Tumor initiation, growth, and spread are influenced by cancer cell intrinsic and tissue microenvironment factors of the organ the tumor resides in. Here, we provide a protocol on utilizing murine gastric cancer (GC) organoids as transplantable mouse models for subcutaneous, orthotopic primary, and liver metastatic disease. We provide detailed instructions for organoid expansion; processing of GC organoids; and their subsequent subcutaneous, intra-stomach wall, and intra-splenic transplantation. We then detail steps for post-procedure tumor and metastasis monitoring and outcomes. For complete details on the use and execution of this protocol, please refer to Huber et al.1.

Abstract Tissue-resident immune cells reside within the gastrointestinal tract known as intraepithelial lymphocytes (T-IELs), including αβ and γδ T-IELs. This unique population of T cells constantly survey and are critical in maintaining the gastrointestinal epithelium. We show that T-IELs in various regions of the gastrointestinal tract have distinct features. T-IELs in the small intestine exhibit high expression of cytotoxic molecules important for cancer defense while colon T-IELs are distinctively regulated by the transcription factor, TCF-7/TCF-1, which suppresses their effector and cytotoxic properties, including reduced expression of granzymes, and their abundance is dependent on the microbiome. Targeted deletion of TCF-1 in γδ T-IELs using pre-clinical mouse models resulted in a distinct effector profile and reduced colon tumor burden. Furthermore, TCF-1 expression was significantly reduced in γδ T-IELs present in human colorectal cancers compared with normal healthy colon, strongly correlating with an enhanced γδ T-IEL effector phenotype and improved patient survival. Further investigation aims to elucidate diverse mechanisms by which TCF-1 controls tissue-specific anti-tumor immunity and uncover the important factors controlling TCF-1 expression. Our study underscores the necessity to consider tumor and organ microenvironment-specific factors in optimizing immunotherapy, advancing our understanding of T cell function in the colon to pave the way for innovative CRC treatments. Citation Format: Marina H. Yakou, Sonia Ghilas, Kelly Tran, Yang Liao, Shoukat Afshar-Sterle, Anita Kumari, Kevin Schmid, Christine Dijkstra, Chantelle Inguanti, Simone Ostrouska, Jordan Wilcox, Maxine Smith, Pavitha Parathan, Amr Allam, Hai-Hui Xue, Gabrielle T. Belz, John M. Mariadason, Andreas Behren, Grant R. Drummond, Roland Ruscher, David S. Williams, Bhupinder Pal, Wei Shi, Matthias Ernst, Dinesh Raghu, Lisa A. Mielke. TCF-1 is a critical regulator of intraepithelial lymphocytes in colorectal 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 2698.

Although aberrant activation of the KRAS and PI3K pathway alongside TP53 mutations account for frequent aberrations in human gastric cancers, neither the sequence nor the individual contributions of these mutations have been clarified. Here, we establish an allelic series of mice to afford conditional expression in the glandular epithelium of KrasG12D;Pik3caH1047R or Trp53R172H and/or ablation of Pten or Trp53. We find that KrasG12D;Pik3caH1047R is sufficient to induce adenomas and that lesions progress to carcinoma when also harboring Pten deletions. An additional challenge with either Trp53 loss- or gain-of-function alleles further accelerated tumor progression and triggered metastatic disease. While tumor-intrinsic STAT3 signaling in response to gp130 family cytokines remained as a gatekeeper for all stages of tumor development, metastatic progression required a mutant Trp53-induced interleukin (IL)-11 to IL-6 dependency switch. Consistent with the poorer survival of patients with high IL-6 expression, we identify IL-6/STAT3 signaling as a therapeutic vulnerability for TP53-mutant gastric cancer.

Fig S1. IL-33 and St2 protein expression in sporadic colon cancer.

