Immune Cell Composition of Liver Hepatocellular Carcinoma and its clinical relevance: A research based on TCGA database

Nk Cells ◽

Survival Time ◽

Clinical Data ◽

Immune Cells ◽

Immune Cell ◽

Transcriptome Profiling ◽

Statistical Analyses ◽

Lower Amount ◽

Abstract Background Liver hepatocellular carcinoma (LIHC), as the main type of liver cancer, has become a main health issue as the third-most common cause of mortality in cancer patients. However, conventional chemo- or radio- therapies shows little improvement in survival, which calls for novel therapies. Because of the immunotolerance mechanism existing naturally in liver, immunotherapy provides significant effect in treatment of LIHC patients. Up to now, various immunotherapies have been proposed, but due to the complex pathways from which LIHC cancerous cell escape immunosurveillance, combined therapies are often needed, which are still under development. Methods In the current study, with data downloaded from TCGA database, CIBERSORT was performed for identifying the composition of infiltrating immune cells and further statistical analyses using R 3.5.3 were carried out, aiming at connecting specific immune cells with clinical survival. Results With data of immune and stromal scores downloaded from the website of MD Anderson Cancer Centre, both showed significance in survival time. Further analyses based on the result of CIBERSORT demonstrated that the number of macrophages M0 and T cells CD8 infiltration between para-carcinoma and tumour tissues are markedly different. With combination of clinical data, we were able to identify that a higher amount of activated NK cells (p=0.008) and a lower amount of resting NK cells (p=0.047) presented a longer survival time. Conclusion With the help of the TCGA database and multiple techniques, statistical analyses of transcriptome profiling data and clinical data were successfully carried out. The results in this study may pave the way for a new therapeutic strategy which could be combined with current treatments to further improve the clinical outcome of LIHC patients. Further and deeper investigation of other available data, however, were needed in order to verify the results of current study.

Identification of Biomarkers Related to Immune Cell Infiltration in Hepatocellular Carcinoma Using Gene Co-Expression Network

Pathology & Oncology Research ◽

10.3389/pore.2021.601693 ◽

2021 ◽

Vol 27 ◽

Author(s):

Wanbang Zhou ◽

Yiyang Chen ◽

Ruixing Luo ◽

Zifan Li ◽

Guanwei Jiang ◽

...

Keyword(s):

Network Analysis ◽

Tumor Progression ◽

Protein Interactions ◽

Immune Cells ◽

Immune Cell ◽

Immune Microenvironment ◽

Hub Genes ◽

Expression Levels ◽

Immune Infiltration

Hepatocellular carcinoma (HCC) is a common cancer with poor prognosis. Due to the lack of effective biomarkers and its complex immune microenvironment, the effects of current HCC therapies are not ideal. In this study, we used the GSE57957 microarray data from Gene Expression Omnibus database to construct a co-expression network. The weighted gene co-expression network analysis and CIBERSORT algorithm, which quantifies cellular composition of immune cells, were used to identify modules related to immune cells. Four hub genes (EFTUD2, GAPDH, NOP56, PA2G4) were identified by co-expression network and protein-protein interactions network analysis. We examined these genes in TCGA database, and found that the four hub genes were highly expressed in tumor tissues in multiple HCC groups, and the expression levels were significantly correlated with patient survival time, pathological stage and tumor progression. On the other hand, methylation analysis showed that the up-regulation of EFTUD2, GAPDH, NOP56 might be due to the hypomethylation status of their promoters. Next, we investigated the correlations between the expression levels of four hub genes and tumor immune infiltration using Tumor Immune Estimation Resource (TIMER). Gene set variation analysis suggested that the four hub genes were associated with numerous pathways that affect tumor progression or immune microenvironment. Overall, our results showed that the four hub genes were closely related to tumor prognosis, and may serve as targets for treatment and diagnosis of HCC. In addition, the associations between these genes and immune infiltration enhanced our understanding of tumor immune environment and provided new directions for the development of drugs and the monitoring of tumor immune status.

