Extent Of Immune Cell Infiltration Research Articles

FAM171B as a Novel Biomarker Mediates Tissue Immune Microenvironment in Pulmonary Arterial Hypertension.

The purpose of this study was to uncover potential diagnostic indicators of pulmonary arterial hypertension (PAH), evaluate the function of immune cells in the pathogenesis of the disease, and find innovative treatment targets and medicines with the potential to enhance prognosis. Gene Expression Omnibus was utilized to acquire the PAH datasets. We recognized differentially expressed genes (DEGs) and investigated their functions utilizing R software. Weighted gene coexpression network analysis, least absolute shrinkage and selection operators, and support vector machines were used to identify biomarkers. The extent of immune cell infiltration in the normal and PAH tissues was determined using CIBERSORT. Additionally, the association between diagnostic markers and immune cells was analyzed. In this study, 258DEGs were used to analyze the disease ontology. Most DEGs were linked with atherosclerosis, arteriosclerotic cardiovascular disease, and lung disease, including obstructive lung disease. Gene set enrichment analysis revealed that compared to normal samples, results from PAH patients were mostly associated with ECM-receptor interaction, arrhythmogenic right ventricular cardiomyopathy, the Wnt signaling pathway, and focal adhesion. FAM171B was identified as a biomarker for PAH (area under the curve = 0.873). The mechanism underlying PAH may be mediated by nave CD4 T cells, resting memory CD4 T cells, resting NK cells, monocytes, activated dendritic cells, resting mast cells, and neutrophils, according to an investigation of immune cell infiltration. FAM171B expression was also associated with resting mast cells, monocytes, and CD8 T cells. The results suggest that PAH may be closely related to FAM171B with high diagnostic performance and associated with immune cell infiltration, suggesting that FAM171B may promote the progression of PAH by stimulating immune infiltration and immune response. This study provides valuable insights into the pathogenesis and treatment of PAH.

Analysis of combination therapy of immune checkpoint inhibitors in osteosarcoma.

One of the most common primary bone malignant tumors is osteosarcoma (OS), possessing a high tendency of local invasion and distant metastasis. Although surgery combined with chemotherapy can extend the patients’ survival time, the prognosis for most patients with metastases or relapses is poor. Immunotherapy has been proved to be a promising treatment alternative for malignant tumors. Although there is a significant amount of animal- and cell-based evidence supporting the relationship between immune checkpoint inhibitors (anti-PD-1, anti-PD-L1, anti-CTLA-4) and cancers, no pan-cancer analysis is available. Simultaneously, immune checkpoint inhibitors have demonstrated satisfactory clinical results in some tumors; however, only a small fraction of patients with certain cancer types have been benefitted. Therefore, based on the TCGA dataset, we first explored the potential roles of immune checkpoints in 33 tumors. Programmed death receptor 1 (PD-1), programmed cell death ligand 1 (PD-L1), and cytotoxic T lymphocyte antigen 4 (CTLA-4) were not consistently expressed in the same direction in all tumors; however, the direction of expression change was the same in most immune cells. Although there is no well-established relationship between the expression of PD-1/PD-L1/CTLA-4 genes and the prognosis of patients with sarcomas, their interaction and extent of immune cell infiltration into sarcomas are probably the key determinants of therapeutic response. Our first pan-cancer study provides a relatively comprehensive understanding of immune checkpoint inhibitors in different sarcomas.

Identification of Effective Diagnostic Biomarkers and Immune Cell Infiltration in Atopic Dermatitis by Comprehensive Bioinformatics Analysis

