Patient-derived Cultures Research Articles

Abstract 4683: Developing human Ewing sarcoma in vitro models to prioritise new treatments

Abstract Models that more accurately reflect Ewing sarcoma (ES) will enable the prioritization of novel targeted agents from bench to clinic. To date, development of an ES mouse model have been unsuccessful1 and engraftment of human ES in mice is variable2. Coupled with a moral obligation to minimize the use of mammals, we have established and characterized models using patient-derived ES cultures in vitro and in larval zebrafish. The transcriptomes of ES cell lines and patient-derived ES cultures3 were analyzed and compared using total RNAseq followed by DESeq2 and Gene Set Enrichment analysis. Cells in 2D, as 3D spheroids, in combination with cells of the tumor microenvironment and in larval zebrafish (Danio rerio) were characterized. Six cell lines clustered independently from patient-derived ES cultures (n=20), reflecting differential expression of 15,709 RNAs (p<0.01). Interrogation of the differentially expressed genes using Reactome, KEGG and Gene Ontology identified up regulation of genes associated with mitotic spindle and G2/M G1/S DNA damage spindle checkpoints, homologous recombination and the cell cycle in the cell lines compared to patient-derived cultures (p<0.01). These data are consistent with the quicker doubling time (DT) and increased sensitivity of ES cell lines to chemotherapy (actinomycin D, doxorubicin, vincristine, etoposide; DT range=19-33h, EC50 range=4-34nM) compared to patient-derived cultures (DT range=55-197h, EC50>10μM, p<0.05). All patient-derived ES cultures formed spheroids of similar diameter (range 105-258µm) at 96h (p>0.05), although there was heterogeneity in spheroid weight (range 205-3639ng, p<0.05) and migration index (MI; range 30-170, p<0.05). Treatment with actinomycin D (1-10 µM) significantly increased spheroid diameter (p<0.05), whereas 4-hyperoxyifosfamide (active metabolite of ifosfamide, 7-30µM) decreased spheroid diameter (p<0.05). Doxorubicin did not significantly change the diameter of spheroids. When propagated in combination with mesenchymal stem cells there was a 2-fold increase in viable cell number (p<0.0001) compared to ES cultures alone. Patient-derived ES cultures in zebrafish were observed at the injection site (perivitelline space). Some cells were detected in circulation 3 days post injection. This is consistent with heterogeneity and the high MI of patient-derived ES cultures. The transcriptome of ES cell lines is significantly different from that of ES patient-derived cultures and is associated with increased doubling times and response to chemotherapies. This highlights the importance of developing preclinical models using patient-derived ES cultures. Patient-derived ES cultures in 2D and 3D models in vitro and in zebrafish may provide a reliable cost-effective preclinical pipeline 1Minas et al. 2017.Oncotarget,8(21):34141-34163.2Nanni et al. 2019.Sci Rep,9(1):12174 3Roundhill et al. 2021.Cell Oncol,44(5):1065-1085. Citation Format: Elizabeth A. Roundhill, Elton J. Vasconcelos, David R. Westhead, Sarah Grissenberger, Martin Distel, Susan A. Burchill. Developing human Ewing sarcoma in vitro models to prioritise new treatments. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4683.

Abstract 4122: TIL-containing patient-derived explant cultures reveal role of metformin on antigen presenting cell activation

Abstract Globally, breast cancer is among the most diagnosed cancer types for women. Current and upcoming breast cancer therapies are being investigated in combination with compounds that stimulate an immune response, but whether the therapeutic agents themselves have unexpected immunomodulatory effects is often overlooked. Here, we have developed a method to grow 3D cultures of intact fragments of patient-derived tissue (Patient-Derived Explant Cultures; PDECs) to assess the preclinical potential of studying human tumor cells and immune cells simultaneously ex vivo Single cell sequencing, flow cytometry, gene expression profiling and cytokine profiling data show that the tumor immunocontexture is conserved in PDECs and that these resident immune cells respond to distinct immune stimulus We performed gene expression profiling, flow cytometry, and cytokine profiling of drug-treated human explants and found that metformin has antitumor potential through the activation of antigen presenting cells. We further validated in vitro that metformin-mediated APC activation is largely through mitochondrial respiration inhibition irrespective of the presence of tumor cells. Our PDEC platform highlights the preclinical potential of ex vivo explants by simultaneously offering information of tumor and immune cell toxicity and mechanism. Citation Format: Rita J. Turpin, Ruixian Liu, Pauliina Munne, Aino Peura, Jenna Rannikko, Gino Philips, Natasha Salmelin, Elina Hurskainen, Ilida Suleymanova, Minna Mutka, Tuomo Meretoja, Johanna Mattson, Satu Mustjoki, Päivi Saavalainen, Diether Lambrechts, Jeroen Pouwels, Maija Hollmén, Juha Klefström. TIL-containing patient-derived explant cultures reveal role of metformin on antigen presenting cell activation. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4122.