Roles of Immune Cells in the Concurrence of Echinococcus Granulosus Infection and Hepatocellular Carcinoma

10.21203/rs.3.rs-98853/v1 ◽

2020 ◽

Author(s):

Aimaiti Yasen ◽

Bo Ran ◽

Maolin Wang ◽

Guodong Lv ◽

Renyong Lin ◽

...

Keyword(s):

T Cell ◽

Immune Responses ◽

Nk Cells ◽

Echinococcus Granulosus ◽

Immune Cells ◽

Hepg2 Cells ◽

Control Group ◽

Cell Markers ◽

Hepg2 Cell Lines

Abstract Background/aims: Immune cells are pivotal players in the immune responses against both parasitic infection and malignancies. Substantial evidence demonstrated that there may exist possible relationship between Echinococcus granulosus (E.granulosus) infection and hepatocellular carcinoma (HCC) development. Thus, this study aimed to observe crucial roles of immune cells in the formation of subcutaneous lesions after transplanting HepG2 cell lines with or without E.granulosus protoscoleces (PSCs).Methods: HepG2 cell lines were subcutaneously injected into nude mice in the control group. In the co-transplantation group, HepG2 cells were subcutaneously co-injected with high dosage of E.granulosus PSCs. From the 25th day of transplantation, volume of subcutaneous lesions was measured every four days, which were removed at the 37th day for further studies. Basic pathological and functional changes were observed. Moreover, expression of Ki67, Bal-2, Caspase3, α-smooth muscle actin (α-SMA), T cell markers (CD3, CD4, CD8), PD1/PD-L1, nature killer (NK) cell markers (CD16, CD56) were further detected by immunohistochemistry.Results: Subcutaneous lesions were gradually increased in volume and there occurred pathologically heterogeneous tumor cells, which were more significant in the co-transplantation group. Compared to the control group, expression of proliferation markers Ki67 and Bcl-2 was at higher levels in the co-transplantation group. Reversely, apoptotic marker Caspase3 was highly detected in the control group, suggesting promoting effects of E.granulosus PSCs on HCC development. Interestingly, subcutaneous lesions of the co-transplantation group were more functional in synthesizing and storing glycogen. Collagen and α-SMA+ cells were also at higher levels in the co-transplantation group than those in the control group. Most importantly, co-transplantation of HepG2 cells with E.granulosus PSCs led to significant increase in the expression of T cell markers (CD3, CD4 and CD8), immune inhibitory checkpoint PD1/PD-L1 and NK cells markers (CD16 and CD56). Conclusions: E.granulosus may have promoting effects on HCC development, which was closely associated with the immune responses of T cells and NK cells.

Landscape of associations between long non‐coding RNAs and infiltrating immune cells in liver hepatocellular carcinoma

Journal of Cellular and Molecular Medicine ◽

10.1111/jcmm.15690 ◽

2020 ◽

Vol 24 (19) ◽

pp. 11243-11253 ◽

Cited By ~ 1

Author(s):

Li Li ◽

Xiaowei Song ◽

Yanju Lv ◽

Qiuying Jiang ◽

Chengjuan Fan ◽

...

Keyword(s):

Immune Cells ◽

Non Coding Rnas ◽

3363 Prognostic Value of Immune-Related Biomarkers in Resected Non-Small Cell Lung Cancer

Journal of Clinical and Translational Science ◽

10.1017/cts.2019.349 ◽

2019 ◽

Vol 3 (s1) ◽

pp. 153-153

Author(s):

Rajwanth R Veluswamy ◽

Stephanie Tuminello ◽

Francesca Petralia ◽

Wil Lieberman-Cribbin ◽

Pei Wang ◽

...

