Tumor-infiltrating Immune Cells Research Articles

Prognostic significance of NUAK1 and its association with immune infiltration in stomach adenocarcinoma

BackgroundStomach adenocarcinoma (STAD) represents a significant global health burden, accounting for a considerable proportion of cancer-related mortalities, and NUAK1, a protein kinase, plays a crucial role in cellular metabolism, cell cycle regulation, migration, and tumor progression. However, its relationship with prognosis and immune infiltration in STAD has not been thoroughly investigated.MethodsRNA sequencing data from the Cancer Genome Atlas (TCGA) and Genotypic Tissue Expression Project (GTEx) databases were employed to assess disparities in NUAK1 expression between STAD tumour and normal tissues. Additionally, we investigated the correlation between NUAK1 expression and patient prognosis, in addition to the level of immune cell infiltration. The potential functions were elucidated through an examination of the Gene Ontology (GO) Encyclopedia, the Kyoto Encyclopedia of Genes and Genomes (KEGG), and an enrichment analysis (GSEA). The GeneMANIA was used to validate the functions of nuak1-related genes.ResultsOur analysis demonstrated that NUAK1 expression in tumour tissues exhibited a notable disparity from that observed in normal tissues, with elevated levels detected in STAD tissues. We used the GeneMANIA database to identify functionally similar genes with significantly higher expression for some genes in the unpaired group samples. An elevated NUAK1 expression level was found to correlate with a poorer overall survival (OS), disease-specific survival (DSS), and progression-free intervals (PFI). Additionally, immune infiltration analysis indicated a significant positive correlation between NUAK1 expression and various tumor-infiltrating immune cells, while a negative correlation was observed with T helper cell 17(Th17) cells. Furthermore, enrichment analysis was conducted to identify relevant biological features and pathways.ConclusionThe expression levels of NUAK1 are significantly increased in STAD, and this heightened expression correlates with diminished OS, DSS, and PFI among affected patients. These observations indicate that NUAK1 has the potential to function as a prognostic biomarker for STAD and may represent a viable therapeutic target for intervention in its management.

Construction of a novel copper-induced-cell-death-related gene signature for prognosis in colon cancer, with focus on KIF7

BackgroundColon cancer (CC) is a leading cause of cancer-related mortality worldwide. Accurate prognostic markers are essential for patient risk stratification and personalized treatment. Copper-induced cell-death-related genes (CRG) have emerged as potential players in cancer prognosis, yet their role in CC remains unclear.MethodsThis study aimed to comprehensively evaluate the expression of CRG and their roles in CC using gene expression and clinical data from TCGA and GEO databases. Univariate Cox regression and least absolute shrinkage and selection operator (LASSO) analyses identified prognostic genes, leading to the construction of a CRG prognostic signature. The signature’s predictive accuracy was validated using Kaplan-Meier survival curves, Receiver Operating Characteristic (ROC) curves, and a nomogram model. Additionally, we conducted experiments including immunofluorescence staining and cellular assays to validate the key genes’ biological functions.ResultsA 12-gene CRG signature was significantly associated with overall survival in CC patients. The high-risk group, as classified by median risk score, exhibited significantly shorter survival times compared to the low-risk group. The signature’s predictive accuracy was further confirmed with Area Under the Curve (AUC) scores exceeding 0.75 in TCGA and GSE17536 cohorts. Notably, the risk score was significantly correlated with immune checkpoints, chemotherapy sensitivity, and tumor microenvironment. Furthermore, the risk score showed a strong association with immunotherapy response in patients from GSE78220 and GSE39688 cohorts. Bioinformatics analysis of KIF7, a key gene within the signature, revealed its upregulation in CC and significant associations with tumor mutation burden, microsatellite instability, and immune cell infiltration across various cancers. Experiments confirmed that KIF7 was upregulated in CC and its knockdown reduced cell proliferation, migration, and invasion.ConclusionThe CRG prognostic signature can effectively predict overall survival, immune microenvironment and chemotherapy response in CC. KIF7, as a potential prognostic marker, has significant potential for the prediction and treatment of CC.

The landscape in telomere related gene prognostic signature for survival and medication treatment effectiveness prediction in hepatocellular carcinoma

ObjectiveTelomeres, made of repetitive DNA sequences and shelterin complexes, which were found at the ends of chromosomes and had been extensively studied in cancer research. However, in hepatocellular carcinoma (HCC) was still relatively scarce. In this study, we investigated the correlation between telomerase-related genes (TRGs) and the prognosis and immunotherapy of HCC patients to enhance clinical outcomes.MethodsIn this work, TRGs were gathered using TelNet, while clinical information and gene expression data for HCC patients were retrieved from the Cancer Genome Atlas (TCGA) database. A risk prediction model based on TRGs was created using COX and Lasso regression analyses, with ROC curves used to assess prognostic efficacy. Univariate and multifactorial COX regression analyses were used to determine if the risk model had an independent impact on prognosis. Nomograms were created to enhance clinical usability, and calibration curves were used to assess predictive ability at various time points. The Tumor Immune Dysfunction and Exclusion (TIDE) score was used to analyze differences in immune infiltrating cells between risk groups. The study analyzed the relationship between risk ratings and drug treatment effectiveness using data from the CellMiner database. The hub gene was identified and its relationship to prognostic markers of HCC patients was examined. The expression of hub genes in immune cell subpopulations was also investigated by single-cell data.Results2093 TRGs were identified, with 949 showing significant differences in expression between HCC and paracancerous tissues. Seven risk genes were overexpressed in tumor tissues, leading to lower survival rates in high-risk patients. Risk model could independently predict the prognosis of HCC patients. Analysis of tumor immune infiltrating cells revealed significant differences in cell abundance between risk groups, with notable variations in immune subset enrichment between subgroups. Higher risk scores correlated with increased sensitivity to sorafenib, mitoxantrone, oxaliplatin, gemcitabine, and entinostat, while sensitivity decreased for vincristine, etc. CDCA8 was identified as a key gene in the Protein Interaction Network, while high expression associated with poorer overall survival, tumor proliferation and metastasis. The results of single-cell data analysis suggest that CDCA8 may promote the development of HCC by affecting T lymphocytes.ConclusionThe TRG-based risk model could predict HCC patient prognosis and closely linked to tumor immune environment, which could offer new possibilities for clinical treatment.

