as patient-derived tumor organoids (PDTOs). Indeed, irradiating established PDTOs may not necessarily abrogate their growth as multicellular units, unless their stem-like compartment is completely eradicated. Moreover, irradiating PDTO-derived single-cell suspensions may not properly recapitulate the sensitivity of malignant cells to RT in the context of established PDTOs. Here, we detail an adaptation of conventional clonogenic assays that involves exposure of established PDTOs to ionizing radiation, followed by single-cell dissociation, replating in suitable culture conditions and live imaging. Non-irradiated (control) PDTO-derived stem-like cells reform growing PDTOs with a PDTO-specific efficiency, which is negatively influenced by irradiation in a dose-dependent manner. In these conditions, PDTO-forming efficiency and growth rate can be quantified as a measure of radiosensitivity on time-lapse images collected until control PDTOs achieve a predefined space occupancy.

Tumour organoids and assembloids: Patient-derived cancer avatars for immunotherapy.

Organoid technology is an emerging and rapidly growing field that shows promise in studying organ development and screening therapeutic regimens. Although organoids have been proposed for a decade, concerns exist, including batch-to-batch variations, lack of the native microenvironment and clinical applicability. The concept of organoids has derived patient-derived tumour organoids (PDTOs) for personalized drug screening and new drug discovery, mitigating the risks of medication misuse. The greater the similarity between the PDTOs and the primary tumours, the more influential the model will be. Recently, 'tumour assembloids' inspired by cell-coculture technology have attracted attention to complement the current PDTO technology. High-quality PDTOs must reassemble critical components, including multiple cell types, tumour matrix, paracrine factors, angiogenesis and microorganisms. This review begins with a brief overview of the history of organoids and PDTOs, followed by the current approaches for generating PDTOs and tumour assembloids. Personalized drug screening has been practised; however, it remains unclear whether PDTOs can predict immunotherapies, including immune drugs (e.g. immune checkpoint inhibitors) and immune cells (e.g. tumour-infiltrating lymphocyte, T cell receptor-engineered T cell and chimeric antigen receptor-T cell). PDTOs, as cancer avatars of the patients, can be expanded and stored to form a biobank. Fundamental research and clinical trials are ongoing, and the intention is to use these models to replace animals. Pre-clinical immunotherapy screening using PDTOs will be beneficial to cancer patients. The current PDTO models have not yet constructed key cellular and non-cellular components. PDTOs should be expandable and editable. PDTOs are promising preclinical models for immunotherapy unless mature PDTOs can be established. PDTO biobanks with consensual standards are urgently needed.

Targeting PARG induces tumor cell growth inhibition and antitumor immune response by reducing phosphorylated STAT3 in ovarian cancer

BackgroundOvarian cancer is the most lethal gynecological malignancy, with limited treatment options after failure of standard therapies. Despite the potential of poly(ADP-ribose) polymerase inhibitors in treating DNA damage response (DDR)-deficient...

Abstract 222: Establishment of patient-derived tumor organoids from head and neck cancers for predicting response to treatments

Abstract The risk of relapse or recurrence of Head and Neck Squamous Cell Carcinoma (HNSCC) is high despite the combination of surgery and radiochemotherapy, responsible for high toxicity. It is crucial to develop new therapeutic strategies and to identify patients likely to benefit from these treatments. Patient-Derived Tumor Organoids (PDTO) are three-dimensional multicellular structures derived from patient tumor samples and faithfully reproduce the histological and molecular characteristics of the original tumor. A growing body of research indicates that PDTO may predict the clinical response, representing a major opportunity for the development of new therapeutic strategies and precision medicine. The purpose of this translational study is to generate PDTO from HNSCC patients to evaluate their predictive value. PDTO were obtained after dissociation of tumor specimen of HNSCC patients through the setup of the clinical study ORGAVADS (NCT04261192). Tumor cells were embedded in extracellular matrix and cultured in specific medium. Histological and immunohistochemical characterizations were performed to validate the resemblance between PDTO and their original tumor. Response of PDTO to chemotherapy, radiotherapy and innovative therapies were evaluated by live-cell imaging and viability assays. The culture conditions were optimized to improve the success rate of PDTO establishment which now exceeded 50%. Twenty-one PDTO lines have been established and showed histological characteristics close to the original tumor. Expression of immunohistochemical tumor markers p53, p40, p63, and p16 were similar in tumors and paired PDTO. Functional assays were performed on 15 PDTO to analyze the response to treatments (cisplatin, olaparib, X-Rays) and heterogeneity of response was observed between the models. When clinical response was available, PDTO derived from good responders showed high sensitivity to treatments while PDTO from bad responders showed low sensitivity to treatments. Interestingly, two PDTO lines derived from HPV+ oropharyngeal tumors displayed very high sensitivity to cisplatin, matching with the patient's profile and response. Our results showed feasibility to derive PDTO from HNSCC and to perform functional assay to assess their response to different treatments. The first studies of correlation between PDTO and patient responses are promising and will be further investigated in more patients. This will allow to demonstrate the predictive value of PDTO from HNSCC with the purpose to develop a clinically compatible predictive functional assay. Citation Format: Marion Perréard, Vianney Bastit, Lucie Lecouflet, Guillaume Desmartin, Romane Florent, Corinne Jeanne, Juliette Thariat, Emmanuel Babin, Laurent Poulain, Louis-Bastien Weiswald. Establishment of patient-derived tumor organoids from head and neck cancers for predicting response to treatments [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 222.

