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http://dx.doi.org/10.1164/rccm.202308-1331LE | DOI Listing |
PLoS One
September 2025
Department of Haematology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia.
Acute myeloid leukaemia-normal karyotype (AML-NK) exhibits heterogeneity in expression profiles, influencing the treatment response and survival outcome. Transcriptome sequencing allows a comprehensive analysis of differentially expressed genes (DEGs) and dysregulated pathways in AML-NK, shedding light on the molecular mechanisms and their implications in patients' management. DEG analyses utilising transcriptome sequencing were conducted using a customised DESeq2 pipeline on 51 AML-NK patients at diagnosis (DX), 12 AML-NK patients who attained first remission (CR1) and 12 healthy controls.
View Article and Find Full Text PDFRNA can fold to form complex three-dimensional tertiary structures, with large roles in RNA biology. However, accurate discovery of motifs that form true tertiary structures remains an unsolved challenge. Here we demonstrate that at rare but distinctive sites, RNA tertiary folding creates electronegative pockets that undergo selective chemistry with a small positively-charged chemical probe, trimethyloxonium (TMO).
View Article and Find Full Text PDFAm J Hum Genet
August 2025
Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA. Electronic address:
Transcriptome-wide association studies (TWASs) have been developed to identify candidate genes associated with complex traits by integrating genome-wide association studies (GWASs) with expression quantitative trait loci (eQTL) data. However, most existing TWAS methods assess the marginal association between a single gene and a trait of interest, ignoring the influence of other genes in the same genomic region. Furthermore, false-positive gene-trait associations may arise due to correlations between eQTLs and nearby causal genetic variants.
View Article and Find Full Text PDFNucleic Acids Res
August 2025
Department of Chemistry and State Key Laboratory of Marine Environmental Health, City University of Hong Kong, Hong Kong SAR, 000000, China.
TDP-43 is a hallmark protein associated with neurodegenerative diseases. Recent studies revealed TDP-43 as an RNA G-quadruplex (rG4)-binding protein, impacting mRNA transport and function. However, our knowledge of the TDP-43-RNA secondary structure interaction and information on its specific rG4 targets are limited.
View Article and Find Full Text PDFPLoS Comput Biol
September 2025
Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.
Root causal genes correspond to the first gene expression levels perturbed during pathogenesis by genetic or non-genetic factors. Targeting root causal genes has the potential to alleviate disease entirely by eliminating pathology near its onset. No existing algorithm has been designed to discover root causal genes from observational data alone.
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