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Genetic ancestry superpopulations show distinct prevalence and outcomes across pediatric central nervous system tumors from the PBTA and PNOC.
Neuro Oncol
January 2025
Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
Background: Central nervous system (CNS) tumors lead to cancer-related mortality in children. Genetic ancestry-associated cancer prevalence and outcomes have been studied, but is limited.
Methods: We performed genetic ancestry prediction in 1,452 pediatric patients with paired normal and tumor whole genome sequencing from the Open Pediatric Cancer (OpenPedCan) project to evaluate the influence of reported race and ethnicity and ancestry-based genetic superpopulations on tumor histology, molecular subtype, survival, and treatment.
Predicting transcriptional changes induced by molecules with MiTCP.
Brief Bioinform
November 2024
Department of Automation, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 200240, China.
Studying the changes in cellular transcriptional profiles induced by small molecules can significantly advance our understanding of cellular state alterations and response mechanisms under chemical perturbations, which plays a crucial role in drug discovery and screening processes. Considering that experimental measurements need substantial time and cost, we developed a deep learning-based method called Molecule-induced Transcriptional Change Predictor (MiTCP) to predict changes in transcriptional profiles (CTPs) of 978 landmark genes induced by molecules. MiTCP utilizes graph neural network-based approaches to simultaneously model molecular structure representation and gene co-expression relationships, and integrates them for CTP prediction.
View Article and Find Full Text PDFIdentification of glycogen synthase kinase 3alpha/beta as a host factor required for hepatitis B virus transcription using high-throughput screening.
Hepatology
January 2025
Genome Medical Science Project, National Center for Global Health and Medicine, Ichikawa, Japan.
Background Aims: Hepatitis B virus (HBV) leads to severe liver diseases, such as cirrhosis and hepatocellular carcinoma. Identification of host factors that regulate HBV replication can provide new therapeutic targets. The discovery of sodium taurocholate cotransporting polypeptide (NTCP) as an HBV entry receptor has enabled the establishment of hepatic cell lines for analyzing HBV infection and propagation.
View Article and Find Full Text PDFButyl Imidates: Highly Stable and Isolable Synthetic Intermediates.
J Org Chem
January 2025
U.S. Process Chemistry, CMC Synthetics Platform, Sanofi, 350 Water Street, Cambridge, Massachusetts 02141, United States.
Imidates are versatile synthetic intermediates that contain ambiphilic reactivity, making them valuable pharmaceutically relevant synthons. Despite their extensive utility, imidates are typically generated in situ rather than isolated due to their inherent instability. This report details a systematic study that led to the discovery of an isolable imidate hydrogen chloride (HCl) salt that exhibits high tolerance to hydrolysis, thereby improving process control and facilitating downstream transformations.
View Article and Find Full Text PDFHigh-Throughput Chemotherapeutic Drug Screening System for Gastric Cancer (Cure-GA).
Ann Surg Oncol
January 2025
Department of Surgery, Seoul National University Bundang Hospital, Seongnam, Republic of Korea.
Background: Three dimensional (3D) cell cultures can be effectively used for drug discovery and development but there are still challenges in their general application to high-throughput screening. In this study, we developed a novel high-throughput chemotherapeutic 3D drug screening system for gastric cancer, named 'Cure-GA', to discover clinically applicable anticancer drugs and predict therapeutic responses.
Methods: Primary cancer cells were isolated from 143 fresh surgical specimens by enzymatic treatment.
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