Abstract 4727: Large scale drug response comparison across different neuroblastoma cell model systems

Abstract Traditionally neuroblastoma research has predominantly used 2D cell lines, which, despite their simplicity, often fall short in mirroring the physiological complexity of actual tumors. Recently, 3D models like patient-derived tumor organoids (PDO) and patient-derived xenografts (PDX) have emerged as superior alternatives, offering more realistic predictions of patient treatment responses. This study aims to discern the differences in drug response between conventional 2D cell lines and the more advanced 3D neuroblastoma models - specifically, patient-derived organoids (nPDO) and patient-derived xenograft organoids (nPDXO). Employing high-throughput drug screening of 528 cancer drugs, we evaluated the drug responses across traditional 2D cell lines, nPDOs, and nPDXOs. Additionally, focused experiments with 29 selected drugs were conducted to determine the influence of culture topology on drug efficacy. The findings were compared to a study by Hansson et al.1 that used nPDXO. Our study discovered a pronounced difference in drug sensitivity between 2D cell lines and 3D models, with 3D models showing heightened sensitivity. Interestingly, 2D cell cultures had a more heterogenous drug response compared to 3D models. The drug response correlation between nPDOs and nPDXOs was relatively high (Spearman ~0.8), indicating consistent responses across these models. Our comparison underscores the impact of model system choice on drug response studies in neuroblastoma. The study highlights important differences in drug response between neuroblastoma 2D and 3D cell culture models. However, only subtle differences were found between PDO and PDX-derived organoid lines, despite differences in treatment centers and media compositions. This suggests that while the choice of cell culture topology greatly impacts drug response, PDO and PDX derived lines can largely be used interchangeably for drug screening experiments.

Abstract 3093: Combining lab automation with data analysis automation to enable high-throughput screening of patient-derived organoids

Abstract Although patient-derived tumor organoids (PDOs) better-represent patient tumors compared to traditional in vitro cell cultures, limitations of PDO analysis remain a major hurdle for high-throughput screening (HTS) applications. In particular, current PDO analysis fall short in at least 1 of 2 major criteria: 1) accurate recapitulation of patient tumor or 2) scalability. To address this, we have developed an automation-compatible protocol to satisfy these 2 major criteria to facilitate the adoption of PDOs for HTS applications1. Our novel protocol leverages live-cell imaging techniques to capture the dynamic interactions and intricate complexities of PDOs, which allowed for more precise and comprehensive analysis. To further enhance the accuracy and efficiency of our approach, we developed a fully automated image and data analysis pipeline (Orbits). Using label-free detection of organoids from brightfield images, Orbits integrates growth-rate-based drug response metrics with drug synergy metrics to significantly improve the identification of synergistic drug interactions. Here, present the results of our HTS protocol on 10 distinct drug combination strategies, specifically focusing on the repurposed drug candidate Auranofin, a Thioredoxin reductase inhibitor. We screened on 10 PDOs sourced from healthy lung, non-small cell lung cancer, and pancreatic ductal adenocarcinoma. Not only were we able to distinguishing cytostatic from cytotoxic drug responses at a single-organoid level, we identified drug candidates that can synergistically enhanced the efficacy of Auranofin in a tumor selective manner. Our study presents a major step forward in the field of PDO-based drug discovery, offering a robust protocol for HTS and automated data analysis. The implementation of our method will accelerate the discovery of effective therapeutic strategies, ultimately translating to improved patient outcomes. 1 Le Compte, M., et al JoVE 190 (2022) Citation Format: Abraham Lin, Maxim Le Compte, Tyler Gilcrest, Edgar Cardenas De La Hoz, Geert Roeyen, Jeroen Hendriks, Filip Lardon, Christophe Deben. Combining lab automation with data analysis automation to enable high-throughput screening of 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 3093.