Abstract 1256: Transglutaminase-2 is elevated in the invasive cell state and modulates the tumor immune microenvironment in cutaneous melanoma

Abstract Cutaneous melanoma is the most fatal skin cancer; resistance to targeted therapies contributes to poor prognosis. In some cases, resistance arises from pre-existing tumor heterogeneity, which allows subpopulations of drug-tolerant cells with distinct transcriptional states to survive in the presence of drug. The loss of SOX10, a lineage-specific transcription factor, is known to drive melanoma phenotype switching from a proliferative to an invasive drug-tolerant state. Here, we found that knocking out SOX10 in human and mouse melanoma cell lines leads to the upregulation of transglutaminase-2 (TGM2), a calcium-dependent cross-linking enzyme. Analysis of publicly available bulk and single-cell RNA-sequencing data showed that TGM2 is highly expressed in the invasive cell state in melanoma cell lines and patient-derived melanoma cultures, respectively. Furthermore, knockdown of SOX10 in patient-derived melanoma cultures increases TGM2 mRNA expression. 3D spheroid assays and extracellular matrix production/remodeling assays showed that knockdown of TGM2 has no effect on the invasiveness of SOX10-deficient cells. However, we found that TGM2 is secreted by SOX10-deficient cells and hypothesized that it could modulate the tumor immune microenvironment (TIME) given that TGM2 has been associated with increased immune infiltration in melanoma patient samples. To investigate the effect of TGM2 on the TIME, we stably overexpressed TGM2/Tgm2 in syngeneic mouse melanoma cell lines and allowed tumors to grow in immune-competent C57BL/6 mice. As compared to empty vector, TGM2/Tgm2-overexpression led to an increase in the percentage and number of CD4+ T cells and B cells, and a decrease in the number of myeloid cells, in the tumor immune compartment by flow cytometry analysis. Future studies will assess which subsets of CD4+ T cells and B cells infiltrate TGM2/Tgm2-overexpressing tumors, how these changes to the TIME affect melanoma invasiveness, and if TGM2 expression affects response to targeted therapy in vivo. Overall, our data suggest that TGM2 is highly expressed in the invasive melanoma cell state, is regulated by the SOX10 transcription factor, and can modulate adaptive immune cells in the TIME. Citation Format: Signe Caksa, Nicole A. Wilski, Erica L. Kitterman, McKenna Q. Glasheen, Jacob S. Heilizer, Timothy J. Purwin, Claudia Capparelli, Andrew E. Aplin. Transglutaminase-2 is elevated in the invasive cell state and modulates the tumor immune microenvironment in cutaneous melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1256.

Abstract 363: Modelling cancer cachexia using a comprehensive panel of heterogeneous esophageal squamous cell carcinoma xenografts for therapeutic application

Abstract Background: Esophageal squamous cell carcinoma (ESCC) is one of deadliest esophageal malignancies in Asia. Cancer cachexia is a multifactorial body wasting syndrome and is one of the major causes of death in late-stage patients (1). It is characterized by skeletal muscle loss and atrophy, adipose and body wasting, and metabolic dysregulations and stress (1). ESCC is one of the cancer types with the highest morbidity and mortality rates due to cancer cachexia (2). However, there are few effective and approved treatments targeting cancer cachexia. Currently, cancer cachexia animal models are highly limited with few cancer types available as a pre-clinical drug testing platform, with none related to esophageal carcinoma (3). Results: Here we have developed a panel of ESCC patient-derived organoid xenograft (PDOX) mouse model based on our latest patient-derived organoid cultures originating from Hong Kong patients. Our immunodeficient mouse-based PDOX model resembles different cachexic phenotypes that cell line-derived xenograft lacks, including body (skeletal muscle and adipose tissue) wasting and functional signs (e.g. lack of body movement, reduced muscle strength, and loss of appetite). The slow-proliferating characteristic of the ESCC PDOX allows development of a cachexic condition before humane endpoint. Furthermore, our full panel of PDOX lines allowed us to identify the full spectrum, differential cachexia severity across mice bearing different PDOXs, indicating a heterogenous nature. We have comprehensively characterized the cachexia phenotypes and performed proof-of-concept preclinical drug tests using established anti-cachexic drugs; treated PDOX-bearing mice have improved body condition and function compared to the control, which were further verified by histological examinations of tissue samples. Molecular analysis showed that several classic cachexia related gene expressions were down-regulated in isolated liver (Il1b) and inguinal adipose tissues (adipose triglyceride lipase). Conclusions: Our ESCC PDOX model potentially serves as a great pre-clinical cachexia-targeted drug testing platform, providing more treatment options for ESCC patients for better disease management. Acknowledgement: We acknowledge the Research Grants Council (TRS T12-701/17-R to MLL) and the Food and Health Bureau (HMRF 06171566 to VZY) of Hong Kong Special Administrative Region for funding supports. We acknowledge DSMZ for the KYSE cell lines. We acknowledge the HKUMed-CPOS for providing imaging facilities.

Abstract 1425: TTFields reduce sensitivity in glioblastoma is associated with the functional expression of the chloride intracellular channel 1 and with voltage dependent sodium channel