Background: Atopic dermatitis (AD) is a dermatological disorder characterized by symptoms such as chronically inflamed skin and frequently intolerable itching. The mechanism underlying AD development is still unclear. Our study aims to identify the diagnostic and therapeutic biomarkers for AD and provide insight into immune mechanisms at the molecular level through bioinformatics analysis. Methods: The GSE6012, GSE32924, and GSE36842 gene expression profiles were obtained for analysis from the Gene Expression Omnibus database. Differentially expressed genes (DEGs) were segregated using the “Batch correction” and “RobustRankAggreg” methods. Weighted gene co-expression network analysis (WGCNA) was performed to screen for module genes with AD traits. Then, common DEGs (co-DEGs) were screened out via combined differential expression analysis and WGCNA. Functional enrichment analysis was performed for these co-DEGs using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG), followed by protein-protein interaction network analysis. Candidate hub genes were identified using the “cytoHubba” plugin in Cytoscape, and their value for AD diagnosis was validated using receiver operating characteristic curve analysis in the external database GSE120721. Immunohistochemical staining was performed for further validation. The CIBERSORT algorithm was used to evaluate skin samples obtained from healthy controls (HCs) and lesions of AD patients, to determine the extent of immune cell infiltration. The association between the identified hub genes and significant differential immune cells was analyzed using Pearson correlation analysis. Results: A total of 259 DEGs were acquired from the intersection of DEGs obtained by the two independent procedures, and 331 AD-trait module genes were separated out from the blue module via WGCNA analysis. Then, 169 co-DEGs arising from the intersection of the 259 DEGs and the 331 AD-trait module genes were obtained. We found that co-DEGs were significantly enhanced in the type I interferon and IL-17 signal transduction pathways. Thirteen potential hub genes were identified using Cytoscape. Five hub genes (CCR7, CXCL10, IRF7, MMP1, and RRM2) were identified after screening via external dataset validation and immunohistochemical analysis. We also identified four significant differential immune cells, i.e., activated dendritic cells, plasma cells, resting mast cells, and CD4+ naïve T cells, between AD patients and HCs. Moreover, the relationship between the identified hub genes and significant differential immune cells was analyzed. The results showed that the CCR7 expression level was positively correlated with the number of CD4+ naïve T cells (R = 0.42, p = 0.011). Conclusion: CCR7, CXCL10, IRF7, MMP1, and RRM2 could be potential diagnostic and therapeutic biomarkers for AD. CCR7 expression level was positively correlated with the number of CD4+ naïve T cells in AD. These findings need to be corroborated in future studies.

Clinical Diagnostic and Prognostic Potential of NDRG1 and NDRG2 in Hepatocellular Carcinoma Patients.

BackgroundPrimary liver cancer is still the most common lethal malignancy. The N-myc downstream-regulated gene family (NDRG1–4) is a group of multifunctional proteins associated with carcinogenesis. However, systematic evaluation of the diagnostic and prognostic values of NDRG1 or NDRG2 expression in liver cancer is poorly investigated.MethodThe gene expression matrix of liver hepatocellular carcinoma (LIHC) was comprehensively analyzed by the “limma” and “Dseq2” R packages. The Gene Ontology (GO) and Gene Set Enrichment Analysis (GSEA) were used to identify the biological functional differences. A single-sample GSEA (ssGSEA) was conducted to quantify the extent of immune cell infiltration. Finally, the clinical and prognostic information of LIHC patients was systematically investigated using Kaplan–Meier analysis and logistic and Cox regression analysis.ResultsCompared with normal tissues, NDRG1 expression was higher, whereas NDRG2 expression was lower in tumor tissues (P <0.001). The area under the receiver operator characteristic curve (AUROC) of NDRG1 and NDRG2 for LIHC was 0.715 and 0.799, respectively. Kaplan–Meier analysis revealed that NDRG1 and NDRG2 were independent clinical prognostic biomarkers for the overall survival (OS, P = 0.001 and 2.9e−06), progression-free interval (PFI, P = 0.028 and 0.005) and disease-specific survival (DSS, P = 0.027 and P <0.001). The C-indexes and calibration plots of the nomogram suggest that NDRG1 and NDRG2 have an effective predictive performance for OS (C-index: 0.676), DSS (C-index: 0.741) and PFI (C-index: 0.630) of liver cancer patients. The mutation rate of NDRG1 in liver cancer reached up to 14%, and DNA methylation levels of NDRG1 and NDRG2 promoters correlated significantly with clinical prognosis.ConclusionsThe mRNA expression and DNA methylation of NDRG superfamily members have the potential for LIHC diagnosis and prognosis via integrative analysis from multiple cohorts.

Diagnostic gene biomarkers for predicting immune infiltration in endometriosis

ObjectiveTo determine the potential diagnostic markers and extent of immune cell infiltration in endometriosis (EMS).MethodsTwo published profiles (GSE7305 and GSE25628 datasets) were downloaded, and the candidate biomarkers were identified by support vector machine recursive feature elimination analysis and a Lasso regression model. The diagnostic value and expression levels of biomarkers in EMS were verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR) and western blotting, then further validated in the GSE5108 dataset. CIBERSORT was used to estimate the composition pattern of immune cell components in EMS.ResultsOne hundred and fifty-three differential expression genes (DEGs) were identified between EMS and endometrial with 83 upregulated and 51 downregulated genes. Gene sets related to arachidonic acid metabolism, cytokine–cytokine receptor interactions, complement and coagulation cascades, chemokine signaling pathways, and systemic lupus erythematosus were differentially activated in EMS compared with endometrial samples. Aquaporin 1 (AQP1) and ZW10 binding protein (ZWINT) were identified as diagnostic markers of EMS, which were verified using qRT-PCR and western blotting and validated in the GSE5108 dataset. Immune cell infiltrate analysis showed that AQP1 and ZWINT were correlated with M2 macrophages, NK cells, activated dendritic cells, T follicular helper cells, regulatory T cells, memory B cells, activated mast cells, and plasma cells.ConclusionAQP1 and ZWINT could be regarded as diagnostic markers of EMS and may provide a new direction for the study of EMS pathogenesis in the future.