Machine learning-based selection of immune cell markers in osteosarcoma: prognostic determination and validation of CLK1 in disease progression

IntroductionOsteosarcoma (OS) is a malignancy of the bone that mainly afflicts younger individuals. Despite existing treatment approaches, patients with metastatic or recurrent disease generally face poor prognoses. A greater understanding of the tumor microenvironment (TME) is critical for enhancing outcomes in OS patients.MethodsThe clinical and RNA expression data of OS patients were extracted from the TARGET database. The single-cell RNA sequencing (scRNA-seq) data of 11 OS samples was retrieved from the GEO database, and analyzed using the Seurat package of R software. Copy number variation (CNV) was analyzed using the InferCNV software. The potential interactions between the different cells in the TME was analyzed with the CellChat package. A multi-algorithm-based computing framework was used to calculate the tumor-infiltrating immune cell (TIIC) scores. A prognostic model was constructed using 20 machine learning algorithms. Maftools R package was used to characterize the genomic variation landscapes in the patient groups stratified by TIIC score. The human OS cell lines MG63 and U2OS were used for the functional assays. Cell proliferation and migration were analyzed by the EdU assay and Transwell assay respectively. CLK1 protein expression was measured by immunoblotting.ResultsWe observed higher CNV in the OS cells compared to endothelial cells. In addition, there was distinct transcriptional heterogeneity across the OS cells, and cluster 1 was identified as the terminal differentiation state. S100A1, TMSB4X, and SLPI were the three most significantly altered genes along with the pseudo-time trajectory. Cell communication analysis revealed an intricate network between S100A1+ tumor cells and other TME cells. Cluster 1 exhibited significantly higher aggressiveness features, which correlated with worse clinical outcomes. A prognostic model was developed based on TIIC-related genes that were screened using machine learning algorithms, and validated in multiple datasets. Higher TIIC signature score was associated with lower cytotoxic immune cell infiltration and generally inferior immune response and survival rate. Moreover, TIIC signature score was further validated in the datasets of other cancers. CLK1 was identified as a potential oncogene that promotes the proliferation and migration OS cells.ConclusionA TIIC-based gene signature was developed that effectively predicted the prognosis of OS patients, and was significantly associated with immune infiltration and immune response. Moreover, CLK1 was identified as an oncogene and potential therapeutic target for OS.

Increased expression of HBXIP (LAMTOR5) predicts poor prognosis and is correlated with immune-cell infiltration in glioma.

The poor response of patients with gliomas to existing immunotherapy has resulted in negligible improvement in prognosis. It is widely acknowledged that HBXIP serves as a transcriptional activator implicated in tumorigenesis across various cancer types. However, its specific role within glioma remains unclear. The aim of this study was to determine the association between HBXIP expression and survival and tumor-infiltrating immune cells. In addition, to construct a prognostic model to predict the overall survival (OS) of patients with glioma. Transcriptome sequencing data of 325 patients with glioma in the Chinese Glioma Genome Atlas (CGGA) database and 702 patients with glioma in The Cancer Genome Atlas (TCGA) were included for retrospective analysis and were used as the training group and the validation group, respectively. The expression of HBXIP in pancancer was detected in the database. A t-test and one-way analysis of variance were used to determine the differential expression levels of HBXIP across distinct subgroups of glioma. Functional annotations pertaining specifically to HBXIP's biological relevance underwent scrutiny via Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. The prognostic significance of HBXIP in glioma was ascertained through Kaplan-Meier curves and Cox regression models, a nomogram was used to establish a prognostic model, and the predictive power was evaluated with calibration curves and the concordance index. HBXIP's association with inhibitory immune checkpoints and tumor immune cell infiltration was examined using Pearson correlation coefficients via Tumor Immune Estimation Resource database. We found that HBXIP was upregulated in glioma, and that elevated HBXIP expression correlated significantly with adverse clinicopathological features and decreased OS. Multivariate analysis showed that HBXIP was an independent prognostic biomarker for glioma, and the established prognostic model could accurately predict the OS of patients. We also found that HBXIP expression was positively correlated with inhibitory immune checkpoint expression, HBXIP overexpression was associated with increased levels of tumor immunoinfiltrating cells in glioma that resulted in poor survival, and HBXIP demonstrated a positive correlation with the expression of immune cell marker genes. HBXIP is closely related to the clinicopathologic factors in glioma and may function as an oncogene. Its high expression is associated with poor prognosis, which may potentially be linked to immune escape and immune cell infiltration. HBXIP is a potential biomarker of prognostic and immune infiltration in glioma.

