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Comprehensive assessment of the significance of cellular senescence-associated genes in neuroblastoma.
Genes Genomics
January 2025
Department of Pediatric Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China.
Background: The clinical course of high-risk neuroblastoma patients remains suboptimal, and the dynamic and reversible nature of cellular senescence provides an opportunity to develop new therapies.
Objective: This study aims to identify unique markers of cellular senescence in neuroblastoma and to explore their clinical significance.
Methods: The impact of multiple genetic regulatory mechanisms on cellular senescence-associated genes (CSAGs) was first assessed.
Advances in cancer genomics and precision oncology.
Genes Genomics
January 2025
Department of Smart Farm and Agricultural Industry, Kangwon National University, Chuncheon, 24341, Republic of Korea.
Background: Next-generation sequencing has revolutionized genome science over the last two decades. Indeed, the wealth of sequence information on our genome has deepened our understanding on cancer. Cancer is a genetic disease caused by genetic or epigenetic alternations that affect the expression of genes that control cell functions, particularly cell growth and division.
View Article and Find Full Text PDFMapping the topography of spatial gene expression with interpretable deep learning.
Nat Methods
January 2025
Department of Computer Science, Princeton University, Princeton, NJ, USA.
Spatially resolved transcriptomics technologies provide high-throughput measurements of gene expression in a tissue slice, but the sparsity of these data complicates analysis of spatial gene expression patterns. We address this issue by deriving a topographic map of a tissue slice-analogous to a map of elevation in a landscape-using a quantity called the isodepth. Contours of constant isodepths enclose domains with distinct cell type composition, while gradients of the isodepth indicate spatial directions of maximum change in expression.
View Article and Find Full Text PDFRapid change in red cell blood group systems after the main Out of Africa of Homo sapiens.
Sci Rep
January 2025
Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.
Despite the advances in paleogenomics, red cell blood group systems in ancient human populations remain scarcely known. Pioneer attempts showed that Neandertal and Denisova, two archaic hominid populations inhabiting Eurasia, expressed blood groups currently found in sub-Saharans and a rare "rhesus", part of which is found in Oceanians. Herein we fully pictured the blood group genetic diversity of 22 Homo sapiens and 14 Neandertals from Eurasia living between 120,000 and 20,000 years before present (yBP).
View Article and Find Full Text PDFIdentification of potential biomarkers for 2022 Mpox virus infection: a transcriptomic network analysis and machine learning approach.
Sci Rep
January 2025
Department of Biochemistry and Molecular Biology, Shahjalal University of Science and Technology, Sylhet, 3114, Bangladesh.
Monkeypox virus (MPXV), a zoonotic pathogen, re-emerged in 2022 with the Clade IIb variant, raising global health concerns due to its unprecedented spread in non-endemic regions. Recent studies have shown that Clade IIb (2022 MPXV) is marked by unique genomic mutations and epidemiological behaviors, suggesting variations in host-virus interactions. This study aimed to identify the differentially expressed genes (DEGs) induced by the 2022 MPXV infection through comprehensive bioinformatics analyses of microarray and RNA-Seq datasets from post-infected cell types with different MPXV clades.
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