Comprehensive Landscape of Prognostic Significance and Immune Characteristics of Myosins in Squamous Cell Carcinoma of the Head and Neck.

Myosin superfamily, a large and diverse family of molecular motors important for cell motility and migration, has been illustrated to play contradictory roles during the development of several kinds of tumors. However, the function and prognostic values of MYOs in head and neck squamous cell carcinoma (HNSCC) still remain largely unknown. In the current manuscript, the expression levels and clinical data of MYOs in HNSCC were investigated by online databases, including Oncomine, GEPIA, GEO, TCGA, HPA, UALCAN, Kaplan-Meier plotter, and CancerSEA; we found that the expression levels of MYO1B, MYO5A, and MYO10 were significantly elevated in HNSCC tissues, which were also correlated with the unfavorable overall survival (OS) of the patients. Furthermore, MYO1B/MYO5A/MYO10 interacting genes were identified, and the protein-protein interaction (PPI) networks were constructed by STRING and GeneMANIA. The enrichment analysis revealed that MYO1B/MYO5A/MYO10 associated genes mainly participated in cell metastasis and EMT processes, which were also confirmed by cell functional experiments. At last, the ssGSEA method was conducted to investigate the extent of immune cell infiltration, and we found that both the expression of MYO1B/MYO5A/MYO10 were closely correlated with the infiltration of immune cells in HNSCC. These findings implied that MYO1B, MYO5A, and MYO10 as novel prognostic factors for HNSCC and provided new strategy for HNSCC treatment.

Aconitate Decarboxylase 1 Deficiency Exacerbates Mouse Colitis Induced by Dextran Sodium Sulfate.

Ulcerative colitis is a complex inflammatory bowel disorder disease that can induce rectal and colonic dysfunction. Although the prevalence of IBD in Western countries is almost 0.5% of the general population, genetic causes are still not fully understood. In a recent discovery, itaconate was found to function as an immune-modulating metabolite in mammalian immune cells, wherein it is synthesized as an antimicrobial compound from the citric acid cycle intermediate cis-aconitic acid. However, the association between the Acod1 (Aconitate decarboxylase 1)-itaconate axis and ulcerative colitis has rarely been studied. To elucidate this, we established a DSS-induced colitis model with Acod1-deficient mice and then measured the mouse body weights, colon lengths, histological changes, and cytokines/chemokines in the colon. We first confirmed the upregulation of Acod1 RNA and protein expression levels in DSS-induced colitis. Then, we found that colitis symptoms, including weight loss, the disease activity index, and colon shortening, were worsened by the depletion of Acod1. In addition, the extent of intestinal epithelial barrier breakdown, the extent of immune cell infiltration, and the expression of proinflammatory cytokines and chemokines in Acod1-deficient mice were higher than those in wild-type mice. Finally, we confirmed that 4-octyl itaconate (4-OI) alleviated DSS-induced colitis in Acod1-deficient mice and decreased the expression of inflammatory cytokines and chemokines. To our knowledge, this study is the first to elucidate the role of the Acod1-itaconate axis in colitis. Our data clearly showed that Acod1 deletion resulted in severe DSS-induced colitis and substantial increases in inflammatory cytokine and chemokine levels. Our results suggest that Acod1 may normally play an important regulatory role in the pathogenesis of colitis, demonstrating the potential for novel therapies using 4-OI.

Accounting for B-cell Behavior and Sampling Bias Predicts Anti-PD-L1 Response in Bladder Cancer.