Keyword(s):

Nk Cells ◽

Immune Cells ◽

Immune Cell ◽

Meta Analysis ◽

Stage I ◽

Resected Stage ◽

Iiia Nsclc ◽

Nsclc Patients ◽

Lung Adenocarcinomas ◽

The Impact

OBJECTIVES/SPECIFIC AIMS: Immune cells within the tumor microenvironment (TME) play an important role in the development and progression of non-small cell lung cancer (NSCLC). However, data evaluating the impact of individual immune cell types on NSCLC outcomes is limited and often conflicting. We performed a meta-analysis of existing data and used The Cancer Genome Atlas (TCGA) to evaluate the effect of several immune cells on surgical outcomes of stage I-IIIA NSCLC. METHODS/STUDY POPULATION: PubMed was searched to identify eligible studies evaluating survival of surgically resected stage I-IIIA NSCLC patients according to immune cell infiltration. Meta-analysis was performed using a linear mixed-effects model to determine overall, disease specific and progression free survival. We then used a similar patient subset found in the TCGA to validate the meta-analysis findings. For the TCGA analysis, sample-specific scores for different immune cells were computed via xCell using level three RNAseq data. After stratifying the cohort by histologic subtype, the association between each cell type and survival was assessed via Cox Regression, while adjusting for stage, gender and smoking status. RESULTS/ANTICIPATED RESULTS: From the meta-analysis (37 articles eligible; N = 8,162 patients), high levels of CD20+ B cells (hazard ratio [HR]: 0.36, 95% confidence interval [CI]: 0.15-0.85), natural killer (NK) cells (HR: 0.64, 95% CI: 0.41-1.0), and dendritic cells (0.34, 95% CI: 0.13-0.84) were significantly associated with better overall survival (OS); T regulatory cells (HR: 1.85, 95% CI: 1.35-2.54) were associated with worst OS. High CD8+ T cell infiltrates were associated with improved disease-free survival (DFS; HR: 0.85, 95% CI 0.73-0.99), while CD68+ macrophages (HR> 2.83, 95% CI: 1.28-6.24) were associated with worst DFS. In the TCGA cohort, lung adenocarcinomas rich in CD4 T cells, CD8 T cells, B cells, and NK cells were associated with improved OS in unadjusted analysis. In adjusted analysis, only NK cells were associated with improved OS (HR: 0.82, 95% CI: 0.69-0.98). There was no significant association of any immune cell type for DFS in lung adenocarcinomas and with both OS and DFS in Squamous Cell Lung Cancers (p>0.05 for all comparisons). DISCUSSION/SIGNIFICANCE OF IMPACT: The presence of tumor infiltration by specific immune cell subsets may potentially predict survival outcomes in resected stage I-III NSCLC patients. However, the impact of immune cells may not be similar in all histologic types and after adjusting for important clinical confounders.

Global immune characterization of HBV/HCV-related hepatocellular carcinoma identifies macrophage and T-cell subsets associated with disease progression

Cell Discovery ◽

10.1038/s41421-020-00214-5 ◽

2020 ◽

Vol 6 (1) ◽

Author(s):

Guohe Song ◽

Yang Shi ◽

Meiying Zhang ◽

Shyamal Goswami ◽

Saifullah Afridi ◽

...

Keyword(s):

T Cells ◽

T Cell ◽

Single Cell ◽

Immune Cells ◽

Immune Cell ◽

T Cell Subsets ◽

M2 Macrophage ◽

Advanced Hcc ◽

Immune Cell Subsets

AbstractDiverse immune cells in the tumor microenvironment form a complex ecosystem, but our knowledge of their heterogeneity and dynamics within hepatocellular carcinoma (HCC) still remains limited. To assess the plasticity and phenotypes of immune cells within HBV/HCV-related HCC microenvironment at single-cell level, we performed single-cell RNA sequencing on 41,698 immune cells from seven pairs of HBV/HCV-related HCC tumors and non-tumor liver tissues. We combined bio-informatic analyses, flow cytometry, and multiplex immunohistochemistry to assess the heterogeneity of different immune cell subsets in functional characteristics, transcriptional regulation, phenotypic switching, and interactions. We identified 29 immune cell subsets of myeloid cells, NK cells, and lymphocytes with unique transcriptomic profiles in HCC. A highly complex immunological network was shaped by diverse immune cell subsets that can transit among different states and mutually interact. Notably, we identified a subset of M2 macrophage with high expression of CCL18 and transcription factor CREM that was enriched in advanced HCC patients, and potentially participated in tumor progression. We also detected a new subset of activated CD8+ T cells highly expressing XCL1 that correlated with better patient survival rates. Meanwhile, distinct transcriptomic signatures, cytotoxic phenotypes, and evolution trajectory of effector CD8+ T cells from early-stage to advanced HCC were also identified. Our study provides insight into the immune microenvironment in HBV/HCV-related HCC and highlights novel macrophage and T-cell subsets that could be further exploited in future immunotherapy.

