Medical Genetics, Genomics and Bioinformatics—2022

Климонтов, Вадим Валерьевич; Koshechkin, Konstantin; Орлова, Н. А.; Sekacheva, Marina; Orlov, Yuriy L.

doi:10.3390/ijms24108968

Cited by 6 publications

(2 citation statements)

References 28 publications

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“…Fundamental research on the actions of cancer factors has been vigorously conducted in the field of bioinformatics, particularly in genomics and proteomics, due to the progress of sequencing technology and the human genome project in several nations ( 30 ). Researcher participation in the analysis of biological data, the development of untested and unexamined information in biological data, and the execution of follow-up external experimental studies have all been made possible by the growing quantity and quality of public databases, thus contributing to the advancement of various disciplines and fields of research ( 31 , 32 ).…”

Section: Discussionmentioning

confidence: 99%

Identification of prognostic RNA editing profiles for clear cell renal carcinoma

Chen,

Li,

Huang

et al. 2024

Front. Med.

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ObjectiveClear cell renal cell carcinoma (ccRCC) is the most common type of renal cancer and currently lacks effective biomarkers. This research aims to analyze and identify RNA editing profile associated with ccRCC prognosis through bioinformatics and in vitro experiments.MethodsTranscriptome data and clinical information for ccRCC were retrieved from the TCGA database, and RNA editing files were obtained from the Synapse database. Prognostic models were screened, developed, and assessed using consistency index analysis and independent prognostic analysis, etc. Internal validation models were also constructed for further evaluation. Differential genes were investigated using GO, KEGG, and GSEA enrichment analyses. Furthermore, qPCR was performed to determine gene expression in human renal tubular epithelial cells HK-2 and ccRCC cells A-498, 786-O, and Caki-2.ResultsAn RNA editing-based risk score, that effectively distinguishes between high and low-risk populations, has been identified. It includes CHD3| chr17:7815229, MYO19| chr17:34853704, OIP5-AS1| chr15:41590962, MRI1| chr19:13883962, GBP4| chr1:89649327, APOL1| chr22:36662830, FCF1| chr14:75203040 edited sites or genes and could serve as an independent prognostic factor for ccRCC patients. qPCR results showed significant up-regulation of CHD3, MYO19, MRI1, APOL1, and FCF1 in A-498, 786-O, and Caki-2 cells, while the expression of OIP5-AS1 and GBP4 was significantly down-regulated.ConclusionRNA editing site-based prognostic models are valuable in differentiating between high and low-risk populations. The seven identified RNA editing sites may be utilized as potential biomarkers for ccRCC.

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Section: Discussionmentioning

confidence: 99%

Identification of prognostic RNA editing profiles for clear cell renal carcinoma

Chen,

Li,

Huang

et al. 2024

Front. Med.

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“…The BGRS conference series has a history of initiating successful Special Issues on bioinformatics in the bioinformatics journals. The recent examples include special issues at Frontiers in genetics and MDPI International Journal of Molecular Sciences on biomedical applications – “High-Throughput Sequencing-Based Investigation of Chronic Disease Markers and Mechanisms” [ 29 ], “Medical Genetics, Genomics and Bioinformatics” [ 30 , 31 ], and on plant biology – special issue “Plant Biology and Biotechnology” [ 32 ]. We have presented special issues “Research Topics of the Bioinformatics of Gene Regulation” [ 33 ], and the series of the matical issues on genome regulation and systems biology at Frontiers in Genetics journal – Research Topic “Bioinformatics of genome regulation and systems biology” repeating the BGRS conference name and collecting the materials discussed at BGRS\SB meetings [ 34 , 35 ].…”

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confidence: 99%