Cancer immunotherapy is predominantly based on T cell-centric approaches. At the same time, the adaptive immune response in the tumor environment also includes clonally produced immunoglobulins and clonal effector/memory B cells that participate in antigen-specific decisions through their interactions with T cells. Here, we investigated the role of infiltrating B cells in bladder cancer via patient dataset analysis of intratumoral immunoglobulin repertoires. We showed that the IgG1/IgA ratio is a prognostic indicator for several subtypes of bladder cancer and for the whole IMVigor210 anti-PD-L1 immunotherapy study cohort. A high IgG1/IgA ratio associated with the prominence of a cytotoxic gene signature, T-cell receptor signaling, and IL21-mediated signaling. Immunoglobulin repertoire analysis indicated that effector B-cell function, rather than clonally produced antibodies, was involved in antitumor responses. From the T-cell side, we normalized a cytotoxic signature against the extent of immune cell infiltration to neutralize the artificial sampling-based variability in immune gene expression. Resulting metrics reflected proportion of cytotoxic cells among tumor-infiltrating immune cells and improved prediction of anti-PD-L1 responses. At the same time, the IgG1/IgA ratio remained an independent prognostic factor. Integration of the B-cell, natural killer cell, and T-cell signatures allowed for the most accurate prediction of anti-PD-L1 therapy responses. On the basis of these findings, we developed a predictor called PRedIctive MolecUlar Signature (PRIMUS), which outperformed PD-L1 expression scores and known gene signatures. Overall, PRIMUS allows for reliable identification of responders among patients with muscle-invasive urothelial carcinoma, including the subcohort with the low-infiltrated "desert" tumor phenotype.

CAV1 is a prognostic predictor for patients with idiopathic pulmonary fibrosis and lung cancer

The extremely high mortality of both lung cancer and Idiopathic pulmonary fibrosis (IPF) is a global threat. Early detection and diagnosis can reduce their mortality. Since fibrosis is a necessary process of cancer, identifying the common potential prognostic genes involved in these two diseases will significantly contribute to disease prevention and targeted therapy. Microarray datasets of IPF and lung cancer were extracted from the GEO database. GEO2R was exploited to retrieve the differentially expressed genes (DEGs). The intersecting DEGs were obtained by the Venn tool. DAVID tools were used to perform GO and KEGG pathway enrichment analysis of DEGs. Then, the Kaplan-Meier plotter was employed to determine the prognostic value and verify the expression, pathological stage, and phosphorylation level of the hub gene in the TCGA and GTEx database. Finally, the extent of immune cell infiltration in lung cancer was estimated by the TIMER2 tool. The Venn diagram revealed 1 upregulated gene and 15 downregulated genes from GSE32863, GSE43458, GSE118370, and GSE75037 of lung cancer, as well as GSE2052 and GSE53845 of IPF. CytoHubba identified the top three genes [TEK receptor tyrosine kinase (TEK), caveolin 1 (CAV1), and endomucin (EMCN)] as hub genes following the connectivity degree. Survival analysis claimed the association of only TEK and CAV1 expression to both overall survival (OS) and first progression (FP). Pathological stage analyses revealed the relationship of only CAV1 expression to the pathological stage and the significant correlation of only CAV1 phosphorylation expression level for lung cancer. Furthermore, a statistically positive correlation was observed between the immune infiltration of cancer-associated fibroblasts, endothelial, and neutrophils with the CAV1 expression in lung cancer, whereas the contradictory result was noted for the immune infiltration of T cell follicular helper. Early detection and diagnostic potential of lung cancer are ameliorated by the combined selection of key genes among IPF and lung cancer.

Tumor Heterogeneity and Consequences for Bladder Cancer Treatment.

Simple SummaryBladder cancer is a heterogeneous disease that is composed of epithelia with varying transcriptional, mutational and lineage signatures. The epithelia of bladder tumors can also undergo pronounced changes in transcriptional and phenotypical qualities in response to progression, treatment related stresses and cues from the tumor microenvironment (TME). We hypothesize that changes in epithelial tumor heterogeneity (EpTH) occur due to the evolving content of epithelial subpopulations through both Darwinian and Lamarckian-like natural selection processes. We further conjecture that lineage-defined subpopulations can change through nongenomic and genomic cellular mechanisms that include cellular plasticity and acquired driver mutations, respectively. We propose that such processes are dynamic and contribute towards clinical treatment challenges including progression to drug resistance. In this article, we assess mechanisms that may support dynamic tumor heterogeneity with the overall goal of emphasizing the application of these concepts to the clinical setting.Acquired therapeutic resistance remains a major challenge in cancer management and associates with poor oncological outcomes in most solid tumor types. A major contributor is tumor heterogeneity (TH) which can be influenced by the stromal; immune and epithelial tumor compartments. We hypothesize that heterogeneity in tumor epithelial subpopulations—whether de novo or newly acquired—closely regulate the clinical course of bladder cancer. Changes in these subpopulations impact the tumor microenvironment including the extent of immune cell infiltration and response to immunotherapeutics. Mechanisms driving epithelial tumor heterogeneity (EpTH) can be broadly categorized as mutational and non-mutational. Mechanisms regulating lineage plasticity; acquired cellular mutations and changes in lineage-defined subpopulations regulate stress responses to clinical therapies. If tumor heterogeneity is a dynamic process; an increased understanding of how EpTH is regulated is critical in order for clinical therapies to be more sustained and durable. In this review and analysis, we assess the importance and regulatory mechanisms governing EpTH in bladder cancer and the impact on treatment response.

