Tumor Immune Response Research Articles

Identification of two distinct head and neck squamous cell carcinoma subtypes based on fatty acid metabolism-related signatures: Implications for immunotherapy and chemotherapy.

The dysregulation of lipid metabolism is a critical factor in the initiation and progression of tumors. In this investigation, we aim to characterize the molecular subtypes of head and neck squamous cell carcinoma (HNSCC) based on their association with fatty acid metabolism and develop a prognostic risk model. The transcriptomic and clinical data about HNSCC were obtained from public databases. Clustering analysis was conducted on fatty acid metabolism genes (FAMG) associated with prognosis, utilizing the non-negative matrix factorization algorithm. The immune infiltration, response to immune therapy, and drug sensitivity between molecular subtypes were evaluated. Differential expression genes were identified between subtypes, and a prognostic model was constructed using Cox regression analyses. A nomogram for HNSCC was constructed and evaluated. Thirty FAMGs have been found to exhibit differential expression in HNSCC, out of which three are associated with HNSCC prognosis. By performing clustering analysis on these 3 genes, 2 distinct molecular subtypes of HNSCC were identified that exhibit significant heterogeneity in prognosis, immune landscape, and treatment response. Using a set of 7778 genes that displayed differential expression between the 2 molecular subtypes, a prognostic risk model for HNSCC was constructed comprising 11 genes. This model has the ability to stratify HNSCC patients into high-risk and low-risk groups, which exhibit significant differences in prognosis, immune infiltration, and immune therapy response. Moreover, our data suggest that this risk model is negatively correlated with B cells and most T cells, but positively correlated with macrophages, mast cells, and dendritic cells. Ultimately, we constructed a nomogram incorporating both the risk signature and radiotherapy, which has demonstrated exceptional performance in predicting prognosis for HNSCC patients. A molecular classification system and prognostic risk models were developed for HNSCC based on FAMGs. This study revealed the potential involvement of FAMGs in modulating tumor immune microenvironment and response to treatment.

Oxygen-Independent Radiodynamic Therapy: Radiation-Boosted Chemodynamics for Reprogramming the Tumor Immune Environment and Enhancing Antitumor Immune Response.

Radiodynamic therapy (RDT) has emerged as a promising modality for cancer treatment, offering notable advantages such as deep tissue penetration and radiocatalytic generation of oxygen free radicals. However, the oxygen-dependent nature of RDT imposes limitations on its efficacy in hypoxic conditions, particularly in modulating and eliminating radioresistant immune suppression cells. A novel approach involving the creation of a "super" tetrahedron polyoxometalate (POM) cluster, Fe12-POM, has been developed for radiation boosted chemodynamic catalysis to enable oxygen-independent RDT in hypoxic conditions. This nanoscale cluster comprises four P2W15 units functioning as energy antennas, while the Fe3 core serves as an electron receptor and catalytic center. Under X-ray radiation, a metal-to-metal charge transfer phenomenon occurs between P2W15 and the Fe3 core, resulting in the valence transition of Fe3+ to Fe2+ and a remarkable 139-fold increase in hydroxyl radical generation compared to Fe12-POM alone. The rapid generation of hydroxyl radicals, in combination with PD-1 therapy, induces a reprogramming of the immune environment within tumors. This reprogramming is characterized by upregulation of CD80/86, downregulation of CD163 and FAP, as well as the release of interferon-γ and tumor necrosis factor-α. Consequently, the occurrence of abscopal effects is facilitated, leading to significant regression of both local and distant tumors in mice. The development of oxygen-independent RDT represents a promising approach to address cancer recurrence and improve treatment outcomes.

Functional analysis and validation of oncodrive gene AP3S1 in ovarian cancer through filtering of mutation data from whole-exome sequencing

BackgroundHigh-grade serous ovarian carcinoma (HGSOC) is the most aggressive and prevalent subtype of ovarian cancer and accounts for a significant portion of ovarian cancer-related deaths worldwide. Despite advancements in cancer treatment, the overall survival rate for HGSOC patients remains low, thus highlighting the urgent need for a deeper understanding of the molecular mechanisms driving tumorigenesis and for identifying potential therapeutic targets. Whole-exome sequencing (WES) has emerged as a powerful tool for identifying somatic mutations and alterations across the entire exome, thus providing valuable insights into the genetic drivers and molecular pathways underlying cancer development and progression.MethodsVia the analysis of whole-exome sequencing results of tumor samples from 90 ovarian cancer patients, we compared the mutational landscape of ovarian cancer patients with that of TCGA patients to identify similarities and differences. The sequencing data were subjected to bioinformatics analysis to explore tumor driver genes and their functional roles. Furthermore, we conducted basic medical experiments to validate the results obtained from the bioinformatics analysis.ResultsWhole-exome sequencing revealed the mutational profile of HGSOC, including BRCA1, BRCA2 and TP53 mutations. AP3S1 emerged as the most weighted tumor driver gene. Further analysis of AP3S1 mutations and expression demonstrated their associations with patient survival and the tumor immune response. AP3S1 knockdown experiments in ovarian cancer cells demonstrated its regulatory role in tumor cell migration and invasion through the TGF-β/SMAD pathway.ConclusionThis comprehensive analysis of somatic mutations in HGSOC provides insight into potential therapeutic targets and molecular pathways for targeted interventions. AP3S1 was identified as being a key player in tumor immunity and prognosis, thus providing new perspectives for personalized treatment strategies. The findings of this study contribute to the understanding of HGSOC pathogenesis and provide a foundation for improved outcomes in patients with this aggressive disease.

