Comprehensive analysis of PD-L1 expression, tumor-infiltrating lymphocytes, and tumor microenvironment in LUAD: differences between Asians and Caucasians

Abstract Backgrounds The characteristics of programmed cell death protein-1 (PD-L1) expression, tumor-infiltrating lymphocytes (TILs), and tumor microenvironment (TME) in lung adenocarcinoma (LUAD) patients are closely related to immunotherapy, and there are differences between Asians and Caucasians. Methods Acquire the transcriptome data of the Cancer Genome Atlas and Chinese LUAD patients. R software was used to analyze the differential expression of genes, prognosis, and gene function. Use CIBERSORT for TIL-related analysis and ESTIMATE for TME-related analysis. Results The expression of PD-L1 in tumor tissues of Caucasian LUAD patients was lower than that in normal tissues, while there was no significant difference in Asians. There was no statistical difference between PD-L1 expression and prognosis. The composition of TILs between Caucasian and Asian LUAD patients was quite different. There was no correlation between TILs and prognosis in Caucasians. However, the higher content of resting mast cells indicated a better prognosis in Asians. The Caucasian patients with higher immune and estimate scores had a better prognosis (p = 0.021, p = 0.025). However, the Asian patients with a higher estimate score had a worse prognosis (p = 0.024). The high expression of COL5A2 (p = 0.046, p = 0.027) and NOX4 (p = 0.020, p = 0.019) were both associated with the poor prognosis in Caucasians and Asians. Conclusion There are many differences in the characteristics of PD-L1 expression, TILs, and TME between Caucasian and Asian LUAD patients. This provides a certain hint for the selection of specific immunotherapy strategies separately for Caucasian and Asian LUAD patients.

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Predicted CD4+ T cell infiltration levels could indicate better overall survival in sarcoma patients

Journal of International Medical Research ◽

10.1177/0300060520981539 ◽

2021 ◽

Vol 49 (1) ◽

pp. 030006052098153

Author(s):

Qing Bi ◽

Yang Liu ◽

Tao Yuan ◽

Huizhen Wang ◽

Bin Li ◽

...

Keyword(s):

Overall Survival ◽

T Cell ◽

Survival Data ◽

Tumor Infiltrating Lymphocytes ◽

The Cancer Genome Atlas ◽

Cell Infiltration ◽

T Cell Infiltration ◽

Whole Exome ◽

Cancer Genome Atlas ◽

Infiltrating Lymphocytes

Objective The role of tumor-infiltrating lymphocytes (TILs) has not yet been characterized in sarcomas. The aim of this bioinformatics study was to explore the effect of TILs on sarcoma survival and genome alterations. Methods Whole-exome sequencing, transcriptome sequencing, and survival data of sarcoma were obtained from The Cancer Genome Atlas. Immune infiltration scores were calculated using the Tumor Immune Estimation Resource. Potential associations between abundance of infiltrating TILs and survival or genome alterations were examined. Results Levels of CD4+ T cell infiltration were associated with overall survival of patients with pan-sarcomas, and higher CD4+ T cell infiltration levels were associated with better survival. Somatic copy number alterations, rather than mutations, were found to correlate with CD4+ T cell infiltration levels. Conclusions This data mining study indicated that CD4+ T cell infiltration levels predicted from RNA sequencing could predict sarcoma prognosis, and higher levels of CD4+ T cells infiltration indicated a better chance of survival.

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Spatial heterogeneity and organization of tumor mutation burden and immune infiltrates within tumors based on whole slide images correlated with patient survival in bladder cancer

10.1101/554527 ◽

2019 ◽

Cited By ~ 5

Author(s):

Hongming Xu ◽

Sunho Park ◽

Jean René Clemenceau ◽

Jinhwan Choi ◽

Nathan Radakovich ◽

...

Keyword(s):

Bladder Cancer ◽

Spatial Heterogeneity ◽

Tumor Cells ◽

Tumor Infiltrating Lymphocytes ◽

The Cancer Genome Atlas ◽

Mutation Burden ◽

Prognostic Utility ◽

Cancer Genome Atlas ◽

Infiltrating Lymphocytes ◽

Whole Slide Images

AbstractHigh-TMB (TMB-H) could result in an increased number of neoepitopes from somatic mutations expressed by a patient’s own tumor cell which can be recognized and targeted by neighboring tumor-infiltrating lymphocytes (TILs). Deeper understanding of spatial heterogeneity and organization of tumor cells and their neighboring immune infiltrates within tumors could provide new insights into tumor progression and treatment response. Here we developed and applied computational approaches using digital whole slide images (WSIs) to investigate spatial heterogeneity and organization of regions harboring TMB-H tumor cells and TILs within tumors, and its prognostic utility. In experiments using WSIs from The Cancer Genome Atlas bladder cancer (BLCA), our findings show that WSI-based approaches can reliably predict patient-level TMB status and delineate spatial TMB heterogeneity and co-organization with TILs. TMB-H patients with low spatial heterogeneity enriched with high TILs show improved overall survival indicating a prognostic role of spatial TMB and TILs information in BLCA.