Abstract 122: Highly multiplexed, spatially-resolved tissue imaging of genetically engineered mouse models of cancer to discover and characterize immune regulators of tumorigenesis

Abstract Despite the encouraging success of immunotherapy for certain malignancies, most patients with solid tumors do not yet benefit from such therapies. It is therefore critical that we identify factors dictating responsiveness to immunotherapy by more completely characterizing tumor-immune interactions. Even though immunotherapies are used in humans, in-depth analysis of murine models is essential for a mechanistic understanding of the crosstalk among tumor, immune, and stromal components of the tumor microenvironment (TME): only animal models have the necessary manipulability and reproducibility for causal, mechanistic studies. However, murine modelling must be combined with spatially resolved analytical methods such as highly multiplexed tissue imaging that enable accurate characterization of the TME at a single-cell level. Here we use tissue cyclic immunofluorescence (t-CyCIF) multiplexed imaging to characterize the immune microenvironment of a mouse lung adenocarcinoma model initiated via lentiviral delivery of Cre recombinase into the lungs of KrasLSL-G12D/+;p53fl/fl (KP) mice. Using this new platform, we identify tumor cells and immune cell types (dendritic cells, NK cells, macrophages, B cells, helper T cells, regulator T cells and cytotoxic T cells). We characterize the effects of expressing tumor antigen (i.e., LucOS), of CRISPRa based upregulation of the chemokines (e.g., CXCL10), and of combination immune check point inhibitor treatments (e.g., one-week treatment with anti-PD-1 and anti-CTLA-4 (PC)). Remarkably the total immune composition of the mouse lungs remains relatively unchanged following these perturbations, but there are marked changes in the immune cell localization in tumor nodules, in the number and size of immune cell networks and in the functional activation states of cytotoxic T cells. For example, one week of PC treatment did not affect tumor burden and did not change the extent of immune cell infiltration however, it did drastically change cytotoxic T cell phenotypes with increased effector phenotypes (i.e., GzmB and Perforin expression and proliferation) and decreased exhaustion-like phenotypes (i.e., PD-1 and Tim-3 expression). Lymphocyte networks decreased in number but were closer to tumors. Using high-dimensional protein expression data to characterize GEMM models following in situ genetic or therapeutic perturbation is a powerful new platform to investigate tumor-immune interactions. Citation Format: Giorgio Gaglia, Megan Burger, Claire Ritch, Danae Argyropoulou, Yang Dai, Shannon Coy, Jia-Ren Lin, Peter Sorger, Tyler Jacks, Sandro Santagata. Highly multiplexed, spatially-resolved tissue imaging of genetically engineered mouse models of cancer to discover and characterize immune regulators of tumorigenesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 122.

Decreased infiltration of CD4+ Th1 cells indicates a good response to ursodeoxycholic acid (UDCA) in primary biliary cholangitis

BackgroundPrimary biliary cholangitis (PBC) is characterized by nonsuppurative destructive cholangitis and is thought to be an autoimmune disorder. Currently, ursodeoxycholic acid (UDCA) is the only FDA approved first-line therapy for PBC, but up to nearly one-third of patients do not achieve a complete response to this treatment. Adaptive immune cells, including T cells and B cells, have been found in the portal tracts and the bile duct epithelium and play a role in the pathogenesis of PBC, but the importance of these cells for evaluating the therapeutic response to UDCA in PBC has not yet been studied. MethodsIn this study, we collected liver puncture biopsy specimens from 34 matched patients with PBC before and after UDCA treatment and investigated the relationship between the infiltration of adaptive immune cells and the treatment response to UDCA. The extent of immune cell infiltration was determined by immunohistochemical analysis. Responses were defined based on Paris-I criteria. ResultsAfter 1 year of treatment, 25/34 patients responded to UDCA treatment according to Paris-I criteria (responders), and 9/34 patients were nonresponders. Immunohistochemical analysis showed that UDCA responders exhibited significantly less CD4+ T cell infiltration after UDCA treatment than before (50.4 ± 7.5/HPF vs 30.0 ± 7.9/HPF, P = 0.002). In contrast, UDCA nonresponders exhibited significantly more CD4+ T cell infiltration after UDCA treatment than before (32.2 ± 8.0/HPF vs 75.0 ± 13.9/HPF, P = 0.045). Moreover, patients who exhibited a reduction in CD4+ T cell infiltration after UDCA treatment had a higher response rate than those that exhibited an increase in CD4+ T cell infiltration (85.7 % vs 53.8 %, P = 0.041). However, CD3+ T cell, CD8+ T cell, and CD20+ B cell infiltration was not significantly different before and after treatment in either UDCA responders or nonresponders. Furthermore, we found that the number of infiltrating T-bet+ Th1 cells was much lower after UDCA treatment than before in responders (10.5 ± 5.7/HPF vs. 5.16 ± 4.0/HPF, P = 0.0214) but much higher in nonresponders after treatment than before (1.89±1.2/HPF vs. 12.3±5.4/HPF, P = 0.043). However, there was no difference in the extent of GATA3+ Th2 or FOXP3+ Treg infiltration before and after treatment in either UDCA responders or nonresponders. ConclusionCollectively, our results suggest that a decrease in the number of liver-infiltrating CD4+ Th1 cells is associated with a good response of PBC patients to UDCA treatment. Immunohistochemical analysis of CD4 and T-bet in PBC liver specimens may be a potential approach for evaluating the therapeutic response to UDCA.

