Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma

Background Hepatocellular carcinoma (HCC) is an inflammation-associated tumor involved in immune tolerance and evasion in the immune microenvironment. Heat shock proteins (HSPs) are involved in the occurrence, progression, and immune regulation of tumors. Therefore, HSPs have been considered potential therapeutic targets. Here, we aimed to elucidate the value of HSP family A (Hsp70) member 4 (HSPA4) in the diagnosis and predicting prognosis of HCC, and its relationship with immune cell infiltration, immune cell biomarkers, and immune checkpoints. Gene mutation, DNA methylation, and the pathway involved in HCC were also analyzed. Methods The gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to compare HSPA4 expression, and the results were confirmed by immunohistochemical staining of clinical samples. R package was used to analyze the correlation between HSPA4 and cancer stage, and to establish receiver operating characteristic (ROC) curve of diagnosis, time-dependent survival ROC curve, and a nomogram model. cBioPortal and MethSurv were used to identify genetic alterations and DNA methylation, and their effect on prognosis. The Tumor Immune Estimation Resource (TIMER) was used to analyze immune cell infiltration, immune cell biomarkers, and immune checkpoints. The STRING database was used to analyze protein–protein interaction network information. Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the functions of HSPA4 and its functional partner genes. Results Overexpression of HSPA4 was identified in 25 cancers. Overexpression of HSPA4 considerably correlated with cancer stage and alpha-fetoprotein (AFP) level in HCC. Patients with higher HSPA4 expression showed poorer prognosis. HSPA4 expression can accurately identify tumor from normal tissue (AUC = 0.957). The area under 1-, 3-, and 5-year survival ROCs were above 0.6. The HSPA4 genetic alteration rate was 1.3%. Among the 14 DNA methylation CpG sites, seven were related to the prognosis of HCC. HSPA4 was positively related to immune cell infiltration and immune checkpoints (PD-1 and CTLA-4) in HCC. The KEGG pathway enrichment analysis revealed HSPA4 enrichment in antigen processing and presentation together with HSPA8 and HSP90AA1. We verified the value of HSPA4 in the diagnosis and predicting prognosis of HCC. HSPA4 may not only participate in the occurrence and progression but also the immune regulation of HCC. Therefore, HSPA4 can be a potential diagnostic and prognostic biomarker and a therapeutic target for HCC.

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Hypoxic Characteristic in the Immunosuppressive Microenvironment of Hepatocellular Carcinoma

Frontiers in Immunology ◽

10.3389/fimmu.2021.611058 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhuomao Mo ◽

Daiyuan Liu ◽

Dade Rong ◽

Shijun Zhang

Keyword(s):

Hepatocellular Carcinoma ◽

Immune Cell ◽

Cox Regression ◽

Cancer Genome ◽

Gene Set Enrichment Analysis ◽

The Cancer Genome Atlas ◽

Cell Infiltration ◽

Immune Checkpoints ◽

Immune Cell Infiltration ◽

Immunosuppressive Microenvironment

Background: Generally, hepatocellular carcinoma (HCC) exists in an immunosuppressive microenvironment that promotes tumor evasion. Hypoxia can impact intercellular crosstalk in the tumor microenvironment. This study aimed to explore and elucidate the underlying relationship between hypoxia and immunotherapy in patients with HCC.Methods: HCC genomic and clinicopathological datasets were obtained from The Cancer Genome Atlas (TCGA-LIHC), Gene Expression Omnibus databases (GSE14520) and International Cancer Genome Consortium (ICGC-LIRI). The TCGA-LIHC cases were divided into clusters based on single sample gene set enrichment analysis and hierarchical clustering. After identifying patients with immunosuppressive microenvironment with different hypoxic conditions, correlations between immunological characteristics and hypoxia clusters were investigated. Subsequently, a hypoxia-associated score was established by differential expression, univariable Cox regression, and lasso regression analyses. The score was verified by survival and receiver operating characteristic curve analyses. The GSE14520 cohort was used to validate the findings of immune cell infiltration and immune checkpoints expression, while the ICGC-LIRI cohort was employed to verify the hypoxia-associated score.Results: We identified hypoxic patients with immunosuppressive HCC. This cluster exhibited higher immune cell infiltration and immune checkpoint expression in the TCGA cohort, while similar significant differences were observed in the GEO cohort. The hypoxia-associated score was composed of five genes (ephrin A3, dihydropyrimidinase like 4, solute carrier family 2 member 5, stanniocalcin 2, and lysyl oxidase). In both two cohorts, survival analysis revealed significant differences between the high-risk and low-risk groups. In addition, compared to other clinical parameters, the established score had the highest predictive performance at both 3 and 5 years in two cohorts.Conclusion: This study provides further evidence of the link between hypoxic signals in patients and immunosuppression in HCC. Defining hypoxia-associated HCC subtypes may help reveal potential regulatory mechanisms between hypoxia and the immunosuppressive microenvironment, and our hypoxia-associated score could exhibit potential implications for future predictive models.