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Tumor Microenvironment Macrophage Inhibitory Factor Directs the Accumulation of Interleukin-17-producing Tumor-infiltrating Lymphocytes and Predicts Favorable Survival in Nasopharyngeal Carcinoma Patients

Journal of Biological Chemistry ◽

10.1074/jbc.m112.367532 ◽

2012 ◽

Vol 287 (42) ◽

pp. 35484-35495 ◽

Cited By ~ 45

Author(s):

Jiang Li ◽

Hao-Yuan Mo ◽

Geng Xiong ◽

Lin Zhang ◽

Jia He ◽

...

Keyword(s):

Tumor Microenvironment ◽

Tumor Cells ◽

Peripheral Blood ◽

Th17 Cells ◽

Tumor Tissue ◽

Tumor Infiltrating Lymphocytes ◽

Interleukin 17 ◽

Tumor Tissues ◽

Macrophage Inhibitory Factor ◽

Infiltrating Lymphocytes

The accumulation of an intratumoral CD4+ interleukin-17-producing subset (Th17) of tumor-infiltrating lymphocytes (TILs) is a general characteristic in many cancers. The relationship between the percentage of Th17 cells and clinical prognosis differs among cancers. The mechanism responsible for the increasing percentage of such cells in NPC is still unknown, as is their biological function. Here, our data showed an increase of Th17 cells in tumor tissues relative to their numbers in normal nasopharynx tissues or in the matched peripheral blood of NPC patients. Th17 cells in tumor tissue produced more IFNγ than did those in the peripheral blood of matched NPC patients and healthy controls. We observed high levels of CD154, G-CSF, CXCL1, IL-6, IL-8, and macrophage inhibitory factor (MIF) out of 36 cytokines examined in tumor tissue cultures. MIF promoted the generation and recruitment of Th17 cells mediated by NPC tumor cells in vitro; this promoting effect was mainly dependent on the mammalian target of rapamycin pathway and was mediated by the MIF-CXCR4 axis. Finally, the expression level of MIF in tumor cells and in TILs was positively correlated in NPC tumor tissues, and the frequency of MIF-positive TILs was positively correlated with NPC patient clinical outcomes. Taken together, our findings illustrate that tumor-derived MIF can affect patient prognosis, which might be related to the increase of Th17 cells in the NPC tumor microenvironment.

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BTBD10 is a Prognostic Biomarker Correlated With Immune Infiltration in Hepatocellular Carcinoma

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.762541 ◽

2022 ◽

Vol 8 ◽

Author(s):