Cancer stem cell, chromosomal instability, and cancer immunity

Cancer stem cells (CSCs) are a unique population of tumor cells with stem cell-like properties. They are believed to be involved in drug resistance, potential therapy failure, tumor relapse after treatment, and ultimately reduced overall survival of cancer patients. One of the causal factors that may lead to CSC formation is chromosomal instability (CIN), a dynamic event leading to numerical and structural changes in the chromosomes. The CIN is also proposed to aid the maintenance of CSCs, contribute towards their heterogeneity, and facilitate their immune escape. However, the role of CIN in the modulation of the immune system in tumors remains contradictory. Studies have revealed that it can lead to both activation and suppression of the immune system. Previous literature suggests that the CIN, CSCs, and cancer immunity (3Cs), interact with and complement each other to create a pro-tumor environment. However, the mechanisms underlying such an interaction are poorly understood. So, in this review article, an attempt has been made to understand the nature of the interaction between the triad of CIN, CSC, and the immune response in tumors and some of the pathways governing the same. Understanding the above may be a positive step towards the complete cure for malignant diseases.

Synergistic effects of Ω-3 polyunsaturated fatty acid supplementation and programmed cell death protein 1 blockade on tumor growth and immune modulation in a xenograft model of esophageal cancer

Esophageal cancer, especially esophageal squamous cell carcinoma (ESCC), remains a significant global health challenge with limited survival rates. This study aimed to elucidate the combined effects of immune-modulating nutrition (IMN) with Ω-3 polyunsaturated fatty acid (PUFA) supplementation and anti-programmed cell death protein 1 (PD-1) treatment on tumor growth and immune responses in a xenograft model of ESCC. A total of 36 C57BL/6 mice were used to construct a xenograft model using the mouse esophageal cancer cell line AKR. Mice were subjected to treatment with anti- PD-1 antibody combined with either Ω-3 PUFA-rich or Ω-3 PUFA-deficient nutrition. Tumor growth, immune markers, cytokine profiles, and metabolic changes were evaluated. The combination of anti-PD-1 and Ω-3 PUFA supplementation significantly inhibited tumor growth more effectively than anti-PD-1 treatment alone. Enhanced expression of immune markers PD-L1 and CD3 was observed in Ω-3 PUFA-fed mice. Additionally, compared with anti-PD-1 therapy and anti-PD-1 plus Ω-3 PUFA-deficient nutrition, Ω-3 PUFAs intensified alterations in key chemokines and cytokines, including elevated IL-12, IFN-γ, and GM-CSF levels, and reduced CXCL12 levels. However, Ω-3 PUFAs did not significantly alter the glycolysis and tryptophan metabolic program induced by anti-PD-1. Our findings indicated the potential synergetic therapeutic benefits of combining anti-PD-1 treatment with Ω-3 PUFA supplementation in ESCC, which offered promising avenue for further research.

Deciphering cutaneous melanoma prognosis through LDL metabolism: Single-cell transcriptomics analysis via 101 machine learning algorithms.

Cutaneous melanoma poses a formidable challenge within the field of oncology, marked by its aggressive nature and capacity for metastasis. Despite extensive research uncovering numerous genetic and molecular contributors to cutaneous melanoma development, there remains a critical knowledge gap concerning the role of lipids, notably low-density lipoprotein (LDL), in this lethal skin cancer. This article endeavours to bridge this knowledge gap by delving into the intricate interplay between LDL metabolism and cutaneous melanoma, shedding light on how lipids influence tumour progression, immune responses and potential therapeutic avenues. Genes associated with LDL metabolism were extracted from the GSEA database. We acquired and analysed single-cell sequencing data (GSE215120) and bulk-RNA sequencing data, including the TCGA data set, GSE19234, GSE22153 and GSE65904. Our analysis unveiled the heterogeneity of LDL across various cell types at the single-cell sequencing level. Additionally, we constructed an LDL-related signature (LRS) using machine learning algorithms, incorporating differentially expressed genes and highly correlated genes. The LRS serves as a valuable tool for assessing the prognosis, immunity and mutation status of patients with cutaneous melanoma. Furthermore, we conducted experiments on A375 and WM-115 cells to validate the function of PPP2R1A, a pivotal gene within the LRS. Our comprehensive approach, combining advanced bioinformatics analyses with an extensive review of current literature, presents compelling evidence regarding the significance of LDL within the cutaneous melanoma microenvironment.