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Development and validation of a LRP1B mutation-associated prognostic model for hepatocellular carcinoma

10.21203/rs.3.rs-266054/v1 ◽

2021 ◽

Author(s):

Jian Xu ◽

Xiaomin Shen ◽

Bo Zhang ◽

Rui Su ◽

Mingxuan Cui ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Gene Mutation ◽

Prognostic Model ◽

Immune Cell ◽

Low Risk ◽

Cell Infiltration ◽

Immune Checkpoints ◽

Immune Cell Infiltration ◽

Significant Difference ◽

Patient Prognosis

Abstract Purpose: To develop a LRP1B gene mutation based prognostic model for hepatocellular carcinoma (HCC) patients risk prediction. Methods: The LRP1B gene mutation rate was calculated from HCC patient samples. Meanwhile, differentially expressed genes according to LRP1B mutant were screened out for prognostic model establishment. Based on this innovative model, HCC patients were categoried into high and low-risk group. The immune status including immune cell infiltration ratio and checkpoints have been explored in two groups. Results: It can be shown here 11 genes demonstrate significant differences according to LRP1B status, which can better predict HCC patient prognosis. The accuracy of the model prediction is evaluated and approved by the AUC value. From the immune cell infiltration ratio analysis, there is a significant difference in the infiltration degree of 7 types of immune cells and 2 immune checkpoints between high and low-risk HCC patients. Meanwhile, LRP1B was tested as a prognostic marker in clinic to predict different stages for HCC with satisfied accurancy. Conclusion: This study has explored a potential prognostic biomarker and developed a novel LRP1B mutation-associated prognostic model for hepatocellular carcinoma, which provides a systematic reference for future better understanding of clinical research.

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Development and validation of a LRP1B mutation-associated prognostic model for hepatocellular carcinoma

Bioscience Reports ◽

10.1042/bsr20211053 ◽

2021 ◽

Author(s):

Jian Xu ◽

Xiaomin Shen ◽

Bo Zhang ◽

Rui Su ◽

Mingxuan Cui ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Gene Mutation ◽

Prognostic Model ◽

Immune Cell ◽

Low Risk ◽

Cell Infiltration ◽

Immune Checkpoints ◽

Immune Cell Infiltration ◽

Significant Difference

Purpose: To develop a LRP1B gene mutation based prognostic model for hepatocellular carcinoma (HCC) patients risk prediction. Methods: The LRP1B gene mutation rate was calculated from HCC patient samples. Meanwhile, differentially expressed genes according to LRP1B mutant were screened out for prognostic model establishment. Based on this innovative model, HCC patients were categoried into high and low-risk group. The immune status including immune cell infiltration ratio and checkpoints have been explored in two groups. The functions of LRP1B and risk factors in the model were verified using both in vivo and in vitro experiments. Results: It could be demonstrated that LRP1B was a potential negative predictor for HCC patients prognosis with high mutation frequency. The functions of LRP1B was verified with ELISA assay and Quantitative Real-time PCR method based on clinical recruited HCC participants. 11 genes displayed significant differences according to LRP1B status, which could better predict HCC patient prognosis. The functions of these genes were examined using HCC cell line HCCLM3, suggesting they played a pivotal role in determining HCC cell proliferation and apoptosis. From the immune cell infiltration ratio analysis, there was a significant difference in the infiltration degree of 7 types of immune cells and 2 immune checkpoints between high and low-risk HCC patients. Conclusion: This study hypothesized a potential prognostic biomarker and developed a novel LRP1B mutation-associated prognostic model for hepatocellular carcinoma, which provided a systematic reference for future understanding of clinical research.