Abstract Glioblastoma (GBM) is the most aggressive type of brain tumor, and existing treatments are inadequate at preventing recurrence. Tumor Treating Fields (TTFields) is a novel treatment that has been proven to extend patients' lives during the previous two decades. The antitumoral impact of TTFields involve different mechanism and is an optional add-on to standard temozolomide maintenance. Although TTFields therapy slows tumor progression initially, it does not prevent tumor relapse in most patients. We subjected patient-derived GBM primary cultures to continuous TTFields stimulation to mimic the GBM standard of care and examine the molecular pathways behind GBM sensitivity to TTFields treatment. TTFields initially limit cellular growth well. However, even under constant TTFields administration, the remaining cells regain their ability to proliferate at their own rate in long-term trials. Prolonged treatment with TTFields increases the expression of many stemness markers as well as the overexpression of different genes involved in cell cycle progression. There is also a rise in membrane ionic conductance activity. After sustained exposure to TTFields, sodium, potassium, and chloride channels are functionally increased. This influences the properties of tumor cells. Increased sodium channel functional activity, for example, promotes membrane potential depolarization. Furthermore, earlier research has shown that the membrane form of the chloride intracellular channel 1 (tmCLIC1) is important in the development of GBM. In patient-derived GBM cells exposed to TTFields, tmCLIC1 is significantly concentrated, and membrane depolarization improves its function. The evaluation of GBM tissues obtained from many patients who were treated with TTFields validates the in vitro tumor relapse model.Our findings imply that the process by which GBM cells develop a decrease in sensitivity to TTFields correlates with an increase in stemness markers and an increase in ionic channel functional expression. Citation Format: Stefania Castiglione, Gaetano Cannavale, Francesca Cianci, Ivan Verduci, Chiara Biella, Chiara Mercurio, Emanuela Pastorelli, Monica Lupi, Laura Paracchini, Laura Mannarino, Dietmar Krex, Federico Brandalise, Michele Mazzanti. TTFields reduce sensitivity in glioblastoma is associated with the functional expression of the chloride intracellular channel 1 and with voltage dependent sodium channel [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1425.

Abstract 160: Derivation and long-term maintenance of patient-derived tumoroid lines in a defined, serum-free medium

Abstract In vitro cancer research often fails to translate to the clinic, in part due to the use of traditional 2D cancer cell lines as models, which fail to resemble primary cancer cells by a variety of measures, including high mutational burden. An emerging solution to this problem is to replace traditional cell lines with patient tissue-derived cells expanded in 3D, also known as tumoroids or cancer organoids. We developed a defined, serum- and conditioned medium-free system, GibcoTM OncoProTM Tumoroid Culture Medium, that can be used to derive stable tumoroid lines from a variety of tissue sources and maintains the phenotype and genotype of patient-derived tumor cells. By supplementing the base medium with indication-specific growth factors, tumoroid lines were derived from colorectal, lung, and endometrial cancers from both fresh surgical resections and cryopreserved primary cancer cells. To demonstrate the utility of these patient-derived cells as long-term in vitro models, colorectal and lung tumoroid lines were derived from multiple donors and cultured for up to 50 passages. Brightfield microscopy, cell counts, and next-generation sequencing were used to assess maintenance of tumoroid morphology, growth rate, gene expression patterns, and genomic mutations. Patient-derived tumoroid cultures adopted donor-specific morphologies that were maintained during long-term culture. Cell doubling time tended to stabilize within the first few passages as cultures established, was donor-dependent, and averaged around 65 hours for colorectal tumoroids - on par with that of traditional 2D cancer cell lines - and 90-100 hours for lung and endometrial tumoroids, respectively. Importantly, tumoroid lines maintained their gene expression pattern for over 20,000 human RefSeq genes during long-term culture, with correlation between initial tumor material and late-passage samples of R>0.8. Distinct molecular subtypes of colorectal cancer were preserved in cultured tumoroids. The allelic frequency of single nucleotide variations (SNVs) in 161 highly relevant cancer genes was also highly correlated (R>0.9) between uncultured tissue and late-passage tumoroids. Within SNVs, transition/transversion mutation ratios were conserved. Tumoroids were cryopreserved and recovered during this study, demonstrating that biobanking of colorectal and lung tumoroids should not impact their long-term stability. Finally, a subset of the derived colorectal and lung tumoroids were tested and shown to be tumorigenic in mice, where subsequent histology of the tumor was similar to that of in vitro cultures. Altogether, tumoroid derivation and culture in this novel medium enables the long-term preservation of patient-specific cellular genotype and phenotype, which should allow for expansion, biobanking, and performance of experimental repeats within the same patient tissue-derived cultures across labs and over time. Citation Format: Chris Yankaskas, Brittany Balhouse, Colin Paul, Shyanne Salen, Sybelle Djikeng, Pradip Shahi Thakuri, Mark Kennedy, Matt Dallas, David Kuninger. Derivation and long-term maintenance of patient-derived tumoroid lines in a defined, serum-free medium [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 160.

Abstract 5500: Patient-derived organotypic cultures (PDOCs) from melanoma metastases as a precision medicine test to improve patient management

