Targeting intracellular oncoproteins with dimeric IgA promotes expulsion from the cytoplasm and immune-mediated control of epithelial cancers

Dimeric IgA (dIgA) can move through cells via the IgA/IgM polymeric immunoglobulin receptor (PIGR), which is expressed mainly on mucosal epithelia. Here, we studied the ability of dIgA to target commonly mutated cytoplasmic oncodrivers. Mutation-specific dIgA, but not IgG, neutralized KRASG12D within ovarian carcinoma cells and expelled this oncodriver from tumor cells. dIgA binding changed endosomal trafficking of KRASG12D from accumulation in recycling endosomes to aggregation in the early/late endosomes through which dIgA transcytoses. dIgA targeting of KRASG12D abrogated tumor cell proliferation in cell culture assays. In vivo, KRASG12D-specific dIgA1 limited the growth of KRASG12D-mutated ovarian and lung carcinomas in a manner dependent on CD8+ T cells. dIgA specific for IDH1R132H reduced colon cancer growth, demonstrating effective targeting of a cytoplasmic oncodriver not associated with surface receptors. dIgA targeting of KRASG12D restricted tumor growth more effectively than small-molecule KRASG12D inhibitors, supporting the potential of this approach for the treatment of human cancers.

Grading of lung adenocarcinomas with simultaneous segmentation by artificial intelligence (GLASS-AI)

Preclinical genetically engineered mouse models (GEMMs) of lung adenocarcinoma are invaluable for investigating molecular drivers of tumor formation, progression, and therapeutic resistance. However, histological analysis of these GEMMs requires significant time and training to ensure accuracy and consistency. To achieve a more objective and standardized analysis, we used machine learning to create GLASS-AI, a histological image analysis tool that the broader cancer research community can utilize to grade, segment, and analyze tumors in preclinical models of lung adenocarcinoma. GLASS-AI demonstrates strong agreement with expert human raters while uncovering a significant degree of unreported intratumor heterogeneity. Integrating immunohistochemical staining with high-resolution grade analysis by GLASS-AI identified dysregulation of Mapk/Erk signaling in high-grade lung adenocarcinomas and locally advanced tumor regions. Our work demonstrates the benefit of employing GLASS-AI in preclinical lung adenocarcinoma models and the power of integrating machine learning and molecular biology techniques for studying the molecular pathways that underlie cancer progression.

Abstract 678: Investigating the mechanisms involved in HMGB1-dependent DNA uptake and STING activation in dendritic cells

Background: The cGAS-STING pathway is critical for the development of anti-tumor immunity. Activation of host STING can occur by sensing of extracellular DNA by intratumoral dendritic cells (DCs). After chemotherapy and under conditions of chromosomal instability, tumor cells release double-stranded DNA. We have previously shown DCs are able to internalize DNA in a dynamin-dependent manner, suggesting that a membrane receptor might mediate DNA endocytosis. DNA uptake also requires the presence of the high mobility group box protein 1 (HMGB1). HMGB1 has multiple known receptors such as TLR2, TLR4, RAGE and CD24. However, whether these receptors are involved in DNA engulfment by DCs remains unknown. Here, we sought to elucidate the mechanisms facilitating DNA uptake and subsequent STING activation in DCs.

Methods: Bone marrow derived (BM)DCs obtained from wild type (WT), RAGE, TLR2 or TLR4-deficient mice, as well as and WT or CD24-deficient MutuDC1940 cells, were cultured in the presence or absence of Cy5-labeled plasmid DNA, a recombinant Flag-tagged HMGB1 protein (rHMGB1) and/or DMXAA. Cy5-DNA uptake, Flag-HMGB1 binding and IRF3 phosphorylation was analyzed by flow cytometry or immunofluorescence microscopy. MutuDC1940 cells were also treated with plasmid DNA, rHMGB1, tumor debris (HS) and/or L-Leucyl-L-Leucine methyl ester (LLOMe) and galectin-3 clustering was quantified by immunofluorescence. Statistically significant differences were determined by ANOVA test.

