scholarly journals Identification of Therapeutic Targets and Prognostic Biomarkers among Genes from the Mediator Complex Family in the Hepatocellular Carcinoma Tumour-Immune Microenvironment

2022 ◽  
Vol 2022 ◽  
pp. 1-22
Author(s):  
Wei Tan ◽  
Shuai Peng ◽  
Zhuokai Li ◽  
Ruiqian Zhang ◽  
Yangrui Xiao ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
B Cells ◽  
Functional Enrichment ◽  
High Expression ◽  
Mediator Complex ◽  
Immune Microenvironment ◽  
Expression Levels ◽  
Study Results ◽  
Liver Cancers

Background. Hepatocellular carcinoma (HCC) is predominant among all types of primary liver cancers characterised by high morbidity and mortality. Genes in the mediator complex (MED) family are engaged in the tumour-immune microenvironment and function as regulatory hubs mediating carcinogenesis and progression across diverse cancer types. Whereas research studies have been conducted to examine the mechanisms in several cancers, studies that systematically focused on the therapeutic and prognostic values of MED in patients with HCC are limited. Methods. The online databases ONCOMINE, GEPIA, UALCAN, GeneMANIA, cBioPortal, OmicStudio, STING, Metascape, and TIMER were used in this study. Results. The transcriptional levels of all members of the MED family in HCC presented an aberrant high expression pattern. Significant correlations were found between the MED1, MED6, MED8, MED10, MED12, MED15, MED17, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, and MED27 expression levels and the pathological stage in the patients with HCC. The patients with high expression levels of MED6, MED8, MED10, MED17, MED19, MED20, MED21, MED22, MED24, and MED25 were significantly associated with poor prognosis. Functional enrichment analysis revealed that the members of the MED family were mainly enriched in the nucleobase-containing compound catabolic process, regulation of chromosome organisation, and transcriptional regulation by TP53. Significant correlations were found between the MED6, MED8, MED10, MED17, MED19, MED20, MED21, MED22, MED24, and MED25 expression levels and all types of immune cells (B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells). B cells and MED8 were independent predictors of overall survival. We found significant correlations between the somatic copy number alterations of the MED6, MED8, MED10, MED20, MED21, MED22, MED24, and MED25 molecules and the abundance of immune infiltrates. Conclusions. Our study delineated a thorough landscape to investigate the therapeutic and prognostic potentials of the MED family for HCC cases, which yielded promising results for the development of immunotherapeutic drugs and construction of a prognostic stratification model.

scholarly journals High Expression Levels of SLC38A1 Are Correlated with Poor Prognosis and Defective Immune Infiltration in Hepatocellular Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-15
Author(s):  
Yun Liu ◽  
Yong Yang ◽  
Linna Jiang ◽  
Hongrui Xu ◽  
Junwei Wei
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Death ◽  
Programmed Cell Death ◽  
Protein Expression ◽  
Prognostic Significance ◽  
Functional Enrichment ◽  
High Expression ◽  
Expression Levels ◽  
Immune Infiltration ◽  
Mrna And Protein Expression

Solute Carrier Family 38 Member 1 (SLC38A1) is a principal transporter of glutamine and plays a crucial role in the transformation of neoplastic cells. However, the correlation between SLC38A1 expression, prognosis, and immune infiltration in hepatocellular carcinoma (HCC) has yet to be elucidated. We used two independent patient cohorts, namely, a Cancer Genome Atlas (TCGA) cohort and a Clinical Proteomic Tumor Analysis Consortium (CPTAC) cohort, to analyze the role of SLC38A1 in HCC at the mRNA and protein levels, respectively. In these two cohorts, SLC38A1 mRNA and protein expression levels were higher in HCC tissues than in adjacent nontumor tissues. Both SLC38A1 mRNA and protein expression were positively associated with clinicopathological characteristics (clinical stage, T stage, pathological grade, tumor size, and tumor thrombus), were negatively associated with survival, and were independent prognostic factors in HCC patients. Functional enrichment analyses further indicated that SLC38A1 was involved in multiple pathways related to amino acid metabolism, tumors, and immunity. High expression levels of SLC38A1 were inversely proportional to CD8+ T cells and directly proportional to macrophages M0, neutrophils, programmed cell death-1/programmed cell death ligand 1 (PD-1/PD-L1), and cytotoxic T lymphocyte-associated protein 4 (CTLA-4). Moreover, we used immunohistochemical analysis of tissue samples and other online databases to further validate the expression levels and prognostic significance of SLC38A1 in HCC. Collectively, our study demonstrated that the upregulated expression of SLC38A1 was related to an unfavorable prognosis and defective immune infiltration in HCC.

scholarly journals High Expression of ANXA2 Pseudogene ANXA2P2 Promotes an Aggressive Phenotype in Hepatocellular Carcinoma