Enhanced B7-H4 expression in gliomas with low PD-L1 expression identifies super-cold tumors

BackgroundCharacterizing expression profiles of different immune checkpoint molecules are promising for personalized checkpoint inhibitory immunotherapy. Gliomas have been shown as potential targets for immune checkpoint inhibitors recently. Our study was...

TMIC-11. ENHANCED B7-H4 EXPRESSION IN GLIOMAS WITH LOW PD-L1 EXPRESSION IDENTIFIES COLD TUMORS

Abstract The expression profiles of different immune checkpoint molecules are promising for triaging personalized targeted immunotherapy. Gliomas have been shown as potential targets for immune checkpoint inhibitors. Our study was performed to determine co-expression levels of two major B7 immune molecules PD-L1 and B7-H4 in gliomas in which both have demonstrated to inhibit anti-tumor host immunity. We assessed tumor issues from primary gliomas stage II–IV(n=505) by immunohistochemistry (IHC) for protein levels of both PD-L1 and B7-H4. Gene co-expression analysis assessing clusters based on extent of PD-L1/B7-H4 classifier genes expression were investigated in two transcriptome datasets (TCGA and CGGA) to validate IHC expression profiles. Here, we found that 61% and 54% of patient samples were positive for PD-L1 and B7-H4 respectively, whereby high-expression of either protein was limited to 23% and 20% respectively. Co-expression of PD-L1 and B7-H4 in high levels was limited to 2%. Comparable results were seen in RNA-seq datasets when PD-L1 mRNA expression level corelated negatively with B7-H4. Gene co-expression modules clustered in each grade gliomas without Double-High modules (glioma cluster with high mRNA expression of both PD-L1 and B7-H4 classifier genes) also verified restricted co-expression pattern. B7-H4 mRNA expression level had negative correlation with extent of immune cell infiltration, including tumor-infiltrating lymphocytes (TILs), and High-B7-H4 module gliomas (high B7-H4 but low PD-L1 classifier genes expression) were related to a cold tumor with less TILs. The majority of gliomas express PD-L1 or B7-H4, however, co-expression of both at high levels is minimal. The High-B7-H4 module was significantly lacking in TILs, suggesting that B7-H4 might inhibit T cell trafficking into the central nervous system (CNS). This study demonstrates that PD-L1 expression alone is not fully informative in gliomas for immune targeted or active-specific immunotherapy, and PD-L1 and B7-H4 probably inhibit different aspects of the T cell functions.

The Immune Contexture Associates with the Genomic Landscape in Lung Adenomatous Premalignancy.

Epithelial cells in the field of lung injury can give rise to distinct premalignant lesions that may bear unique genetic aberrations. A subset of these lesions may escape immune surveillance and progress to invasive cancer; however, the mutational landscape that may predict progression has not been determined. Knowledge of premalignant lesion composition and the associated microenvironment is critical for understanding tumorigenesis and the development of effective preventive and interception strategies. To identify somatic mutations and the extent of immune cell infiltration in adenomatous premalignancy and associated lung adenocarcinomas, we sequenced exomes from 41 lung cancer resection specimens, including 89 premalignant atypical adenomatous hyperplasia lesions, 15 adenocarcinomas in situ, and 55 invasive adenocarcinomas and their adjacent normal lung tissues. We defined nonsynonymous somatic mutations occurring in both premalignancy and the associated tumor as progression-associated mutations whose predicted neoantigens were highly correlated with infiltration of CD8+ and CD4+ T cells as well as upregulation of PD-L1 in premalignant lesions, suggesting the presence of an adaptive immune response to these neoantigens. Each patient had a unique repertoire of somatic mutations and associated neoantigens. Collectively, these results provide evidence for mutational heterogeneity, pathway dysregulation, and immune recognition in pulmonary premalignancy.Significance: These findings identify progression-associated somatic mutations, oncogenic pathways, and association between the mutational landscape and adaptive immune responses in adenomatous premalignancy.See related commentary by Merrick, p. 4811.