Results: DCs take-up Cy5-DNA when rHMGB1 was added, and it was HMGB1 dose-dependent, supporting HMGB1 as a key factor for DNA uptake. We found that TLR2, TLR4, RAGE or CD24 deficient DCs were capable of internalizing Cy5-DNA in the presence of rHMGB1 to the same extent as WT DCs, indicating that none of these receptors are necessary for HMGB1-mediated DNA uptake. DNA-HMGB1 stimulation triggered IRF3 phosphorylation in DCs, suggesting extracellular DNA enters the cytosol and is sensed by cGAS, leading to STING activation. In support of this, DNA-HMGB1 treatment induced an increase in lysosomal membrane permeabilization, as measured by the extent of galectin-3 clusters within cells.

Conclusion: HMGB1 promotes DNA uptake by DCs independently of TLR2, TLR4, RAGE or CD24, suggesting other receptor(s) mediate the process of HMGB1-dependent DNA internalization. Further, DNA-HMGB1 induced lysosomal membrane destabilization which may facilitate DNA release into the cytosol for sensing and trigger activation of the cGAS-STING pathway.

Citation Format: Daiana P. Celias, Kay Hänggi, Brian Ruffell. Investigating the mechanisms involved in HMGB1-dependent DNA uptake and STING activation in dendritic cells [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 678.

Ovarian cancer immunogenicity is governed by a narrow subset of progenitor tissue-resident memory T cells

Despite repeated associations between T cell infiltration and outcome, human ovarian cancer remains poorly responsive to immunotherapy. We report that the hallmarks of tumor recognition in ovarian cancer-infiltrating T cells are primarily restricted to tissue-resident memory (TRM) cells. Single-cell RNA/TCR/ATAC sequencing of 83,454 CD3+CD8+CD103+CD69+ TRM cells and immunohistochemistry of 122 high-grade serous ovarian cancers shows that only progenitor (TCF1low) tissue-resident T cells (TRMstem cells), but not recirculating TCF1+ T cells, predict ovarian cancer outcome. TRMstem cells arise from transitional recirculating T cells, which depends on antigen affinity/persistence, resulting in oligoclonal, trogocytic, effector lymphocytes that eventually become exhausted. Therefore, ovarian cancer is indeed an immunogenic disease, but that depends on ∼13% of CD8+ tumor-infiltrating T cells (∼3% of CD8+ clonotypes), which are primed against high-affinity antigens and maintain waves of effector TRM-like cells. Our results define the signature of relevant tumor-reactive T cells in human ovarian cancer, which could be applicable to other tumors with unideal mutational burden.

TIM-3 blockade enhances IL-12-dependent antitumor immunity by promoting CD8+ T cell and XCR1+ dendritic cell spatial co-localization

BACKGROUND

T cell immunoglobulin and mucin domain containing-3 (TIM-3) blocking antibodies are currently being evaluated in clinical trials for solid and hematological malignancies. Despite its identification on T cells, TIM-3 is predominantly expressed by myeloid cells, including XCR1+ type I conventional dendritic cells (cDC1s). We have recently shown that TIM-3 blockade promotes expression of CXCR3 chemokine ligands by tumor cDCs, but how this drives a CD8+ T cell-dependent response to therapy is unclear.

METHODS

T cell infiltration, effector function, and spatial localization in relation to XCR1+ cDC1s were evaluated in a murine orthotopic mammary carcinoma model during response to TIM-3 blockade and paclitaxel chemotherapy. Mixed bone marrow chimeras and diphtheria toxin depletion were used to determine the role of specific genes in cDC1s during therapeutic responses.

RESULTS

TIM-3 blockade increased interferon-γ expression by CD8+ T cells without altering immune infiltration. cDC1 expression of CXCL9, but not CXCL10, was required for response to TIM-3 blockade. CXCL9 was also necessary for the increased proximity observed between CD8+ T cells and XCR1+ cDC1s during therapy. Tumor responses were dependent on cDC1 expression of interleukin-12, but not MHCI.

CONCLUSIONS

TIM-3 blockade increases exposure of intratumoral CD8+ T cells to cDC1-derived cytokines, with implications for the design of therapeutic strategies using antibodies against TIM-3.