2019 ◽  
Vol 2019 ◽  
pp. 1-11 ◽  
Author(s):  
Qiu-shuang Wang ◽  
Liang-Liang Shi ◽  
Fei Sun ◽  
Yi-fan Zhang ◽  
Ren-Wang Chen ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Disease Free Survival ◽  
Annexin A2 ◽  
The Cancer Genome Atlas ◽  
High Expression ◽  
Migration And Invasion ◽  
Targeted Drugs ◽  
Noncancerous Tissue ◽  
Expression Levels ◽  
Hcc Cells

Objective. Accumulating evidence suggests that pseudogenes play potential roles in the regulation of their cognate wild-type genes, oncogenes, and tumor suppressor genes. ANXA2P2 (annexin A2 pseudogene 2) is one of three pseudogenes of annexin A2 that have recently been shown to be aberrantly transcribed in hepatocellular carcinoma (HCC) cells. However, its clinical meaning and biological function in HCC have remained unclear. Therefore, the present study was aimed at exploring the prognostic value of a high expression of ANXA2P2 in HCC tissue and at identifying whether it can affect the efficacy of targeted drugs (sorafenib, regorafenib, and lenvatinib). Methods. We obtained ANXA2P2 mRNA expression levels from The Cancer Genome Atlas (TCGA) RNA sequence database. The expression levels of ANXA2P2 in 49 pairs of intratumoral and peritumoral liver tissues were examined by RT-PCR. Wound healing and transwell assays were performed to confirm the tumor-promoting properties of ANXA2P2 in HCC cells. CCK8 assay was conducted to identify whether ANXA2P2 can affect the growth of HCC cells when administered with targeted drugs (sorafenib, regorafenib, and lenvatinib). Results. The expression of ANXA2P2 in HCC tissues was significantly higher than that in adjacent cancerous tissues from TCGA database and validation group. Additionally, patients with high ANXA2P2 expression in HCC tissue had a shorter overall survival, whereas no statistically significant correlation was found between ANXA2P2 expression and disease-free survival (p=0.08) as well as other clinical parameters, such as age, gender, histological grade, T classification, stage, albumin level, alpha-fetoprotein, and vascular invasion (p=0.7323, 0.8807, 0.5762, 0.8515, 0.7113, 0.242, 1.0000, and 0.7685, respectively). Furthermore, in vitro experiments showed that knockdown of ANXA2P2 inhibited migration and invasion of HCC cells but did not have an influence on the HCC cell proliferation when treated with targeted drugs (sorafenib, regorafenib, and lenvatinib). Conclusion. Our study confirmed elevated ANXA2P2 expression levels in HCC tissue compared with adjacent noncancerous tissue and a worse prognosis of patients with high ANXA2P2 levels in the HCC tissue. The newly found properties of promoting migration and invasion of ANXA2P2 in HCC help to explain this phenomenon. ANXA2P2 could be a novel and suitable predicative biomarker for the risk assessment of recurrence or metastasis of HCC patients but may not be effective to predict the efficacy of targeted drugs.

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

2021 ◽  
Vol 27 ◽  
Author(s):  
Wanbang Zhou ◽  
Yiyang Chen ◽  
Ruixing Luo ◽  
Zifan Li ◽  
Guanwei Jiang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
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.

scholarly journals Interaction between tumour-infiltrating B cells and T cells controls the progression of hepatocellular carcinoma

Gut ◽  
2015 ◽  
Vol 66 (2) ◽  
pp. 342-351 ◽  
Author(s):  
Marta Garnelo ◽  
Alex Tan ◽  
Zhisheng Her ◽  
Joe Yeong ◽  
Chun Jye Lim ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
B Cells

scholarly journals Deep Profiling of the Immune Microenvironment throughout Myeloma Disease Stages

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 727-727
Author(s):  
Megan Darrington ◽  
Frits van Rhee ◽  
Carolina Schinke ◽  
Maurizio Zangari ◽  
Sharmilan Thanendrarajan ◽  
...  
Keyword(s):  
T Cells ◽  
B Cells ◽  
Nk Cells ◽  
Board Of Directors ◽  
Lower Percentage ◽  
Population Abundance ◽  
Regulatory Cells ◽  
Immune Microenvironment ◽  
Advisory Committees ◽  
B Regulatory Cells

