Comprehensive analysis of N6-methyladenosine -related long non-coding RNAs and immune cell infiltration in hepatocellular carcinoma

Yu, Zhong Lin; Zhu, Zheng

doi:10.1080/21655979.2021.1923381

Cited by 17 publications

(12 citation statements)

References 35 publications

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“…Transcription and human configuration data were matched by Perl to obtain the precise mRNA gene expression data. The gene IDs were transformed into gene names by R4.1.0 [16]. In order to evaluate the difference of NRGs expression (DEGs) with statistical significance, FDR <0.05 and |log2FC|≥0.585 as a selection criteria.…”

Section: Annotation Of Genes Identification Of Nrgs and Its Mutation Ratesmentioning

confidence: 99%

Novel necroptosis-related gene signature for predicting the prognosis of pancreatic adenocarcinoma

Huang

Cai

et al. 2022

Aging

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Pancreatic adenocarcinoma (PAAD) is a deadly digestive system tumor with a poor prognosis. Recently, necroptosis has been considered as a type of inflammatory programmed cell death. However, the expression of necroptosis-related genes (NRGs) in PAAD and their associations with prognosis remain unclear. NRGs' prediction potential in PAAD samples from The TCGA and GEO datasets was investigated. The prediction model was constructed using Lasso regression. Co-expression analysis showed that gene expression was closely related to necroptosis. NRGs were shown to be somewhat overexpressed in high-risk people even when no other clinical symptoms were present, indicating that they may be utilized in a model to predict PAAD prognosis. GSEA showed immunological and tumor-related pathways in the high-risk group. Based on the findings, immune function and m6A genes differ significantly between the low-risk and high-risk groups. MET, AM25C, MROH9, MYEOV, FAM111B, Y6D, and PPP2R3A might be related to the oncology process for PAAD patients. Moreover, CASKIN2, TLE2, USP20, SPRN, ARSG, MIR106B, and MIR98 might be associated with low-risk patients with PAAD. NRGs and the relationship of the immune function, immune checkpoints, and m6A gene expression with NRGs in PAAD may be considered as potential therapeutic targets that should be further studied.

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Section: Annotation Of Genes Identification Of Nrgs and Its Mutation Ratesmentioning

confidence: 99%

Novel necroptosis-related gene signature for predicting the prognosis of pancreatic adenocarcinoma

Huang

Cai

et al. 2022

Aging

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“…Emerging evidence has demonstrated that m6A-related genes could be prognostic markers for predicting the survival time of patients [ 42 – 44 ]. In recent years, the role of m6A related lncRNAs has been recognized profoundly in HCC [ 45 , 46 ]. And studies in terms of prognosis of HCC patients were also accumulated.…”

Section: Resultsmentioning

confidence: 99%

“…As an instance, high expression level of LINC00958 which is mediated by m6A modification predicts poor overall survival of HCC patients independently [ 47 ]. Moreover, studies using a comprehensive informatics analysis based on data from TCGA database revealed that m6A methylated lncRNA was closely related to the prognosis of HCC [ 48 – 50 ]. However, more effective and specific prognostic biomarkers still needed.…”

Section: Resultsmentioning

confidence: 99%

Identification of m6A-Related lncRNA to Predict the Prognosis of Patients with Hepatocellular Carcinoma

Wang

2022

BioMed Research International

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Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. In the past decades, HCC treatment has achieved great progress; however, the overall prognosis remains poor. Therefore, it is the need of the hour to identify new prognostic biomarkers which can advance our understanding related to the underlying molecular mechanism of adverse prognosis and apply them to clinical work in prognosis prediction. In the present study, data of 576 HCC patients and 292 normal control cases from TCGA and ICGC databases were enrolled to our bioinformatic analysis. SNHG1 and SNHG3 were identified as overlapping genes in TCGA and ICGC databases using Pearson correlation analysis and univariate Cox regression analysis. Further, we used the median of the SNHG1 and SNHG3 expression values as the cutoff values to define the HCC patient groups with high or low expression level. The subsequent analysis revealed that abnormal high expression of SNHG1 or SNHG3 affected the immune infiltration patterns and the crosstalk among immune cells. Moreover, high expression of SNHG1 or SNHG3 resulted in drug resistant to AKT inhibitor VII, bexarotene, bicalutamide, dasatinib, erlotinib, and gefitinib. In addition, lower tumor neoantigen burden was observed in high SNHG1 or SNHG3 group. Further, we found significant relation between the aberrant upregulation of SNHG1 and SNHG3 in tumor grade and stage. We established a nomogram to systematically predict the 5- and 8-year overall survival of liver cancer patients with good accuracy. Finally, the in vitro assays suggest that SNHG1 and SNHG3 promote the proliferative, migratory, and invasive abilities of HCC cells.

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“…Therefore, we suggest that AL157392.3 may influence the development of AML through the glycolytic pathway. Moreover, AC145207.5 was only found to play a role in developing hepatocellular carcinoma, but not in AML ( Yu and Zhu, 2021 ; Zhou et al, 2021 ). The other six lncRNAs were rarely reported in cancers and further research should be conducted to reveal their potential role in AML development.…”

Section: Discussionmentioning

confidence: 98%

Comprehensive Analysis of N6-Methyladenosine-Related Long Noncoding RNA Prognosis of Acute Myeloid Leukemia and Immune Cell Infiltration

et al. 2022

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N6-Methyladenosine-related long noncoding RNAs play an essential role in many cancers’ development. However, the relationship between m6A-related lncRNAs and acute myelogenous leukemia (AML) prognosis remains unclear. We systematically analyzed the association of m6A-related lncRNAs with the prognosis and tumor immune microenvironment (TME) features using the therapeutically applicable research to generate effective treatment (TARGET) database. We screened 315 lncRNAs associated with AML prognosis and identified nine key lncRNAs associated with m6A by the LASSO Cox analysis. A model was established based on these nine lncRNAs and the predictive power was explored in The Cancer Genome Atlas (TCGA) database. The areas under the ROC curve of TARGET and TCGA databases for ROC at 1, 3, and 5 years are 0.701, 0.704, and 0.696, and 0.587, 0.639, and 0.685, respectively. The nomogram and decision curve analysis (DCA) showed that the risk score was more accurate than other clinical indicators in evaluating patients’ prognoses. The clusters with a better prognosis enrich the AML pathways and immune-related pathways. We also found a close correlation between prognostic m6A-related lncRNAs and tumor immune cell infiltration. LAG3 expression at the immune checkpoint was lower in the worse prognostic cluster. In conclusion, m6A-related lncRNAs partly affected AML prognosis by remodeling the TME and affecting the anticarcinogenic ability of immune checkpoints, especially LAG3 inhibitors. The prognostic model constructed with nine key m6A-related lncRNAs can provide a method to assess the prognosis of AML patients in both adults and children.

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Comprehensive analysis of N6-methyladenosine -related long non-coding RNAs and immune cell infiltration in hepatocellular carcinoma

Cited by 17 publications

References 35 publications

Novel necroptosis-related gene signature for predicting the prognosis of pancreatic adenocarcinoma

Novel necroptosis-related gene signature for predicting the prognosis of pancreatic adenocarcinoma

Identification of m6A-Related lncRNA to Predict the Prognosis of Patients with Hepatocellular Carcinoma

Comprehensive Analysis of N6-Methyladenosine-Related Long Noncoding RNA Prognosis of Acute Myeloid Leukemia and Immune Cell Infiltration

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