Abstract 1216: Pan-RAS inhibition by a tumor-targeted biotherapeutic

Abstract Oncogenic RAS signaling drives tumor growth in about 30% of human malignancies. In recent years the first mutant-specific inhibitors of KRAS G12C (sotorasib and adagrasib) entered the clinic. While some durable responses were noted in KRAS-mutant non-small cell lung cancer, the clinical experience of KRAS G12C inhibitors is marked by rapid drug resistance, either intrinsic or acquired, causing re-activation of the MAPK pathway. Common resistance mechanisms include compensatory signaling through the related RAS isoforms NRAS and HRAS, as well as the selection of non-G12C KRAS mutations, among others. The bacterial peptidase RRSP potently cleaves all RAS mutants and isoforms in the conserved Switch I region. We have shown that receptor-mediated intracellular delivery of RRSP using an engineered protein delivery system (RASx) can inactivate all RAS signaling in a cell, causing apoptosis in RAS-addicted tumor cells in vitro and in vivo. Since systemic pan-RAS inhibition is not likely to be tolerated therapeutically, precise tumor targeting is a necessary feature of a true pan-RAS inhibitor. Here, we describe the unique ability of the RASx system to specify the cell surface receptor used by RRSP to enter cells, allowing exquisite targeting and killing of KRAS, NRAS and HRAS-driven tumor cells while sparing healthy tissues. We screened a panel of patient-derived tumor organoids (PDOs), to demonstrate broad tumor cell killing across pancreatic and colorectal cancer-derived PDOs. 97% of KRAS mutant organoids were sensitive to RASx, independent of the specific mutation. Intriguingly, 46% of wildtype RAS PDOs were sensitive to RASx, including organoids with activating mutations in EGFR. In contrast, PDOs with mutations downstream of RAS such as BRAF V600E were resistant to RASx. Indeed, RASx is effective not only against RAS-addicted tumors, but also wildtype RAS tumors driven by upstream receptor tyrosine kinases, potentially expanding the clinical utility of this platform. RASx is a first-in-class, tumor-targeted pan-RAS inhibitor that represents a unique entry into the growing armamentarium against oncogenic RAS. Citation Format: Greg L. Beilhartz, Huazhu Liang, Molly Udaskin, Christine Ng, Nikolina Radulovich, Roman A. Melnyk. Pan-RAS inhibition by a tumor-targeted biotherapeutic [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 1216.

Abstract 6219: Type V collagen promotes lung adenocarcinoma metastasis by regulating tumor mechanical stress and the implication for prognosis and therapeutic strategies