SLC12A9 is an immunological and prognostic biomarker for glioma

BackgroundGlioma is one of the most common malignant brain tumors. It has a high rate of progression and a poor prognosis, and effective biomarkers still need to be identified. The solute carrier family 12 (SLC12) family has been reported to be involved in various physiological and pathological processes, but their functional roles in glioma remain unclear. MethodsUsing public datasets, we studied the mutation and expression level of SLC12 family genes in glioma and identified the significantly differentially expressed member solute carrier family 12 member 9 (SLC12A9). We further predicted the prognostic role of SLC12A9 in glioma by using the Kaplan–Meier method and Cox regression analysis. Then, we performed biological functional enrichment analysis. We focused on the relationships between SLC12A9 expression and immune infiltration in glioma. Meanwhile, we conducted in vitro experiments to evaluate the effect of SLC12A9 expression on glioma cells. ResultsAmong the members of the SLC12 family, SLC12A9 had the highest mutation rate in glioma, with gene amplification as the major mutation type, and its expression was significantly upregulated in glioma. Higher SLC12A9 expression was significantly associated with older age, higher grade, wild-type isocitrate dehydrogenase (IDH), and a worse prognosis. The functional enrichment analysis indicated that SLC12A9 is mainly related to ion channel annotation. Gene set enrichment analysis (GSEA) revealed that SLC12A9 was mainly related to the DNA replication pathway. Furthermore, we found that SLC12A9 correlated with tumor-infiltrating immune cells and immune checkpoints. Thus, SLC12A9 may be involved in regulating the immune response of glioma. Finally, our in vitro experiments revealed that silencing SLC12A9 dramatically inhibited glioma cell growth and migration. ConclusionsWe showed that SLC12A9 may be a new predictive biomarker for glioma diagnosis, prognosis, and immunotherapy response, offering helpful guidelines to advance glioma treatment.

CRHBP, a novel multiple cancer biomarker connected with better prognosis and anti-tumorigenicity

BackgroundThe corticotropin-releasing hormone-binding protein (CRHBP) plays a crucial role in regulating corticotropin release. Little is known about the role of CRHBP, a major regulator of neuroendocrine, autonomic, and stress adaptation, in tumors. In this study, we aimed to investigate the clinical and molecular landscapes of CRHBP in various types of tumors.MethodsWe investigated the role of CRHBP in different types of tumors using publicly available databases and performed a comparative expression analysis of CRHBP-related genes in pan-cancer prognosis using methylation profiling, tumor-infiltrating immune cell expression analysis, gene enrichment analysis, and protein-protein interaction analysis, identified common pathways, and in vitro evaluation.ResultsWe evaluated CRHBP expression across tumor and corresponding normal tissues using the data from The Cancer Genome Atlas and the Genotype-Tissue Expression database. CRHBP was downregulated in most tumors and was identified as an important factor for predicting the prognosis of patients with cancer. Intracellular metabolic pathways and hormone-related processes were involved in the functional mechanisms of CRHBP. Mechanistically, the downregulation of CRHBP was attributed to the upregulation of four miRNAs in most tumors, and CRHBP expression was related to tumor-infiltrating immune cells in tumors. Overexpression of CRHBP significantly inhibited cell proliferation of LUAD, LIHC, and KIRC cell lines, while inhibition of cell mobility was found only in KIRC and HCC cells.ConclusionsThis study provides a comprehensive summary of the systemic role of CRHBP expression in various types of tumors, highlighting the prognostic importance and clinical significance of tumors. Furthermore, CRHBP decreases cell proliferation and mobility in cancer cell lines associated with OS and DFS, further research is needed to understand the underlying mechanisms and explore clinical applications.

Deciphering potential molecular mechanisms in clear cell renal cell carcinoma based on the ubiquitin-conjugating enzyme E2 related genes: Identifying UBE2C correlates to infiltration of regulatory T cells.