Jianhui Li ◽

Xiaojuan Tian ◽

Ye Nie ◽

Ying He ◽

Wenlong Wu ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Cell Lines ◽

Tumor Infiltrating Lymphocytes ◽

Normal Liver ◽

The Cancer Genome Atlas ◽

Immune Checkpoints ◽

Phosphatase 2A ◽

Cancer Genome Atlas ◽

Infiltrating Lymphocytes ◽

The Impact

Background: BTBD10 serves as an activator of Akt family members through decreasing the protein phosphatase 2A-mediated dephosphorylation. The present study attempted to investigate the prognostic value of BTBD10 in hepatocellular carcinoma (HCC), specially, its relationship with tumor-infiltrating lymphocytes (TILs).Methods: BTBD10 expression was evaluated in HCC using The Cancer Genome Atlas (TCGA) and Xijing Hospital database, and verified in HCC cell lines. Cox analyses were performed to analyze independent prognostic risk factors for HCC. The optimal cut-off value of BTBD10 was calculated, by which all patients were divided into two groups to compare the overall survival (OS). The signaling pathways were predicted, by which BTBD10 may affect the progression of HCC. To investigate the impact of BTBD10 on HCC immunotherapy, correlations between BTBD10 and TILs, immune checkpoints, m6A methylation-related genes and ferroptosis-related genes were assessed. The distribution of half-maximal inhibitory concentration (IC50) of diverse targeted drugs was observed based on the differential expression of BTBD10.Results: BTBD10 expression was higher in HCC tissues and cell lines than that of normal liver tissues and cells. The patients with high expression of BTBD10 showed a worse OS, as compared to that of BTBD10 low-expressing group. Cox analyses indicated that BTBD10 was an independent prognostic risk factor for HCC. Several molecular pathways of immune responses were activated in HCC patients with high-expressing of BTBD10. Furthermore, BTBD10 expression was demonstrated to be positively correlated with tumor-infiltrating B cells, T cells, macrophages, neutrophils and dendritic cells. Meanwhile, the expression of BTBD10 was synchronized with that of several m6A methylation-related genes, ferroptosis-related genes and immune checkpoints. The IC50 scores of Sorafenib, Navitoclax, Veliparib, Luminespib, and Imatinib were found to be lower in BTBD10 high-expressing HCC group.Conclusion: BTBD10 negatively regulates tumor immunity in HCC and exhibits adverse effect on the prognosis of HCC, which could be a potential target for immunotherapy.

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A Comprehensive Survey of Immune Cytolytic Activity-Associated Gene Co-Expression Networks across 17 Tumor and Normal Tissue Types

Cancers ◽

10.3390/cancers10090307 ◽

2018 ◽

Vol 10 (9) ◽

pp. 307

Author(s):

Tian Tian ◽

Ji Wan ◽

Yan Han ◽

Haoran Liu ◽

Feng Gao ◽

...

Keyword(s):

Cytolytic Activity ◽

The Cancer Genome Atlas ◽

Immune Activity ◽

Multiple Tumor ◽

Normal Tissues ◽

Tumor Tissues ◽

Comprehensive Survey ◽

Cancer Genome Atlas ◽

Normal Networks ◽

Tumor Types

Cytolytic immune activity in solid tissue can be quantified by transcript levels of two genes, GZMA and PRF1, which is named the CYT score. A previous study has investigated the molecular and genetic properties of tumors associated CYT, but a systematic exploration of how co-expression networks across different tumors are shaped by anti-tumor immunity is lacking. Here, we examined the connectivity and biological themes of CYT-associated modules in gene co-expression networks of 14 tumor and 3 matched normal tissues constructed from the RNA-Seq data of the “The Cancer Genome Atlas” project. We first found that tumors networks have more diverse CYT-correlated modules than normal networks. We next identified and investigated tissue-specific CYT-associated modules across 14 tumor types. Finally, a common CYT-associated network across 14 tumor types was constructed. Two common modules have mixed signs of correlation with CYT in different tumors. Given the tumors and normal tissues surveyed, our study presents a systematic view of the regulation of cytolytic immune activity across multiple tumor tissues.

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Higher Expression of SPP1 Predicts Poorer Survival Outcomes in Head and Neck Cancer

Journal of Immunology Research ◽

10.1155/2021/8569575 ◽

2021 ◽

Vol 2021 ◽

pp. 1-11

Author(s):

Tongwu Bie ◽

Xuewen Zhang

Keyword(s):

Head And Neck ◽

Prognostic Biomarker ◽

The Cancer Genome Atlas ◽

Biological Processes ◽

Clinical Genetic ◽

Normal Tissues ◽

Tumor Tissues ◽

Cancer Genome Atlas ◽

Biological Methods ◽

Secreted Phosphoprotein 1

Secreted phosphoprotein 1 (SPP1) participated in various biological processes in many cancers, including immune response, tumor progression, and prognosis. However, SPP1 in head and neck squamous cell carcinoma (HNSCC) remains unknown. Clinical-genetic data of HNSCC were obtained from The Cancer Genome Atlas (TCGA) database. The differential expression of SPP1 in HNSCC tissues and adjacent normal tissues was quantified by bioinformatics methods and verified by western blot and other differential biological methods. We concluded that SPP1 is significantly upregulated in tumor tissues and can become a prognostic biomarker for HNSCC.

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Differential flora in the microenvironment of lung tumor and paired adjacent normal tissues

Carcinogenesis ◽

10.1093/carcin/bgaa044 ◽

2020 ◽

Vol 41 (8) ◽

pp. 1094-1103

Author(s):

Qixing Mao ◽

Weidong Ma ◽

Zhongqiu Wang ◽

Yingkuan Liang ◽

Te Zhang ◽

...