The inhibitory receptor TIM-3 limits activation of the cGAS-STING pathway in intra-tumoral dendritic cells by suppressing extracellular DNA uptake

Blockade of the inhibitory receptor TIM-3 shows efficacy in cancer immunotherapy clinical trials. TIM-3 inhibits production of the chemokine CXCL9 by XCR1⁺ classical dendritic cells (cDC1), thereby limiting antitumor immunity in mammary carcinomas. We found that increased CXCL9 expression by splenic cDC1s upon TIM-3 blockade required type I interferons and extracellular DNA. Chemokine expression as well as combinatorial efficacy of TIM-3 blockade and paclitaxel chemotherapy were impaired by deletion of Cgas and Sting. TIM-3 blockade increased uptake of extracellular DNA by cDC1 through an endocytic process that resulted in cytoplasmic localization. DNA uptake and efficacy of TIM-3 blockade required DNA binding by HMGB1, while galectin-9-induced cell surface clustering of TIM-3 was necessary for its suppressive function. Human peripheral blood cDC1s also took up extracellular DNA upon TIM-3 blockade. Thus, TIM-3 regulates endocytosis of extracellular DNA and activation of the cytoplasmic DNA sensing cGAS-STING pathway in cDC1s, with implications for understanding the mechanisms underlying TIM-3 immunotherapy.

Abstract PO-082: Automated tumor segmentation, grading, and analysis of tumor heterogeneity in preclinical models of lung adenocarcinoma

Preclinical mouse models of lung adenocarcinoma are invaluable for the discovery of molecular drivers of tumor formation, progression, and therapeutic resistance. Histological analyses of these preclinical models require significant investments of time and training to ensure accuracy and consistency. Analysis by a clinical pathologist is the gold standard in this approach, but may be difficult to obtain due to the cost and availability of their services. As an alternative we have developed a digital pathology tool to identify, segment, grade, and analyze tumors in mouse models of lung adenocarcinoma. This convolutional neural network (CNN) model, based on ResNet18, was trained to classify normal lung tissue, normal airways, and the different grades (1 – 4) of lung adenocarcinoma from 100,000 224 × 224 pixel image patches (~16,000 patches per class). Our training dataset was constructed from whole slide images of hematoxylin and eosin stained lung sections from 4 different mouse models of lung adenocarcinoma with oncogenic Kras (KrasG12D/+), in combination with oncogenic p53 mutations (KrasG12D/+; p53R172H/+ and KrasG12D/+;p53R270H/+), or with the loss of the tumor suppressive TAp73 (KrasG12D/+;TAp7fltd/fltd). Our CNN demonstrated a strong correspondence with human pathologists on our holdout dataset, achieving a micro-F1 score of 0.81 on a pixel-by-pixel basis. As a test of our CNN, we analyzed two mouse models to better understand the role of TAp73 in lung adenocarcinoma: KrasG12D/+ (“K”) and KrasG12D/+;TAp73fltd/fltd (“TK”). Both human raters and our CNN reported a significant increase in the tumor burden of the compound mutant “TK” mice compared to the single mutant “K” mice. According to our CNN, this increased tumor burden was driven primarily by an increase in tumor size and not an increased number of tumors in “TK” mice. Because our CNN can assign different grades to regions within the same image patch and tumor, we also uncovered a high degree of intratumor heterogeneity that was not reported by the human pathologists, who are trained to assign one grade to a single tumor with a bias for the highest grade present in a given tumor. The finer grading resolution allowed our CNN to uncover the increased tumor size observed in the “TK” mice was due to expansion of Grade 2 regions (characterized by enlarged nuclei without irregular shape) within tumors that would be considered a higher grade by pathologists. Our CNN also provides a detailed map of tumor grades overlaid on the H&E images used for analysis, allowing for precise targeting of regions within tumors with other assays. We are currently utilizing these outputs in conjunction with other assays, such as spatial transcriptomic analysis and immunohistochemistry, to investigate the molecular mechanisms that underlie the expansion of Grade 2 tumor regions in “TK” mice. Future work will expand this tool into a multidimensional digital pathology pipeline that can accelerate current investigations and reveal new therapeutic targets and prognostic markers.

