Clear cell renal carcinoma (ccRCC) is one of the most common renal carcinomas worldwide, which has worse prognosis compared with other subtypes of tumors. We propose a potential RNA regulatory mechanism associated with ccRCC progression. Accordingly, we screened out clinical factors and the expression of RNAs and miRNAs of ccRCC from the TCGA database. 9 lncRNAs (FGF12-AS2, WT1-AS, TRIM36-IT1, AC009093.1, LINC00443, TCL6, COL18A1-AS1, AC110619.1, HOTTIP), 2 miRNAs (mir-155 and mir-21), and 3 mRNAs (COL4A4, ERMP1, PRELID2) were selected from differential expression RNAs and built predictive survival models. The survival models performed very well in predicting prognosis and were found to be highly correlated with tumor stage. In addition, the survival-related lncRNA-miRNA-mRNA (ceRNA) network was constructed by 18 RNAs including 12 mRNAs, 2 miRNAs, and 4 lncRNAs. It is found that the "ECM-receptor interaction," "Pathways in cancer," and "Chemokine signaling pathway" as the main pathways in KEGG pathway analysis. Overall, we established predictive survival model and ceRNA network based on multivariate Cox regression analysis. It may open a new approach and potential biomarkers for clinical prognosis and treatment of ccRCC patients.
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http://dx.doi.org/10.1155/2022/8504441 | DOI Listing |
Nan Fang Yi Ke Da Xue Xue Bao
January 2025
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Guangxi Medical University //Key Laboratory of Biological Molecular Medicine Research, Education Department of Guangxi Zhuang Autonomous Region, Nanning 530021, China.
Objectives: To investigate the association of NUF2 expression with tumor prognosis and its regulatory role in tumor microenvironment.
Methods: We analyzed NUF2 expression, its prognostic value, and is immune-related functions across different cancer types using datasets from the Human Protein Atlas (HPA), TCGA, GTEx, CCLE, and TIMER. RT-qPCR, Western blotting, and immunohistochemistry were used to detect NUF2 expression in liver cancer cell lines and tissue and blood samples from patients with liver cancer.
BMC Genomics
January 2025
MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences / Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao / Sanya, China.
Background: The golden pompano (Trachinotus ovatus) is an economically significant warm-water aquaculture species in China. The time required for sexual maturity of T. ovatus is relatively long.
View Article and Find Full Text PDFHeliyon
July 2024
Cancer Center, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China.
Background: Breast cancer is a highly malignant disease worldwide, but there are currently no sufficient molecular biomarkers to predict patient prognosis and guide radiotherapy. The tumor microenvironment (TME) is an important factor affecting tumor biological function, and changes in its composition are equally relevant to tumor progression and prognosis during radiotherapy.
Methods: Here, we performed bioinformatic analyses using data obtained from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases to screen for molecular biomarkers related to the TME that may influence radiotherapy sensitivity.
Funct 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 PDFSci 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.
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