Blocking senescence and tolerogenic function of dendritic cells induced by γδ Treg cells enhances tumor-specific immunity for cancer immunotherapy

BackgroundRegulatory T (Treg) cells are a key component in maintaining the suppressive tumor microenvironment and immune suppression in different types of cancers. A precise understanding of the molecular mechanisms used...

Combination Nano-Delivery Systems Remodel the Immunosuppressive Tumor Microenvironment for Metastatic Triple-Negative Breast Cancer Therapy.

Triple-negative breast cancer (TNBC) is an aggressive type of breast cancer for which effective therapies are lacking. Targeted remodeling of the immunosuppressive tumor microenvironment (TME) and activation of the body's immune system to fight tumors with well-designed nanoparticles have emerged as pivotal breakthroughs in tumor treatment. To simultaneously remodel the immunosuppressive TME and trigger immune responses, we designed two potential therapeutic nanodelivery systems to inhibit TNBC. First, the bromodomain-containing protein 4 (BRD4) inhibitor JQ1 and the cyclooxygenase-2 (COX-2) inhibitor celecoxib (CXB) were coloaded into chondroitin sulfate (CS) to obtain CS@JQ1/CXB nanoparticles (NPs). Then, the biomimetic nanosystem MM@P3 was prepared by coating branched polymer poly(β-amino ester) self-assembled NPs with melittin embedded macrophage membranes (MM). Both in vitro and in vivo, the CS@JQ1/CXB and MM@P3 NPs showed excellent immune activation efficiencies. Combination treatment exhibited synergistic cytotoxicity, antimigration ability, and apoptosis-inducing and immune activation effects on TNBC cells and effectively suppressed tumor growth and metastasis in TNBC tumor-bearing mice by activating the tumor immune response and inhibiting angiogenesis. In summary, this study offers a novel combinatorial immunotherapeutic strategy for the clinical TNBC treatment.

Pharmacological suppression of the OTUD4/CD73 proteolytic axis revives antitumor immunity against immune-suppressive breast cancers.

Despite widespread utilization of immunotherapy, treating immune-cold tumors remains a challenge. Multiomic analyses and experimental validation identified the OTUD4/CD73 proteolytic axis as a promising target in treating immune-suppressive triple negative breast cancer (TNBC). Mechanistically, deubiquitylation of CD73 by OTUD4 counteracted its ubiquitylation by TRIM21, resulting in CD73 stabilization inhibiting tumor immune responses. We further demonstrated the importance of TGF-β signaling for orchestrating the OTUD4/CD73 proteolytic axis within tumor cells. Spatial transcriptomics profiling discovered spatially resolved features of interacting malignant and immune cells pertaining to expression levels of OTUD4 and CD73. In addition, ST80, a newly developed inhibitor, specifically disrupted proteolytic interaction between CD73 and OTUD4, leading to reinvigoration of cytotoxic CD8+ T cell activities. In preclinical models of TNBC, ST80 treatment sensitized refractory tumors to anti-PD-L1 therapy. Collectively, our findings uncover what we believe to be a novel strategy for targeting the immunosuppressive OTUD4/CD73 proteolytic axis in treating immune-suppressive breast cancers with the inhibitor ST80.

Regulation of cancer progression by CK2: an emerging therapeutic target.

Casein kinase II (CK2) is an enzyme with pleiotropic kinase activity that catalyzes the phosphorylation of lots of substrates, including STAT3, p53, JAK2, PTEN, RELA, and AKT, leading to the regulation of diabetes, cardiovascular diseases, angiogenesis, and tumor progression. CK2 is observed to have high expression in multiple types of cancer, which is associated with poor prognosis. CK2 holds significant importance in the intricate network of pathways involved in promoting cell proliferation, invasion, migration, apoptosis, and tumor growth by multiple pathways such as JAK2/STAT3, PI3K/AKT, ATF4/p21, and HSP90/Cdc37. In addition to the regulation of cancer progression, increasing evidence suggests that CK2 could regulate tumor immune responses by affecting immune cell activity in the tumor microenvironment resulting in the promotion of tumor immune escape. Therefore, inhibition of CK2 is initially proposedas apivotal candidate for cancer treatment. In this review, we discussed the role of CK2 in cancer progression and tumor therapy.

