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Some patients with advanced clear-cell ovarian cancer (CCOC) respond to immunotherapy; however, little is known about the tumor microenvironment (TME) of this relatively rare disease. Here, we describe a comprehensive quantitative and topographical analysis of biopsies from 45 patients, 9 with Federation Internationale des Gynaecologistes et Obstetristes (FIGO) stage I/II (early CCOC) and 36 with FIGO stage III/IV (advanced CCOC). We investigated 14 immune cell phenotype markers, PD-1 and ligands, and collagen structure and texture. We interrogated a microarray data set from a second cohort of 29 patients and compared the TMEs of ARID1A-wildtype (ARID1Awt) versus ARID1A-mutant (ARID1Amut) disease. We found significant variations in immune cell frequency and phenotype, checkpoint expression, and collagen matrix between the malignant cell area (MCA), leading edge (LE), and stroma. The MCA had the largest population of CD138+ plasma cells, the LE had more CD20+ B cells and T cells, whereas the stroma had more mast cells and αSMA+ fibroblasts. PD-L2 was expressed predominantly on malignant cells and was the dominant PD-1 ligand. Compared with early CCOC, advanced-stage disease had significantly more fibroblasts and a more complex collagen matrix, with microarray analysis indicating “TGFβ remodeling of the extracellular matrix” as the most significantly enriched pathway. Data showed significant differences in immune cell populations, collagen matrix, and cytokine expression between ARID1Awt and ARID1Amut CCOC, which may reflect different paths of tumorigenesis and the relationship to endometriosis. Increased infiltration of CD8+ T cells within the MCA and CD4+ T cells at the LE and stroma significantly associated with decreased overall survival.

List of antibodies used in flow cytometry and sorting

Supplementary Data from The Tumor Microenvironment of Clear-Cell Ovarian Cancer

Neoadjuvant chemotherapy (NACT) may stimulate anticancer adaptive immune responses in high-grade serous ovarian cancer (HGSOC), but little is known about effects on innate immunity. Using omental biopsies from HGSOC, and omental tumors from orthotopic mouse HGSOC models that replicate the human tumor microenvironment, we studied the impact of platinum-based NACT on tumor-associated macrophages (TAM). We found that chemotherapy reduces markers associated with alternative macrophage activation while increasing expression of proinflammatory pathways, with evidence of inflammasome activation. Further evidence of a shift in TAM functions came from macrophage depletion via CSF1R inhibitors (CSF1Ri) in the mouse models. Although macrophage depletion in established disease had no impact on tumor weight or survival, CSF1Ri treatment after chemotherapy significantly decreased disease-free and overall survival. This decrease in survival was accompanied by significant inhibition of adaptive immune response pathways in the tumors. We conclude that chemotherapy skews the TAM population in HSGOC toward an antitumor phenotype that may aid adaptive immune responses, and therapies that enhance or sustain this during remission may delay relapse.

Supplementary Figures 1-6 with legends.

Cell motility is an important component of anti-tumor responses, allowing immune cells like myeloid and cytotoxic T cells to infiltrate tumors. Using ex vivo human and mouse high-grade serous ovarian cancer (HGSOC) tumor slices combined with time-lapse imaging, we monitored the movement of CD8+ T and myeloid cells in live tumors, in real-time. To analyze the recordings and characterize immune cell movements, we developed a semi-supervised analysis, identifying four types of cell behavior: migrating, long migrating, static and wobbling. Tumor slices were maintained 24h ex vivo, retaining viability and cell movements. We show that ex vivo treatments with LPS altered CD8+ T and myeloid cell behavior. In vivo chemotherapy reduced ex vivo cell movements in human and mouse tumors, and differentially affected CD8+ T and myeloid cells in 60577 and HGS2 murine tumors, respectively chemo-sensitive and chemo-resistant mouse models, suggesting those cell types have different roles in the response to chemotherapy. Ex vivo tumor slices can extend in vivo mouse work to human, providing a stepping stone to translate mouse cancer studies to clinical trials. Citation Format: Florian Laforets, Panoraia Kotantaki, Beatrice Malacrida, Samar Elorbany, Ranjit Manchanda, Emmanuel Donnadieu, Frances Balkwill. Semi-supervised analysis of myeloid and T cell behavior in ex vivo ovarian tumor slices reveals changes in cell motility after 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 5913.