Background Intraepithelial lymphocytes (IELs), including αβ and γδ T cells (T-IELs) constantly survey and play a critical role in maintaining the gastrointestinal (GI) epithelium. Recent reports highlight a critical function for γδ T-IELs in defense again colorectal carcinoma (CRC).1–3 Methods Tumor biopsies from patients with stage III CRC were analysed by multiplex immunohistochemistry to investigate immune cell location and immune cell phenotypes were correlated with patient outcome data. We used mouse models, flow cytometry and single cell RNA sequencing to analyse T-IELs in different regions of the gastrointestinal tract. In addition, targeted deletion of transcriptional regulators in γδ T-IELs was used to interrogate the function of γδ T-IELs in controlling tumor growth. Results We show that cytotoxic molecules important for defense against cancer, were highly expressed by T-IELs in the small intestine. In contrast, abundance of colonic T-IELs was dependent on the microbiome, displayed higher expression of TCF-1/TCF7 and a reduced effector and cytotoxic profile, including low expression of granzymes. Targeted deletion of TCF-1 in γδ T-IELs induced a unique T-IEL effector profile and reduced colon tumor formation in mice. Finally, TCF-1 expression was significantly reduced in γδ T-IELs present in human CRCs compared to normal healthy colon, which strongly correlated with an enhanced γδ T-IEL effector phenotype and improved patient survival. Conclusions Our findings highlight the exciting potential for exploiting colon-resident T cells subsets, including γδ T-IELs in the development of new immunotherapy strategies to treat CRC. References Dasgupta S, Liu H, Bailey B, Wyrick C, Grieves J, DeBoever C, et al. gammadelta T Cells Control Gut Pathology in a Chronic Inflammatory Model of Colorectal Cancer. Cell Mol Gastroenterol Hepatol. 2021;12(3):1163–5 e8. de Vries NL, van de Haar J, Veninga V, Chalabi M, Ijsselsteijn ME, van der Ploeg M, et al. gammadelta T cells are effectors of immunotherapy in cancers with HLA class I defects. Nature. 2023;613(7945):743–50. Reis BS, Darcy PW, Khan IZ, Moon CS, Kornberg AE, Schneider VS, et al. TCR-Vgammadelta usage distinguishes protumor from antitumor intestinal gammadelta T cell subsets. Science. 2022;377(6603):276–84. Ethics Approval Use of human samples were approved by the Austin Health Human Ethics Committee (Heidelberg, Australia protocol H2013/05077). Informed consent was obtained from all patients. All mice used in accordance with Austin Health Animal Ethics Committee or the James Cook University Animal Ethics Committee, Australia. Consent None of the patient data in this abstract is identifiable.

Intraepithelial lymphocytes (IELs), including αβ and γδ T cells (T-IELs), constantly survey and play a critical role in maintaining the gastrointestinal epithelium. We show that cytotoxic molecules important for defense against cancer were highly expressed by T-IELs in the small intestine. In contrast, abundance of colonic T-IELs was dependent on the microbiome and displayed higher expression of TCF-1/TCF7 and a reduced effector and cytotoxic profile, including low expression of granzymes. Targeted deletion of TCF-1 in γδ T-IELs induced a distinct effector profile and reduced colon tumor formation in mice. In addition, TCF-1 expression was significantly reduced in γδ T-IELs present in human colorectal cancers (CRCs) compared with normal healthy colon, which strongly correlated with an enhanced γδ T-IEL effector phenotype and improved patient survival. Our work identifies TCF-1 as a colon-specific T-IEL transcriptional regulator that could inform new immunotherapy strategies to treat CRC.

Fig S2. MC38 tumor growth is enhanced in St2-deficient hosts.

Fig S6. St2-deficiency did not alter Treg frequency in untreated naïve colons.

Gene-of-interest knockout organoids present a powerful and versatile research tool to study a gene’s effects on many biological and pathological processes. Here, we present a straightforward and broadly applicable protocol to generate gene knockouts in mouse organoids using CRISPR-Cas9 technology. We describe the processes of transient transfecting organoids with pre-assembled CRISPR-Cas9 ribonucleoprotein complexes, organoid cell sorting, and establishing clonal organoid culture pairs. We then detail how to confirm the knockout via Western blot analysis.

Suppl Table 1. Oligonucleotide Sequences

Fig S3. St2 is not expressed by Lgr5+ stem cells within the colon.

Fig S4. St2 is expressed by colon-derived mesenchymal cells.

Fig S5. Loss of IL-33 signalling does not affect the recruitment of macrophages, mast cells and total T cells to the colon tumors.