Expression and prognosis analysis of JMJD5 in human cancers

10.21203/rs.3.rs-67707/v2 ◽

2020 ◽

Author(s):

Hui Li ◽

Qun Li ◽

Hong Jing ◽

Jianghai Zhao ◽

Hui Zhang ◽

...

Keyword(s):

T Cells ◽

B Cells ◽

Lung Adenocarcinoma ◽

Immune Cells ◽

Prognostic Value ◽

Normal Tissues ◽

Human Cancers ◽

Stomach Adenocarcinoma ◽

Abstract BackgroundJumonjiC (JmjC) domain-containing protein 5 (JMJD5) plays an important role in cancer metabolism. However, the prognostic value of JMJD5 in most human cancers is still unknown. In this study, we aim to investigate the expression and prognostic value of JMJD5, immune cells infiltration, and the correlations among them. MethodsWe performed a detailed cancer vs. normal analysis of JMJD5 mRNA expression via online Tumor Immune Estimation Resource (TIMER). The protein expressions of JMJD5 in various cancers vs. adjacent normal tissues were examined by immunohistochemistry (IHC) of tissue microarray sections (TMAs). Moreover, the Kaplan-Meier Plotter databases were used to evaluate the prognostic values in above cancers. The correlations between JMJD5 expression level and abundances of six immune infiltrating cells (B cells, CD4+ T cells, CD8+ T cells, macrophages, neutrophils and dendritic cells) were explored by TIMER database in breast cancer (BRCA), liver hepatocellular carcinoma (LIHC), lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC) and stomach adenocarcinoma (STAD). The prognostic values of tumor- infiltrating immune cells were also investigated by TIMER in above four cancers. Finally, the COX proportional hazards model was used to investigate the correlations among clinical outcome, the abundance of immune cell infiltrates and the expression of JMJD5 in above four cancer types.ResultsThe expression of JMJD5 was significantly lower in human breast carcinoma (BRCA), cholangiocarcinoma (CHOL), liver hepatocellular carcinoma (LIHC) and lung cancer (LUC) but higher in prostate adenocarcinoma (PRAD) and stomach adenocarcinoma (STAD) comparing to their respective normal tissues. And high expression of JMJD5 has better prognosis only in BRCA, LIHC, LUC but the opposite effect in STAD. JMJD5 expression is significant correlation with the abundance of six immune cells infiltration in above four cancers. Both the BRCA or lung adenocarcinoma (LUAD) patients with abundance of B cell and the STAD patients with low level of macrophage have a better cumulative survival. ConclusionsWe provided novel evidence of JMJD5 as an essential prognostic biomarker in cancers through analyses the correlation of the JMJD5 expression, tumor-infiltrating B cells and macrophages and prognostic value. This study offers new perspectives therapeutic target in BRCA, LUAD and STAD.

Inhibition of RFX6 Suppresses the Invasive Ability of Tumor Cells Through the Notch Pathway and Affects Tumor Immunity in Hepatocellular Carcinoma

Frontiers in Oncology ◽

10.3389/fonc.2021.801222 ◽

2021 ◽

Vol 11 ◽

Author(s):

Mu Song ◽

Mulati Kuerban ◽

Lu Zhao ◽

Xiaolin Peng ◽

Youqin Xu

Keyword(s):