Chimeric antigen receptor (CAR)-T cell therapies have promising outcomes in hematologic malignancies but limited activity in solid tumors. We used 3-dimentional (3D) in vitro human cell models of increasing complexity to investigate resistance to CAR-T cell therapy in high grade serous ovarian cancer (HGSOC), a disease with poor response to immunotherapy. We identified mucin-1 (MUC1) and TnMUC1 as target antigens in HGSOC omental metastasis and the HGSOC cell lines, OvCAR3 and G164. We then generated CAR-T cells against these targets and tested them in spheroids, collagen gels and microfluidic models. In spheroids, OvCAR3 cells were killed by CAR-T cells whereas, G164 cells were resistant to CAR-T cell cytotoxicity. RNA sequencing suggested that the impaired apoptotic signaling in G164 cells caused malignant cell-intrinsic resistance to CAR-T cell cytotoxicity. Treating G164 spheroids with birinapant, an antagonist of cellular inhibitor of apoptosis protein, induced CAR-T cell cytotoxicity. Moreover, when resistant cells were co-cultured as spheroids with primary omental fibroblasts from ovarian cancer patients, CAR-T cells were activated and cytotoxic. G164 spheroids cultured in fibroblast-conditioned medium also induced CAR-T cell cytotoxicity due to C-C motif chemokine ligand 2 (CCL2) produced by fibroblasts. CCL2 activated CCR2/4+ CAR-T cells to induce cytotoxicity in an antigen-dependent manner. We then investigated CAR-T cell migration and cytotoxicity in malignant cell/fibroblast co-culture collagen gels. CAR-T cell migrated into OvCAR3 gels and were cytotoxic against the malignant cells. However, a dense extracellular matrix (ECM) produced primarily by fibroblasts prevented CAR-T cell migration and cytotoxicity in G164 gels. Treating G164 gels with transforming growth factor beta (TGFβ) receptor inhibitor SB431542 reduced ECM content and altered ECM structure, thus stimulating CAR-T cell penetration and restoring cytotoxicity against G164 cells. We also developed an ovarian cancer-on-a-chip model which involved culturing cell-seeded collagen gels in vascularized tri-channel microfluidic devices. CAR-T cells successfully penetrated and killed malignant cells in co-culture collagen gels when delivered through vascularized microfluidic devices. To our knowledge, this is the first report to use microfluidic tumor models to successfully deliver CAR-T cells. Using these different human 3D in vitro models, we uncovered malignant cell-intrinsic factors and novel mechanisms involving fibroblasts which may influence CAR-T cell activity. Complex human cell models may accelerate preclinical research into CAR-T cell therapies in solid tumors. Citation Format: Joash Dominic Joy, Beatrice Malacrida, Florian Laforêts, Panoraia Kotantaki, Eleni Maniati, Sarah Hopkins, Ianire Garrobo-Calleja, Julien Gautrot, Frances Balkwill. 3D in vitro models uncover malignant cell intrinsic and extrinsic mechanisms of CAR-T cell resistance in high grade serous ovarian cancer. [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 4576.

In this study we explored the effects of chemotherapy on the extracellular matrix of high-grade serous ovarian cancer metastasis (HGSOC) at structural-textural protein level and transcriptionally, in order to identify the microenvironmental features that accompany a successful response. We studied two murine orthotopic, transplantable syngeneic models of HGSOC, one that displays excellent response to carboplatin/paclitaxel (60577) and one that is resistant to treatment (HGS2)1. Using immunohistochemistry, we stained omental tumors from both models for the ECM components fibronectin (FN1), collagen 1A1 (COL1A1) and versican (VCAN), also using Masson’s Trichrome to stain for collagen. We analyzed their abundance, textural features (Haralick features) and structure with the image analysis softwares, QuPath and TWOMBLI respectively. A compilation of 44 ECM metrics, which we named the “structure index”, correlated with response to chemotherapy, as measured by reduction in omental tumor weight. In parallel, we performed RNAseq on the omental tumors, identifying clusters of genes that change over time with chemotherapy treatment of the responsive model 60577, while the chemoresistant model HGS2 displayed limited alteration of gene expression. We integrated RNAseq and ECM structure and texture data, and showed the structure index was correlated with 144 core matrisome genes. To identify potential therapeutic targets, we then focused our study on genes that remained highly expressed in resistant tumors post chemotherapy, but were originally low or decreased with treatment in the sensitive tumors. Members of the LOX and P4HA family were found amongst these genes. We confirmed by immunohistochemical analysis that expression of LOX, LOXL2, P4HA1 and P4HA2 was downregulated by chemotherapy in the 60577 chemo-sensitive tumors while their levels remained relatively unaffected in the resistant HGS2 tumors. This study refines our understanding of the mechanisms of microenvironmental chemoresistance in HGSOC, highlighting putative therapeutic targets to increase the efficacy of platinum-based chemotherapy in ovarian cancer. 1 Maniati, E. et al. Mouse Ovarian Cancer Models Recapitulate the Human Tumor Microenvironment and Patient Response to Treatment. Cell Rep 30, 525-540.e527, doi:10.1016/j.celrep.2019.12.034 (2020). Citation Format: Panoraia Kotantaki, Florian Laforêts, Eleni Maniati, Chiara Berlato, Anna Malliouri, Michael John Devlin, Beatrice Malacrida, Samar Elorbany, Ranjit Manchanda, Frances R. Balkwill. Chemotherapy-induced extracellular matrix remodeling in HGSOC [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 5957.