Citation Format: John H. Lockhart, Hayley D. Ackerman, Kyubum Lee, Mahmoud Abdalah, Andrew Davis, Nicole Montey, Theresa Boyle, James Saller, Ayensur Keske, Kay Hänggi, Brian Ruffell, Olya Stringfield, Aik Choon Tan, Elsa R. Flores. Automated tumor segmentation, grading, and analysis of tumor heterogeneity in preclinical models of lung adenocarcinoma [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-082.

The Unfolded Protein Response Mediator PERK Governs Myeloid Cell-Driven Immunosuppression in Tumors through Inhibition of STING Signaling

The primary mechanisms supporting immunoregulatory polarization of myeloid cells upon infiltration into tumors remain largely unexplored. Elucidation of these signals could enable better strategies to restore protective anti-tumor immunity. Here, we investigated the role of the intrinsic activation of the PKR-like endoplasmic reticulum (ER) kinase (PERK) in the immunoinhibitory actions of tumor-associated myeloid-derived suppressor cells (tumor-MDSCs). PERK signaling increased in tumor-MDSCs, and its deletion transformed MDSCs into myeloid cells that activated CD8⁺ T cell-mediated immunity against cancer. Tumor-MDSCs lacking PERK exhibited disrupted NRF2-driven antioxidant capacity and impaired mitochondrial respiratory homeostasis. Moreover, reduced NRF2 signaling in PERK-deficient MDSCs elicited cytosolic mitochondrial DNA elevation and, consequently, STING-dependent expression of anti-tumor type I interferon. Reactivation of NRF2 signaling, conditional deletion of STING, or blockade of type I interferon receptor I restored the immunoinhibitory potential of PERK-ablated MDSCs. Our findings demonstrate the pivotal role of PERK in tumor-MDSC functionality and unveil strategies to reprogram immunosuppressive myelopoiesis in tumors to boost cancer immunotherapy.

The Immune Microenvironment and Cancer Metastasis

The dynamic interplay between neoplastic cells and the immune microenvironment regulates every step of the metastatic process. Immune cells contribute to invasion by secreting a cornucopia of inflammatory factors that promote epithelial-to-mesenchymal transition and remodeling of the stroma. Cancer cells then intravasate to the circulatory system assisted by macrophages and use several pathways to avoid recognition by cytotoxtic lymphocytes and phagocytes. Circulating tumor cells that manage to adhere to the vasculature and encounter premetastic niches are able to use the associated myeloid cells to extravasate into ectopic organs and establish a dormant microscopic colony. If successful at avoiding repetitive immune attack, dormant cells can subsequently grow into overt, clinically detectable metastatic lesions, which ultimately account to most cancer-related deaths. Understanding how disseminated tumor cells evade and corrupt the immune system during the final stages of metastasis will be pivotal in developing new therapeutic modalities that combat metastasis.

Oncogenic KRAS Drives Immune Suppression in Colorectal Cancer

In this issue of Cancer Cell, Liao et al. demonstrate that oncogenic KRAS drives an immune suppressive program in colorectal cancer by repressing IRF2 expression, which leads to downregulation of interferon responsive genes, enhanced expression of CXCL3 and recruitment of suppressive myeloid cells, and subsequent resistance to immune checkpoint blockade.

Necroptosis Execution Is Mediated by Plasma Membrane Nanopores Independent of Calcium

Necroptosis is a form of regulated necrosis that results in cell death and content release after plasma membrane permeabilization. However, little is known about the molecular events responsible for the disruption of the plasma membrane. Here, we find that early increase in cytosolic calcium in TNF-induced necroptosis is mediated by treatment with a Smac mimetic via the TNF/RIP1/TAK1 survival pathway. This does not require the activation of the necrosome and is dispensable for necroptosis. Necroptosis induced by the activation of TLR3/4 pathways does not trigger early calcium flux. We also demonstrate that necroptotic plasma membrane rupture is mediated by osmotic forces and membrane pores around 4 nm in diameter. This late permeabilization step represents a hallmark in necroptosis execution that is cell and treatment independent and requires the RIP1/RIP3/MLKL core. In support of this, treatment with osmoprotectants reduces cell damage in an in vivo necroptosis model of ischemia-reperfusion injury.