Abstract 5343: Depletion of gut microbiota with broad spectrum antibiotics drives Pten-null prostate cancer growth in mice

Abstract Gut microbes have the potential to be either promoters or inhibitors of cancer. Use of antibiotics during cancer therapy can lead to dysbiosis, which may affect treatment outcomes. Here, we examine the effects of broad-spectrum antibiotics on cancer progression in mice with Pten-null castration resistant prostate cancer (CRPC). After five or eight weeks, orchiectomized conditional Pten-null knockout (KO) mice aged 50 and 90 weeks were given two biweekly cycles of a broad-spectrum antibody cocktail (BSAbx), respectively. The effects of BSAbx on tumor burden were compared, and molecular and immunological responses were analyzed by quantitative IHC (qIHC) and qRt-PCR at week four after antibiotic treatment. BSAbx treatment resulted in tumor burdens of 1.2 and 2.4-fold higher than in control mice in mice aged 50 and 90 weeks, respectively. qIHC analysis of KI67 showed increased proliferation in stromal and cancer cells. Additionally, androgen receptor (AR) protein and gene expression levels of Ar and Ar target genes (Fkbp5, Tmprss2, and Timp4) were elevated in tumors of BSAbx-treated mice. Restoring gut microbiota by fecal microbiota transplantation (FMT) from KO mice CRPC after BSAbx restored AR transcriptional activity to basal levels and lessened tumor growth. FMT from non-castrated KO with castration-naïve prostate cancer or heathy wildtype mice further reduced AR Transcriptional activity. Moreover, altering the gut microbiota of CRPC mice with FMT from heathy mice resulted in a tendency for lower tumor burden, 21% reduction versus control mice. Immunologically, BSAbx treatment resulted in decreased CD11b+/GR1+ cells in tumors and were associated with decreased interferon-gamma (IFN-gamma), dendritic cell functions and T cell-mediated cytotoxicity gene signatures. Mice that received FMT form health mice showed enhanced T cell mediated immunity as demonstrated by higher IFN-gamma signatures and tumor abundances of CD8+ T cells expression IFN-gamma, TNF-alpha and the cytotoxic granule granzyme B. Our study shows that broad spectrum antibiotics caused dysbiosis and promoted prostate cancer growth in mice with Pten-null prostate cancer. The effects were partly mediated through the upregulation of AR signaling and the impairment of neutrophil and T cell-mediated immune responses in tumors. Citation Format: Marco A. De Velasco, Yurie Kura, Kazuko Sakai, Mitsuhisa Nishimoto, Yasunori Mori, Kazuhiro Yoshimura, Kazutoshi Fujita, Kazuto Nishio, Hirotsugu Uemura. Depletion of gut microbiota with broad spectrum antibiotics drives Pten-null prostate cancer growth in mice [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 5343.

Abstract 693: The effect of butyrophilin 1A1 blockade in combination with radiation treatment in tumor models

Abstract Expression of radiation-induced immune escape molecules, including PD-L1, contributes to the efficacy of cancer immunotherapy. We used an unbiased in vivo gene knockdown screen in naïve T-cells and introduced them into irradiated host tumors to identify novel immunosuppressive genes activated during radiation. From the screen, we found that butyrophilin 1A1 (BTN1A1) knockdown causes T-cell expansion in irradiated tumors. This points to the potential immune checkpoint role of BTN1A1. We validated that BTN1A1 expression is inducible in activated T-cells and that blocking BTN1A1 contributes to T-cell activation. We tested an anti-mouse BTN1A1 antibody (STC109) in mouse colon tumor models (CT26 tumors), we observed partial anti-tumor efficacy using single agent STC109, which was enhanced by the combination of STC109 with radiation. We also got similar result in in mouse lung tumor models (LLC tumors) using anti-mouse BTN1A1 antibody, and the combination treatment showed an improved suppression of tumor growth and lung metastasis compared to single agent. Moreover, our data shown that knockout of BTN1A1 in 4T1 tumor models shown dramatic defect of tumor growth, and the BTN1A1 ko tumors are more sensitive to radiotherapy. These findings indicate the role of BTN1A1 in tumor immune response from radiation stress, and that anti-BTN1A1 has strong potential to enhance efficacy of radiotherapy for cancer treatment. Citation Format: Nan Li, Chen Braun, Young-Seung Kim, Andrew Park, Stephen S Yoo, Steven H. Lin. The effect of butyrophilin 1A1 blockade in combination with radiation treatment in tumor models [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 693.