Some patients with advanced clear-cell ovarian cancer (CCOC) respond to immunotherapy; however, little is known about the tumor microenvironment (TME) of this relatively rare disease. Here, we describe a comprehensive quantitative and topographical analysis of biopsies from 45 patients, 9 with Federation Internationale des Gynaecologistes et Obstetristes (FIGO) stage I/II (early CCOC) and 36 with FIGO stage III/IV (advanced CCOC). We investigated 14 immune cell phenotype markers, PD-1 and ligands, and collagen structure and texture. We interrogated a microarray data set from a second cohort of 29 patients and compared the TMEs of ARID1A-wildtype (ARID1Awt) versus ARID1A-mutant (ARID1Amut) disease. We found significant variations in immune cell frequency and phenotype, checkpoint expression, and collagen matrix between the malignant cell area (MCA), leading edge (LE), and stroma. The MCA had the largest population of CD138+ plasma cells, the LE had more CD20+ B cells and T cells, whereas the stroma had more mast cells and αSMA+ fibroblasts. PD-L2 was expressed predominantly on malignant cells and was the dominant PD-1 ligand. Compared with early CCOC, advanced-stage disease had significantly more fibroblasts and a more complex collagen matrix, with microarray analysis indicating “TGFβ remodeling of the extracellular matrix” as the most significantly enriched pathway. Data showed significant differences in immune cell populations, collagen matrix, and cytokine expression between ARID1Awt and ARID1Amut CCOC, which may reflect different paths of tumorigenesis and the relationship to endometriosis. Increased infiltration of CD8+ T cells within the MCA and CD4+ T cells at the LE and stroma significantly associated with decreased overall survival.

We have assessed the utility of 3-dimensional (3D) in vitro human cell models to understand barriers to chimeric antigen receptor (CAR)-T cell activity in high-grade serous ovarian cancer, (HGSOC) a disease with a poor response to immunotherapy. We defined mucin-1 (MUC1) as a potential target in HGSOC biopsies and the HGSOC cell lines, OvCAR3 and G164. We then generated CAR-T cells against MUC1 and tested them in spheroid and collagen gel cultures. In spheroids, although CAR-T cells killed OvCAR3 cells, G164 cells failed to induce CAR-T cell activation or cytotoxicity. However, when we added primary omental fibroblasts from ovarian cancer patients to G164 spheroids, CAR-T cells were activated and cytotoxic. Fibroblast conditioned medium also activated CAR-T cells to kill G164 cells in spheroids and this was due to their production of C-C motif chemokine ligand 2 (CCL2). Further experiments revealed that CCL2 produced by fibroblast stimulated CCR2/4 positive CAR-T cells to a higher state of activation, which enhanced the cytotoxicity of CAR-T cells against G164 cells. We then investigated CAR-T cell activity in co-cultures of OvCAR3 or G164 cells and primary fibroblasts embedded in collagen. CAR-T cells migrated into OvCAR3 gels and killed the malignant cells during a three-day period. However, CAR-T cells failed to migrate into gels with G164 cells and there was no malignant cell killing. Gels containing G164 cells had denser extracellular matrix (ECM) than OvCAR3 gels, as measured by staining for collagens and fibronectin. Previously, we showed that transforming growth factor-beta (TGFβ) secreted by HGSOC cells acted on fibroblasts to induce the production of ECM in collagen gels.1 Treating G164 gels with the TGFβ receptor inhibitor SB431542 reduced ECM density, stimulated CAR-T cell migration and restored CAR-T cell cytotoxicity against G164 cells. Using these different human 3D models we have demonstrated that malignant cell intrinsic factors can cause resistance to CAR-T cells. Sensitivity to CAR-T cell killing can be modulated both positively and negatively by fibroblasts. Targeting ECM along with CAR-T cell therapy might improve the efficiency of CAR-T cells in solid tumors. 1Delaine-Smith et al, iScience, 2021 Citation Format: Joash Dominic Joy, Beatrice Malacrida, Florian Laforêts, Panoraia Kotantaki, Eleni Maniati, Sarah Hopkins, Ianire Calleja, Sara Brett, Takis Athanasopoulos, Sadfer Ali, Peter Emery-Billcliff, Ida Ricciardelli, Charlotte Kay, Jayne Colebrook, Magda Ali, Katherine Strong, Frances Balkwill. TGFβ-mediated targeting of the extracellular matrix enhances the migration and cytotoxicity of CAR-T cells in 3D models of ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 693.