Keyword(s):

Tumor Microenvironment ◽

Lung Tumor ◽

Lung Carcinogenesis ◽

Microbial Composition ◽

Lung Cancer Patients ◽

Normal Tissues ◽

Β Diversity ◽

Tumor Tissues ◽

Α Diversity ◽

Significant Difference

Abstract Recent evidence demonstrates the existence of diversified microbiota in the lung. However, the effect of lung carcinogenesis on the flora in lung microenvironment has yet not been well investigated. In this study, we surveyed the microbial composition and diversity in lung tumor and paired adjacent normal tissues obtained from 55 lung cancer patients to test whether any specific tumor-associated microbial features in lung microenvironment can be identified. Compared with non-malignant adjacent tissues, the tumor samples showed significantly lower community richness (α diversity), but no significant difference in overall microbiome dissimilarity (β diversity). Strong intrasubject correlations were observed between tumor sample and its paired non-malignant adjacent tissues. In addition, correlation network analysis found more significant taxa–taxa correlations (adjusted q-value < 0.05) in tumor microenvironment than non-malignant adjacent tissues. At taxa level, we found Propionibacterium genus were significantly reduced in tumor tissues compared with non-malignant adjacent tissues. In summary, the microbiota in tumor tissues showed the lower richness, higher taxa–taxa interaction, and reduction of potential pro-inflammatory microbial genera compared with non-malignant tissues, suggesting the potential link between the tumor microbiota and the altered tumor microenvironment for the further investigation.

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Deep Learning for Automatic Subclassification of Gastric Carcinoma Using Whole-Slide Histopathology Images

Cancers ◽

10.3390/cancers13153811 ◽

2021 ◽

Vol 13 (15) ◽

pp. 3811

Author(s):

Hyun-Jong Jang ◽

In-Hye Song ◽

Sung-Hak Lee

Keyword(s):

Deep Learning ◽

Relative Proportion ◽

The Cancer Genome Atlas ◽

Cancer Tissue ◽

Mucinous Tumor ◽

Receiver Operating Characteristic Curves ◽

Tumor Tissues ◽

Cancer Genome Atlas ◽

Stomach Adenocarcinoma ◽

Tumor Types

Histomorphologic types of gastric cancer (GC) have significant prognostic values that should be considered during treatment planning. Because the thorough quantitative review of a tissue slide is a laborious task for pathologists, deep learning (DL) can be a useful tool to support pathologic workflow. In the present study, a fully automated approach was applied to distinguish differentiated/undifferentiated and non-mucinous/mucinous tumor types in GC tissue whole-slide images from The Cancer Genome Atlas (TCGA) stomach adenocarcinoma dataset (TCGA-STAD). By classifying small patches of tissue images into differentiated/undifferentiated and non-mucinous/mucinous tumor tissues, the relative proportion of GC tissue subtypes can be easily quantified. Furthermore, the distribution of different tissue subtypes can be clearly visualized. The patch-level areas under the curves for the receiver operating characteristic curves for the differentiated/undifferentiated and non-mucinous/mucinous classifiers were 0.932 and 0.979, respectively. We also validated the classifiers on our own GC datasets and confirmed that the generalizability of the classifiers is excellent. The results indicate that the DL-based tissue classifier could be a useful tool for the quantitative analysis of cancer tissue slides. By combining DL-based classifiers for various molecular and morphologic variations in tissue slides, the heterogeneity of tumor tissues can be unveiled more efficiently.

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C4b-binding protein α-chain enhances antitumor immunity by facilitating the accumulation of tumor-infiltrating lymphocytes in the tumor microenvironment in pancreatic cancer

Journal of Experimental & Clinical Cancer Research ◽

10.1186/s13046-021-02019-0 ◽

2021 ◽

Vol 40 (1) ◽

Author(s):

Kosuke Sasaki ◽

Shigetsugu Takano ◽

Satoshi Tomizawa ◽

Yoji Miyahara ◽

Katsunori Furukawa ◽

...