Gastric cancer (GC) remains the third leading cause of cancer-related death worldwide. Unfortunately, only a subset of GC patients, characterized by tumors with high microsatellite instability (MSI), responds to immune checkpoint (ICI) therapy. In the context of GC, the mechanisms of how MSI improves ICI therapy responses remain poorly understood. Here we are undertaking a proof of principle study to demonstrate in novel GC mouse models that loss of mismatch repair protein MLH1 confers MSI phenotype and impairs tumor growth via altered anti-tumor immune responses. To study the functional and mechanistic effects of loss of MLH1 protein, we established MLH1-deficient (Kras-, Pi3kca-, Tp53-mutant) murine tumor organoids via CRISPR/Cas9 technology. These organoids were subcutaneously allografted into immunocompetent C57BL/6 mice to study tumor progression, immune surveillance, and responses to immunotherapy in vivo. MSI testing confirmed that MLH1-proficient parental organoids are MSI low, whereas MLH1-deficient organoids are MSI high. Low passage MLH1-deficient organoid tumors grew similarly to MLH1-proficient tumors. However, after culturing of organoids in vitro for a prolonged time prior to injection to allow accumulation of mutations, subcutaneous allograft MLH1-deficient tumors were considerably smaller compared to MLH1-proficient tumors. MLH1-deficient tumors showed a significantly higher number of CD8+ T cells. Additionally, MLH1-deficient tumors were similar in size to MLH1-proficient tumors when allografted into Rag1-/- mice. Interestingly, CD8- and CD4-depleting experiments showed an involvement of CD4+ T cells in the impairment of MLH1-deficient tumor growth. Treatment with anti-PD-1, but not anti-CTLA-4, reduced tumor mass further. We are currently investigating the underlying mechanism for the impaired growth of MLH1-deficient organoid allograft tumors via tumor mutational burden analysis and neoantigen testing. Taken together, we provide evidence that loss of MLH1 leads to high MSI in gastric tumors, reduces tumor growth after prolonged in vitro culture and increases response to anti-PD-1 therapy. Our findings encourage further studies to investigate the mechanisms of impaired tumor growth after MLH1 loss in GC and may provide insights leading to improve ICI therapy responses for GC patients. Citation Format: Anne Huber, Christine Dijkstra, Vicki Whitehall, Matthias Ernst, Moritz Eissmann. Proof of principle that loss of mismatch repair protein reduces tumor burden in mouse model of gastric cancer [abstract]. In: Proceedings of the AACR Special Conference: Tumor Immunology and Immunotherapy; 2022 Oct 21-24; Boston, MA. Philadelphia (PA): AACR; Cancer Immunol Res 2022;10(12 Suppl):Abstract nr A49.

Aberrant expression of the oncoprotein c-Myc (Myc) is frequently observed in solid tumors and is associated with reduced overall survival. In addition to well-recognized cancer cell-intrinsic roles of Myc, studies have also suggested tumor-promoting roles for Myc in cells of the tumor microenvironment, including macrophages and other myeloid cells. Here, we benchmark Myc inactivation in tumor cells against the contribution of its expression in myeloid cells of murine hosts that harbor endogenous or allograft tumors. Surprisingly, we observe that LysMCre-mediated Myc ablation in host macrophages does not attenuate tumor growth regardless of immunogenicity, the cellular origin of the tumor, the site it develops, or the stage along the tumor progression cascade. Likewise, we find no evidence for Myc ablation to revert or antagonize the polarization of alternatively activated immunosuppressive macrophages. Thus, we surmise that systemic targeting of Myc activity may confer therapeutic benefits primarily through limiting Myc activity in tumor cells rather than reinvigorating the anti-tumor activity of macrophages.