Enhanced B7-H4 Expression in Gliomas With Low PD-L1 Expression Identifies Cold Tumors

Abstract INTRODUCTION The expression profiles of different immune checkpoint molecules are promising for triaging personalized targeted immunotherapy. Our study was performed to determine co-expression levels of 2 major B7 immune molecules, PD-L1 and B7-H4, in gliomas where both have demonstrated to inhibit antitumor host immunity. METHODS We assessed tumor issues from primary gliomas stage II to IV (n = 505) by immunohistochemistry (IHC) for protein levels of both PD-L1 and B7-H4. Gene co-expression analysis assessing clusters based on extent of PD-L1/B7-H4 classifier genes expression were investigated in 2 transcriptome datasets (TCGA and CGGA) to validate IHC expression profiles and explore properties of the glioma immune microenvironment among specific co-expression PD-L1/B7-H4 cluster groups. RESULTS PD-L1 was detected in 61% of patients whereby 23% expressed high levels. B7-H4 was expressed in 54% whereby 20% were identified as high expression. Co-expression of PD-L1 and B7-H4 in high levels was limited to 2% cases. Comparable results were seen in RNA-sequencing datasets when PD-L1 mRNA expression level corelated negatively with B7-H4. Gene co-expression modules clustered in each grade gliomas without double-high modules (gliomas cluster with high mRNA expression of both PD-L1 and B7-H4 classifier genes) also verified restricted coexpression pattern. B7-H4 mRNA expression level had negative correlation with extent of immune cell infiltration, including tumor-infiltrating lymphocytes (TILs), and high-B7-H4 module gliomas (high B7-H4 but low PD-L1 classifier genes expression) was related to a cold tumor with less TILs. CONCLUSION The majority of gliomas express PD-L1 or B7-H4, however, co-expression of both at high levels is minimal. The high-B7-H4 module was significantly lacking in TILs, suggesting that B7-H4 might inhibit T cell trafficking into the central nervous system (CNS). This study demonstrates that PD-L1 expression alone is not fully informative in gliomas for immune targeted or active-specific immunotherapy, and PD-L1 and B7-H4 probably inhibit different aspects of the T cell functions.

Better prognostic determination and feature characterization of cutaneous melanoma through integrative genomic analysis.

Melanoma is the most dangerous type of skin cancer and has highly heterogeneous features. Despite progress in melanoma classification, interpatient heterogeneity remains difficult to predict, especially in terms of long-term survival. Here, based on mRNA-seq, miRNA-seq and DNA methylation data from 447 cutaneous melanoma patients in the Cancer Genome Atlas, we performed integrative and single-dataset clustering analyses. A novel group of patients was identified, including 301 with better, 55 with poorer and 91 with intermediate prognoses. Immune genes were upregulated in the better prognostic group, and higher immune scores (representing a greater extent of immune cell infiltration into tumor tissues) were associated with better prognoses. Higher expression of 115 genes was determined to predict better outcomes. The better prognostic group also exhibited DNA hypomethylation, and immune pathways were enriched among the hypomethylated genes. Using exome-seq data from the same patients, we observed that the better prognostic group harbored the highest number of mutations. The mutational signature in the better prognostic group was associated with ultraviolet light exposure. These integrated investigations have potential therapeutic significance, as they clarify the molecular heterogeneity of cutaneous melanoma and enhance its classification.

Identification of a high-risk subtype of intestinal-type Japanese gastric cancer by quantitative measurement of the luminal tumor proportion.

BackgroundWe hypothesized that the relative proportion of tumor (PoT) at the luminal surface can predict gastric cancer (GC) patient survival.MethodsWe measured the luminal PoT in resection specimens from 231 GC patients with stage II/III disease who had surgery at the Kanagawa Cancer Center, Yokohama, Japan. Tissue microarrays were used to assess the extent of immune cell infiltration by CD45 immunohistochemistry. Results were related to histopathological features and patient overall survival (OS).ResultsPoT was significantly lower in diffuse‐type (30%) compared to intestinal‐type GC (41%), P = 0.03. Patients with low PoT intestinal‐type GC survived significantly longer than patients with high PoT intestinal‐type GC (5 years OS: 78% vs 47%, P = 0.0112). Low PoT was an independent favorable prognostic factor in multivariate analysis in intestinal‐type GC. Low PoT was correlated with high content of CD45‐positive immune cells (P = 0.035). There was no relationship between PoT and survival in diffuse‐type GC.ConclusionsThis is the first study to identify a subgroup of patients with stage II/III intestinal‐type GC at high risk of recurrence by measuring PoT at the luminal surface. The relationship between PoT and immune cell content provides an initial insight into potential underlying biological mechanisms.