Abstract Introduction: The mechanical environment of the human body influences physiological and pathological processes, and understanding these biomechanical aspects holds promise for medical research. Tumor microenvironment changes, including extracellular matrix (ECM) alterations, result the changing of mechanical characteristics of the tissue, play a crucial role in cancer progression and metastasis, including lung adenocarcinoma (LUAD), one of a major histology type of lung cancer. This study focuses on elucidating how mechanical characteristics, especially those related to the ECM, influence LUAD and the signaling pathways involved. Methods: Cell culture, transfection, Western blot, immunofluorescence, immunohistochemistry, Transwell assay, scratch wound-healing assay were used to investigate the behavior changes of LUAD cells under different treatment. Bioinformatics analyses, and machine learning-based integrative approaches were employed to build the SVM_Score, which was built with relevant base membrane (BM) genes. Patient-derived tumor organoids, myofibroblasts, and co-culture systems were established. Sorafenib, which can inhibited collagen and fibronectin synthesis, was used to explore the proliferation and migration changing of lung cancer cells co-cultured with myofibroblasts. Results: Mechanical stress, simulated by matrix application, enhanced LUAD cell migration and invasion, correlating with ECM alterations and EMT pathway activation. SVM_Score predicted LUAD patient prognosis and EMT propensity across multiple datasets, revealing its robust prognostic capabilities. Lower SVM_Scores were associated with worse survival outcomes, increased cancer-related pathways, higher Tumor Mutation Burden and altered immune microenvironment characteristics. SVM_Score was also linked to myofibroblast-secreted COL5A1, a key marker for mechanical stress. Patient tissues with low SVM_Scores exhibited higher COL5A1 expression, enhanced EMT propensity, and increased internal mechanical stress. Sorafenib, by inhibiting COL5A1 secretion, attenuated the pro-tumor effects of myofibroblasts, inhibiting proliferation and migration of LUAD cells, and rendering LUAD cells more sensitive to chemotherapy. Conclusion: This comprehensive study unveils the intricate relationship between mechanical stress, ECM alterations, and LUAD progression. SVM_Score emerges as a potent prognostic tool, reflects tumor mechanical characteristics. Sorafenib intervention targeting COL5A1 secretion provides a potential therapeutic strategy to mitigate LUAD aggressiveness. These findings contribute to a deeper understanding of the biomechanical aspects of LUAD, offering insights for future research and clinical applications. Citation Format: Guangsheng Zhu, Yanan Wang, Yingjie Wang, Chen, Yongwen Li, Hongyu Liu, Jun Chen. Type V collagen promotes lung adenocarcinoma metastasis by regulating tumor mechanical stress and the implication for prognosis and therapeutic strategies [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 6219.

Abstract 6590: Novel WRN helicase inhibitors selectively target microsatellite unstable cancer cells

Abstract Microsatellite-unstable (MSI) cancers depend on the WRN helicase to resolve replication stress from expanded (TA)-dinucleotide repeats. WRN is a promising synthetic lethal target for MSI tumours and WRN inhibitors are being developed. Here, we used CRISPR-Cas9 base editing to map WRN residues critical for MSI synthetic lethality, validating the helicase domain as the primary target and guiding inhibitor discovery. Fragment-based screening led to the discovery of potent and highly selective WRN helicase covalent inhibitors from the same chemical series. These compounds strikingly and selectively suppressed MSI model growth in vitro and in vivo by mimicking genetic WRN loss, inducing DNA double-strand breaks at expanded TA repeats and DNA damage response. We characterized WRN inhibition across cancer cell lines and patient-derived tumour organoids, enabling biomarker assessment of TA-repeat expansions and MMR status to refine patient selection, with compound efficacy correlating with TA-repeat expansions in MSI cells. Efficacy was also confirmed in patient-derived organoids and PDX models refractory to immunotherapy. The discovery of potent and selective covalent WRN inhibitors provides proof-of-concept for targeting MSI cancers and provides tools to unlock the molecular dissection of the WRN biology and MSI synthetic lethality. Citation Format: Gabriele Picco, Yanhua Rao, Angham Al Saedi, Sara F. Vieira, Yang Lee, Ray Shenje, Shriram Bhosle, Samantha Walker, Kieron May, Carmen Herranz-Ors, Cansu Dicer, Freddy Gibson, Ruby Banerjee, Thilo Werner, Josh Cottom, Yang Peng, Nanhua Deng, Phil Landis, Thomas Angel, Jacob Bush, Matthew G. Rees, Melissa M. Ronan, Jennifer A. Roth, Howard Lightfoot, Francesca Zappacosta, Jonathan Pettinger, Syd Barthorpe, Chris Eberl, Brian Jones, Jess Schneck, Dennis Murphy, Josh Taygerly, Mike DeMartino, Matthew Coelho, Jon Houseley, Benjamin Schwartz, Mathew J. Garnett. Novel WRN helicase inhibitors selectively target microsatellite unstable cancer cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6590.

Abstract 3994: N glycosylation inhibition hinders immunosuppressive tumor microenvironment cells improving CAR T cell efficacy