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Early calcium signaling in TSZ necroptosis correlates with cellular levels of cIAP1/2

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Calcium flux is induced by a Smac mimetic and is dispensable for necroptosis execution

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Pores ∼4 nm in diameter mediate final plasma membrane disruption in necroptosis

Inhibitor of Apoptosis Protein-1 Regulates Tumor Necrosis Factor-Mediated Destruction of Intestinal Epithelial Cells

BACKGROUND AND AIMS

Tumor necrosis factor (TNF) is a cytokine that promotes inflammation and contributes to pathogenesis of inflammatory bowel diseases. Unlike other cells and tissues, intestinal epithelial cells undergo rapid cell death upon exposure to TNF, by unclear mechanisms. We investigated the roles of inhibitor of apoptosis proteins (IAPs) in the regulation of TNF-induced cell death in the intestinal epithelium of mice and intestinal organoids.

METHODS

RNA from cell lines and tissues was analyzed by quantitative polymerase chain reaction, protein levels were analyzed by immunoblot assays. BIRC2 (also called cIAP1) was expressed upon induction from lentiviral vectors in young adult mouse colon (YAMC) cells. YAMC cells, the mouse colon carcinoma cell line MC38, the mouse macrophage cell line RAW 264.7, or mouse and human organoids were incubated with second mitochondrial activator of caspases (Smac)-mimetic compound LCL161 or recombinant TNF-like weak inducer of apoptosis (TNFSF12) along with TNF, and cell death was quantified. C57BL/6 mice with disruption of Xiap, Birc2 (encodes cIAP1), Birc3 (encodes cIAP2), Tnfrsf1a, or Tnfrsf1b (Tnfrsf1a and b encode TNF receptors) were injected with TNF or saline (control); liver and intestinal tissues were collected and analyzed for apoptosis induction by cleaved caspase 3 immunohistochemistry. We also measured levels of TNF and alanine aminotransferase in serum from mice.

RESULTS

YAMC cells, and mouse and human intestinal organoids, died rapidly in response to TNF. YAMC and intestinal crypts expressed lower levels of XIAP, cIAP1, cIAP2, and cFLIP than liver tissue. Smac-mimetics reduced levels of cIAP1 and XIAP in MC38 and YAMC cells, and Smac-mimetics and TNF-related weak inducer of apoptosis increased TNF-induced cell death in YAMC cells and organoids-most likely by sequestering and degrading cIAP1. Injection of TNF greatly increased levels of cell death in intestinal tissue of cIAP1-null mice, compared with wild-type C57BL/6 mice, cIAP2-null mice, or XIAP-null mice. Excessive TNF-induced cell death in the intestinal epithelium was mediated TNF receptor 1.

CONCLUSIONS

In a study of mouse and human cell lines, organoids, and tissues, we found cIAP1 to be required for regulation of TNF-induced intestinal epithelial cell death and survival. These findings have important implications for the pathogenesis of TNF-mediated enteropathies and chronic inflammatory diseases of the intestine.

RIPK1/RIPK3 promotes vascular permeability to allow tumor cell extravasation independent of its necroptotic function