Renal clear cell carcinoma (ccRCC) is a highly aggressive and common form of kidney cancer, with limited treatment options for advanced stages. Recent studies have highlighted the importance of the ubiquitin-proteasome system in tumor progression, particularly the role of ubiquitin-conjugating enzyme E2 (UBE2) family members. However, the prognostic significance of UBE2-related genes (UBE2RGs) in ccRCC remains unclear. In this study, bulk RNA-sequencing and single-cell RNA-sequencing data from ccRCC patients were retrieved from the Cancer Genome Atlas and Gene Expression Omnibus databases. Differential expression analysis was performed to identify UBE2RGs associated with ccRCC. A combination of 10 machine learning methods was applied to develop an optimal prognostic model, and its predictive performance was evaluated using area under the curve (AUC) values for 1-, 3-, and 5-year overall survival (OS) in both training and validation cohorts. Functional enrichment analyses of gene ontology and Kyoto Encyclopedia of Genes and Genomes were conducted to explore the biological pathways involved. Correlation analysis was conducted to investigate the association between the risk score and tumor mutational burden (TMB) and immune cell infiltration. Immunotherapy and chemotherapy sensitivity were assessed by immunophenoscore and tumor immune, dysfunction, and exclusion scores to identify potential predictive significance. In vitro, knockdown of the key gene UBE2C in 786-O cells by specific small interfering RNA to validate its impact on apoptosis, migration, cell cycle, migration, invasion of tumor cells, and induction of regulatory T cells (Tregs). Analysis of sc-RNA revealed that UBE2 activity was significantly upregulated in malignant cells, suggesting its role in tumor progression. A three-gene prognostic model comprising UBE2C, UBE2D3, and UBE2T was constructed by Lasoo Cox regression and demonstrated robust predictive accuracy, with AUC values of 0.745, 0.766, and 0.771 for 1-, 3-, and 5-year survival, respectively. The model was validated as an independent prognostic factor in ccRCC. Patients in the high-risk group had a worse prognosis, higher TMB scores, and low responsiveness to immunotherapy. Additionally, immune infiltration and chemotherapy sensitivity analyses revealed that UBE2RGs are associated with various immune cells and drugs, suggesting that UBE2RGs could be a potential therapeutic target for ccRCC. In vitro experiments confirmed that the reduction of UBE2C led to an increase in apoptosis rate, as well as a decrease in tumor cell invasion and metastasis abilities. Additionally, si-UBE2C cells reduced the release of the cytokine Transforming Growth Factor-beta 1 (TGF-β1), leading to a decreased ratio of Tregs in the co-culture system. This study presents a novel three-gene prognostic model based on UBE2RGs that demonstrates significant predictive value for OS, immunotherapy, and chemotherapy in ccRCC patients. The findings underscore the potential of UBE2 family members as biomarkers and therapeutic targets in ccRCC, warranting further investigation in prospective clinical trials.

Flow Cytometry Analyses of Meningioma Immune Cell Composition Using a Short, Optimized Digestion Protocol.

Current challenges in meningioma treatment, including post-surgical complications and cognitive impairments, highlight the need for new treatment alternatives. Immunological interventions have shown promise. However, there is a knowledge gap in characterizing infiltrating immune cells in meningioma and their interplay. Further studies on immune cells in single-cell suspensions from digested meningioma tissues could identify targetable mechanisms for non-surgical treatment options with fewer side effects. This study aimed to optimize a protocol for faster digestion of meningioma tissues into viable single-cell suspensions and to identify infiltrating immune cell populations. We modified a commercial kit intended for whole skin dissociation to digest resected meningioma tissues into viable single-cell suspensions. Tumor-infiltrating immune cell populations were characterized using flow cytometry. Flow cytometry analyses revealed that the digested tissue was composed of viable immune cells, including predominantly CD14+ macrophages and CD3+ T cells, with minor populations of CD56+ NK cells and CD19+ B cells. In both of the two patient samples tested, half of the tumor-associated macrophages were TIM-3+, with a small proportion co-expressing CD83. Women were more likely to have a lower proportion of immune cells, B cells, and NK cells. Female patients with a high proportion of immune cells had a higher proportion of macrophages. We successfully optimized a protocol for generating single-cell suspensions with viable immune cells from meningioma tissues, revealing infiltrating antigen-presenting cells with an immunosuppressive phenotype, and lymphocytes. This short protocol allows advanced analyses of tumor-infiltrating cells using techniques such as single-cell RNA sequencing and flow cytometry, which require live, dissociated cells.

Blockade of purine metabolism reverses macrophage immunosuppression and enhances anti-tumor immunity in non-small cell lung cancer

AimsImmune checkpoint blockade therapy is not effective in most patients with non-small cell lung cancer (NSCLC) due to the immunosuppressive tumor microenvironment. Macrophages are key components of tumor-infiltrating immune cells and play a critical role in immunosuppression, which can be mediated by cell-intrinsic metabolism. This study aimed to evaluate whether macrophages regulate NSCLC progression through metabolic crosstalk with cancer cells and affect immunotherapy efficacy. MethodsThe macrophage landscape of NSCLC tissues were analyzed by single-cell sequencing and verified through flow cytometry and immunofluorescence. Multiplex assay, single-cell sequencing data, ELISA, immunofluorescence, and RNA-seq et al. were used to investigate and verify the mechanism of macrophage-mediated metabolic regulation on immunosuppression. The tumor-bearing model was established in C57BL/6 J mice to explore in vivo efficacy. ResultsWe found that tumor tissue-derived macrophages exhibited an anti-inflammatory phenotype and had a prognostic value for NSCLC. NSCLC cell-secreted CXCL8 recruited macrophages from peritumor tissues to tumor sites and promoted programmed death-ligand 1 (PD-L1) expression by activating purine metabolism with increasing xanthine dehydrogenase and uric acid production. Moreover, purine metabolism-mediated macrophage immunosuppression was dependent on NLRP3/caspase-1/IL-1β signaling. Blockade of purine metabolism signaling enhanced anti-tumor immunity and the efficacy of anti-PD-L1 therapy. ConclusionsCollectively, our findings reveal a key role of purine metabolism in macrophage immunosuppression and suggest that blockade of purine metabolism combined with immune checkpoint blockade could provide synergistic effects in NSCLC treatment.

