ncRNAs-mediated high expression of SEMA3F correlates with poor prognosis and tumor immune infiltration of hepatocellular carcinoma

Lou, Weiyang; Wang, Wenlong; Chen, Jing; Wang, Shuqian; Huang, Yuan

doi:10.1016/j.omtn.2021.03.014

Cited by 47 publications

(39 citation statements)

References 42 publications

(44 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Another study reported that interventional treatment of primary liver cancer can reduce serum HTATIP2/TIP30 and B7-H4 levels, improve liver function and quality of life and prolong the survival times of patients (20). A number of studies reported that SEMA3F, UCK2, NOL10, RAP2A, ZIC2 and SAC3D1 are associated with prognosis and tumour immune infiltration in hepatocellular carcinomas (21)(22)(23)(24)(25). In addition, KIF18A was reported to be associated with tumour immune cell infiltration in adrenocortical carcinomas (26).…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics Analysis Using ATAC-seq and RNA-seq for the Identification of 15 Gene Signatures Associated With the Prediction of Prognosis in Hepatocellular Carcinoma

Yang¹,

Li²,

Qiu³

2021

Front. Oncol.

View full text Add to dashboard Cite

BackgroundGene expression (RNA-seq) and overall survival (OS) in TCGA were combined using chromosome accessibility (ATAC-seq) to search for key molecules affecting liver cancer prognosis.MethodsWe used the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) to analyse chromatin accessibility in the promoter regions of whole genes in liver hepatocellular carcinoma (LIHC) and then screened differentially expressed genes (DEGs) at the mRNA level by transcriptome sequencing technology (RNA-seq). We obtained genes significantly associated with overall survival (OS) by a one-way Cox analysis. The three were screened by taking intersection and further using a Kaplan–Meier (KM) for validation. A prognostic model was constructed using the obtained genes by LASSO regression analysis.The expression of these genes in hepatocellular carcinomas was then analysed. The protein expression of these genes was verified using the Human Protein Atlas(HPA) online datasets and immunohistochemistry.ResultsATAC-seq, RNA-seq and survival analysis, combined with a LASSO prediction model, identified signatures of 15 genes (PRDX6, GCLM, HTATIP2, SEMA3F, UCK2, NOL10, KIF18A, RAP2A, BOD1, GDI2, ZIC2, GTF3C6 SLC1A5, ERI3 and SAC3D1), all of which were highly expressed in hepatocellular carcinoma. The LASSO prognostic model showed that this risk score had high predictive accuracy for the survival prognosis at 1, 3 and 5 years. A KM curve analysis showed that high expression of all 15 gene signatures was significantly associated with a poor prognosis in LIHC patients. HPA analysis of protein expression showed that PRDX6, GCLM, HTATIP2, NOL10, KIF18A, RAP2A and GDI2 were highly expressed in the hepatocellular carcinoma tissues compared with normal control tissues.ConclusionsPRDX6, GCLM, HTATIP2, SEMA3F, UCK2, NOL10, KIF18A, RAP2A, BOD1, GDI2, ZIC2, GTF3C6, SLC1A5, ERI3 and SAC3D1 may affect the prognosis of LIHC.

show abstract

Section: Discussionmentioning

confidence: 99%

Bioinformatics Analysis Using ATAC-seq and RNA-seq for the Identification of 15 Gene Signatures Associated With the Prediction of Prognosis in Hepatocellular Carcinoma

Yang¹,

Li²,

Qiu³

2021

Front. Oncol.

View full text Add to dashboard Cite

show abstract

“…Upstream binding miRNAs of LOX was forecasted through the ENCORI pan-cancer analysis platform ( http://starbase.sysu.edu.cn/panCancer.php ), which consists of PITA, RNA22, miRmap, microT, miRanda, PicTar, and TargetScan programs. Only the forecasted miRNAs that simultaneously presented in five or more programs as described above were considered for following analyses ( Lou et al, 2021 ) ( Supplementary Table S1 ). The correlation between miRNAs and LOX in STAD was analyzed by the Spearman method.…”

Section: Methodsmentioning

confidence: 99%

lncRNA/miR-29c-Mediated High Expression of LOX Can Influence the Immune Status and Chemosensitivity and Can Forecast the Poor Prognosis of Gastric Cancer