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Identification of lncRNA FAM99A gene as a prognostic biomarker of hepatocellular carcinoma

10.21203/rs.3.rs-16068/v1 ◽

2020 ◽

Author(s):

Manyi Sun ◽

Shuhua Lv ◽

Jin Zhong

Keyword(s):

Hepatocellular Carcinoma ◽

Dna Methylation ◽

Molecular Mechanism ◽

Immune Cell ◽

Sequence Similarity ◽

Enrichment Analysis ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Hepatic Cancer ◽

Clinical Prognosis

Abstract Background The complicated pathogenesis of hepatic cancer involves multiple clinical prognosis-associated oncogenes. Methods We utilized the bioinformatics approach to analyze the data from hepatic cancer cases collected by TCGA repository. Results We first found that the FAM99A (Family With Sequence Similarity 99 Member A) gene, a long non-coding RNA (lncRNA), is lowly expressed in hepatocellular carcinoma and closely related to clinical prognosis. We further analyzed the underling molecular mechanism from the perspectives of copy number variation (CNV), DNA methylation, immune cell infiltration, and related cellular pathway. Even though we did not observe a strong correlation between the FAM99A expression and the CNV or immune cell infiltration, the high methylation levels of the five methylated probe sites (cg24218935, cg01745044, cg04353359, cg04938738, cg25356611) were found to be negatively correlated with low expression level of FAM99A. Besides, we performed the enrichment analysis to screen out a group of FAM99A-correlated genes and molecular pathways, such as complement cascade, RNA metabolism, drug metabolic process, PPAR signaling pathway, or cell cycle. Conclusions The liver-specific FAM99A gene was first identified as a prognosis marker of hepatocellular carcinoma, and the underlying molecular mechanism involves DNA methylation and a series of cellular pathways.

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Glucose-6-Phosphate Dehydrogenase is a Prognostic Biomarker and Correlated with Immune Infiltrates in Hepatocellular Carcinoma

10.21203/rs.3.rs-1232206/v1 ◽

2022 ◽

Author(s):

Yang Bu ◽

Kejun Liu ◽

Yiming Niu ◽

Ji Hao ◽

Lei Cui ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Tumor Microenvironment ◽

Liver Cancer ◽

Immune Cell ◽

Cox Regression ◽

Functional Enrichment ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Potential Biomarker ◽

Glucose 6 Phosphate Dehydrogenase

Abstract Background: Glucose-6-phosphate dehydrogenase (G6PD) plays an important role in the metabolic and immunological aspects of tumors. In hepatocellular carcinoma (HCC), the alteration of tumor microenvironment influences recurrence and metastasis. We extracted G6PD-related data from public databases of HCC tissues and used a bioinformatics approach to explore the correlation between G6PD expression and clinicopathological features and prognosis of immune cell infiltration in HCC.Methods: We extract G6PD expression information from TCGA and GEO databases in liver cancer tissues and normal tissues, validated by immunohistochemistry, and the correlation between G6PD expression and clinical features is analyzed, and the clinical significance of G6PD in liver cancer is assessed by Kaplan-Meier, Cox regression and prognostic line graph models. Functional enrichment analysis is performed by protein-protein interaction (PPI) network, GO/KEGG, GSEA and G6PD-associated differentially expressed genes (DEGs). TIMER and ssGSEA packages are used to assess the correlation between expression and the level of immune cell infiltration.Results: Our results show that G6PD expression is significantly upregulated in hepatocellular carcinoma tissues (P < 0.001). G6PD expression is associated with histological grade, pathological stage, T-stage, vascular infiltration and AFP level (P < 0.05); HCC patients in the low G6PD expression group had longer overall survival and better prognosis compared with the high G6PD expression group (P < 0.05). The level of G6PD expression also affects the levels of macrophages, unactivated dendritic cells, B cells, and follicular helper T cells in the tumor microenvironment.Conclusion: High expression of G6PD is a potential biomarker for poor prognosis of hepatocellular carcinoma, and G6PD may be a target for immunotherapy of HCC.

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Comprehensive analysis of epigenetic modifications and immune-cell infiltration in tissues from patients with systemic lupus erythematosus

Epigenomics ◽

10.2217/epi-2021-0318 ◽

2021 ◽

Author(s):

Zhenghao He ◽

Shihang Zhou ◽

Ming Yang ◽

Zhidan Zhao ◽

Yang Mei ◽

...

Keyword(s):

Systemic Lupus Erythematosus ◽

Dna Methylation ◽

Lupus Erythematosus ◽

Immune Cell ◽

Epigenetic Modifications ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Methylation Analysis ◽

Systemic Lupus ◽

Dna Methylation Analysis

Aim: To explore potential abnormal epigenetic modifications and immune-cell infiltration in tissues from systemic lupus erythematosus (SLE) patients. Materials & methods: To utilize bioinformatics analysis and ‘wet lab' methods to identify and verify differentially expressed genes in multiple targeted organs in SLE. Results: Seven key genes, IFI44, IFI44L, IFIT1, IFIT3, PLSCR1, RSAD2 and OAS2, which are regulated by epigenetics and may be involved in the pathogenesis of SLE, are identified by combined long noncoding RNA–miRNA–mRNA network analysis and DNA methylation analysis. The results of quantitative reverse transcription PCR, immunohistochemistry and DNA methylation analysis confirmed the potential of these genes as biomarkers. Conclusion: This study reveals the potential mechanisms in SLE from epigenetic modifications and immune-cell infiltration, providing diagnostic biomarkers and therapeutic targets for SLE.