Cell cycle inhibitors activate the hypoxia-induced DDX41/STING pathway to mediate antitumor immune response in liver cancer.

Cell cycle inhibitors have a long history as cancer treatment. Here, we report that these inhibitors combated cancer partially via the stimulator of IFN genes (STING) signaling pathway. We demonstrated that paclitaxel (microtubule stabilizer), palbociclib (cyclin-dependent kinase 4/6 inhibitor), and AZD1152 and GSK1070916 (aurora kinase B inhibitors) have anticancer functions beyond arresting the cell cycle. They consistently caused cytosolic DNA accumulation and DNA damage, which inadvertently triggered the cytosolic DNA sensor DEAD-box helicase 41 (DDX41) and activated STING to secrete pro-inflammatory senescence-associated secretory phenotype factors (SASPs). Interestingly, we found that DDX41 was a transcriptional target of HIF. Hypoxia induced expression of DDX41 through HIF-1, making hypoxic hepatocellular carcinoma (HCC) cells more sensitive to the antimitotic agents in STING activation and SASP production. The SASPs triggered immune cell infiltration in tumors for cancer clearance. The treatment with cell cycle inhibitors, especially paclitaxel, extended survival by perturbing mouse HCC growth when used in combination with anti-PD-1. We observed a trend that paclitaxel suppressed Sting wild-type HCC more effectively than Sting-KO HCC, suggesting that STING might contribute to the antitumor effects of paclitaxel. Our study revealed the immune-mediated tumor-suppressing properties of cell cycle inhibitors and suggested combined treatment with immunotherapy as a potential therapeutic approach.

DSN1 may predict poor prognosis of lower-grade glioma patients and be a potential target for immunotherapy

ABSTRACT DSN1 has been previously found to be positively correlated with various cancers. However, the effect of DSN1 or its methylation on the prognosis, molecular characteristics, and immune cell infiltration of low-grade glioma (LGG) has not yet been studied. We obtained 1046 LGG samples from the The Cancer Genome Atlas, The Chinese Glioma Genome Atlas (CGGA) microarray, and CGGA RNA-Seq databases. Bioinformatic methods (gene set enrichment analysis (GSEA), chi-square test, multivariate), and laboratory validation were used to investigate DSN1 in LGG. The expression levels of DSN1 mRNA and protein in LGG were substantially higher than those in normal brain tissue, and their expression was negatively regulated by methylation. The survival time of patients with low expression of DSN1 and cg12601032 hypermethylation was considerably prolonged. DSN1 was a risk factor, and of good diagnostic and prognostic value for LGG. Importantly, the expression of DSN1 is related to many types of tumor-infiltrating immune cells and has a positive correlation with PDL1. DSN1 promoted the activation of multiple cancer-related pathways, such as the cell cycle. Additionally, knockdown of DSN1 substantially inhibited the proliferation and invasion of LGG cells. To the best of our knowledge, this study is the first comprehensive analysis of the mechanism of DSN1 leading to poor prognosis of LGG, which provides a new perspective for revealing the pathogenesis of LGG. DSN1 or its methylation has diagnostic value for the prognosis of glioma, and may become a new biological target of anti-tumor immunotherapy.

Abstract C022: Exercise reduces pancreatic tumor in a gut microbiome dependent manner

Abstract Preclinical studies suggest that aerobic exercise influences the tumor microenvironment by normalizing vasculature and reducing immunosuppression in Pancreatic Ductal Adenocarcinoma (PDAC). Gut microbes can influence PDAC progression by modulating metabolic and immune pathways. However, a knowledge gap remains regarding the role of the gut microbiome in the anti-tumor effects of exercise. We hypothesized that the exercise-induced anti-tumor effect in PDAC is regulated by gut microbiome. We compared the effect of treadmill running on growth of orthotopic PDAC in C57BL/6 mice from Taconic Biosciences (Tac) and Jackson Laboratories (Jax), which have different microbiomes. Tumor-bearing mice performed treadmill exercise (ex, 12 meters/minute (m/min) for 45 minutes (min) daily) or were non-exercised controls (no-ex). Exercise reduced tumor weight compared to no-ex controls in Jax (no-ex, 0.72±0.05 grams (g); ex, 0.54±0.04g; p=0.04) but not in Tac mice (no-ex, 0.72±0.05g; ex, 0.78±0.05g; p=0.47). Interestingly, in Tac mice treated with antibiotics (ATBx) ad libitum, treadmill exercise reduced tumor growth (no-ex, 0.74±0.04 g; ex, 0.53±0.03g; p= 0.006). Taken together, this data indicates that the anti-tumor effect of exercise is affected by gut microbiome. We considered potential mechanisms by which exercise suppresses tumor growth. Tumor infiltrating immune cells were measured by flow cytometry and immunohistochemistry. No significant differences in the tumor infiltrating immune cells were observed between no-ex and ex mice from Tac or Jax, regardless of ATBx, indicating that gut microbiome mediated anti-tumor effect is independent of immune pathways. Previous studies have demonstrated that exercise reduces tumor growth in an intensity dependent manner. Therefore, to determine exercise intensity as percentage of Peak Velocity (VPeak), exercise capacity (ExCap) test was performed. VPeak (m/min), time to exhaustion (min), and distance to exhaustion (m) were used as indicators for treadmill ExCap. Treadmill ExCap was significantly lower in tumor bearing Tac mice (24.86±3.55m/min, 12.56±1.79min, 217.17±31.02m) compared to Jax mice (30.50±3.81m/min; 16.58±2.07min; 320.15±40.02m; p=0.01). However, ATBx treatment did not change the treadmill ExCap in the Tac mice (25.50±3.19m/min; 12.62±1.58min; 209.26±26.16m; p=0.97) despite significantly changing the effect of exercise on tumor growth, indicating that ExCap may not regulate differences observed in the tumor weight. Overall, these results indicate that gut microbiome regulates anti-tumor effects of exercise, that are independent of tumor infiltrating immune cells or exercise intensity. Analysis of serum and tumor metabolites, 16s rRNAseq to evaluate microbial differences, and bulk RNAseq on tumors, is underway with the goal of identifying microbial-derived metabolites which mediate the anti-tumor effect of exercise. Understanding how the gut microbiome mediates the efficacy of exercise to suppress tumor growth will be critical for maximizing the benefits of exercise for patients with PDAC. Citation Format: Sumedha Pareek, Vidhi Chandra, Le Li, Hetal Patel, Truong Lam, Olivereen LeRoux, Haoyue Liu, Jonghae Lee, Florencia McAllister, Keri Schadler. Exercise reduces pancreatic tumor in a gut microbiome dependent manner [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C022.