Abstract Adoptive transfer of CAR T cells demonstrated impressive results against B-cell malignancies, but still limited efficacy against solid tumors. In this context, multiple challenges need to be overcome, including poor tumor recognition and strong immunosuppression within the tumor microenvironment (TME). Our Unit has recently reported that pharmacological inhibition of N-glycan synthesis in cancer cells increases CAR T cell efficacy by improving tumor recognition and preventing T cell exhaustion. In this project, we investigated the role of N-glycosylation blockade on TME cells in the context of colorectal cancer (CRC) and pancreatic adenocarcinoma (PDAC)-derived liver metastases, exploiting CEA-specific CAR T cell therapy. To understand the effect of N-glycosylation blockade on TME cells (both M2-like macrophages, M2-M and Hepatic stellate cells, HepSCs), we analyzed the phenotypic and transcriptional profile and we performed in vitro functional assays, such as tripartite co-cultures, suppressive assays and released-cytokines analysis. In vitro studies revealed that N-glycosylation inhibition abolishes the ability of both TME cells to restrain T cell proliferation and increases the elimination of cancer cell lines and patient-derived tumor organoids (PDOs from CRC-liver metastases). Interestingly, these effects were associated with profound phenotypic and transcriptional changes in M2-M and HepSCs. In particular, the treatment was able to inhibit M2-polarization in terms of surface markers expression, IL-10 secretion and gene expression profile, and was shown to hinder the activation of HepSCs. Moreover, to evaluate the effect of N-glycosylation inhibition on TME cells in vivo, we exploited immunodeficient mice reconstituted with a human immune system (huSGM3), engrafted intra-liver with tumor cells and treated with CEA CAR T cells. Interestingly, in this in vivo model, the presence of human immune cells supports CAR T cell responses and helps recreate an immune TME more representative of the human disease. Importantly, using these mice we observed that N-glycosylation inhibition improves CEA CAR T cells fitness, enhancing their antitumor activity in terms of survival. This effect is associated with a modulation of human immune TME populations and in particular with the downregulation of immunosuppressive genes in tumor-infiltrating human immune cells (from scRNAseq and Nanostring analysis). Overall, these data suggest that blocking N-glycosylation can help overcome multiple barriers that currently limit CAR T cell efficacy in solid tumors, acting not only on tumor cells, but also on immunosuppressive tumor microenvironment cells. Citation Format: Camilla Sirini, Beatrice Greco, Chiara Balestrieri, Barbara Camisa, Laura Falcone, Rita El Khoury, Oronzina Botrugno, Giulio Giovannoni, Giovanni Tonon, Emanuela Brunetto, Maria Giulia Cangi, Federica Pedica, Alice Bergamini, Fabio Ciceri, Chiara Bonini, Monica Casucci. N glycosylation inhibition hinders immunosuppressive tumor microenvironment cells improving CAR T cell efficacy [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 3994.

Abstract 2325: NUWA-ms: A network-based method to infer quantification of missing proteins using multi-cohort proteomics profiles

Abstract Although mass spectrometry is powerful for proteomic quantification, the inherent issue of missing values remains a significant challenge. We found a prevalent lack of quantification of valuable proteins (e.g., immune cell markers and drug targets) in published datasets, limiting the functional utilities of quantitative proteomic profiles. This was exemplified by the substantial lack of quantification of immune cell marker, which impede the dissection of tissue-infiltrating immune cells by deconvolution analysis of cancer proteomic profiles. Thus, we introduce a network-based method NUWA-ms for robust abundance inference of missing proteins using multi-cohort proteomic profiles. By evaluating 561 tumors with paired proteomic and transcriptomic profiles, a significant improvement of deconvolution performance was shown with the aid of NUWA-ms. This was further validated by the comparison between scRNA-seq and proteomic analyses of a same gastric cancer tumor tissue. NUWA-ms applications to cancer proteomic profiles facilitated the inference of CD8+ T cell markers and effector proteins, enabling the associations of CD8+ T cell infiltration with MSI status in colorectal cancer and anti-PD-1 therapy response in melanoma. These findings demonstrated the utilities of NUWA-ms in depicting infiltrating lymphocytes in the tumor microenvironment using proteomic profiles. Furthermore, based on the proteomic profiles of six patient-derived tumor organoids (PDOs), NUWA-ms application helped identifying PDOs sensitive to a targeted therapeutic agent including the ones neglected by the raw MS quantification, and aided in revealing the resistant mechanism. Together, NUWA-ms could enable a robust inference of protein abundance, to help identifying protein biomarkers and therapeutic targets for cancer and other complex diseases. Citation Format: Lihua Cao, Yuhao Xie, Jiale Chen, Man Wang, Tingting Zhao, Heli Yang, Yang Du, Yang Yang, Zhaode Bu, Jiafu Ji, Jianmin Wu. NUWA-ms: A network-based method to infer quantification of missing proteins using multi-cohort proteomics profiles [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 2325.