Pan-cancer deconvolution of tumour composition using DNA methylation

The nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated analysis of tumour composition and genomics across a wide spectrum of solid cancers. Initially studying head and neck squamous cell carcinoma, we identify two distinct tumour subgroups: ‘immune hot’ and ‘immune cold’, which display differing prognosis, mutation burden, cytokine signalling, cytolytic activity and oncogenic driver events. We demonstrate the existence of such tumour subgroups pan-cancer, link clonal-neoantigen burden to cytotoxic T-lymphocyte infiltration, and show that transcriptional signatures of hot tumours are selectively engaged in immunotherapy responders. We also find that treatment-naive hot tumours are markedly enriched for known immune-resistance genomic alterations, potentially explaining the heterogeneity of immunotherapy response and prognosis seen within this group. Finally, we define a catalogue of mediators of active antitumour immunity, deriving candidate biomarkers and potential targets for precision immunotherapy.

Abstract 5353: Single cell RNA sequencing of pancreatic ductal adenocarcinoma reveals tumor heterogeneity

Abstract Background: Pancreatic ductal adenocarcinoma (PDAC) accounts for ~95% of pancreatic cancer cases and is currently the 3rd leading cause of adult cancer deaths in the US. Due to the lack of methods for early detection and limited treatment options, PDAC has a dismal 5-year survival rate at just &amp;lt;9%. The desmoplastic PDAC tumor microenvironment (TME) is complex and heterogeneous. With recent advances in technology, the characterization of tumors to investigate cellular diversity and evolution in cancer is rapidly accelerating. Here we employed single cell RNA sequencing (scRNA-Seq) to profile transcriptomes of individual cells from dissociated pancreatic tumors isolated from either patients or transgenic mice developing spontaneous PDAC (KPC). This approach elucidated the cellular makeup of individual tumor to reveal distinct cell types like epithelial, endothelial and immune cells, cancer associated fibroblasts (CAFs) and cells undergoing epithelial-to-mesenchymal transition (EMT). Deregulated pathways specific to distinctly identified cell populations were also mapped. Methods: Freshly harvested human or mouse PDAC tumors were mechanically and enzymatically dissociated to single cells using a Miltenyi gentleMACS Tissue Dissociator. The 10X Genomics Chromium Single Cell 3′ Solution was employed for capture, amplification and labeling of mRNA from single cells and for library preparation. scRNA-Seq was performed on Illumina HiSeq 2500. Custom R packages were used for clustering and bioinformatics data analyses. Results: Viability of single cell suspensions used for library preps from all samples was &amp;gt;81%. By unsupervised clustering of the scRNA-Seq matrix and using known signature genes for various cell types we revealed the cellular heterogeneity in a human PDAC to identify distinct cell types. These included epithelial tumor cells (EPCAM+, KRT19+); CD133+ tumor stem cells; CAFs (COL5A1+, COL6A2+, SPARC+); endothelial cells CDH5+ VWF+; and CD45 (PTPRC)+ immune cells also positive for CD3D, CD2, FCGR2A; and cells undergone EMT (CDH2+, ITGA5+, SNAI2+). Using a similar strategy, mouse PDAC diversity was represented by epithelial and EMT tumor cells, CAFs, endothelial cells, macrophages and MDSCs. KRAS and glycolysis signaling pathways in epithelial tumor cells, while hypoxia in the EMT cluster were up regulated. KPC tumors differed in the extent of immune cell infiltration, with a low influx in the smaller versus large tumor, both perhaps representing distinct stages of tumor progression. Conclusions: Our data supports high throughput scRNA-Seq of solid tumors like PDAC as a powerful method to probe and elucidate the underlying tumor heterogeneity. Understanding diversity and complexity of the PDAC TME in individual tumors may help identify unique therapeutic targets and potentially inform treatment/maintenance strategies for patients with advanced disease. Citation Format: Pawan Noel, Wei Lin, Erkut Borazanci, Albert Amini, Ruben Muñoz, Emily Rodela, Serina Ng, Daniel Von Hoff, Haiyong Han. Single cell RNA sequencing of pancreatic ductal adenocarcinoma reveals tumor heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5353.