Liver Cancer ◽

Cancer Cells ◽

Immune Cell ◽

Biological Effects ◽

Biological Significance ◽

Notch Pathway ◽

Luciferase Assay ◽

Migration And Invasion ◽

BackgroundThe DNA-binding protein RFX6 was overexpressed in hepatocellular carcinoma, and its expression level was correlated with the prognosis and immune cell infiltration in liver hepatocellular carcinoma. However, the mechanism of the abnormal expression and the biological effects of RFX6 in liver cancer remains unknown.MethodsTo understand the specific expression mechanism of RFX6 in liver cancer, we performed bioinformatic prediction, CHIP-qPCR assay, co-IP, and dual-luciferase assay to assess the regulating mechanism of RFX6. In the meantime, a series of biological experiments in vivo and in vitro were conducted to analyze the biological significance of RFX6 in hepatocellular carcinoma.ResultsWe demonstrated that knockdown of RFX6 in liver cancer cells significantly suppressed the proliferation, migration, and invasion of cancer cells. Moreover, inhibition of RFX6 could affect the immune response of T cells. Among a number of interacting proteins, we revealed that RFX6 directly binds to DTX2, a regulator of the Notch signaling pathway by targeting NOTCH1, and helps in its transcription stability. Furthermore, we discovered that miRNA-542-3p, the expression of which was decreased in hepatocellular carcinoma, was directly involved in the negative regulation of the expression of RFX6.ConclusionIn summary, we discovered that the miRNA-542-3p–RFX6–DTX2–NOTCH1 regulatory pathway played significant roles in the tumor progression of liver hepatocellular carcinoma.

A dual immune signature of CD8+ T Cells and MMP9 improves the survival of hepatocellular carcinoma patients

Bioscience Reports ◽

10.1042/bsr20204219 ◽

2021 ◽

Author(s):

Huan Ding ◽

Huan Hu ◽

Feifei Tian ◽

Huaping Liang

Keyword(s):

T Cells ◽

Cd8 T Cells ◽

Immune Cells ◽

Immune Cell ◽

Cox Regression ◽

Gene Expression Omnibus ◽

The Cancer Genome Atlas ◽

High Recurrence Rate ◽

Immune Signature

The 5-year survival of hepatocellular carcinoma (HCC) is difficult due to the high recurrence rate and metastasis. Tumor infiltrating immune cells (TICs) and immune-related genes (IRGs) bring hope to improve survival and treatment of HCC patients. However, there are problems in predicting immune signatures and identifying novel therapeutic targets. In the study, the CIBERSORT algorithm was used to evaluate 22 immune cell infiltration patterns in gene expression omnibus (GEO) and the cancer genome atlas (TCGA) data. Eight immune cells were found to have significant infiltration differences between the tumor and normal groups. The CD8+ T Cells immune signature was constructed by least absolute shrinkage and selection operator (LASSO) algorithm. The high infiltration level of CD8+ T Cells could significantly improve survival of patients. The weighted gene co-expression network analysis (WGCNA) algorithm identified MMP9 was closely related to the overall survival of HCC patients. K-M survival and tROC analysis confirmed that MMP9 had an excellent prognostic prediction. Cox regression showed that a dual immune signature of CD8+ T Cells and MMP9 was independent survival factor in HCC. Therefore, a dual prognostic immune signature could improve the survival of patient and may provide a new strategy for the immunotherapy of HCC.

671 Biological impacts of standard of care chemotherapies on immune effector cells from AML patients

Journal for ImmunoTherapy of Cancer ◽

10.1136/jitc-2021-sitc2021.671 ◽

2021 ◽

Vol 9 (Suppl 3) ◽

pp. A699-A699

Author(s):

Dmitry Zhigarev ◽

Alexander MacFarlane ◽

Christina Drenberg ◽

Reza Nejati ◽

Asya Varshavsky ◽

...

Keyword(s):