Necroptosis is an inflammatory form of programmed cell death requiring receptor-interacting protein kinase 1, 3 (RIPK1, RIPK3) and mixed lineage kinase domain-like protein (MLKL). The kinase of RIPK3 phosphorylates MLKL causing MLKL to form a pore-like structure, allowing intracellular contents to release and cell death to occur. Alternatively, RIPK1 and RIPK3 have been shown to regulate cytokine production directly influencing inflammatory immune infiltrates. Recent data suggest that necroptosis may contribute to the malignant transformation of tumor cells in vivo and we asked whether necroptosis may have a role in the tumor microenvironment altering the ability of the tumor to grow or metastasize. To determine if necroptosis in the tumor microenvironment could promote inflammation alone or by initiating necroptosis and thereby influencing growth or metastasis of tumors, we utilized a syngeneic tumor model of metastasis. Loss of RIPK3 in the tumor microenvironment reduced the number of tumor nodules in the lung by 46%. Loss of the kinase activity in RIPK1, a member of the necrosome also reduced tumor nodules in the lung by 38%. However, the loss of kinase activity in RIPK3 or the loss of MLKL only marginally altered the ability of tumor cells to form in the lung. Using bone marrow chimeras, the decrease in tumor nodules in the Ripk3^-/- appeared to be due to the stromal compartment rather than the hematopoietic compartment. Transmigration assays showed decreased ability of tumor cells to transmigrate through the vascular endothelial layer, which correlated with decreased permeability in the Ripk3^-/- mice after tumor injection. In response to permeability factors, such as vascular endothelial growth factor, RIPK3 null endothelial cells showed decreased p38/HSP27 activation. Taken together, our results suggest an alternative function for RIPK1/RIPK3 in vascular permeability leading to decreased number of metastasis.

Targeting p38 or MK2 Enhances the Anti-Leukemic Activity of Smac-Mimetics

Birinapant is a smac-mimetic (SM) in clinical trials for treating cancer. SM antagonize inhibitor of apoptosis (IAP) proteins and simultaneously induce tumor necrosis factor (TNF) secretion to render cancers sensitive to TNF-induced killing. To enhance SM efficacy, we screened kinase inhibitors for their ability to increase TNF production of SM-treated cells. We showed that p38 inhibitors increased TNF induced by SM. Unexpectedly, even though p38 is required for Toll-like receptors to induce TNF, loss of p38 or its downstream kinase MK2 increased induction of TNF by SM. Hence, we show that the p38/MK2 axis can inhibit or promote TNF production, depending on the stimulus. Importantly, clinical p38 inhibitors overcame resistance of primary acute myeloid leukemia to birinapant.

FANCD2 and CtIP cooperate to repair DNA interstrand crosslinks

The resolution of DNA interstrand crosslinks (ICLs) requires a complex interplay between several processes of DNA metabolism, including the Fanconi anemia (FA) pathway and homologous recombination (HR). FANCD2 monoubiquitination and CtIP-dependent DNA-end resection represent key events in FA and HR activation, respectively, but very little is known about their functional relationship. Here, we show that CtIP physically interacts with both FANCD2 and ubiquitin and that monoubiquitinated FANCD2 tethers CtIP to damaged chromatin, which helps channel DNA double-strand breaks generated during ICL processing into the HR pathway. Consequently, CtIP mutants defective in FANCD2 binding fail to associate with damaged chromatin, which leads to increased levels of nonhomologous end-joining activity and ICL hypersensitivity. Interestingly, we also observe that CtIP depletion aggravates the genomic instability in FANCD2-deficient cells. Thus, our data indicate that FANCD2 primes CtIP-dependent resection during HR after ICL induction but that CtIP helps prevent illegitimate recombination in FA cells.

Prolyl isomerase PIN1 regulates DNA double-strand break repair by counteracting DNA end resection

The regulation of DNA double-strand break (DSB) repair by phosphorylation-dependent signaling pathways is crucial for the maintenance of genome stability; however, remarkably little is known about the molecular mechanisms by which phosphorylation controls DSB repair. Here, we show that PIN1, a phosphorylation-specific prolyl isomerase, interacts with key DSB repair factors and affects the relative contributions of homologous recombination (HR) and nonhomologous end-joining (NHEJ) to DSB repair. We find that PIN1-deficient cells display reduced NHEJ due to increased DNA end resection, whereas resection and HR are compromised in PIN1-overexpressing cells. Moreover, we identify CtIP as a substrate of PIN1 and show that DSBs become hyperresected in cells expressing a CtIP mutant refractory to PIN1 recognition. Mechanistically, we provide evidence that PIN1 impinges on CtIP stability by promoting its ubiquitylation and subsequent proteasomal degradation. Collectively, these data uncover PIN1-mediated isomerization as a regulatory mechanism coordinating DSB repair.