Abstract INTRODUCTION Despite significant improvements in advanced melanoma therapy, there is still a pressing need for innovative therapies. Here, we optimized a method for testing the drug sensitivity of PDOCs and evaluated whether this preclinical model could be a valid tool for rapidly determining the patient’s tumor response profile to approved and alternative therapies. METHODS PDOCs were generated from melanoma metastases (> 60 specimens) after mechanical or enzymatic dissociation. Tissue fragments (<70um) were harvested, embedded in 3D collagen beads (1.5 mg/mL type I collagen), and cultured in a 96-well plate for 6 days, maintaining tumor and stromal viability. More than 20 primary cell lines from the same samples were also stabilized. The melanoma cells or the PDOCs were left untreated or treated with the patient’s own therapy or with alternative drugs, and the efficacy of treatments was evaluated by MTT assay and flow cytometry. CD8+ T cell infiltration and cytokine secretion were also investigated. RESULTS The first experiments were set up to validate PDOCs as predictive preclinical models of patient response to therapy. We tested approved melanoma therapies (i.e., the combination of BRAF and MEK inhibitors, or anti-PD-1 antibodies) on the same melanoma specimens at the IDI and IEO institutes. More than 10 different samples were compared, finding reproducible results between the two Institutions. Furthermore, drug response in PDOCs was comparable to the clinical response of matched patients undergoing the tested therapy, demonstrating PDOCs are reliable predictive tools. Then, we used primary cell lines to screen a pool of ten different targeted agents selected through functional screening of a bioactive library of 512 compounds on patient-derived xenografts, and based on known drug resistance mechanisms in melanoma. The three best-performing compounds were subsequently studied in PDOCs as single agents or in combination with immunotherapy. We found high heterogeneity of drug efficacy in different melanoma samples with no obvious correlation to BRAF or NRAS mutations, metastasis type, or patients’ prior therapies. Of note, in some cases, the combination with an anti-PD-1 inhibitor significantly improved the efficacy of one or more of the three drugs. CONCLUSIONS We optimized and validated PDOCs as personalized preclinical models suitable for assessing the drug sensitivity/resistance profile of individual patient-derived melanomas. By retaining tumor stromal components and heterogeneity, PDOCs could be used to predict patients’ clinical response to currently approved agents, helping oncologists expedite decision-making when several treatment options are possible. Furthermore, the model could be used to evaluate the effectiveness of alternative treatments on tumors resistant to approved therapies, and to explore new drug combinations. Citation Format: Antonella Bresin, Fiorenza Lotti, Lauretta Levati, Pier F. Ferrucci, Francesca Ricci, Francesco Scicchitano, Zorika C. Di Rocco, Giandomenico Russo, Luisa Lanfrancone. Patient-derived organotypic cultures (PDOCs) from melanoma metastases as a precision medicine test to improve patient management. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5500.

Abstract 2419: A multimodel preclinical platform to evaluate photodynamic therapy as a strategy to reduce local recurrence in myxofibrosarcoma and osteosarcoma

Abstract Sarcomas are heterogeneous and rare malignant tumors that develop from connective tissues. Myxofibrosarcoma (MFS) and Osteosarcoma (OS) are the main representative subtypes of Soft tissues and Bone sarcomas. Conventional treatment consists of surgical resection and neo/adjuvant chemotherapy. However, a challenging clinical feature is a high local recurrence rate, calling for the development of novel strategies to eradicate MFS and OS. Fluorescence-guided surgery (FGS), coupled with photodynamic therapy (PDT), enables to detect and eradicate malignant tissues using a light-sensitive photosensitizer (PS). These compounds could be retained by neoplastic cells to a greater extent than by healthy tissue. Thus, when photoactivated, they lead to cancer cell death, minimizing normal tissues toxicity. The project aims to provide a preclinical proof of concept of FGS and PDT for MFS and OS, allowing us to pave the way for a more effective treatment strategy. A multimodel preclinical platform of MFS and OS comprising 2D, 3D-collagen based scaffold was developed. A MFS stabilized cell line (IM-MFS-1) and four OS cell lines (Saos-2, U-2 OS, MG-63, 143B) were used. NIH-3T3 fibroblast cell line was used as healthy counterpart. We tested a panel of synthetic PSs: Toluidine Blue, 5-Aminolevulinic Acid hydrochloride (ALA), Methylene Blue, Chlorin e6 (Ce6), Pheophorbide a (Pba) and Al(III) Phthalocyanine Chloride Tetrasulfonic Acid (AlPcS4) that can be photoactivated with light in the 630-660 nm wavelengths’ range. The PSs were ranked on (a) selective uptake by tumor cells, respect to healthy cells and (b) the cytotoxic effect, after photoactivation. PSs cell uptake was evaluated by Countess II FL automated cell counter. Cytotoxicity was evaluated by WST-1 and Presto Blue assays. For each PS we determined the highest concentration, causing less than 50% dark toxicity in IM-MFS-1, OS cell lines and fibroblast NIH-3T3, seeded in 2D and 3D collagen-based models. Then, we evaluated the cell viability upon light irradiation (λ=630 or 660 nm; 10 mW/cm^2, 5 min). For all PSs, dark toxicity was very low. However, only Ce6 was effectively uptaken by tumor cells (% uptake > 60%) and not by NIH-3T3 cells (% uptake = 27%). Moreover, upon photoactivation, Ce6 induced significantly higher cell death in cancer cells as compared to NIH-3T3 cells, e.g. 1-3% cell viability in tumor cells and 76% cell viability in NIH-3T3. Results from our multimodel platform highlight PDT as a powerful strategy for the treatment of MFS and OS. Among the screened PSs, Ce6 is the most promising, showing a remarkable selectivity in tumor cells uptake and cytotoxicity. To increase the clinical significance of our approach, we will confirm its efficacy in patient-derived primary cultures; xenograft zebrafish in vivo embryos will be used to evaluate how PDT affects the disease aggressiveness and metastatic potential. Citation Format: Chiara Spadazzi, Micaela Pannella, Chiara Bellotti, Elisa Martella, Silvia Vanni, Alessandro De Vita, Chiara Liverani, Giacomo Miserocchi, Claudia Cocchi, Chiara Calabrese, Valentina Fausti, Roberto Casadei, Federica Pieri, Ania Naila Guerrieri, Giovanni Martinelli, Greta Varchi, Enrico Lucarelli, Laura Mercatali, Toni Ibrahim. A multimodel preclinical platform to evaluate photodynamic therapy as a strategy to reduce local recurrence in myxofibrosarcoma and osteosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2419.