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CMET-30. COMPREHENSIVE METHYLOME ANALYSIS OF EGFR-MUTANT PRIMARY LUNG ADENOCARCINOMA AND MATCHED BRAIN METASTASIS

Neuro-Oncology ◽

10.1093/neuonc/noz175.231 ◽

2019 ◽

Vol 21 (Supplement_6) ◽

pp. vi58-vi58

Author(s):

Yasin Mamatjan ◽

Michael Cabanero ◽

Jeffrey Zuccato ◽

Jessica Weiss ◽

Shirin Karimi ◽

...

Keyword(s):

Dna Methylation ◽

Brain Metastasis ◽

Lung Adenocarcinoma ◽

Immune Cell ◽

Methylation Status ◽

Cell Infiltration ◽

Immune Cell Infiltration ◽

Promoter Regions ◽

Primary Lung Adenocarcinoma ◽

Egfr Mutant

Abstract Brain metastasis (BM) in patients with EGFR-mutant lung adenocarcinoma is a major determinant of overall survival. Novel insight into the genetic and epigenetic underpinnings of BM development is lacking. The aim of this study is to compare the methylome of EGFR-mutant primary lung adenocarcinoma (EGFRM-PLA) and matched BM to identify important alterations for the mechanisms of BM. Matched EGFRM-PLA and BM tumors from seven patients were profiled using the Illumina Infinium MethylationEPIC BeadChip array. Unsupervised clustering analyses of the 14 samples showed a similar whole DNA methylation signatures between EGFRM-PLA and BM tumors. Furthermore, PCA plot highlighted that seven matched BM and lung tumor samples were clustered together closely based on matching pairs for the most variable probes (2.5K to 10K). These observations indicate high level of concordance and the same cell of origin. However, these fourteen samples clustered into two groups based on tumor site being lung or brain based on 83K differentially methylated CpG sites. Of the 83K probes, 2.4K were either hypermethylated or hypomethylated in all lung samples. A quarter of these 2.4K probes were located in promoter regions. Specifically, we identified differences in methylation status of EGFR/ALK promoter regions in lung tumors versus BM. CNV analyses showed higher deep deletions of chromosomes and genes in BM compared to EGFRM-PLA. Leukocytes unmethylation for purity (LUMP) scores which indicate immune cell infiltration were similar between lung and BM pairs (Mean LUMP_score=0.64) consistent with high immune cell infiltration. Our results indicated a similar whole DNA methylation signature of EGFRM-PLA and matched BM, while comprehensive analysis identified important differentially methylated probes. Distinct differences in CNV alterations were observed in lung versus brain samples. The BM and EGFRM-PLA showed similar tumor purity and immune cell components. Overall, tumor methylation profiling provides clinically important information regarding biology of BM in EGFRM-PLA.

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Prognostic Significance of STC2 and DNA methylation in Head and Neck Squamous Cell Carcinoma: A Study Based on the TCGA and GEO Databases

10.21203/rs.3.rs-191202/v1 ◽

2021 ◽

Author(s):

Guangyao Li ◽

Daquan Wu ◽

Lei Zhou ◽

Dan You ◽

Xinsheng Huang

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Squamous Cell Carcinoma ◽

Survival Rate ◽

Cell Carcinoma ◽

Head And Neck ◽

Tp53 Mutation ◽

Immune Cell ◽

Cell Infiltration ◽

Immune Cell Infiltration

Abstract Background: Head and neck squamous cell carcinoma (HNSC) is a popular malignancy type that brings about poor prognosis with a low survival rate worldwide. Stanniocalcin 2 (STC2) is a glycosylated peptide hormone and shows the potential to become a new biomarker for the evaluation of malignant tumors. The purpose of this study was to explore the prognostic implications of STC2 and DNA methylation in HNSC and the role of STC2 expression in immune cell infiltration.Methods: STC2 gene expression data were collected from Gene Expression Omnibus (GEO) and the Cancer Genome Atlas (TCGA) databases. Univariate and multivariate analyses were employed to screen prognostic risk factors. The relationship between STC2 expression and TP53 mutation in HNSC was explored. TCGA data were utilized to analyze how STC2 expression affected immune cell infiltration in HNSC.Results: STC2 was highly expressed in HNSC patients (P < 0.01), especially those with a lower overall survival rate (P < 0.0001). TP53 mutation might be a risk factor of STC2 overexpression in HNSC (P = 0.0015). STC2 expression was negatively correlated with STC2 methylation (Spearman: -0.43, P < 0.001). Hypermethylation or hypomethylation at the eight CpG sites most related to STC2 expression was identified as independent factors for HNSC prognosis. STC2 was positively correlated with cancer-associated fibroblasts infiltration and associated with the infiltration of various immune cells.Conclusion: STC2 can be regarded as a vital prognostic biomarker of HNSC due to its essential roles in immune cell infiltration.