Keyword(s):

T Cell ◽

Tumor Microenvironment ◽

Binding Protein ◽

Combined Treatment ◽

Tumor Infiltrating Lymphocytes ◽

Pdac Cell ◽

Α Chain ◽

Infiltrating Lymphocytes

Abstract Background Recent studies indicate that complement plays pivotal roles in promoting or suppressing cancer progression. We have previously identified C4b-binding protein α-chain (C4BPA) as a serum biomarker for the early detection of pancreatic ductal adenocarcinoma (PDAC). However, its mechanism of action remains unclear. Here, we elucidated the functional roles of C4BPA in PDAC cells and the tumor microenvironment. Methods We assessed stromal C4BPA, the C4BPA binding partner CD40, and the number of CD8+ tumor-infiltrating lymphocytes in resected human PDAC tissues via immunohistochemical staining. The biological functions of C4BPA were investigated in peripheral blood mononuclear cells (PBMCs) and human PDAC cell lines. Mouse C4BPA (mC4BPA) peptide, which is composed of 30 amino acids from the C-terminus and binds to CD40, was designed for further in vitro and in vivo experiments. In a preclinical experiment, we assessed the efficacy of gemcitabine plus nab-paclitaxel (GnP), dual immune checkpoint blockades (ICBs), and mC4BPA peptide in a mouse orthotopic transplantation model. Results Immunohistochemical analysis revealed that high stromal C4BPA and CD40 was associated with favorable PDAC prognosis (P=0.0005). Stromal C4BPA strongly correlated with the number of CD8+ tumor-infiltrating lymphocytes (P=0.001). In in vitro experiments, flow cytometry revealed that recombinant human C4BPA (rhC4BPA) stimulation increased CD4+ and CD8+ T cell numbers in PBMCs. rhC4BPA also promoted the proliferation of CD40-expressing PDAC cells. By contrast, combined treatment with gemcitabine and rhC4BPA increased PDAC cell apoptosis rate. mC4BPA peptide increased the number of murine T lymphocytes in vitro and the number of CD8+ tumor-infiltrating lymphocytes surrounding PDAC tumors in vivo. In a preclinical study, GnP/ICBs/mC4BPA peptide treatment, but not GnP treatment, led to the accumulation of a greater number of CD8+ T cells in the periphery of PDAC tumors and to greater tumor regression than did control treatment. Conclusions These findings demonstrate that the combination of GnP therapy with C4BPA inhibits PDAC progression by promoting antitumor T cell accumulation in the tumor microenvironment.

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Tumor-Infiltrating Lymphocytes in the Tumor Microenvironment of Laryngeal Squamous Cell Carcinoma: Systematic Review and Meta-Analysis

Biomedicines ◽

10.3390/biomedicines9050486 ◽

2021 ◽

Vol 9 (5) ◽

pp. 486

Author(s):

Juan P. Rodrigo ◽

Mario Sánchez-Canteli ◽

Fernando López ◽

Gregory T. Wolf ◽

Juan C. Hernández-Prera ◽

...

Keyword(s):

Systematic Review ◽

Squamous Cell Carcinoma ◽

Tumor Microenvironment ◽

Cell Carcinoma ◽

Squamous Cell ◽

Prognostic Value ◽

Laryngeal Squamous Cell Carcinoma ◽

Meta Analysis ◽

Tumor Infiltrating Lymphocytes ◽

Infiltrating Lymphocytes

The presence of tumor-infiltrating lymphocytes (TIL) in the tumor microenvironment has been demonstrated to be of prognostic value in various cancers. In this systematic review and meta-analysis, we investigated the prognostic value of TIL in laryngeal squamous cell carcinoma (LSCC). We performed a systematic search in PubMed for publications that investigated the prognostic value of TIL in LSCC. A meta-analysis was performed including all studies assessing the association between TIL counts in hematoxylin-eosin (HE)-stained sections, for CD8+ and/or CD3+/CD4+ TIL and overall survival (OS) or disease-free survival (DFS). The pooled meta-analysis showed a favorable prognostic role for stromal TIL in HE sections for OS (HR 0.57, 95% CI 0.36–0.91, p = 0.02), and for DFS (HR 0.56, 95% CI 0.34–0.94, p = 0.03). High CD8+ TIL were associated with a prolonged OS (HR 0.62, 95% CI 0.4–0.97, p = 0.04) and DFS (HR 0.73, 95% CI 0.34–0.94, p = 0.002). High CD3+/CD4+ TIL demonstrated improved OS (HR 0.32, 95% CI 0.16–0.9, p = 0.03) and DFS (HR 0.23, 95% CI 0.10–0.53, p = 0.0005). This meta-analysis confirmed the favorable prognostic significance of TIL in LSCC. High stromal TIL evaluated in HE sections and intra-tumoral and stromal CD3+, CD4+ and/or CD8+ TIL might predict a better clinical outcome.

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