Abstract 1132: Exploiting MGMT loss using a new class of DNA modifiers which selectively target tumor DNA and overcome therapy resistance mechanisms across multiple tumor types

Abstract DNA damage response (DDR) defects are common in cancer, and it is well established that these tumor-associated DNA repair vulnerabilities can be exploited for a therapeutic gain. Small molecule inhibitors of DDR proteins have been developed to target these cancers, which are now FDA-approved and/or currently being tested in clinical trials. Our team recently reported on an entirely new approach to exploit DDR defects in cancer, via DNA modification, eliminating the need to target proteins (Lin et al., Science 2022). In this recent study, we demonstrated that our new class of “DNA modifiers (DMs)” can be engineered to exploit loss of O6-methylguanine methyltransferase (MGMT), which leads to robust and selective killing of MGMT-deficient glioma tumors, both in vivo and in vitro. We also found that our approach could overcome acquired and intrinsic defects in another DDR pathway, mismatch repair (MMR), which is a known resistance mechanism to standard-of-care cytotoxic therapies in glioma, including TMZ. Here, we sought to determine the extent to which our approach can be expanded to selectively target a wide range of cancers beyond glioma in which loss of MGMT, as well as acquired and intrinsic MMR defect, are commonly seen at various frequencies. To this end, we profiled over 900 cell line models, as well as several collections of patient-derived cultures derived from several tumor types for sensitivity to our DMs based on MGMT and MMR status in vitro. We then validated our findings in cell line xenograft and patient-derived xenograft models, in vivo. In parallel, we compared the activity of DMs to commonly used, standard-of-care cytotoxic drugs, in vitro and in vivo. Our data indicate that DMs can effectively target MGMT loss, as well as intrinsic and acquired MMR defects, in multiple non-CNS tumor types. Taken together, the findings reported here support an entirely new approach to selectively exploit DDR defects via direct DNA modification. This new approach has the potential to overcome known resistance mechanisms to currently used small molecule inhibitors of DDR proteins, across a broad range of cancers. Citation Format: Bruce Ruggeri, Kyle Tarantino, Ranjini Sundaram, Kingson Lin, Seth Herzon, Joseph Park, Spenser Johnson, Susan Gueble, Ranjit S. Bindra. Exploiting MGMT loss using a new class of DNA modifiers which selectively target tumor DNA and overcome therapy resistance mechanisms across multiple tumor types [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1132.

463 Tandem CAR T Cells Targeting EGFRvIII and IL-13R⍺2 are Effective Against Heterogeneous Glioblastoma

INTRODUCTION: Chimeric antigen receptor (CAR) T cells have achieved remarkable responses in patients with hematological malignancies; however, the potential of this therapeutic platform for solid tumors like glioblastoma (GBM) has been limited, due in large part to the targeting of single antigens in a heterogenous disease. Strategies that allow CAR T cells to engage multiple antigens concomitantly may broaden therapeutic responses and mitigate the effects of immune escape. METHODS: We generated a TanCART construct with dual specificity consisting of both the humanized anti-EGFRvIII scFv and IL-13 zetakine translated in tandem separated by a flexible glycine-serine linker. We also employed two monospecific CAR T cells, CART-EGFRvIII and CART-IL-13Rɑ2 as controls. We used both standard immunological assays and multiple orthotopic preclinical models including patient-derived xenograft to demonstrate efficacy of this approach against heterogenous tumors. RESULTS: Tandem CAR T cells displayed enhanced cytotoxicity in vitro against heterogeneous GBM populations, including patient-derived brain tumor cultures (P < 0.05). Compared to CAR T cells targeting single antigens, dual antigen engagement through the tandem construct was necessary to achieve long-term, complete and durable responses in orthotopic murine models of heterogeneous GBM, including patient-derived xenografts (P < 0.05). CONCLUSIONS: We demonstrate that TanCART is effective against heterogenous tumors in the brain. To our knowledge, this is the first report of a tandem CAR T cell targeting EGFRvIII and IL-13Rɑ2 simultaneously. These data lend further credence to the development of multi-specific CAR T cells in the treatment of GBM and other cancers.

892 Validation of Docetaxel as a Radiosensitizer in High-Risk Meningiomas Based on DNA Methylation Profiling

INTRODUCTION: Genome-wide methylation profiling has emerged as a transformative prognostic tool in meningiomas, and has identified discrete epigenetic clusters that share distinct clinical and biological features. The association of these signatures with underlying pathological mechanisms has not been well-explored. METHODS: From a collection of over two-hundred well-annotated tumors, we found 981 genes in which methylation signal was predictive of recurrence. Using pathway enrichment analysis, Docetaxel was identified as a candidate therapeutic agent; a medication that is frequently utilized in other common malignancies. This chemotherapy was validated in vitro and in vivo using patient derived meningiomas, and also tested in combination with radiotherapy. RESULTS: Based on 15 patient-derived cultures from our institution and 2 public cell lines, we found that Docetaxel could inhibit meningioma growth at concentrations that were favorable relative to other cancers. This drug triggered apoptosis in meningiomas of all tumor grades and methylation classes, with IC50 values ranging from 0.8 nm to 4.4 nm in vitro. Combining Docetaxel with radiation therapy resulted in synergistic cytotoxic effects on meningioma cultures, associated with elevated markers of cell death and dsDNA breaks. We confirmed our results via orthotopic meningioma models of the cell lines CH157 and IOMM-Lee, which exhibited dose-dependent improvements in mortality and tumor volume in response to Docetaxel and radiation. CONCLUSIONS: Our results leverage DNA methylation patterns to repurpose FDA-approved medications in the treatment of meningiomas, and suggest a clinical trial of Docetaxel with radiotherapy may be efficacious in aggressive lesions.