Abstract A043: Senescent CAFs modulate tumor immunity and promote breast cancer progression

Abstract Cellular senescence is characterized by a series of markers such as p16INKA4(p16) positivity and a distinctive profile of secretory factors including mitogens, cytokines, and extracellular matrix (ECM) proteins that are collectively recognized as senescence-associated secretory phenotype (SASP). Interestingly, high p16 positivity in stroma strongly correlates with ductal carcinoma in situ (DCIS) recurrence, raising the possibility that p16+ senescent stromal cells contribute to breast cancer progression. To explore the hypothesis, we carried out single-cell RNA sequencing (scRNA-seq) analyses of murine and human HER2+/ER+/TNBC tumor samples and found that senescence was restricted to a specific cancer-associated fibroblasts (CAF) subpopulation that expresses numerous SASP factors that could impact tumor immunosurveillance, including cytokine SASP factors and ECM SASP factors such as collagens. We refer to these cells as senescent CAFs (senCAFs). To investigate how senCAFs impact tumorigenesis, we crossed MMTV-PyMT (PyMT) mice that spontaneously develop mammary tumors to INK-ATTAC (INK) mice, which allows selective elimination of p16+ senescent cells. Depletion of senCAFs in PyMT/INK mice led to significantly delayed tumor onset and changes in various tumor-infiltrating immune cells including natural killer (NK) cells, both of which could be recapitulated by treating PyMT mice with a senolytic drug. Monoclonal antibody- mediated NK cell depletion in the PyMT model further indicated that NK cells are indispensable for senCAF’s tumor-promoting effect. Finally, our bulk RNA-sequencing and cytotoxicity assays revealed that ECM derived from senescent but not cycling myofibroblastic mammary fibroblasts potently inhibited NK cell killing of tumor cells. Importantly, PyMT mice treated with Losartan (DuP-753), an inhibitor for collagen I synthesis, showed lower tumor burden and improved tumor-infiltrating NK cell status. Together our data highlight that senCAFs contribute to mammary gland tumorigenesis by modulating tumor ECM and immunity and suggest that senolytic treatment may limit breast cancer progression. Citation Format: Jiayu Ye, John M. Baer, Douglas V. Faget, Vasilios A. Morikis, Qihao Ren, Anupama Melam, Ana Paula Delgado, Erik Knudsen, Agnieszka Witkiewicz, Robert S. Powers, Gregory D. Longmore, David G. DeNardo, Sheila A. Stewart. Senescent CAFs modulate tumor immunity and promote breast cancer progression [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr A043.

Abstract C019: IL27R signaling regulates neutrophils maturation, activation and function in colorectal cancer-liver metastases

Abstract Colorectal cancer (CRC) is the third most common cancer and fourth cause of cancer death worldwide. The liver is the most common organ for CRC metastasis, which is a major cause of death for CRC patients. Therefore, a better understanding of mechanisms facilitating CRC liver metastasis is in urgent need. IL27 is a member of IL6/IL12 cytokines superfamily which have a critical role in tumor microenvironment to affect tumorigenesis and metastasis. IL27 is secreted by activated macrophages and dendritic cells, and IL27R is expressed in various immune cells, mediating IL27-dependent pro-inflammatory or anti-inflammatory immune responses. However, the role of myeloid IL27 signaling in CRC-liver metastasis remains unclear. To study the role of IL27R signaling in myeloid cells, we generated Il27ra fl/fl mice and crossed them with LysM cre deleter to obtain LysM cre+ Il27ra f/f mice. Using MC-38 CRC cells portal vein injection model, we found that myeloid IL27Ra deletion leads to increased CRC-liver metastasis accompanied by increase in neutrophils, particularly Ly6G+Cxcr2-CD101- immature neutrophils, in circulation as well as tumors in LysM cre+ Il27ra f/f mice. Single-cell sequencing of tumor-infiltrating immune cells revealed that lack of IL27Ra in myeloid cells promoted neutrophil recruitment and degranulation as well as reactive oxygen species (ROS) and reactive nitrogen species (RNS) production but inhibited neutrophil maturation and production of pro-inflammatory chemokines and cytokines such as CXCL10, CSF1 and TNF. Furthermore, IL27Ra deficient neutrophils displayed heightened inflammatory response when stimulated with LPS in vitro. Collectively, our work reveals novel role of myeloid IL27Ra signaling that inhibits metastatic liver colonization by promoting neutrophil maturation, restricting neutrophil infiltration and degranulation. Citation Format: Jiani Zhu, Zhengzheng Shi, Ekaterina Koltsova. IL27R signaling regulates neutrophils maturation, activation and function in colorectal cancer-liver metastases [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer; 2024 Nov 17-20; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(22_Suppl):Abstract nr C019.