Microsatellite instability-high (MSI-H) phenotype arises from defective DNA repair mechanisms and is found in many malignancies, including colorectal and endometrial cancers. Due to high neoantigen loads derived from tumor-specific mutations, evidence of tumor-infiltrating T cells and high response rates to checkpoint blockade (30-60%), MSI-H cancers can be leveraged to study the features of neoantigen-induced anti-tumor immunity in response to therapy and disease outcome. Previously we identified a set of recurrent frameshift (fs) mutations in MSI-H cancers that yielded immunogenic polyepitope neoantigens (neoAgs) eliciting CD8+ T cell responses. Here we investigate whether these shared fs-neoAgs engendered spontaneous T cell responses in MSI-H colorectal and endometrial cancer patients. Using peripheral blood mononuclear cells (PBMCs), we evaluated the frequency of the fs-neoAg-specific T cells by ex vivo IFN-γ ELISPOT upon fs-peptide stimulation. Additionally, we isolated naïve and memory T cells from MSI-H patient PBMCs and expanded fs-neoAg-specific T cells within each subset. Fs-neoAg-induced effector cytokine (IFN-γ, TNF-α) production was measured by flow cytometry and was detected only in the memory subset, supporting the hypothesis that shared fs-neoAgs prime CD8+ T cells in vivo to generate clonally-expanded memory T cells in MSI-H patients. To further evaluate the clonal expansion of fs-neoAg-specific T cells in MSI-H cancer patients, we identified fs-neoAg-specific T cell receptors (TCRs). T cell lines enriched for fs-neoAg-specific T cells were generated from patient PBMCs and sequenced for variable β chains of TCRs. These fs-neoAg-specific TCRs were monitored in the blood and tumor tissues, including those from primary and recurrent sites. Finally, to determine the spatial relationships between the infiltrating immune cells and the malignant cells at single cell resolution, we performed multiplexed immunohistochemistry using CODEX technology. A panel of 35 markers was used to evaluate the myeloid (HLA-DR, CD11c, CD14, CD68, CD206) and T (CD4, CD8, Foxp3) cell subsets, the activation (CD107a, CD69, Ki67) and exhaustion (PD-1, TIM3, LAG3) status of T cells, T cell states (TCF-1, TOX, PD-1) and the presence of tertiary lymphoid structures/antigen presenting cell niches (CD19, CD20, HLA-DR) in the tumor microenvironment of primary or recurrent MS-stable and MSI-H tumors from endometrial cancer patients. We also investigated potential immune escape mechanisms in MSI-H tumors, such as the loss of B2M and MHC-I expression. This study will provide insights into the quality and quantity of shared anti-tumor T cells within the periphery and tumor tissues and will help identify the immune correlates of response or resistance to therapy in MSI-H cancer patients. Citation Format: Cansu Cimen Bozkus, Mona Saleh, Rachel Brody, Stephanie V. Blank, Nina Bhardwaj. Analyses of tumor-specific T cell dynamics and tumor immune contexture in microsatellite instability-high cancers in response to first-line therapy [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 253.

Gastric cancer (GC) remains the third leading cause of cancer-related death worldwide. While inflammation is a well-established driver of gastric tumorigenesis, only a small subset of GC patients responds to immunotherapy. One proposed mechanism of immune escape is silencing tumor-antigen expression, and thereby avoiding immune recognition. DNA methyltransferases (DNMTs) are the enzymes responsible for DNA methylation and hence, for the epigenetic silencing of gene expression of tumor-antigens and other immune-related molecules. Interestingly, they are often overexpressed in solid tumors. Epigenetic drugs inhibiting these DNMTs have shown anti-tumor effects in combination with immune checkpoint inhibitors. Here we are studying the role of DNMTs, specifically DNMT3A, in GC mouse models and the possibility of combining DNMT inhibitors with immunotherapy for the treatment of GC. This project utilises various mouse models of GC. We established a Dnmt3a-overexpressing inflammation-driven GC mouse model (gp130FF, A33Dnmt3a). In a second mouse model, mutant Kras, Pi3kca and Tp53 expression results in highly advanced invasive gastric carcinoma formation (KPT model). We successfully established GC organoids of one of these triple mutant tumors, which can be injected subcutaneously into wild type mice and result in allograft tumor formation. DNMT3A overexpression was detected in human GC specimen and associated with bad overall survival of patients. Gastric adenomas of our gp130FF, A33Dnmt3a mouse model have a 10-fold elevated Dnmt3a expression. Importantly, tumor-specific Dnmt3a overexpression significantly increased gastric tumor burden. We have conducted DNA methylation and gene expression analyses to identify differently methylated and expressed genes between gp130FF and gp130FF, A33Dnmt3a gastric adenoma cells. Treatment with the DNMT inhibitor decitabine reduced tumor growth in the inflammation-driven gp130FF gastric adenoma mouse model. In the KPT model, we have identified DNMT3A as being highly expressed in the invasive front of tumors, their liver metastases as well as in the allograft tumors established by the KPT organoids. In this model of advanced GC, treatment with the DNMT inhibitor decitabine significantly decreased tumor growth and we are currently investigating the efficacy of decitabine in combination with anti-PD-1 and/or anti-CTLA-4 immunotherapy. Taken together, we provide evidence for a driver function of Dnmt3a in gastric tumorigenesis and gastric tumor growth. In addition, our findings encourage further studies to investigate the potential of DNMT inhibitors for the treatment of GC. Citation Format: Anne Huber, Christine Dijkstra, Yuba Bhandari, Hariharan Easwaran, Stephen Baylin, Matthias Ernst, Moritz Eissmann. DNA methyltransferase 3A promotes inflammation-associated gastric cancer growth and presents a therapy target for gastric cancer. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Epigenomics; 2022 Oct 6-8; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_2):Abstract nr A008.