Characterization and Clinical Relevance of Endometrial CAFs: Correlation between Post-Surgery Event and Resistance to Drugs.

Cancer-associated fibroblasts (CAFs) within a solid tumor can support the progression of cancer. We studied the identification and characterization of patient-derived endometrial CAFs in the context of their clinical relevance in endometrial cancers. We established patient-derived primary cultures of CAFs from surgically resected tumors (TCAF) and tumor-adjacent normal (NCAF) tissues in 53 consented patients with success rates of 97.7% and 75%, respectively. A passage of CAF was qualified by the (1) absence of CK 8,18,19, EpCAM, CD45, and CD31, and (2) presence of SMAalpha, S100A4, CD90, FAP, TE-7, CD155, PD-L1, TGFB, PDGFRA (qRT-PCR, flow cytometry, Western blot, ICC). Out of the 44 established CAFs, 31 were aggressive (having an early, i.e., 4-7 week, establishment time and/or >3 passages) compared to 13 which were non-aggressive. A post-surgery-event (PSE) was observed in 7 out of 31 patients bearing aggressive CAFs, 2 of whom were also positive for CTCs, while none of the 13 patients bearing non-aggressive CAFs had events. A positive correlation was found between patients with grade 3 (p = 0.025) as well as stage 3/4 diseases (p = 0.0106) bearing aggressive CAFs and the PSE. Finally, aggressive TCAFs from patients with PSE resisted the effects of paclitaxel and lenvatinib on the growth of HUVEC and endometrial tumor cells. Our study is the first to report a correlation between the PSE and the aggressive nature of CAFs in endometrial cancers and provides an undeniable reason to study the in-depth mechanism of CAF function towards the development of treatment resistance in endometrial cancers.

Matrix Gla Protein drives stemness and tumor initiation in ovarian cancer

Ovarian cancer (OC) displays the highest mortality among gynecological tumors, mainly due to early peritoneal dissemination, the high frequency of tumor relapse following primary debulking, and the development of chemoresistance. All these events are thought to be initiated and sustained by a subpopulation of neoplastic cells, termed ovarian cancer stem cells (OCSC), that are endowed with self-renewing and tumor-initiating properties. This implies that interfering with OCSC function should offer novel therapeutic perspectives to defeat OC progression. To this aim, a better understanding of the molecular and functional makeup of OCSC in clinically relevant model systems is essential. We have profiled the transcriptome of OCSC vs. their bulk cell counterpart from a panel of patient-derived OC cell cultures. This revealed that Matrix Gla Protein (MGP), classically known as a calcification-preventing factor in cartilage and blood vessels, is markedly enriched in OCSC. Functional assays showed that MGP confers several stemness-associated traits to OC cells, including a transcriptional reprogramming. Patient-derived organotypic cultures pointed to the peritoneal microenvironment as a major inducer of MGP expression in OC cells. Furthermore, MGP was found to be necessary and sufficient for tumor initiation in OC mouse models, by shortening tumor latency and increasing dramatically the frequency of tumor-initiating cells. Mechanistically, MGP-driven OC stemness was mediated by the stimulation of Hedgehog signaling, in particular through the induction of the Hedgehog effector GLI1, thus highlighting a novel MGP/Hedgehog pathway axis in OCSC. Finally, MGP expression was found to correlate with poor prognosis in OC patients, and was increased in tumor tissue after chemotherapy, supporting the clinical relevance of our findings. Thus, MGP is a novel driver in OCSC pathophysiology, with a major role in stemness and in tumor initiation.

Single cell analysis in head and neck cancer reveals potential immune evasion mechanisms during early metastasis

Profiling tumors at single-cell resolution provides an opportunity to understand complexities underpinning lymph-node metastases in head and neck squamous-cell carcinoma. Single-cell RNAseq (scRNAseq) analysis of cancer-cell trajectories identifies a subpopulation of pre-metastatic cells, driven by actionable pathways including AXL and AURK. Blocking these two proteins blunts tumor invasion in patient-derived cultures. Furthermore, scRNAseq analyses of tumor-infiltrating CD8 + T-lymphocytes show two distinct trajectories to T-cell dysfunction, corroborated by their clonal architecture based on single-cell T-cell receptor sequencing. By determining key modulators of these trajectories, followed by validation using external datasets and functional experiments, we uncover a role for SOX4 in mediating T-cell exhaustion. Finally, interactome analyses between pre-metastatic tumor cells and CD8 + T-lymphocytes uncover a putative role for the Midkine pathway in immune-modulation and this is confirmed by scRNAseq of tumors from humanized mice. Aside from specific findings, this study demonstrates the importance of tumor heterogeneity analyses in identifying key vulnerabilities during early metastasis.

KRAS-specific antibody binds to KRAS protein inside colorectal adenocarcinoma cells and inhibits its localization to the plasma membrane.