Abstract 19: Patient derived tumor-on-a-chip platform potentiates adaptive immune response against primary tumor cells

Abstract Background: Adoptive cellular therapy (ACT) is a promising antitumor immunotherapy showing success in select trials/patients. However, major challenges limit ACT in all tumors including insufficient cell numbers and failure to target heterogeneous tumors. To improve ACT, we developed a novel biomimetic device where patient-derived tumor organoids, enriched with antigen presenting cells, are cocultured with autologous peripheral blood mononuclear cells (PBMCs) in a microfluidic tumor-on-a-chip system (TOC). As PBMCs circulate through the device, they are exposed to dispersed tumor polyclonal neoantigens, leading to formation of patient- and tumor-specific organoid interacting lymphocytes (OILs). Objectives: Demonstrate that a 3D tumor-on-a-chip (TOC) platform generates organoid interacting lymphocytes (OILs) with enhanced antitumor reactivity. Methods: Specimens were collected from 15 surgical patients: melanoma (2), mesothelioma (6), and metastatic appendiceal adenocarcinoma (9). Tumor cells were combined with autologous antigen presenting cells (healthy spleen/lymph node) in a 3D matrix to generate immune-enhanced tumor organoids in the TOC system. Autologous PBMCs circulated through the system to produce OILs (7 days). Uncirculated PBMCs and tumor infiltrating lymphocytes (TILs) were cultured as controls. Resultant CD8+ controls and OILs were examined by single cell proteomics to compare cytokine secretion polyfunctionality. To assess anti-tumor reactivity, OILs and controls were reintroduced to tumor cells via coculture. Secreted bulk cytokine profiles were compared by Isoplexis CodePlex and confirmed by ELISA. NanoString Geomx spatial proteomic analysis of coculture PTOs identified key lymphocyte activity and phenotypes during anti-tumor reactivity. Coculture cytotoxic lymphocyte activation and tumor cell death was confirmed by flow cytometry. Data were analyzed using student t-test and differential expression from linear mixed-effect model. Results: Compared to controls, CD8+ OILs showed increased polyfunctionality within single cells immediately after training, particularly in effector T-cell associated cytokine profiles (INF-γ, Granzyme B, Perforin). Upon re-introduction to PTOs, OILs excreted significantly increased inflammatory-associated proteins IFN-γ, MCP-1, and Granzyme A (p&amp;lt;0.05). Furthermore, OIL re-exposure to tumor led to cytotoxic lymphocyte activation (CD8+CD69+) and significantly increased tumor cell death compared to control (p&amp;lt;0.05). Conclusion: Compared to controls, OILs produced in the TOC system show enhanced cytotoxic lymphocyte polyfunctionality and induce tumor cytotoxicity, independent of tumor type. With further validation of the OILs’ increased tumor-targeting efficacy, we propose a new potential ACT modality to target a broad array of tumors previously untreatable by current therapies. Citation Format: Cecilia R. Schaaf, Tiefu Liu, Damian Hutchins, Mitra Kooshki, Calvin Wagner, Nicholas Edenhoffer, Steven Forsythe, Robyn Greissinger, Lance Miller, Pierre Triozzi, Edward Levine, Shay Soker, Adam R. Hall, Konstantinos I. Votanopoulos. Patient derived tumor-on-a-chip platform potentiates adaptive immune response against primary tumor 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 19.

Abstract 5234: TGFbeta-conditioned K-NK cells are able to counter immune suppression in the tumor micro-environment