Tumor cell intrinsic activation of Signal Transducer and Activator of Transcription 3 (STAT3) signaling has been shown to promote stemness, tumorigenesis and cancer therapy resistance. Therefore, Stat3 inhibitors are being developed and tested pre-clinically and in clinical trials for multiple solid cancers. Importantly, STAT3 signaling also occurs in the non-tumor cells within the tumor microenvironment (TME). The effect of Stat3 signaling within the TME on primary gastric cancers (GC), metastasis formation and therapy responses is unknown. Here, we describe a novel genetically defined, tumor organoid-driven, transplantable, orthotopic gastric cancer model that represents gastric carcinomas with associated metastasis formation in immune competent recipient mice. Utilizing our murine GC organoid model in subcutaneous allograft experiments, we showed that established GC tumors respond to pharmacological Stat3 inhibition. This anti-tumor effect is primarily driven by inhibition of the Stat3 signaling in the TME as tumor growth was increased in Stat3 high TME recipients, while tumor growth was inhibited in Stat3-signaling reduced Stat3+/- mice. Furthermore, Crisp-Cas9 -mediated Stat3 knockout in the GC organoids did not alter their in vitro growth potential. Stat3KO GC allograft tumor growth was not changed compared to Stat3WT GC tumors grown in wildtype host mice. Collectively, this suggests that inhibition of Stat3 signaling within the TME but not the tumor cell intrinsic Stat3 reduction confer anti-tumor responses. Through gastric serosa transplantation of the murine GC organoids into Stat3-elevated gp130FF mutant mice, we confirmed that high Stat3 signaling within the TME promotes distal metastasis formation to the liver. Taken together, we show that Stat3 signaling represents a therapy target, that predominantly acts through the TME. Better understanding of the signaling within the TME in primary and metastatic GC lesions will allow identification of novel tumor cell and TME-centric therapy targets. Combination of therapies targeting tumor cell intrinsic vulnerabilities with novel pro-tumorigenic TME -targeting agents could help to improve responses against primary and metastatic disease and therefore improve outcome for the worst prognosis patients. Citation Format: Moritz Eissmann, Anne Huber, Amr Allam, Christine Dijkstra, Matthias Ernst. STAT3 signaling in the tumor microenvironment promotes primary gastric cancer growth and metastasis formation [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 252.

Homeostasis in the gut is achieved by impeccable functioning of tissue resident immune cells that reside and closely interact with the epithelium. The tissue resident immune cells of the intestinal epithelium are predominantly lymphocytes, known as intraepithelial lymphocytes (IELs) and mainly consist of TCRαβ T cells and TCRgd T cells. These IELs are well known to sense microbes, nutrients, and cellular stress but their role in intestinal cancer progression has been controversial. On one hand, gd Τ cells are the primary source of IL-17, an important proinflammatory cytokine that aid in colorectal cancer (CRC) progression. On the other hand, mice lacking gd Τ cells have been showed to have an increased risk of developing carcinogen-induced CRC. Here we used two different mouse model of colon cancer to investigate the role of gd T IELs in colon tumor growth. We showed that in both orthotopic implantation of cancer cells in the colon, and inflammation-driven colon cancer models, gd T cells are essentials to limit tumor growth. Indeed, mice lacking gd T cells had increased tumor incidence with high-grade adenomas compared to control mice. We also performed gene expression analysis of the adenomas in control mice and in mice lacking gd T cells. They revealed distinct transcription profiles with CRC-associated gene expression profile, including inflammatory genes and epithelial to mesenchymal transition genes, particularly enriched in adenomas from gd T cell deficient mice. Moreover, using human tissue microarrays, we investigated whether the presence of gd T cells in tumors of patients with advanced CRC could be used to predict disease outcomes. We revealed that patient disease-free survival was improved if gd T cells could be detected within tumors. Therefore, we showed that gd T cells are primordial in limiting colorectal cancer progression in both mice and humans. Citation Format: Sonia Ghilas, Dinesh Raghu, Kelly Tran, Yang Liao, Bhupinder Pal, Shoukat Sterle, Christine Dijkstra, Marina Yakou, Pavitha Parathan, John Mariadason, Matthias Ernst, Andreas Behren, Grant Drummond, Wei Shi, Lisa A. Mielke. Intestinal intraepithelial T cells limit colorectal cancer progression [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR007.