Abstract Background The immune system is altered in multiple myeloma (MM) and contributes to therapy resistance. The availability of novel immunotherapies necessitates understanding the influence of the immune microenvironment on disease progression which may inform sensitivity to therapy. The objective of this study is to fully characterize the immune microenvironment in MM precursor diseases and MM and identify any immune contribution to progression. To accomplish this we used high-dimensional mass cytometry (CyTOF) to investigate immune alterations associated with progression in pre-malignant and malignant stages of MM. Methods Cryopreserved bone marrow mononuclear cells (BMMCs) from healthy donors (HD, n=13), MGUS (n=21), SMM (n=19), newly diagnosed MM (NDMM, n=17), and ~3 months post- first autologous stem cell transplant (ASCT, n=21) were assessed using a panel of 35 cell surface and 3 intracellular antibodies that includes cell lineage markers for identification of immune populations and functional markers indicative of positive or negative immune regulation. BMMCs were thawed, stained with antibodies, and analyzed on a Helios mass cytometer. Data were normalized using bead normalization, transformed using the inverse hyperbolic sine function with a cofactor of 5 and gated for 45+ live, intact, singlets for global analysis by gating in FCS express and clustering by viSNE for visualization. Differences in population abundance were identified in an unbiased manner by FlowSOM and in marker intensity by CITRUS. Marker intensity analysis was performed using the multiple testing permutation procedure (SAM), with an FDR of 1% and minimum population size of 0.5%. Results To identify changes in the immune microenvironment associated with progression we compared immune population abundance and marker intensity indicative of immune status including activation, exhaustion, or senescence. MGUS was distinguished from HD by increased abundance of CD4 central memory (CM, p<0.001), effector memory (EM, p<0.001) and plasmacytoid and monocyte-derived dendritic cells (DC, p< 0.01). In MGUS, TIM3 and CD57 were elevated on NK cells and NKT cells, respectively, compared to HD suggesting reduced activity. In SMM increased abundance of B regulatory cells (3.0 vs 5.9 %, p<0.01) but reduced inhibitory markers on T cells including PD1, CTLA4 CD55, FOXP3 and TIGIT was observed compared to MGUS. NDMM was distinguished from SMM by reduced abundance of CD4 EM (p<0.01), CD8 early EM (p< 0.001), and B regulatory cells (p<0.01) and increased abundance of active Tregs (CD38+, P<0.01) and total NK cells (p<0.01) which had increased CD55, a complement inhibitory protein. Post-ASCT changes in immune abundance include increased total CD8 and CD8 terminal effectors (CD57 +, p< 0.0001), B regulatory cells (p<0.0001), and reduced total CD4 and CD4 CM (p<0.0001), compared to NDMM. CD4 T cells post-ASCT were characterized by reduced CD127 and CCR7 and increased CD28, CTLA4, FOXP3 and TIGIT and CD8 T cells had reduced CD28, CD127 and CCR7 and increased CD57 and TIGIT compared to NDMM. Interestingly, significant difference in NK cells were not observed but post-ASCT NK cells may be active as suggested by reduced CD59 and TIM3 compared to NDMM. To determine whether the immune microenvironment had normalized by 3 months post-ASCT we compared population abundance to HD, MGUS, and SMM cases. Immune abundance post-ASCT revealed a significantly lower percentage of CD4 CM, 4 -8 - T cells, normal PCs, and post-switch B cells (25+) and elevated CD8 terminal effector (57+) and B regulatory cells than all 3 other groups. Overall major differences in abundance of total T and B cells and their subsets were observed with differences in NK cells between stages primarily reflected in marker expression (e.g. CD161+ subset) rather than abundance. Conclusions Early changes in the immune microenvironment observed in MGUS/SMM lead to immune suppression and eventually immune evasion allowing MM to emerge. In this study the immune ME did not appear to normalize 3 months post-therapy indicated by an increase in B regulatory cells and markers of inactive effector cells. Profiling of the immune microenvironment throughout MM treatment may allow us to identify novel therapeutic targets and optimal timing of administration of novel immunotherapies and patients that would most benefit from these therapies. Disclosures Walker: Sanofi: Speakers Bureau; Bristol Myers Squibb: Research Funding. Morgan: BMS: Membership on an entity's Board of Directors or advisory committees; Jansen: Membership on an entity's Board of Directors or advisory committees; Karyopharm: Membership on an entity's Board of Directors or advisory committees; Oncopeptides: Membership on an entity's Board of Directors or advisory committees; GSK: Membership on an entity's Board of Directors or advisory committees.

scholarly journals High expression levels of CLEC4M indicate poor prognosis in patients with hepatocellular carcinoma

2020 ◽  
Author(s):  
Liuping Luo ◽  
Lihong Chen ◽  
Kun Ke ◽  
Bixing Zhao ◽  
Lili Wang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Poor Prognosis ◽  
High Expression ◽  
Expression Levels

scholarly journals DUSP12 regulates the tumorigenesis and prognosis of hepatocellular carcinoma

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11929
Author(s):  
Gaoda Ju ◽  
Tianhao Zhou ◽  
Rui Zhang ◽  
Xiaozao Pan ◽  
Bing Xue ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
Immune Cells ◽  
Malignant Tumors ◽  
Critical Role ◽  
Normal Liver ◽  
Functional Enrichment ◽  
Loss Of Function ◽  
Liver Tissues