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KRT17 Serves as an Oncogene and a Predictor of Poor Survival in Hepatocellular Carcinoma Patients

10.21203/rs.3.rs-117723/v1 ◽

2020 ◽

Author(s):

yuyan chen ◽

Jing Chen ◽

Zu-Cheng Tian ◽

Dan-Hua Zhou ◽

Ran Ji ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Tumor Cell ◽

Immune Cell ◽

Gene Set Enrichment Analysis ◽

Cell Infiltration ◽

Cancer Type ◽

Immune Cell Infiltration ◽

Functional Link ◽

Network Analyses ◽

Ppi Networks

Abstract Background: Hepatocellular carcinoma (HCC) is the second most common cancer-associated cause of death globally. It is thus vital that novel diagnostic and prognostic biomarkers associated with early-stage HCC be identified. While keratin 17 (KRT17) has previously been reported to be associated with certain cancer types, its relationship with HCC remains to be defined. Methods：The expression of KRT17 in the TCGA LIHC database and in 44 pairs of HCC patient samples was assessed via qRT-PCR, western blotting, and immunohistochemical staining. The prognostic relevance of KRT17 was assessed using Kaplan-Meir curves, while important cancer- and KRT17-related biological processes were defined through gene set enrichment analysis (GSEA). The functional link between KRT17 expression and tumor cell proliferation/survival was assessed through flow cytometry, colony formation assay, CCK-8 assay, and subcutaneous tumor model approaches. Protein-protein interaction (PPI) networks and analyses of immune cell infiltration were also employed to define key signaling pathways associated with KRT17 expression in HCC. Results：HCC tissue samples exhibited increased KRT17 mRNA and protein expression that was predictive of poorer patient survival (P<0.001). GSEA and functional experiments revealed that KRT17 functioned as a regulator of HCC tumor cell survival, proliferation, and cell cycle progression in vitro and in vivo. PPI network analyses also revealed that KRT17 expression was linked to immune cell infiltration and activation in patients with HCC. Conclusion: We found that increased KRT17 levels were associated with poorer survival, more aggressive disease, and altered immune cell infiltration in patients suffering from HCC. As such, KRT17 may function as an oncogene and a prognostic biomarker in this cancer type.

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ARID1A Is a Prognostic Biomarker and Associated with Immune Infiltrates in Hepatocellular Carcinoma

Canadian Journal of Gastroenterology and Hepatology ◽

10.1155/2022/3163955 ◽

2022 ◽

Vol 2022 ◽

pp. 1-14

Author(s):

Yuanyuan Feng ◽

Xinfang Tang ◽

Changcheng Li ◽

Ying Su ◽

Xiaoyu Wang ◽

...

Keyword(s):

Hepatocellular Carcinoma ◽

Overall Survival ◽

Immune Cell ◽

Enrichment Analysis ◽

Gene Set Enrichment Analysis ◽

Cell Infiltration ◽

Migration And Invasion ◽

Risk Indicator ◽

Immune Cell Infiltration

Objective. ARID1A has been discovered as a potential cancer biomarker. But its role in hepatocellular carcinoma (HCC) is subject to considerable dispute. Methods. The relationship between ARID1A and clinical factors was investigated. Clinicopathological variables related to overall survival in HCC subjects were identified using Cox and Kaplan–Meier studies. The connection between immune infiltrating cells and ARID1A expression was investigated using the tumor Genome Atlas (TCGA) dataset for gene set enrichment analysis (GSEA). Finally, a cell experiment was used to confirm it. Results. The gender and cancer topography (T) categorization of HCC were linked to increased ARID1A expression. Participants with advanced levels of ARID1A expression had a worse prognosis than someone with lower levels. ARID1A was shown to be a risk indicator of overall survival on its own. ARID1A expression is inversely proportional to immune cell infiltration. In vitro, decreasing ARID1A expression substantially slowed the cell cycle and decreased HCC cell proliferation, migration, and invasion. Conclusion. The expression of ARID1A could be used to predict the outcome of HCC. It is closely related to tumor immune cell infiltration.

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