Abstract Recent advances have enabled the use of autologous K-NK cells to treat patients suffering from hematological malignancies. When aiming to treat patients suffering from solid tumors however, the suppressive effects of the tumor microenvironment (TME) and the involvement of other immune cells need to be considered to make a cell therapeutic potentially more effective. TGFβ-conditioning (TGFβ-c), the co-culture of K-NK cells with low-dose TGFβ while undergoing cytokine-mediated expansion, imbues these cells with unique qualities suitable to mitigate immuno-suppressive effects of the TME, making them more efficacious toward solid tumors. The exposure to TGFβ during expansion results in significant downregulation of SMAD3, rendering these cells insensitive to TGFβ-mediated down-regulation of NK cell receptors. TGFβ-c K-NK cells display enhanced in vitro cytotoxicity towards 2D, 3D cultured cell lines as well as against organoid models derived of various indications. These cells infiltrate into patient-derived tumor organoids at higher frequency and have increased IFNγ secretion upon target-specific activation. The effect of the higher IFNγ output on a complementary anti-tumor immune subset was investigated in complex immune cell cultures and was indeed shown to enhance DC maturation. In vivo studies revealed prolonged persistence of TGFβ-c K-NK cells in mice while retaining both altered gene-expression and functional hallmarks for up to 28 days, indicating that the conditioning results in a stable phenotype. In summary, TGFβ-c K-NKs are a platform with enhanced potency to transition cell therapy from treating hematological to solid tumor malignancies. Citation Format: Andre Kunert, Anna Oja, Ieva Cesonyte, Katarzyna Franciszkiewicz, Sukhvinder Sidhu, Hardik Jetani, Giulio Bocconcelli, Robert Igarashi, Valeria R. Fantin. TGFbeta-conditioned K-NK cells are able to counter immune suppression in the tumor micro-environment [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 5234.

Abstract 217: Establishment of a spatially defined co-culture model of non-small cell lung cancer organoids and cancer-associated fibroblasts to investigate phenotypic heterogeneity

Abstract Background: Cancer-associated fibroblasts (CAFs) are heterogeneous, with CAF subtypes being localized in spatially defined areas of tumors. However, it remains unclear which CAF subsets specifically play a role in fundamental processes such as tumor growth, invasion, and response to therapy. This study aims to establish a novel in vitro model that recapitulates the in vivo tumor-stroma spatial relationship to investigate CAF heterogeneity and its impact on tumor cell growth in non-small cell lung cancer (NSCLC). Methods: The in vitro model was established using NSCLC patient-derived CAFs and tumor organoids as a 6:1 ratio. Tumor cells originating from xenograft-derived organoids (XDOs) were embedded in a hydrogel containing CAFs (Day 0) and co-cultured for 5 days. Confocal microscopy was utilized to characterize and measure the proliferation of the XDO tumor cells in the co-culture setup, and the proliferation rate was defined as differences in tumor spheroid area between Day 1 and 5. Single-cell RNA-sequencing (scRNAseq) and gene set enrichment analysis (GSEA) were then used to assess the gene expression and signaling pathways dominant in mono- and co-culture to characterize CAF heterogeneity in this model. Results: Initially, the culture media formulations and the matrix for the growth of both CAFs and tumor cells were screened to assess the compatibility of different culture elements. Both CAFs and XDO tumor cells proliferated well in reduced organoid media (M27RD). This reduced medium and the novel matrix composition (50% Matrigel/50% Rat Tail type I collagen) also allowed for maintaining CAF contractility and XDO proliferation. Utilizing these harmonized media and matrix conditions, a spatially defined co-culture model, which incorporated XDOs as a central cluster surrounded by CAFs, was generated. In confocal microscopy, the proliferation rate of tumor cells was significantly higher in co-cultures with CAFs (adjusted p-value &amp;lt; 0.01), while not significant in mono-culture of tumor cells. The GSEA using the Hallmark gene sets on scRNAseq data generated in three co-cultures identified the heterogeneity among CAFs: two CAFs showed significantly higher effect on tumor cell proliferation with the most highly differential expressed genes (DEGs) enriched with inflammation and mitosis and the top high DEGs associated with epithelial-mesenchymal transition, while the other CAF has no effect. Conclusion: The harmonized co-culture conditions for NSCLC organoids and CAFs enabled the characterization of both cell phenotypes and the building of an informed model architecture to study tumor-stroma communication. The presence of CAFs increased tumor cell growth with enrichment in secreted proteins involved in epithelial-mesenchymal transition. Citation Format: Cheol-Kyu Park, Roya Navab, Elisa D'Arcangelo, Quan Li, Hiroyuki Ogawa, Nikolina Radulovich, Nhu-An Pham, Ming-Sound Tsao. Establishment of a spatially defined co-culture model of non-small cell lung cancer organoids and cancer-associated fibroblasts to investigate phenotypic heterogeneity [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 217.