Single-cell and bulk transcriptome analysis reveals tumor cell heterogeneity and underlying molecular program in uveal melanoma

BackgroundUveal melanoma (UM) is a rare and deadly eye cancer with high metastatic potential. Despite the predominance of malignant cells within the tumor microenvironment, the heterogeneity and underlying molecular features remain to be fully characterized.MethodsWe analyzed single-cell transcriptomic profiling of 37,660 malignant cells from 17 UM tumors. A consensus non-negative factorization algorithm was used to decipher transcriptional programs underlying tumor cell-intrinsic heterogeneity. Tumor-infiltrated immune cells were computationally estimated from bulk transcriptomes and bioinformatics methods. A gene signature was derived for subtyping and prognostic stratification and validated in multicenter cohorts.ResultsScRNA-seq analysis revealed the existence of diverse subpopulations and transcriptional variability among malignant cells within and between tumors. Furthermore, we observed that the heterogeneity of malignant cell states and compositions correlated with genomic, immunological, and clinical characteristics. By identifying gene expression programs associated with malignant cell heterogeneity at the single cell level, UM samples were classified into two distinct intra-tumoral subtypes (ITMHlo and ITMHhi) with different prognoses and immune microenvironments. Finally, a machine learning-derived 9-gene signature was developed to translate single-cell information into bulk tissue transcriptomes for patient stratification and was validated in multicenter cohorts.ConclusionsOur study provides insight into understanding the intra-tumoral heterogeneity of UM and its potential impact on patient stratification.

IMMU-15. CD74/MIF SIGNALING AXIS DISRUPTION IN BONE MARROW-DERIVED MYELOID CELLS DELAYS MALIGNANT PROGRESSION IN A PRECLINICAL MODEL OF GLIOMA

Abstract INTRODUCTION CD74, a chaperone associated with the major histocompatibility complex class II (MHC-II), plays a crucial role in assembling and transporting MHC-II molecules on the cellular surface. Beyond its physiological function in antigen presentation, CD74 is a negative regulator of inflammation, and its dysregulation is associated with inflammatory disorders and cancer. Notably, tumor stem cells release macrophage migration inhibitory factor (MIF) to trigger CD74 immunosuppressive signaling in tumor-infiltrating immune cells, thereby abrogating CD8+ T cell activation and promoting angiogenesis. While CD74 expression is known in dendritic cells, macrophages and B cells, our recent findings reveal its upregulation in immunosuppressive macrophages within the low-grade glioma (LGG) tumor microenvironment, and its negative correlation with the survival of adolescent and young adult patients with LGG. HYPOTHESIS. We hypothesize that inhibiting CD74/MIF in immunosuppressive myeloid cells may affect tumor progression and prevent malignant transformation (MT) to high-grade glioma (HGG). METHODS To test our hypothesis, we isolated bone marrow cells from immunocompetent RCAS n/tv-a LGG bearing animals, differentiated them into bone marrow-derived myeloid cells (BMDMs), silenced CD74 expression, and co-cultured them with primary CD8+T cells. Moreover, we inhibited CD74/MIF signaling in vivo. RESULTS. Deconvolution analysis of tumor-infiltrating immune cells revealed upregulation of CD74 and its network in myeloid cells during LGG compared to HGG. Silencing CD74 in LGG BMDMs in vitro resulted in the downregulation of genes associated with migration, proliferation, and immunosuppression. The co-culture of LGG CD74KD-BMDMs with CD8+ T cells increased the expression of T cell activation genes. In vivo treatment of LGG mice with MIF inhibitors significantly decreased myeloid cell infiltration in the tumor microenvironment (TME) and prolonged survival. CONCLUSIONS These preclinical studies highlight a role for the CD74/MIF signaling axis in glioma and present a novel immunotherapeutic target to modulate the activity of immunosuppressive myeloid cells in order to delay MT.