Nk Cells ◽

Immune Cells ◽

Immune Cell ◽

Cell Phenotype ◽

Second Line ◽

Color Flow ◽

Immune Effector ◽

Effector Cells ◽

Immune Effector Cells ◽

And Function

BackgroundAcute myeloid leukemia (AML) is a heterogeneous group of malignant bone marrow diseases, characterized by massive and uncontrolled proliferation of myeloid precursor cells, which alters normal blood cell ratios. This disease is common to older adults and collectively displays one of the lowest 5-year overall survival rates (<25%) among all cancers, currently representing the deadliest form of leukemia. Improved treatments are clearly needed, and immunotherapies are attractive candidate therapies to explore.There are currently several standard chemotherapeutic treatment schemes for AML, which could be divided into two major groups: (1) cytotoxic chemotherapy (“7+3” or daunorubicin-cytarabine) and (2) hypomethylating agents (HMAs). HMAs include both 5-azacytidine and decitabine, which are cytidine analogs that inhibit DNA methyltransferase, resulting in the hypomethylation of DNA and inducing expression of silenced gene loci. Currently, HMAs are routinely delivered in combination with the Bcl-2 inhibitor venetoclax.The goals of this study are to determine how these standard first line therapies can affect the frequency and functional integrity of effector immune cells in patients' blood and establish when the phenotype and function of immune cells are restored to identify time windows when second line immunotherapies could be most effective.MethodsMore than 100 blood samples were obtained from 33 previously untreated AML patients. More than 50 measurable biomarkers were analyzed using 14-color flow cytometry to assess immune phenotypes of T and NK cells in peripheral blood of AML patients prior to treatment and at up to four timepoints after initiation of treatment with HMA or chemotherapy.ResultsWe found several significant changes in immune cell phenotype and function that occur in response to these therapies. Treatment with HMAs was strikingly less impactful on immune cells in patients compared to previously published in vitro studies. Nevertheless, HMA treatment increased perforin levels in T and NK cells, inhibited IFN-gamma secretion by CD8+ T cells, and changed expression of several checkpoint molecules. While chemotherapy caused fewer phenotypic changes it dramatically decreased the total number of immune cells. We also determined viable, functional and phenotypical recovery periods for immune effector cells after the treatments.ConclusionsOur results are important for introducing new second line immunotherapies to these chemotherapeutic regimens for treating AML and to improve overall understanding of immune cell behavior under conditions of anti-tumor treatment.AcknowledgementsSupported by grants from Janssen and the U.S./Israel Binational Science Foundation.Ethics ApprovalThe study was approved by the Fox Chase Cancer Center Institutional Review Board, approval number 17-8010, and all patients provided informed consent before taking part in the study.

Integrated Bioinformatics Analysis Identifies Heat Shock Factor 2 as a Prognostic Biomarker Associated With Immune Cell Infiltration in Hepatocellular Carcinoma

Frontiers in Genetics ◽

10.3389/fgene.2021.668516 ◽

2021 ◽

Vol 12 ◽

Author(s):

Yumei Fan ◽

Jiajie Hou ◽

Xiaopeng Liu ◽

Bihui Han ◽

Yanxiu Meng ◽

...

Keyword(s):

Heat Shock ◽

Immune Cells ◽

Immune Cell ◽

Cox Regression ◽

Critical Role ◽

Enrichment Analysis ◽

Normal Liver ◽

Heat Shock Factor ◽

Gene Set Enrichment Analysis

Hepatocellular carcinoma (HCC) is one of the most common malignancies and ranks as the second leading cause of cancer-related mortality worldwide. Heat shock factor 2 (HSF2) is a transcription factor that plays a critical role in development, particularly corticogenesis and spermatogenesis. However, studies examining the expression and prognostic value of HSF2 and its association with tumor-infiltrating immune cells in HCC are still rare. In the present study, we found that HSF2 expression was significantly upregulated in HCC tissues compared with normal liver tissues using the TCGA, ICGC, GEO, UALCAN, HCCDB and HPA databases. High HSF2 expression was associated with shorter survival of patients with HCC. Cox regression analyses and nomogram were used to evaluate the association of HSF2 expression with the prognosis of patients with HCC. Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and gene set enrichment analysis (GSEA) revealed that HSF2 was associated with various signaling pathways, including the immune response. Notably, HSF2 expression was significantly correlated with the infiltration levels of different immune cells using the TIMER database and CIBERSORT algorithm. HSF2 expression also displayed a significant correlation with multiple immune marker sets in HCC tissues. Knockdown of HSF2 significantly inhibited the proliferation, migration, invasion and colony formation ability of HCC cells. In summary, we explored the clinical significance of HSF2 and provided a therapeutic basis for the early diagnosis, prognostic judgment, and immunotherapy of HCC.