LncRNA THAP9-AS1 highly expressed in tissues of hepatocellular carcinoma and accelerates tumor cell proliferation

In silico analysis of lncRNA-miRNA-mRNA signatures related to Sorafenib effectiveness in liver cancer cells

BACKGROUND

Hepatocellular carcinoma (HCC) is the most common subtype of primary liver cancer with varied incidence and epidemiology worldwide. Sorafenib is still a recommended treatment for a large proportion of patients with advanced HCC. Different patterns of treatment responsiveness have been identified in differentiated hepatoblastoma HepG2 cells and metastatic HCC SNU449 cells.

AIM

To define the long non-codingRNA-microRNA-mRNA (lncRNA-miRNA-mRNA) predicted signatures related to selected hallmarks of cancer (apoptosis, autophagy, cell stress, cell dedifferentiation and invasiveness) in RNAseq studies using Sorafenib-treated HepG2 and SNU449 cells. Various available software analyses allowed us to establish the lncRNA-miRNA-mRNA regulatory axes following treatment in HepG2 and SNU449 cells.

METHODS

HepG2 and SNU449 cells were treated with Sorafenib (10 μmol/L) for 24 hours. Total RNA, including small and long RNA, was extracted with a commercial miRNeasy kit. RNAseq was carried out for the identification of changes in lncRNA-miRNA-mRNA regulatory axes.

RESULTS

MALAT, THAP9-AS1 and SNGH17 appeared to coordinately regulate miR-374b-3p and miR-769-5p that led to upregulation of SMAD7, TIRARP, TFAP4 and FAXDC2 in HepG2 cells. SNHG12, EPB41 L4A-AS1, LINC01578, SNHG12 and GAS5 interacted with let-7b-3p, miR-195-5p and VEGFA in SNU449 cells. The axes MALAT1/hsa-mir-374b-3p/SMAD7 and MALAT1/hsa-mir-769-5p/TFAP4 were of high relevance for Sorafenib response in HepG2 cells, whereas PVT1/hsa-miR-195-5p/VEGFA was responsible for the differential response of SNU449 cells to Sorafenib treatment.

CONCLUSION

Critical lncRNAs acting as sponges of miRNA were identified that regulated mRNA expression, whose proteins mainly increased the antitumor effectiveness of the treatment (SMAD7, TIRARP, TFAP4, FAXDC2 and ADRB2). However, the broad regulatory axis leading to increased VEGFA expression may be related to the side effect of Sorafenib in SNU449 cells.

Genome-wide detection of m6A-associated SNPs in atrial fibrillation pathogenesis

Objective

N6-Methyladenosine (m6A) modification is of great importance in both the pathological conditions and physiological process. The m6A single nucleotide polymorphisms (SNPs) are associated with cardiovascular diseases including coronary artery disease, heart failure. However, it is unclear whether m6A-SNPs are involved in atrial fibrillation (AF). Here, we aimed to explore the relationship between m6A-SNPs and AF.

Method

The relationship between m6A-SNPs and AF was evaluated by analyzing the AF genome-wide association study (GWAS) and m6A-SNPs annotated by the m6AVar database. Further, eQTL and gene differential expression analysis were performed to confirm the association between these identified m6A-SNPs and their target genes in the development of AF. Moreover, we did the GO enrichment analysis to figure out the potential functions of these m6A-SNPs affected genes.

Result

Totally, 105 m6A-SNPs were identified to be significantly associated with AF (FDR < 0.05), among which 7 showed significant eQTL signals on local genes in the atrial appendage. By using four public AF gene expression datasets, we identified genes SYNE2, USP36, and THAP9 containing SNPs rs35648226, rs900349, and rs1047564 were differentially expressed in AF population. Further, SNPs rs35648226 and rs1047564 are potentially associated with AF by affecting m6A modification and both of them might have an interaction with RNA-binding protein, PABPC1.

Conclusion

In summary, we identified m6A-SNPs associated with AF. Our study provided new insights into AF development as well as AF therapeutic target.

Identification and validation of a novel cuproptosis-related lncRNA signature for prognosis and immunotherapy of head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is a highly prevalent and heterogeneous malignancy with a dismal overall survival rate. Nevertheless, the effective biomarkers remain ambiguous and merit further investigation. Cuproptosis is a novel defined pathway of programmed cell death that contributes to the progression of cancers. Meanwhile, long non-coding RNAs (lncRNAs) play a crucial role in the biological process of tumors. Nevertheless, the prognostic value of cuproptosis-related lncRNAs in HNSCC is still obscure. This study aimed to develop a new cuproptosis-related lncRNAs (CRLs) signature to estimate survival and tumor immunity in patients with HNSCC. Herein, 620 cuproptosis-related lncRNAs were identified from The Cancer Genome Atlas database through the co-expression method. To construct a risk model and validate the accuracy of the results, the samples were divided into two cohorts randomly and equally. Subsequently, a prognostic model based on five CRLs was constructed by the Cox regression analysis with the least absolute shrinkage and selection operator (LASSO) algorithm. In addition, the prognostic potential of the five-CRL signature was verified via Cox regression, survival analysis, the receiver operating characteristic (ROC) curve, nomogram, and clinicopathologic characteristics correlation analysis. Furthermore, we explored the associations between the signature risk score (RS) and immune landscape, somatic gene mutation, and drug sensitivity. Finally, we gathered six clinical samples and different HNSCC cell lines to validate our bioinformatics results. Overall, the proposed novel five-CRL signature can predict prognosis and assess the efficacy of immunotherapy and targeted therapies to prolong the survival of patients with HNSCC.