Abstract 7006: Identification of endothelial-cell-specific DNA methylation alterations in breast cancer with deconvolution of the tumor microenvironment

Abstract The tumor microenvironment (TME) plays a pivotal role in cancer progression, with tumor endothelial cells (TECs) emerging as key orchestrators of angiogenesis and vascular remodeling. Tumor-associated vasculature can have increased permeability and irregular blood flow, impacting drug delivery and tumor immune response. Understanding the molecular alterations within TECs may help identify targeted therapies and improve treatment outcomes with existing therapies. We combined TME cell-type deconvolution with modeling to identify cell-specific methylation alterations of TECs in breast cancer. Genome-scale DNA methylation array data accessed in GEO and GTEx from preinvasive, mixed, and invasive breast cancer tissue (n=609) & normal breast tissue (n=230). We applied HiTIMED, a reference-based cell-type deconvolution algorithm, to estimate endothelial and other cell-type proportions in the TME. Next, we applied CellDMC, a statistical algorithm that identifies cell-specific driven differential methylation, to our cell fraction results, unraveling differentially methylated positions occurring in the endothelial compartment of the angiogenic component of our breast tissue DNA methylation profiles. We identified 29 TEC driven differentially methylated positions (FDR ≤ 8e-03), including loci within genes in angiogenic pathways regulated by VEGF, endothelial inflammation and activation genes, and tumor-associated vasculature factors in the TME. Our findings suggest that variation in DNA methylation between TECs and normal endothelial cells is crucial to understanding the TME and providing insights into unknown cancer cell behaviors that contribute to tumor growth and metastasis, thus leading to the design of novel efficient therapies that target the malignant vascular component. Our study demonstrates the power of combining cell-type deconvolution and a modeling framework that identifies cell-specific somatic alterations to unravel the intricate characteristics of TECs in breast cancer. Furthermore, this study highlights the potential of DNA methylation profiling as a robust tool for characterizing TEC heterogeneity and elucidating the molecular basis of angiogenesis beyond breast tissue in the context of diverse cancer types. Our integrative approach holds promise for advancing precision oncology, paving the way for effective and targeted therapies aimed at modulating the tumor vasculature to impede cancer progression in breast cancer and other cancer types. Citation Format: Barbara Karakyriakou, Ze Zhang, Irma Vlasac, Pauline Mochama, Lucas Salas, Brock Christensen. Identification of endothelial-cell-specific DNA methylation alterations in breast cancer with deconvolution of the tumor microenvironment [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 7006.

Abstract 5263: The impact of MRTX1133 on anti-tumor immunity in lung cancer with KRASG12D mutation

Abstract Background: To date, there have been no clinical molecules that are selective for KRASG12D mutant tumors. Although immune checkpoint inhibitors (ICIs) have improved the survival for patients with lung cancer, inferior efficacy of ICIs has been reported in KRASG12D mutant NSCLC. MRTX1133 is a selective KRASG12D inhibitor, which has been investigated in early clinical studies. In this study, we aimed to reveal the immune status using preclinical murine model of KRASG12D mutated lung cancer. In addition, we investigated whether MRTX1133 effects the anti-tumor immunity in mice bearing lung cancer with KRASG12D. Method: CCSP-rtTA/TetO-Cre mice were crossed with LSL-KRASG12D knock-in mice to obtain CCSP-rtTA/TetO-Cre/LSL-KRASG12D conditional mutant mice (KRASG12D mice). These mice were fed an autoclaved rodent diet supplemented with 0.0625% doxycycline when the mice were about 8~12 weeks old. Mice were treated with 10 mg/kg MRTX1133 in vehicle once daily by intraperitoneal injection for 4 or 8 days. After administration of MRTX1133, the lungs and spleens were harvested, and single cell suspensions were labeled with fluorophore-conjugated antibodies for FACS analyses. Results: More regulatory T cells (Tregs) infiltrated the tumors of lung of mice treated with doxycycline for a longer period of time. The expression of immune checkpoint molecules (ICMs), including PD-L1, PD-1, TIGIT, TIM-3, LAG-3, were also upregulated on CD4+ and CD8+ T cells in the KRASG12D mice. Treatment with MRTX1133 strongly inhibited KRASG12D tumor progression, reduced the percentage of Tregs and downregulated the expression of PD-1 on CD4+ and CD8+ T cells infiltrating in lung cancers. The expression of the other ICMs remained high after MRTX1133 administration. In addition, MRTX1133 tended to increase the percentage of tumor-specific CD8+ effector T cells infiltration in lung tumors. Conclusion: T cells were exhausted in mice with KRASG12D mutant lung cancer. MRTX1133 demonstrates the therapeutic efficacy in preclinical murine KRASG12D mutated lung cancer model. This efficacy is more likely to relate not only signal inhibition but also enhances the anti- tumor immune responses. Our findings could aid in developing an alternative immunotherapy strategy in patients with KRASG12D mutant lung cancer. Citation Format: Kunihiro Shono, Satoshi Watanabe, Takaaki Masuda, Ryo Suzuki, Tomoya Wakabayashi, Tomoki Sekiya, Susumu Tanaka, Aya Ohtsubo, Tomohiro Tanaka, Koichiro Nozaki, Rie Kondo, Yu Saida, Satoshi Hokari, Naohiro Yanagimura, Masashi Arita, Riuko Ohashi, Kenjiro Shima, Yosuke Kimura, Nobumasa Aoki, Yasuyoshi Ohshima, Toshiyuki Koya, Toshiaki Kikuchi. The impact of MRTX1133 on anti-tumor immunity in lung cancer with KRASG12D mutation [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 5263.

