In silico identification of novel lncRNAs with a potential role in diagnosis of gastric cancer

GRAS1 non-coding RNA protects against DNA damage and cell death by binding and stabilizing NKAP

Non-coding RNA (ncRNA) gene products are involved in diverse biological processes including splicing, epigenetic regulation, gene expression, proliferation, and metabolism. The biological mechanisms by which ncRNAs contribute to cell survival remain poorly understood. We found that the Growth Regulator Antisense 1 (GRAS1) long non-coding RNA (lncRNA) transcript promotes growth in multiple human cell types by protecting against DNA damage. Knockdown of GRAS1 induced DNA damage and cell death, along with significant expression changes in DNA damage response, intrinsic apoptotic signaling, and cellular response to environmental stimulus genes. Extensive DNA damage occurred after GRAS1 knockdown, with numerous double strand breaks occurring in each cell. The number of cells undergoing apoptosis and with fragmented nuclei increased significantly after GRAS1 knockdown. We used RNA antisense purification and mass spectrometry (RAP-MS) to identify the NF-κB activating protein (NKAP) as a direct protein interaction partner of GRAS1 lncRNA. NKAP protein was degraded after GRAS1 knockdown, in a proteasome-dependent manner. Overexpression of GRAS1 or NKAP mitigated the DNA damage effects of GRAS1 knockdown. In summary, GRAS1 and NKAP directly interact to protect against DNA damage and cell death in multiple human cell lines.

Integrative pan-cancer analysis indicates the prognostic importance of long noncoding RNA SNHG17 in human cancers

BACKGROUND

Cancer is one of the most widespread causes of death today. Early diagnosis can dramatically reduce cancer-related mortality. Studies have shown that the lncRNA Small Nucleolar RNA Host Gene 17 (SNHG17) is aberrantly expressed in various types of solid tumors. Nevertheless, its prognostic value remains to be elucidated. The main objective of this meta-analysis was to elucidate whether SNHG17 can be considered as a potential prognostic biomarker for a variety of cancers.

METHODS

Correlational studies were screened from Cochrane, Embase, PubMed, and Web of Science. Hazard ratios (HRs) and odds ratios (ORs) with 95% confidence intervals (CIs) were pooled, and the role of SNHG17 in cancer was analyzed. The Cancer Genome Atlas (TCGA) database was employed to verify the results.

RESULTS

Seventeen original papers including 1451 patients were included in the meta-analysis. SNHG17 expression was upregulated in various cancers. Overexpression of SNHG17 was significantly correlated with worse overall survival (OS) (HR = 1.92, 95% CI 1.55-2.37, P < 0.001) and relapse-free survival (RFS) (HR = 1.87, 95% CI 1.06-3.30, P = 0.030). Furthermore, overexpression of SNHG17 was predictive of earlier lymph node metastasis (LNM) (OR = 2.94, 95% CI 2.29-3.78, P < 0.001), more advanced tumor-node-metastases (TNM) stage (OR = 3.56, 95% CI 2.22-5.68, P < 0.001), larger tumor size (OR = 2.18, 95% CI 1.65-2.88, P < 0.001), worse differentiation grade (OR = 1.69, 95% CI 1.26-2.25, P < 0.001), and earlier distant metastasis (DM) (OR = 1.63, 95% CI 1.03-2.56, P = 0.033) in human cancers. Moreover, further inquiry based on TCGA dataset validated that SNHG17 was high expression in various tumors and foresaw unfavorable clinical prognosis.

CONCLUSIONS

Overexpression of SNHG17 correlates with poor prognosis and advanced clinicopathological features in cancer patients and may be a potential prognostic indicator and a therapeutic target for cancer treatment.

FOXP4-AS1 May be a Potential Prognostic Biomarker in Human Cancers: A Meta-Analysis and Bioinformatics Analysis

Background

Cancer is one of the leading causes of death worldwide. Early diagnosis can significantly lower cancer-related mortality. Studies have shown that the lncRNA Forkhead box P4 antisense RNA 1 (FOXP4-AS1) is aberrantly expressed in various solid tumors. A meta-analysis was performed to evaluate the correlation of FOXP4-AS1 with the prognosis of cancer patients and determine the clinical value of FOXP4-AS1 as a potential diagnostic marker.

Methods

Correlational studies from the Web of Science, Embase, OVID, Cochrane and PubMed databases were screened (up to April 1, 2021). Meta-analysis was performed using Stata SE12.0 software.

Results

Eleven original studies with 1,332 patients who were diagnosed with a solid cancer (nasopharyngeal carcinoma, hepatocellular carcinoma, colorectal cancer, gastric cancer, osteosarcoma, mantle cell lymphoma, prostate cancer, and pancreatic ductal adenocarcinoma) were included in the meta-analysis. High expression of FOXP4-AS1 was correlated with poor overall survival (OS) (HR = 1.77, 95% CI 1.29-2.44, P < 0.001) and shorter disease-free survival (DFS) (HR = 1.66, 95% CI 1.01-2.72, P = 0.044). Subgroup analysis based on sample size, follow-up time and Newcastle-Ottawa Scale (NOS) score revealed significant differences between FOXP4-AS1 levels and OS (P < 0.05). However, the expression level of FOXP4-AS1 was not significantly correlated with the OS of gastric cancer patients (P = 0.381). High expression of FOXP4-AS1 was predictive of a larger tumor size (OR = 3.82, 95% CI 2.3-6.3, P < 0.001).

Conclusions

Overexpression of FOXP4-AS1 correlates with poor prognosis of cancer patients, and is a potential prognostic biomarker and therapeutic target.

Systematic Review Registration

PROSPERO, identifier CRD42021245267.

In Silico Identification of miRNA-lncRNA Interactions in Male Reproductive Disorder Associated with COVID-19 Infection

Coronavirus disease 2019 (COVID-19), a global pandemic, is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Angiotensin-converting enzyme 2 (ACE2) is the receptor for SARS-CoV-2 and transmembrane serine protease 2 (TMPRSS2) facilitates ACE2-mediated virus entry. Moreover, the expression of ACE2 in the testes of infertile men is higher than normal, which indicates that infertile men may be susceptible to be infected and SARS-CoV-2 may cause reproductive disorder through the pathway induced by ACE2 and TMPRSS2. Little is known about the pathway regulation of ACE2 and TMPRSS2 expression in male reproductive disorder. Since the regulation of gene expression is mediated by microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) at the post-transcriptional level, the aim of this study was to analyze the dysregulated miRNA–lncRNA interactions of ACE2 and TMPRSS2 in male reproductive disorder. Using bioinformatics analysis, we speculate that the predicted miRNAs including miR-125a-5p, miR-125b-5p, miR-574-5p, and miR-936 as regulators of ACE2 and miR-204-5p as a modulator of TMPRSS2 are associated with male infertility. The lncRNAs with a tissue-specific expression for testis including GRM7-AS3, ARHGAP26-AS1, BSN-AS1, KRBOX1-AS1, CACNA1C-IT3, AC012361.1, FGF14-IT1, AC012494.1, and GS1-24F4.2 were predicted. The identified miRNAs and lncRNAs are proposed as potential biomarkers to study the possible association between COVID-19 and male infertility. This study encourages further studies of miRNA–lncRNA interactions to explain the molecular mechanisms of male infertility in COVID-19 patients.