Neoadjuvant chemotherapy (NACT) may stimulate anticancer adaptive immune responses in high-grade serous ovarian cancer (HGSOC), but little is known about effects on innate immunity. Using omental biopsies from HGSOC, and omental tumors from orthotopic mouse HGSOC models that replicate the human tumor microenvironment, we studied the impact of platinum-based NACT on tumor-associated macrophages (TAM). We found that chemotherapy reduces markers associated with alternative macrophage activation while increasing expression of proinflammatory pathways, with evidence of inflammasome activation. Further evidence of a shift in TAM functions came from macrophage depletion via CSF1R inhibitors (CSF1Ri) in the mouse models. Although macrophage depletion in established disease had no impact on tumor weight or survival, CSF1Ri treatment after chemotherapy significantly decreased disease-free and overall survival. This decrease in survival was accompanied by significant inhibition of adaptive immune response pathways in the tumors. We conclude that chemotherapy skews the TAM population in HSGOC toward an antitumor phenotype that may aid adaptive immune responses, and therapies that enhance or sustain this during remission may delay relapse.

The aim of this study is to characterize and validate similarities between the human tumor microenvironment (TME) and the TME of new HGSOC murine models and to use the models to analyze the role of tumor associated macrophages (TAMs) after chemotherapy. HGSOC has seen in the past decades only a modest reduction of mortality. This is in part due to the lack of suitable models, as the origin and mutation patterns of HGSOC were not previously understood. Despite recent advances with organoid models, murine models that represent the TME and in particular the complex interactions with the immune system are needed. We characterized the TME of six orthotopic, transplantable syngeneic murine HGSOC lines established from tumors in genetic models and compared these to patient biopsies. This analysis identified significant correlations between the transcriptome, host cell infiltrates, immune response, matrisome, vasculature and tissue modulus of mouse and human TMEs, with several stromal and malignant cell targets in common. However, each model also showed distinct differences and potential vulnerabilities that will enable us to study potential therapies. These models allowed us to extend our understanding of the role of TAMs following chemotherapy. Chemotherapy reduced the number and changed the phenotype of TAMs both in patient biopsies and in mouse models. Following chemotherapy, inflammasome activation in TAMs was also observed. Depletion of TAMs with CSFR1 inhibitors after carboplatin treatment reduced survival in a mouse model, suggesting that chemotherapy can activate sub-populations of macrophages to an anti-tumor phenotype that can sustain adaptive immunity. In conclusion, we have characterized murine transplantable models that share similarities with human HGSOC and have helped us elucidate the anti-tumor role of TAMs once activated by chemotherapy. Citation Format: Chiara Berlato, Owen Heath, Eleni Maniati, Ganga Gopinathan, Panoraia Kotantaki, Samar Elorbany, Jacqueline McDermott, Colin Pegrum, Ludmila Szabova, Ruth Perets, Ronny Drapkin, Peter Bailey, Alessandro Annibaldi, Desmond P. Barton, Frances R. Balkwill. Murine high grade serous ovarian cancer (HGSOC) models replicate the human tumor microenvironment and suggest anti-tumor activities of macrophages after chemotherapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2745.