Nai

Zeng

et al. 2022

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

Gastric carcinoma is the fourth most prevalent cause of cancer-related deaths worldwide because of dismal prognosis and few therapeutic options. Accumulated studies have indicated that targeting lysyl oxidase (LOX) family members may serve as an anticancer strategy. Nevertheless, the specific mechanisms of LOX in stomach carcinoma are still unclear. In this study, we demonstrated that LOX is significantly different in 13 types of cancers and may act as a potential therapeutic target, especially in stomach carcinoma. Moreover, overexpression of LOX in gastric carcinoma was validated by multiple databases and contributed to the poor overall survival (OS), progression-free survival (PFS) and post-progression survival (PPS) of stomach adenocarcinoma (STAD) patients. Next, based on the ceRNA hypothesis, the HIF1A-AS2/RP11-366L20.2-miR-29c axis was characterized as the upstream regulatory mechanism of LOX gene overexpression in gastric cancer by combining correlation analysis, expression analysis, and survival analysis. Finally, we illustrated that LOX gene overexpression leads to dismal prognosis of gastric cancer, perhaps through promoting M2 macrophage polarization and tumor immune escape and enhancing drug resistance of tumor cells to chemotherapeutic drugs. Our research demonstrate that LOX may be potentially applied as a novel prognostic marker and targeting inhibition of LOX holds promise as a treatment strategy for gastric cancer.

show abstract

“…The co-evolution of metastatic cancer cells with the brain microenvironment is critical for metastatic cells’ escaping dormancy and colonizing the brain. The TME landscape in brain metastases was analyzed and MG, MDMs, neutrophils, and CD8+ and CD4+ T cells have been confirmed to be the major immune cell determinants of the brain TME landscape ( 47 , 62 ). To better predict the functions of the above genes in breast cancer, we explored the correlations between gene expression level and infiltration of immune cells.…”

Section: Discussionmentioning

confidence: 99%

Screening and Identification of Novel Potential Biomarkers for Breast Cancer Brain Metastases

et al. 2022

View full text Add to dashboard Cite

Brain metastases represent a major cause of mortality among patients with breast cancer, and few effective targeted treatment options are currently available. Development of new biomarkers and therapeutic targets for breast cancer brain metastases (BCBM) is therefore urgently needed. In this study, we compared the gene expression profiles of the brain metastatic cell line MDA-MB-231-BR (231-BR) and its parental MDA-MB-231, and identified a total of 84 genes in the primary screening through a series of bioinformatic analyses, including construction of protein-protein interaction (PPI) networks by STRING database, identification of hub genes by applying of MCODE and Cytohubba algorithms, identification of leading-edge subsets of Gene Set Enrichment Analysis (GSEA), and identification of most up-regulated genes. Eight genes were identified as candidate genes due to their elevated expression in brain metastatic 231-BR cells and prognostic values in patients with BCBM. Then we knocked down the eight individual candidate genes in 231-BR cells and evaluated their impact on cell migration through a wound-healing assay, and four of them (KRT19, FKBP10, GSK3B and SPANXB1) were finally identified as key genes. Furthermore, the expression of individual key genes showed a correlation with the infiltration of major immune cells in the brain tumor microenvironment (TME) as analyzed by Tumor Immune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA), suggesting possible roles of them in regulation of the tumor immune response in TME. Therefore, the present work may provide new potential biomarkers for BCBM. Additionally, using GSEA, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Enrichment Analysis, we determined the top enriched cellular functions or pathways in 231-BR cells, which may help better understand the biology governing the development and progression of BCBM.

show abstract

ncRNAs-mediated high expression of SEMA3F correlates with poor prognosis and tumor immune infiltration of hepatocellular carcinoma

Cited by 47 publications

References 42 publications

Bioinformatics Analysis Using ATAC-seq and RNA-seq for the Identification of 15 Gene Signatures Associated With the Prediction of Prognosis in Hepatocellular Carcinoma

Bioinformatics Analysis Using ATAC-seq and RNA-seq for the Identification of 15 Gene Signatures Associated With the Prediction of Prognosis in Hepatocellular Carcinoma

lncRNA/miR-29c-Mediated High Expression of LOX Can Influence the Immune Status and Chemosensitivity and Can Forecast the Poor Prognosis of Gastric Cancer

Screening and Identification of Novel Potential Biomarkers for Breast Cancer Brain Metastases

Contact Info

Product

Resources

About