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Improved ChIP Sequencing for H3K27ac Profiling and Super-Enhancer Analysis Assisted by Fluorescence-Activated Sorting of Formalin-Fixed Paraffin-Embedded Tissues.
Biol Proced Online
January 2025
Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, 610041, China.
Archived clinical formalin-fixed paraffin-embedded tissue (FFPE) is valuable for the study of tumor epigenetics. Although protocol of chromatin immunoprecipitation coupled with next generation sequencing (NGS) (ChIP-seq) using FFPE samples has been established, removal of interference signals from non-target cell components in the samples is still needed. In this study, the protocol of ChIP-seq with purified cells from FFPE lymphoid tissue of nodal T follicular helper cell lymphoma, angioimmunoblastic type (nTFHL-AI) after fluorescence-activated cell sorting (FACS) was established and optimized.
View Article and Find Full Text PDFLeveraging Deep Learning for Immune Cell Quantification and Prognostic Evaluation in Radiotherapy-Treated Oropharyngeal Squamous Cell Carcinomas.
Lab Invest
January 2025
University Clermont Auvergne, INSERM U1240 [Molecular Imaging & Theragnostic Strategies (IMOST)], Clermont-Ferrand, France; Department of Pathology, Centre Jean PERRIN, Clermont-Ferrand, France.
The tumor microenvironment (TME) plays a critical role in cancer progression and therapeutic responsiveness, with the tumor immune microenvironment (TIME) being a key modulator. In head and neck squamous cell carcinomas (HNSCC), immune cell infiltration significantly influences the response to radiotherapy (RT). A better understanding of the TIME in HNSCC could help identify patients most likely to benefit from combining RT with immunotherapy.
View Article and Find Full Text PDFEstablishment of a novel large-scale targeted metabolomics method based on NFSWI-DDA mode utilizing HRMS and TQ-MS.
Talanta
January 2025
State Key Laboratory of Component-based Chinese Medicine, Tianjin Key Laboratory of TCM Chemistry and Analysis, Tianjin University of Traditional Chinese Medicine, 10 Poyanghu Road, Jinghai District, Tianjin, 301617, PR China; Haihe Laboratory of Modern Chinese Medicine, Tianjin, 301617, PR China. Electronic address:
Metabolites identification is the major bottleneck in untargeted LC-MS metabolomics, primarily due to the limited availability of MS information for most detected metabolites in data dependent acquisition (DDA) mode. To solve this problem, we have integrated the iterative, interval, and segmented window acquisition concepts to develop an innovative non-fixed segmented window interval data dependency acquisition (NFSWI-DDA) mode, which achieves comparable MS coverage to data independent acquisition (DIA) mode. This acquisition strategy harnesses the strengths of both DDA and DIA, which could provide extensive coverage and excellent reproducibility of MS spectra.
View Article and Find Full Text PDFIncreased Afferent Nerve Firing Is Correlated With the Detection of Bladder Wall Micromotion in a Perfused Ex-Vivo Porcine Model.
Neurourol Urodyn
January 2025
Department of Surgery, Division of Urology, Virginia Commonwealth University Health System, Richmond, Virginia, USA.
Introduction And Objective: Observable autonomous rhythmic changes in intravesical pressure, termed bladder wall micromotion, is a phenomenon that has been linked to urinary urgency, the key symptom in overactive bladder (OAB). However, the mechanism through which micromotion drives urinary urgency is poorly understood. In addition, micromotion is inherently difficult to study in human urodynamics due to challenges distinguishing it from normal cyclic physiologic processes such as pulse rate, breathing, rectal contractions, and ureteral jetting.
View Article and Find Full Text PDFCryopreservation Method for Preventing Freeze-Fracture of Small Muscle Samples.
Bio Protoc
January 2025
Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA, USA.
Histological techniques to study muscle are crucial for assessing skeletal muscle health. To preserve tissue morphology, samples are usually fixed in formaldehyde or cryopreserved immediately after excision from the body. Freezing samples in liquid nitrogen, using isopentane as a mediator for efficient cooling, preserves the tissue in its natural state.
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