Abstract 3797: Unveiling the spatial dynamics of the tumor microenvironment: Integrated RNA and protein profiling on the same slide through automated spatial multiomics analysis

Abstract Spatial biology techniques have revolutionized our approach towards the study of the tumor microenvironment (TME) and its complex cellular interplay. On the one hand, multiplex immunofluorescence (mIF) methods have enabled a precise profiling of immune cells and other key cellular players of the TME while uncovering their spatial distribution and interactions. On the other hand, in situ hybridization (ISH) technologies have shown to provide complementary information to protein profiling such as the mapping of cytokine- and chemokine-expressing cells, essential for comprehending signaling networks and immune activation statuses. Here, we made use of a novel multiomics approach that combines these two biological inputs by integrating RNAscope™ and sequential immunofluorescence (seqIF™) protocols to achieve same-slide co-detection of RNA and protein targets. The combined workflow is automated on COMET™, an advanced tissue staining and imaging platform. Through precise control over temperature and reagent distribution, the instrument ensures maximum efficiency and reproducibility of the assays. The integrated multiomics protocol allows for up to three RNAscope™ detection cycles combined with twelve seqIF™ cycles, for a final 12-plex RNA + 24-plex protein panel. We first showed the capacity of COMET™ platform to fully automate the RNAscope™ protocol and demonstrated its sensitivity and specificity with the analysis of positive and negative control genes on HeLa cell pellets, highlighting the flexibility of sample selection. To illustrate the potential multiomics in unravelling the complexity of the TME, we designed a panel of 12-RNA-targeting probes for key biomarkers of tumor-infiltrating lymphocytes and their activation status, including multiple secreted molecules (e.g., cytokines and proteases). This was combined with a 24-antibody panel for the detection of protein biomarkers, selected to enable the single-cell profiling of different players within the TME. We applied this panel to characterize different human FFPE tumor tissues and showed that the co-detection of RNA and protein biomarkers on the same slide allows a better characterization of key cellular components involved in tumor progression and immune response. Our results highlight the potential of spatial multiomics technologies in enhancing the efficiency of investigations of immune cell behavior and generally the understanding of cellular interplay in the TME. Their full automation on a platform like COMET™ will accelerate analysis and increase robustness by minimizing user intervention, and ultimately helping in the development of prognostic and predictive biomarkers, in the refinement of cancer diagnoses, and in the selection of new personalized therapies. Citation Format: Paula Juricic, Arec Manoukian, Alice Comberlato, Pino Bordignon, Alix Failletaz, Anushka Dikshit, Emerald Doolittle, Rose Delvillar, Steve Zhou, Ching-wei Chang, Li-chong Wang, Saska Brajkovic, Maithreyan Srinivasan, Diego Dupouy. Unveiling the spatial dynamics of the tumor microenvironment: Integrated RNA and protein profiling on the same slide through automated spatial multiomics analysis [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 3797.

Abstract 1337: Characterization of anti-AXL CAR-NK cell therapy for the treatment of melanoma

Abstract AXL is a receptor tyrosine kinase (RTK) that is commonly expressed in metastatic melanoma and several other forms of cancer. Activation of AXL signaling is linked to tumor cell growth, invasion, metastatic transformation, drug resistance, and immune response regulation. However, treatment of metastatic melanoma continues to present clinical challenges due to its capacity to rapidly develop drug resistance, which manifests under the influence of AXL signaling. As such, AXL may be a viable antigen target for immunotherapies. Despite their successes in hematological malignancies, chimeric antigen receptor (CAR)-T cell therapies remain limited by their susceptibility to causing off-target toxicity. In contrast, natural killer (NK) cells are not associated with such risks, which makes them clinically appealing as an alternative to T cells. However, studies on the application of CAR-NK cells to treat solid tumors remain acutely scarce. To explore the clinical viability of CAR-NK cells for the treatment of metastatic melanoma, AXL-specific CAR-NK cells were generated by transfecting NK cells obtained from NK cell lines. Preliminary data from a cytotoxicity assay indicated that the cytotoxicity of CAR-NK92-MI cells against AXL-positive melanoma cell lines was significantly stronger (up to a 10-fold difference) than the corresponding parental cells. Further in vitro characterization of this CAR-NK cell line and other CAR-NK cell lines, as well as in vivo evaluation of their efficacy in a mouse xenograft model of melanoma metastasis, is underway. Citation Format: Winston Hibler, Glenn Merlino, Yan Lin Yu. Characterization of anti-AXL CAR-NK cell therapy for the treatment of melanoma [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 1337.