Abstract 636: Coculture model for investigating cellular interactions between colorectal tumor organoids and cancer-associated fibroblasts

Abstract The tumor microenvironment (TME) is well recognized for its role in tumor progression, chemoresistance, and recurrence. The TME consists of various components, such as extracellular matrix (ECM), chemical and mechanical cues, as well as stromal cells and their interactions. As the most abundant cells in tumor stroma, cancer-associated fibroblasts (CAFs) have drawn a lot of attention. It has been reported that CAFs not only directly interact with cancer cells via surface proteins and cytokines, but also influence their behaviors by remodeling the ECM. However, due to their heterogenous characteristics and diverse functions, the influence of tumor-CAF interactions on drug response is not fully understood. Here, we present a coculture model for investigating CAF effects on patient-derived colorectal tumor organoids (CTOs) growth, differentiation, and drug response. It consists of normal colon fibroblasts, CCD18-Co, or patient-derived CAFs seeded with CTOs in a mixed hydrogel containing 90% basement membrane extract (BME) and 10% collagen type I. Media conditions were optimized (1:1 mix of CTO culture media plus reduced media excluding growth factors and inhibitors) to achieve similar organoid sizes in the monoculture and coculture conditions at the onset of drug testing. To support higher throughput investigations, our workflow incorporates a liquid handler for automated CTO seeding, media and drug exchange, and an automated microscope with a robotic arm for multi-plate imaging. Briefly, single cell CTOs and fibroblasts were seeded at a 1:1 ratio (3000 total cells/well) in 96-well plates. After 4 days in culture, anti-cancer drugs were administrated in reduced media to the samples. Brightfield images were acquired on days 0, 3, and 5 after drug administration. The collected images were analyzed with a neural network (NN) to dynamically monitor the growth and viability of individual organoids. The CellTiter-Glo assay was performed on day 5 to quantify the total CTO cell viability. The normalized drug response (NDR) was calculated from the NN processed images to determine the drug response. An immunostaining panel, which includes protein markers such as CK20, Ki67, α-SMA, Vimentin, and FAP, was used to evaluate the fibroblast phenotypes and CTO differentiation. Additionally, the cultures were subjected to fluorescent lifetime imaging microscopy (FLIM), a label-free imaging technique, to measure the metabolic adaptations of each cell population. Preliminary studies revealed a CAF-dependent increase in CTO growth and glycolytic signatures in the co-culture setting; however, minimal effects on drug response to common chemotherapy agents such as 5-fluorouracil and irinotecan were observed. In the future, we will use this integrated pipeline as a screening method to identify new treatment strategies aimed at targeting the stromal microenvironment in colorectal cancer. Citation Format: Yuyuan Zhou, Yu-Kai Huang, Emma J. Fong, Elizabeth Elton, Erin McManus, Brandon Choi, Seungil Kim, Shannon M. Mumenthaler. Coculture model for investigating cellular interactions between colorectal tumor organoids and cancer-associated fibroblasts [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 636.

Abstract 4461: Unveiling the links between methionine metabolism and epigenomic reprogramming in upper aerodigestive squamous cell carcinoma

Abstract Upper aerodigestive squamous cell carcinoma (UASCC) presents as a prevalent and aggressive malignancy, posing challenges in terms of effective therapeutic interventions. In this study, we explored the intricacies of amino acid metabolism within UASCC, revealing an unexpected observation that distinguishes UASCC among all human cancers, having the highest methionine levels, driven by the overexpression of its transporter LAT1. Notably, LAT1 exhibits peak expression levels in UASCC, regulated at the transcriptional level by UASCC-specific promoters and enhancers, co-regulated by SCC master regulators TP63/KLF5/SREBF1.Surprisingly, our unbiased bioinformatic screen identifies EZH2 as a pivotal downstream target of the LAT1-methionine pathway, establishing a direct link between methionine metabolism and epigenomic reprogramming. This cascade emerges as crucial for the survival and proliferation of UASCC patient-derived tumor organoids. Furthermore, we find that LAT1 expression closely correlates with cellular sensitivity to inhibition of the LAT1-methionine-EZH2 axis.Significantly, the newly discovered LAT1-methionine-EZH2 cascade emerges as a promising target for intervention, with effective outcomes achievable through both pharmacological approaches and dietary interventions in vivo. In summary, this research unveils a novel mechanistic crosstalk connecting epigenomic reprogramming with methionine metabolism, revealing its biological significance in UASCC. Moreover, it identifies a unique tumor-specific vulnerability, providing avenues for exploitation through both pharmacological and dietary strategies Citation Format: Chehyun Nam. Unveiling the links between methionine metabolism and epigenomic reprogramming in upper aerodigestive squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4461.