Colorectal cancer (CRC) is the third highest incidence cancer and a leading cause of cancer mortality worldwide. To date, chemotherapeutic treatment of advanced CRC that has metastasized has a dismayed success rate of less than 30%. Further, most (80%) sporadic CRCs are microsatellite-stable and are refractory to immune checkpoint blockade therapy. KRAS is a gatekeeper gene in colorectal tumorigenesis. Nevertheless, KRAS is 'undruggable' due to its structure. Thus, focus has been diverted to develop small molecule inhibitors for its downstream effector such as ERK/MAPK. Despite intense research efforts for the past few decades, no small molecule inhibitor has been in clinical use for CRC. Antibody targeting KRAS itself is an attractive alternative. We developed a transient ex vivo patient-derived matched mucosa-tumor primary culture to assess whether anti-KRAS antibody can be internalized to bind and inactivate KRAS. We showed that anti-KRAS antibody can enter live mucosa-tumor cells and specifically aggregate KRAS in the cytoplasm, thus hindering its translocation to the inner plasma membrane. The mis-localization of KRAS reduces KRAS dwelling time at the site where it tethers to activate downstream effectors. We previously showed that expression of SOX9 was KRAS-mutation-dependent and possibly a better effector than ERK in CRC. Herein, we showed that anti-KRAS antibody treated tumor cells have less intense SOX9 cytoplasmic and nuclear staining compared to untreated cells. Our results demonstrated that internalized anti-KRAS antibody inhibits KRAS function in tumor. With an efficient intracellular antibody delivery system, this can be further developed as combinatorial therapeutics for CRC and other KRAS-driven cancers.

Organoids in high-throughput and high-content screenings

Organoids are self-organized three-dimensional (3D) multicellular tissue cultures which derive from cancerous and healthy stem cells, sharing a highly similarity to the corresponding in vivo organs. Since their introduction in 2009, they have emerged as a valuable model for studying early embryogenesis, organ and tissue development, as well as tools in drug screening, disease modeling and personalized therapy. Organoids can now be established for various tissues, including brain, retina, thyroid, gastrointestinal, lung, liver, pancreas, and kidney. These micro-tissues resemble the native organ in terms of gene expression, protein expression, tissue architecture and cell-cell interactions. Despite the success of organoid-based research and the advances in patient-derived organoid culture, important challenges remain. In this review, we briefly showcase the evolution from the primary 3D systems to complex, multilayered 3D structures such as assembloids, gastruloids and ETiX embryoids. We discuss current developments in organoid research and highlight developments in organoid culturing systems and analysis tools which make organoids accessible for high-throughput and high-content screening. Finally, we summarize the potential of machine learning and computational modeling in conjunction with organoid systems.

Patient-Derived Tumor Organoids Can Predict the Progression-Free Survival of Patients With Stage IV Colorectal Cancer After Surgery.

Recent studies have shown patient-derived tumor organoids can predict the drug response of patients with cancer. However, the prognostic value of patient-derived tumor organoid-based drug tests in predicting the progression-free survival of patients with stage IV colorectal cancer after surgery remains unknown. This study aimed to explore the prognostic value of patient-derived tumor organoid-based drug tests in patients with stage IV colorectal cancer after surgery. Retrospective cohort study. Surgical samples were obtained from patients with stage IV colorectal cancer at the Nanfang Hospital. A total of 108 patients who underwent surgery with successful patient-derived tumor organoid culture and drug testing were recruited between June 2018 and June 2019. Patient-derived tumor organoid culture and chemotherapeutic drug testing. Progression-free survival. According to the patient-derived tumor organoid-based drug test, 38 patients were drug sensitive and 76 patients were drug resistant. The median progression-free survival was 16.0 months in the drug-sensitive group and 9.0 months in the drug resistant group ( p < 0.001). Multivariate analyses showed that drug resistance (HR, 3.38; 95% CI, 1.84-6.21; p < 0.001), right-sided colon (HR, 3.50; 95% CI, 1.71-7.15; p < 0.001), mucinous adenocarcinoma (HR, 2.47; 95% CI, 1.34-4.55; p = 0.004), and non-R0 resection (HR, 2.70; 95% CI, 1.61-4.54; p < 0.001) were independent predictors of progression-free survival. The new patient-derived tumor organoid-based drug test model, which includes the patient-derived tumor organoid-based drug test, primary tumor location, histological type, and R0 resection, was more accurate than the traditional clinicopathological model in predicting progression-free survival ( p = 0.001). A single-center cohort study. Patient-derived tumor organoids can predict progression-free survival in patients with stage IV colorectal cancer after surgery. Patient-derived tumor organoid drug resistance is associated with shorter progression-free survival, and the addition of patient-derived tumor organoid drug tests to existing clinicopathological models improves the ability to predict progression-free survival.

Abstract P3-09-01: Characterization of residual disease after neoadjuvant selective estrogen receptor degrader (SERD) therapy using tumor organoids in the I-SPY Endocrine Optimization Protocol (EOP)