Abstract 2634: CRISPR in vivo screen utilizing removable Cas9 system to identify epigenetic immune response modulators in antigen-sensitive mouse syngeneic models

Abstract The application of CRISPR-Cas9 screen in tumor immunology research has promoted the discovery of potential therapeutic targets and provided a deeper understanding of the mechanisms of immunotherapy resistance. Mouse syngeneic tumor model based CRISPR in vivo screen revealed significant features of immunotherapy by better approaching the tumor immune interaction. However, the immunogenicity of CRISPR-Cas9 has been widely observed in a variety of syngeneic models, which greatly limited for the application of CRISPR in vivo screen. Herein, we used two strategies for cancer cell gene editing, Cas9 protein electroporation and loxP-flanked Cas9 with Cre recombinase, to reduce the immunogenicity of CRISPR-Cas9 in CT26 subcutaneous and Renca orthotropic syngeneic models. Encouragingly, we found out that compared with constitutive Cas9-expressing All-In-One based cell pool models, both CT26 subcutaneous model and Renca orthotropic model showed a parental cell tumor comparable growth kinetics and immune checkpoint blockade ICB response by PD-1 antibody treatment. Further immuno-profiling of tumor immune microenvironment indicated limited changes from the parental cell model, which helped the data interpretation of in vivo screen outcome. We then performed a CRISPR in vivo screen by using a focused library against mouse epigenetic regulators in these two models and will discuss the hits from the screen in future. Citation Format: Yuan He, Yafei Liu, Xiao Wang, Xianyi Li, Wenle Dong, Tongrui Hao, Chenyang Zhu, Wenrong Zhou, Zhengang Peng. CRISPR in vivo screen utilizing removable Cas9 system to identify epigenetic immune response modulators in antigen-sensitive mouse syngeneic models [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 2634.

Exploring the NRF2-TP53 Signaling Network Through Machine Learning and Pan-Cancer Analysis: Identifying Potential targets for Cancer Prognosis Related to Oxidative Stress.

Oxidative stress (OXS) is closely related to tumor prognosis and immune response, while TP53 integrated with NRF2 is closely associated with the regulation of cancer-related OXS. Hence, constructing a TP53-NRF2 integrated OXS signature of pan-cancer is essential in predicting survival prognosis and facilitating cancer drug treatment. The pan-cancer analysis acquired the Cancer Genome Atlas (TCGA) transcriptome sequencing data from UCSC Xena, which consisted of 33 cancer types (n = 10440). The Random Forest, Lasso regression, and Cox regression analyses are used to construct an OXS score based on 25 OXS genes. Following this, based on the OXS signature, patients are categorized into low- and high-risk groups. The disparities between the two cohorts regarding survival prognosis, immune infiltration, and drug sensitivity are delved deeply. The expression level of genes is confirmed using immunohistochemistry. The prognosis of pan-cancer patients is adequately predicted by the OXS signature with the assistance of the machine-learning algorithm. A highly accurate nomogram is developed by combining the OXS signature and clinical features. The presence of immune cells indicated that the OXS signature can be associated with the critical pathways of immunotherapy for all types of cancer, and BCL2 showed promising results. Distinct inter-group differences are observed in the OXS signature for frequently utilized antineoplastic medications in clinical settings, including first-line drugs suggested in the guidelines. In summary, by conducting a thorough analysis of OXS genes, a new model based on OXSscore is successfully developed. This model can predict the clinical prognosis and drug sensitivity of pan-cancer with high accuracy. Potential stars in the field of cancer-related anti-OXS may include drugs that target BCL2.

Abstract 4213: Multiplex digital spatial profiling of proteins and RNA in MC38 mouse colorectal cancer syngeneic model

