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LBFextract: Unveiling transcription factor dynamics from liquid biopsy data.
Comput Struct Biotechnol J
December 2024
Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, Berlin 10178, Germany.
Motivation: The analysis of circulating cell-free DNA (cfDNA) holds immense promise as a non-invasive diagnostic tool across various human conditions. However, extracting biological insights from cfDNA fragments entails navigating complex and diverse bioinformatics methods, encompassing not only DNA sequence variation, but also epigenetic characteristics like nucleosome footprints, fragment length, and methylation patterns.
Results: We introduce Liquid Biopsy Feature extract (LBFextract), a comprehensive package designed to streamline feature extraction from cfDNA sequencing data, with the aim of enhancing the reproducibility and comparability of liquid biopsy studies.
The impact of circulating nucleosomes on inflammation in acute lung injury.
FASEB J
December 2024
Clinical and Experimental Therapeutics, College of Pharmacy, University of Georgia and Charlie Norwood VA Medical Center, Augusta, Georgia, USA.
Extracellular histones are released in two major forms: free histones and nucleosomes (DNA-bound histones). However, little distinction has been made between these two forms of circulating extracellular histones. Our study detected increased circulating nucleosomes in acute lung injury patients.
View Article and Find Full Text PDFExtracellular Histones Profiles of Pediatric H3K27-Altered Diffuse Midline Glioma.
Mol Diagn Ther
November 2024
Department of Stem Cell Biology and Transplantology, Research Institute of the Medical University of Varna, Varna, Bulgaria.
Background: Diffuse midline glioma, H3 K27-altered (DMG) is a fatal tumour that arises in the midline structures of the brain. When located in the pons, it is more commonly referred to as diffuse intrinsic pontine glioma (DIPG). DMG/DIPG is usually diagnosed when children are < 10 years, and it has a median overall survival of < 12 months after diagnosis.
View Article and Find Full Text PDFHistone modifications of circulating nucleosomes are associated with changes in cell-free DNA fragmentation patterns.
Proc Natl Acad Sci U S A
October 2024
Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong Special Administrative Region, China.
Article Synopsis
- The study focuses on analyzing cell-free DNA (cfDNA) to determine its tissue origin, which is important for research and diagnostics, utilizing a new technique called FRAGHA that looks at fragmentation patterns linked to histone modifications.
- The research demonstrated strong correlations between specific histone modification signals, such as H3K27ac, and various medical conditions, including fetal DNA presence in maternal plasma and liver cancer detection.
- Machine learning algorithms were employed to improve early detection of liver cancer, showcasing how cfDNA fragmentomics can enhance the effectiveness of liquid biopsies in clinical settings.
Targeting NETosis in Acute Brain Injury: A Systematic Review of Preclinical and Clinical Evidence.
Cells
September 2024
Department of Intensive Care, Erasme Hospital, Brussels University Hospital, Université Libre de Bruxelles, 1070 Brussels, Belgium.
Acute brain injury (ABI) remains one of the leading causes of death and disability world-wide. Its treatment is challenging due to the heterogeneity of the mechanisms involved and the variability among individuals. This systematic review aims at evaluating the impact of anti-histone treatments on outcomes in ABI patients and experimental animals and defining the trend of nucleosome levels in biological samples post injury.
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