Treatment of advanced Clear Cell Ovarian Cancer (CCOC) with immune checkpoint inhibition (ICI) is currently undergoing evaluation in a Phase II clinical trial. ARID1A mutations, which occur in up to 57% of CCOC, influence immune cell infiltration in pre-clinical models, but more information is needed on how it alters the tumor microenvironment (TME) of human CCOC. Methods: FFPE samples from 36 cases of FIGO III-IV CCOC were analyzed. Of the 36 cases; 21 were ARID1A wildtype (ARID1Awt), 14 ARID1A mutant (ARID1Amut) and 1 mixed. Immunohistochemistry was performed for immune markers (CD3, CD8, CD4, CD45RO, FOXP3, CD20, CD68, CD1a, Mast Cell Tryptase, Eosinophil Derived Neurotoxin, alpha-SMA) alongside PD1, PDL1, PDL2 and quantified using QuPath. The malignant cell area (MCA), leading edge (LE) and stroma were measured separately to provide information on immune marker location within the TME. Collagen was identified by Masson's Trichrome with structural analysis using the FIJI plugin TWOMBLI. Statistical analysis was performed on PRISM. Results: In this study we found significant differences between the TME of ARID1Awt and ARID1Amut tumors in terms of both immune infiltrate, collagen density and structure. ARID1Awt tumors had more collagen, with longer fibers and more branchpoints across the MCA, LE and Stroma ( Conclusion: There are significant differences in the collagen matrix, immune cell populations and the PD1-PDL1-PDL2 axis between ARID1Awt and ARID1Amut advanced CCOC tumors. This may influence response to ICI and other therapies. Citation Format: Michael-John Devlin, Rebecca S. Kristeleit, Jacqueline McDermott, Eleni Maniati, Florian Laforêts, Panoraia Kotantaki, Rowan Miller, Frances Balkwill. Impact of ARID1A mutation on the tumor microenvironment of advanced clear cell ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2748.

Summary Although there are many prospective targets in the tumor microenvironment (TME) of high-grade serous ovarian cancer (HGSOC), pre-clinical testing is challenging, especially as there is limited information on the murine TME. Here, we characterize the TME of six orthotopic, transplantable syngeneic murine HGSOC lines established from genetic models and compare these to patient biopsies. We identify significant correlations between the transcriptome, host cell infiltrates, matrisome, vasculature, and tissue modulus of mouse and human TMEs, with several stromal and malignant targets in common. However, each model shows distinct differences and potential vulnerabilities that enabled us to test predictions about response to chemotherapy and an anti-IL-6 antibody. Using machine learning, the transcriptional profiles of the mouse tumors that differed in chemotherapy response are able to classify chemotherapy-sensitive and -refractory patient tumors. These models provide useful pre-clinical tools and may help identify subgroups of HGSOC patients who are most likely to respond to specific therapies., Graphical Abstract, Highlights • Mouse ovarian cancers replicate the human ovarian tumor microenvironment • Stromal, immune, and malignant cell targets in common • Evidence for distinct therapeutic vulnerabilities in individual models • Models may help identify patient subgroups likely to respond to specific therapies, Maniati et al. show how orthotopic transplantable mouse ovarian cancers with appropriate genotypes develop microenvironments that replicate many features of human primary ovarian tumors and metastases. Molecular features of the mouse tumors combined with machine learning may allow the identification of patients who are most likely to respond to specific therapies.

Balancing stem cell self-renewal and initiation of lineage specification programs is essential for the development and homeostasis of the hematopoietic system. We have specifically ablated geminin in the developing murine hematopoietic system and observed profound defects in the generation of mature blood cells, leading to embryonic lethality. Hematopoietic stem cells (HSCs) accumulated in the fetal liver following geminin ablation, while committed progenitors were reduced. Genome-wide transcriptome analysis identified key HSC transcription factors as being upregulated upon geminin deletion, revealing a gene network linked with geminin that controls fetal hematopoiesis. In order to obtain mechanistic insight into the ability of geminin to regulate transcription, we examined Hoxa9 as an example of a key gene in definitive hematopoiesis. We demonstrate that in human K562 cells geminin is associated with HOXA9 regulatory elements and its absence increases HOXA9 transcription similarly to that observed in vivo. Moreover, silencing geminin reduced recruitment of the PRC2 component SUZ12 to the HOXA9 locus and resulted in an increase in RNA polymerase II recruitment and H3K4 trimethylation (H3K4me3), whereas the repressive marks H3K9me3 and H3K27me3 were reduced. The chromatin landscape was also modified at the regulatory regions of HOXA10 and GATA1. K562 cells showed a reduced ability to differentiate to erythrocytes and megakaryocytes upon geminin silencing. Our data suggest that geminin is indispensable for fetal hematopoiesis and regulates the generation of a physiological pool of stem and progenitor cells in the fetal hematopoietic system.