Abstract Introduction Characterization of the tumor microenvironment (TME) has become an essential step for the understanding of the complexity of cell interactions and the discovery of biomarkers for prediction and prognosis of immunotherapy response1. The NanoString GeoMx® Digital Spatial Profiler (DSP) technology includes the ability to quantitatively assess RNA and protein levels as well as sample multiple user-defined regions of interest, specifically focused on defining heterogeneity and TME interactions2. This technology has been widely used to identify biomarkers in clinical surgical specimens, but its applications in preclinical models are still needed. MC38 colorectal cancer syngeneic model is one of the most utilized models for assessing anti-cancer immunotherapies. In this study, we present the spatial profiling of proteins and RNA on MC38 model treated with anti-PD-1 through GeoMx® DSP technology. Methods GeoMx protein panel was used to detect the target protein expression differential in tumor-rich region and immune-rich region within MC38 subcutaneous tumor sections treated. Mice were treated with vehicle or anti-PD-1 (10mg/kg, BIW x 4 doses, ip). Whole Transcriptome Atlas (WTA) was employed, and then a comprehensive assessment of the data and comparison was performed. Results Two morphology markers, CD45 and PanCK, were used to separate tumor-rich region and immune-rich region. The GeoMx® protein data showed that the abundance of VISTA in tumor-rich region differed significantly (log2(fold-change) = 0.67, p < 0.01) in anti-PD-1 group compared to vehicle group. While in immuno-rich region, GITR was significantly altered (log2(fold-change) = 0.79, p < 0.05) in anti-PD-1 group (TGI value = 50.39%). From WTA data, we observed the upregulation of 839 genes, while 1048 genes were downregulated in immuno-rich region in anti-PD-1 group compared with vehicle group (p < 0.05). For tumor-rich regions, 550 genes were upregulated while 782 genes were downregulated in anti-PD-1 group versus vehicle group (p < 0.05). From the gene set enrichment analysis, we found that interferon alpha and interferon gamma, which are related to tumor immunity and immunotherapy response, were upregulated in anti-PD-1 group. Conclusion Both the differential expressing genes and proteins in TME of MC38 syngeneic models treated with anti-PD-1 could be well detected by GeoMx® DSP, which has the potential to provide insightful data for use in biomarker discovery in preclinical cancer models. References Charmsaz S, Collins DM, Perry AS, Prencipe M. Novel Strategies for Cancer Treatment: Highlights From the 55th IACR Annual Conference. Cancers (Basel) 2019; 11(8). Toki MI, et al. High-plex predictive marker discovery for melanoma immunotherapy-treated patients using digital spatial profiling. Clin. Cancer Res. 2019;25:5503-5512. Citation Format: Meihui Chen, Hengyuan Liu, Xiaolong Tu, Sheng Guo, Xiaobo Chen. Multiplex digital spatial profiling of proteins and RNA in MC38 mouse colorectal cancer syngeneic model [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 4213.

Abstract 3718: Deciphering the role of TREM2+ tumor-associated macrophages as mediators of immunoresistance in micro-satellite stable colorectal metastases

Abstract Introduction: Most Colorectal Cancer (CRC)-related deaths are caused by metastatic disease, and more than 95% of CRC metastases (mCRC) are microsatellite stable (MSS) which respond poorly to Immune checkpoint inhibitors (ICI). Tumor-associated macrophages (TAMs) have been recognized as major drivers of immunoresistance in primary CRC; however, their role in mCRC remains poorly understood. We analyzed primary CRC and major metastatic sites (Liver, Peritoneum, Lungs) using single-cell RNA-sequencing (scRNAseq) to elucidate the TAM driven mechanisms of immunoresistance in the mCRC tumor microenvironment (TME) and used a novel TAM directed targeting strategy to improve responses to ICI in a preclinical orthotopic model of MSS-mCRC. Methods: Using scRNA-seq, we analyzed 22 samples from 14 patients with mCRC. Target antigens identified were validated using flow cytometry and immunofluorescence (IF). The antitumor activity of anti-TREM2 and anti-PD1 mABs was evaluated in-vivo using CT26 CRC cell line in BALB-C mice, assessing tumor immune response via flow cytometry. Results: We characterized the TME in MSS-mCRC and identified 17 clusters of malignant epithelial, immune, and stromal cells. Our sub-clustering analysis revealed 6 unique sub-populations of TAMs which were differentially distributed across liver, lung, and peritoneal metastases (PM).Two subsets of TAMs, 5 and 6, were enriched in PM and malignant ascites. TAMs 5/6 expressed canonical lipid-associated genes; TREM2, APOE, and PLTP. TREM2+ TAMs were also enriched in immunosuppressive and pro-angiogenic pathways, and expressed genes known to drive EMT and ECM remodeling in the TME. Thus, TREM2 was identified as a potential therapeutic target. We validated our transcriptomic findings using flow cytometry and IF analysis of MSS-mCRC showing an abundance of TREM2+ TAMs in PM. TREM2+ TAMs co-expressed CD163, known marker for M2-TAMs and stained positive for BODIPY. In an aggressive PM mouse model, treatment with anti-PD1, anti-TREM2, or combination anti-PD1/anti-TREM2 was insufficient to reduce tumor burden. However, a trend towards a reduction in total intratumoral F4/80+CD11b+ TAMs was observed in the combination treatment compared to other groups. All three treatments trended towards increased CD8+ intratumoral T-cell infiltration compared to control mice. Conclusion: Our study provides new insights into the TME of MSS-CRC metastases at a single-cell level. Our findings indicate that TREM2+ TAMs contribute to the immunosuppressive milieu of MSS-CRC metastases. Targeting TREM2 in combination with anti-PD1 resulted in a modulation of TME via reduction of TAMs paralleled by an increased infiltration of CD8+ T cells. This reprogramming of TME suggests that inhibiting TREM2 might augment response to ICI in MSS-CRC metastases, traditionally resistant to ICI. Citation Format: Muhammad Bilal Mirza, Matthew Alexander Cottam, Mustafa Raoof, Kamran Idrees. Deciphering the role of TREM2+ tumor-associated macrophages as mediators of immunoresistance in micro-satellite stable colorectal metastases [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 3718.