EPCO-11. BIASES IN HEALTHY BRAIN SINGLE-CELL DATASETS: FINDING THE BEST COMPARISON FOR GLIOBLASTOMA STUDIES

Abstract Tumor cells undergo metabolic alterations that support their proliferation and simultaneously modify immune populations, resulting in an immunosuppressive tumor microenvironment. This study aims to compare the metabolic expression of immune cells within the tumor microenvironment to those in a healthy environment. However, there is a lack of single-cell transcriptomic data for normal brain cells, necessitating an analysis of different methods to compare immune cells in tumors with those in a healthy brain. To address this, we explored cell-to-cell metabolic variability using public single-cell RNA-seq (scRNA-seq) data of glioblastoma (n=338564), and from immune cells in the brains of post-mortem individuals (n=14177), fetuses (n=40000), and epilepsy patients (n=466), as well as from immune blood cells (n=329762). We employed ssGSEA to generate activity scores for 70 key metabolic pathways from KEGG for each individual cell. Known marker genes were utilized to identify normal cell populations (macrophages, T cells, oligodendrocytes) in datasets lacking cell type annotations. Our results revealed that blood cells exhibited high metabolic activity in macrophages but showed moderate activity in other cell types. Immune blood cells also demonstrated high oxidative phosphorylation (OXPHOS) but low fatty acid activity. Fetal brain cells displayed a lack of heterogeneity and showed high fatty acid activity with low OXPHOS activity. Brain cells from post-mortem individuals displayed heterogeneity but exhibited low metabolic activity across nearly all cells and pathways. Additionally, the hierarchy of pathway activity differed from the other datasets. Epilepsy data revealed a metabolic activity pattern similar to tumor-infiltrating immune cells, with comparable activity hierarchy and heterogeneity, although the sample size was limited for detailed comparison. Understanding the differences between types of datasets is important to choose the most appropriate comparison, allowing us to observe the metabolic alterations in immune cells caused by glioblastoma and to develop better immunotherapy strategies.

IMMU-44. EXTRINSIC ELECTRICAL MODULATION OF THE GLIOBLASTOMA TUMOR MICROENVIRONMENT

Abstract BACKGROUND Approximately 30 to 50% of patients with glioblastoma (GBM) present with glioma-related epilepsy (GRE). Despite morbidity associated with seizures, GRE constitutes an independent positive predictive predictor for survival in GBM. Our prior results showed that repeated seizure induction through extrinsic electrical modulation (EEM, a technique in which an electrical stimulus sufficient to produce a therapeutic seizure is applied) slows intracranial tumor growth and prolongs overall survival in immunocompetent CT-2A glioma-bearing mice. However, the overall survival advantage following EEM treatment was diminished in immunocompromised mice bearing human patient derived xenografts. We hypothesized that EEM induces immune-related tumor microenvironment (TME) changes that prolong survival in mice. METHODS C57BL/6J mice were orthotopically implanted with CT-2A xenografts and subjected to EEM of 2.0 millicoulombs or sham treatment. Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was performed at 3 and 24 hours to determine mRNA level of inflammatory cytokines. Immunohistochemistry (IHC) and bulk RNA sequencing analysis were utilized to assess CD3+ T-cell infiltration and identify immune-related secreted genes, respectively. Flow cytometry at 3 and 96 hours was utilized to characterize tumor-infiltrating immune cell populations. Samples were subjected to Percoll gradient enrichment of immune cell populations and stained for extracellular (CD45, CD4, CD8, CD11b, F4/80, CD80, Ly6G, Ly6C, and CX3CR1) and intracellular (TNF-a, Il-1b, CCL2, and Arg1) antigens. RESULTS RT-qPCR showed an increase in pro-inflammatory cytokines TNF-α (P = 0.0087) and IL-1β (P = 0.000349). IHC analysis demonstrated an increase in intratumoral CD3+ T-cells in EEM-treated samples (P = 0.0171). From 1855 upregulated genes, 3 immune-related secreted genes (C1QTNF4, FAM19A4, and GREM2) were identified. Flow cytometric analysis showed a significant increase in CD11b+, CX3RC1+ microglia (P = 0.0306) and CD45+, CD11b+ tumor-associated myeloid cells (TAMCs) (P = 0.0192) at 3 hours post-EEM. CONCLUSIONS EEM treatment promotes an inflammatory TME with increased intratumoral microglia, TAMCs and T-cell infiltration. These inflammatory changes may prolong survival of CT-2A glioma-bearing mice.

Silver nanoparticle induced immunogenic cell death can improve immunotherapy

Cancer immunotherapy is often hindered by an immunosuppressive tumor microenvironment (TME). Various strategies are being evaluated to shift the TME from an immunologically ‘cold’ to ‘hot’ tumor and hereby improve current immune checkpoint blockades (ICB). One particular hot topic is the use of combination therapies. Here, we set out to screen a variety of metallic nanoparticles and explored their in vitro toxicity against a series of tumor and non-tumor cell lines. For silver nanoparticles, we also explored the effects of core size and surface chemistry on cytotoxicity. Ag-citrate-5 nm nanoparticles were found to induce high cytotoxicity in Renca cells through excessive generation of reactive oxygen species (ROS) and significantly increased cytokine production. The induced toxicity resulted in a shift of the immunogenic cell death (ICD) marker calreticulin to the cell surface in vitro and in vivo. Subcutaneous Renca tumors were treated with anti-PD1 or in combination with Ag-citrate-5 nm. The combination group resulted in significant reduction in tumor size, increased necrosis, and immune cell infiltration at the tumor site. Inhibition of cytotoxic CD8 + T cells confirmed the involvement of these cells in the observed therapeutic effects. Our results suggest that Ag-citrate-5 nm is able to promote immune cell influx and increase tumor responsiveness to ICB therapies.