Objective: This study aims to identify several RNA transcripts associated with the prognosis of kidney renal clear cell carcinoma (KIRC).
Methods: The differentially expressed mRNAs, lncRNAs, and miRNAs (DEmRNAs, DElncRNAs, and DEmiRNAs) between KIRC cases and controls were screened based on an RNA-seq dataset from The Cancer Genome Atlas (TCGA) database. Subsequently, miRcode, miRDB, and TargetScan database were used to predict interactions between lncRNAs, miRNAs and target mRNAs. Then, a ceRNA network was built using miRNAs-mRNAs and lncRNAs-miRNAs pairs. Functional analysis of mRNAs in ceRNA was performed. Finally, the survival analysis of RNA transcripts in ceRNA network and correlation analysis for key RNA regulators were carried out.
Results: There were 1527 DElncRNAs, 54 DEmiRNAs, and 2321 DEmRNAs. A ceRNA network was constructed among 81 lncRNAs, 9 miRNAs, and 197 mRNAs. Functional analysis showed that numerous mRNAs were significantly associated with regulation of cellular glucuronidation. In addition, 35 lncRNAs, 84 mRNAs and two miRNAs were significantly corelated to the survival of patients with KIRC ( < 0.05). Among them, miRNA-21 and miRNA-155 were negatively related to three lncRNAs (LINC00472, SLC25A5.AS1, and TCL6). Seven mRNA targets of miRNA-21 (, , , , , , and ) and 12 mRNAs targets of miRNA-155 (, , , , , , , , , , , and ) also acted as prognostic biomarkers for KIRC patients.
Conclusion: We screened numerous novel prognosis-related RNA markers for KIRC patients by a ceRNA network analysis, providing deeper understandings of prognostic values of RNA transcripts for KIRC.
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http://dx.doi.org/10.3389/fgene.2020.540094 | DOI Listing |
Sci Rep
January 2025
Department of Dermatology, Suining Central Hospital, No. 127, Western Desheng Road, Suining, 629000, People's Republic of China.
Vitiligo is a complex autoimmune skin disorder characterized by depigmentation and immune dysregulation. To elucidate the role of ferroptosis-related genes (FRGs) in vitiligo, we conducted a comprehensive analysis of gene expression data from the GSE53146 and GSE65127 datasets obtained from the GEO database. We identified 31 differentially expressed FRGs (DE-FRGs), with 21 genes upregulated and 10 downregulated.
View Article and Find Full Text PDFFunct Integr Genomics
January 2025
Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, 835215, Jharkhand, India.
Advancements in bioinformatic tools and breakthroughs in high throughput RNA sequencing have unveiled the potential role of non-coding RNAs in influencing the overall expression of disease-responsive genes. Owing to the increasing need to develop resilient crop varieties against environmental constraints, our study explores the functional relationship of various non-coding RNAs in wheat during leaf rust pathogenesis. MicroRNAs (miRNAs) and circular RNAs (circRNAs) were retrieved from SAGE and RNA-Seq libraries, respectively, in the susceptible (HD2329) and resistant (HD2329 + Lr28) wheat Near-Isogenic Lines (NILs).
View Article and Find Full Text PDFAging Dis
January 2025
Institute of Nutrition and Food Technology (INTA), Universidad de Chile, Santiago, Chile.
The gut-brain axis is a bidirectional communication pathway that modulates cognitive function. A dysfunctional gut-brain axis has been associated with cognitive impairments during aging. Therefore, we propose evaluating whether modulation of the gut microbiota through fecal microbiota transplantation (FMT) from young-trained donors (YT) to middle-aged or aged mice could enhance brain function and cognition in old age.
View Article and Find Full Text PDFComb Chem High Throughput Screen
January 2025
Thoracic and Abdominal Radiotherapy Department I, Meizhou People's Hospital, Meizhou 514031, Guangdong, China.
Background: TSPOAP1 antisense RNA 1 (TSPOAP1-AS1) is a long non-coding RNA (lncRNA) that has received widespread attention in oncology research in recent years. Its role and mechanism in some cancers have gradually been revealed. However, it is not clear what role TSPOAP1-AS1 plays in cervical cancer (CESC).
View Article and Find Full Text PDFHeliyon
January 2025
Department of Traditional Chinese Medicine, Yangjiang People's Hospital, Yangjiang, Guangdong, 529525, China.
Objective: Eugenol (EU) from cloves is highly effective against different tumors. The long noncoding ribonucleic acids (lncRNAs), which play a role of competing endogenous RNAs (ceRNAs), suppress microRNAs (miRNAs) involved in post-transcriptional regulatory networks. The present work focused on analyzing how EU affected pre-cancerous breast lesions (PBL).
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