Abstract Background: Treatment of estrogen receptor (ER)-positive breast cancer with selective estrogen receptor degraders (SERDs) frequently results in the loss or reduction of ER expression. Whether these changes are due to on-target effects of SERDs degrading ER or arise as a mechanism of tumor resistance with associated changes in cellular phenotypes remains unknown. It is critical to distinguish between these possibilities to accurately assess treatment response and determine the most appropriate subsequent therapy. To this end, we created and conducted molecular analyses on patient-derived organoid cultures from post-treatment tissue in patients receiving neoadjuvant SERD therapy for early-stage ER+ breast cancer in the I-SPY2 Endocrine Optimization Protocol (EOP). Methods: The I-SPY2 EOP study is a prospective, randomized substudy within the I-SPY TRIAL testing the oral SERD amcenestrant alone or in combination with letrozole or abemaciclib in stage 2/3 ER+ Her2-negative breast cancer. Enrollment is ongoing, with patients receiving amcenestrant neoadjuvantly for 6 months until the day before surgery. Tumor tissue is collected at baseline, 3 weeks, and at surgery. Organoids were generated from post-treatment surgical samples. Organoid cultures were optimized based on established methods (Dekkers et al., Nature Protocols, 2021) to assess ER levels and activity. Pre- and post-treatment tissue samples were also assessed for ER, PR, Ki67, and GATA3, a luminal marker and transcription factor that is functionally linked with ER, via immunohistochemistry. Results: In 7 patients with both pre- and post-treatment tissue samples including fresh surgical samples for organoid generation, the ER in baseline tumor tissue was &amp;gt;=90% in all patients, PR ranged from 40-90%, and Ki67 ranged from 5-30%. In post-treatment surgical tissue from these cases, ER ranged from 0-30%, PR from 0-50%, Ki67 from &amp;lt; 1%-10%, and GATA3 was positive in 5 of 5 cases tested to-date. The creation of organoids from residual disease at surgery was attempted for these 7 patients, with organoids successfully propagated in 5 cases thus far. 3 of 5 organoid cultures were ready for analysis and in all cases strong ER and PR expression in organoids was observed after culture for &amp;gt; 1 month in the absence of amcenestrant. Detailed gene expression profiling (including Mammaprint/Blueprint) and gene set enrichment analyses (GSEA) to assess for intrinsic breast cancer subtype and ER activity in each sample and corresponding organoid culture are in progress and will be reported with the full dataset. Conclusion: Patient-derived organoid culturing of residual disease after neoadjuvant endocrine therapy is feasible. Neoadjuvant treatment with a SERD can render ER and PR low or absent at the time of surgical resection, which does not necessarily imply the presence of endocrine therapy resistant disease. The use of organoids and additional IHC markers (GATA3) demonstrate that receptor negativity may be an indicator of the drug hitting its target, suggesting ER signaling is still intact. In general, patient-derived tumor organoid cultures modeling residual disease states can be a useful adjunct to existing methods used to monitor the effects of neoadjuvant endocrine therapy and is being explored in the I-SPY EOP trial. Citation Format: Jennifer Rosenbluth, Christopher J. Schwartz, Tam Binh Bui, Shruti Warhadpande, Pravin Phadatare, Sigal Eini, Michael Bruck, Julissa Molina-Vega, Kami Pullakhandam, Nicole Schindler, Lamorna A. Brown Swigart, Christina Yau, Gillian Hirst, Rita Mukhtar, Karthik V. Giridhar, Olufunmilayo I. Olopade, Kevin Kalinsky, Cheryl A. Ewing, Jasmine M. Wong, Michael D. Alvarado, Laura Van’t Veer, Laura J. Esserman, Jo Chien. Characterization of residual disease after neoadjuvant selective estrogen receptor degrader (SERD) therapy using tumor organoids in the I-SPY Endocrine Optimization Protocol (EOP) [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-09-01.

106P Synergistic effect of CDK4/6 inhibitors and standard chemotherapy sequential treatment on liposarcoma patient-derived primary culture

106P Synergistic effect of CDK4/6 inhibitors and standard chemotherapy sequential treatment on liposarcoma patient-derived primary culture

Abstract P2-24-02: Analyzing susceptibility to macrophage-activating immunotherapy bexmarilimab in breast cancer by using patient-derived tumor explants

Abstract The immunosuppressive tumor microenvironment governed by tumor-associated macrophages (TAMs) remains a major obstacle to effective cancer immunotherapy. A novel humanized antibody bexmarilimab, targeting the scavenger receptor Clever-1 on TAMs, has shown clinical benefit in ~40% of patients with late-stage ER+ breast cancer (MATINS; NCT03733990). To increase response rates, a comprehensive understanding on how TAM phenotype and the tumor immune landscape affect bexmarilimab-induced immune activation is needed. Single-cell RNA sequencing analysis of breast tumor macrophages shows high phenotypic variation across pathological subtypes and Clever-1 mRNA (STAB1) expression on various immunosuppressive IL4I1+ and TREM2+ monocyte-derived TAMs. STAB1 expressing macrophages were located in both lymphocyte rich and excluded areas in the tumor stroma based on digital spatial profiling with GeoMx. Due to this diversity, we studied bexmarilimab mode-of-action in breast cancer patient-derived tumor explant cultures (PDEC) by RNA sequencing and cytokine profiling. Our results show that bexmarilimab induced TNFα and CXCL10 secretion in 30-40% of the treated explants. In depth analysis of the responsive PDECs revealed a lower baseline expression of interferon responsive genes in their tumor microenvironment. Correspondingly, in vitro assays with primary human macrophages showed that chronic IFNγ priming abolished bexmarilimab-induced immune activation, suggesting potential use of bexmarilimab in patients with immunologically cold breast tumors. Citation Format: Jenna H. Rannikko, Reetta Virtakoivu, Akira Takeda, Pia Boström, Ilkka Koskivuo, Petri Bono, Maija Hollmén. Analyzing susceptibility to macrophage-activating immunotherapy bexmarilimab in breast cancer by using patient-derived tumor explants [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-24-02.