Background Dual specificity protein phosphatase (DUSP)12 is an atypical member of the protein tyrosine phosphatase family, which are overexpressed in multiple types of malignant tumors. This protein family protect cells from apoptosis and promotes the proliferation and motility of cells. However, the pathological role of DUSP12 in hepatocellular carcinoma (HCC) is incompletely understood. Methods We analyzed mRNA expression of DUSP12 between HCC and normal liver tissues using multiple online databases, and explored the status of DUSP12 mutants using the cBioPortal database. The correlation between DUSP12 expression and tumor-infiltrating immune cells was demonstrated using the Tumor Immune Estimation Resource database and the Tumor and Immune System Interaction Database. Loss of function assay was utilized to evaluate the role of DUSP12 in HCC progression. Results DUSP12 had higher expression along with mRNA amplification in HCC tissues compared with those in normal liver tissues, which suggested that higher DUSP12 expression predicted shorter overall survival. Analyses of functional enrichment of differentially expressed genes suggested that DUSP12 regulated HCC tumorigenesis, and that knockdown of DUSP12 expression by short hairpin (sh)RNA decreased the proliferation and migration of HCC cells. Besides, DUSP12 expression was positively associated with the infiltration of cluster of differentiation (CD)4+ T cells (especially CD4+ regulatory T cells), macrophages, neutrophils and dendritic cells. DUSP12 expression was positively associated with immune-checkpoint moieties, and was downregulated in a C3 immune-subgroup of HCC (which had the longest survival). Conclusion These data suggest that DUSP12 may have a critical role in the tumorigenesis, infiltration of immune cells, and prognosis of HCC.

scholarly journals Expression and prognosis analysis of JMJD5 in human cancers

2020 ◽  
Author(s):  
Hui Li ◽  
Qun Li ◽  
Hong Jing ◽  
Jianghai Zhao ◽  
Hui Zhang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
B Cells ◽  
Lung Adenocarcinoma ◽  
Immune Cells ◽  
Prognostic Value ◽  
Normal Tissues ◽  
Human Cancers ◽  
Stomach Adenocarcinoma ◽  
Liver Hepatocellular Carcinoma

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.

scholarly journals Histone Methyltransferase G9a-Promoted Progression of Hepatocellular Carcinoma Is Targeted by Liver-Specific Hsa-miR-122

Cancers ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 2376
Author(s):  
Lan-Ting Yuan ◽  
Wei-Jiunn Lee ◽  
Yi-Chieh Yang ◽  
Bo-Rong Chen ◽  
Ching-Yao Yang ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Cell Lines ◽  
Colony Formation ◽  
Disease Free Survival ◽  
Histone Methyltransferase ◽  
Control Group ◽  
Functional Evaluation ◽  
Expression Levels ◽  
Liver Cancers ◽  
Hcc Cells

Hepatocellular carcinoma (HCC) accounts for the majority of primary liver cancers, which is the second most lethal tumor worldwide. Epigenetic deregulation is a common trait observed in HCC. Recently, increasing evidence suggested that the G9a histone methyltransferase might be a novel regulator of HCC development. However, several HCC cell lines were recently noted to have HeLa cell contamination or to have been derived from non-hepatocellular origin, suggesting that functional validation of G9a in proper HCC models is still required. Herein, we first confirmed that higher G9a messenger RNA and protein expression levels were correlated with poor overall survival (OS) and disease-free survival (DFS) rates of HCC patients from The Cancer Genome Atlas (TCGA) dataset and our recruited HCC cohort. In an in vitro functional evaluation of HCC cells, HCC36 (hepatitis B virus-positive (HBV+) and Mahlavu (HBV−)) cells showed that G9a participated in promoting cell proliferation, colony formation, and migration/invasion abilities. Moreover, orthotopic inoculation of G9a-depleted Mahlavu cells in NOD-SCID mice also resulted in a significantly decreased tumor burden compared to the control group. Furthermore, after surveying microRNA (miRNA; miR) prediction databases, we identified the liver-specific miR-122 as a G9a-targeting miRNA. In various HCC cell lines, we observed that miR-122 expression levels tended to be inversely correlated to G9a expression levels. In clinical HCC specimens, a significant inverse correlation of miR-122 and G9a mRNA expression levels was also observed. Functionally, the colony formation and invasive ability were attenuated in miR-122-overexpressing HCC cells. HCC patients with low miR-122 and high G9a expression levels had the worst OS and DFS rates compared to others. Together, our results confirmed the importance of altered G9a expression during HCC progression and discovered that a novel liver-specific miR-122-G9a regulatory axis exists.

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