Single-cell T cell and B cell antigen receptor-sequencing data analysis can potentially perform in-depth assessments of adaptive immune cells that inform on understanding immune cell development to tracking clonal expansion in disease and therapy. However, it has been extremely challenging to analyze and interpret T cells and B cells and their adaptive immune receptor repertoires at the single-cell level due to not only the complexity of the data but also the underlying biology. In this Review, we delve into the computational breakthroughs that have transformed the analysis of single-cell T cell and B cell antigen receptor-sequencing data.
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http://dx.doi.org/10.1038/s41592-024-02243-4 | DOI Listing |
Sci Adv
January 2025
Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02453, USA.
Circadian neurons within animal brains orchestrate myriad physiological processes and behaviors, but the contribution of these neurons to the regulation of sleep is not well understood. To address this deficiency, we leveraged single-cell RNA sequencing to generate a comprehensive census of transcriptomic cell types of clock neurons. We focused principally on the enigmatic DN3s, which constitute most fly brain clock neurons and were previously almost completely uncharacterized.
View Article and Find Full Text PDFPLoS One
January 2025
Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom.
Epithelial cancers are typically heterogeneous with primary prostate cancer being a typical example of histological and genomic variation. Prior studies of primary prostate cancer tumour genetics revealed extensive inter and intra-patient genomic tumour heterogeneity. Recent advances in machine learning have enabled the inference of ground-truth genomic single-nucleotide and copy number variant status from transcript data.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Anatomy, School of Medicine, Pusan National University, Yangsan, Republic of Korea.
The identification of immune environments and cellular interactions in the colon microenvironment is essential for understanding the mechanisms of chronic inflammatory disease. Despite occurring in the same organ, there is a significant gap in understanding the pathophysiology of ulcerative colitis (UC) and colorectal cancer (CRC). Our study aims to address the distinct immunopathological response of UC and CRC.
View Article and Find Full Text PDFToxicol Sci
January 2025
Department of Chemistry and Environmental Science, New Jersey Institute of Technology, Newark, NJ, 07103.
Phthalates are known endocrine disrupting chemicals and ovarian toxicants that are used widely in consumer products. Phthalates have been shown to exert ovarian toxicity on multiple endpoints, altering transcription of genes responsible for normal ovarian function. However, the molecular mechanisms by which phthalates act on the ovary are not well understood.
View Article and Find Full Text PDFEndocr Relat Cancer
January 2025
X Zheng, Thyroid and Neck Tumor, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China.
Anaplastic Thyroid Cancer (ATC) is an aggressive form of cancer with poor prognosis, heavily influenced by its tumor immune microenvironment (TIME). Understanding the cellular and gene expression dynamics within the TIME is crucial for developing targeted therapies. This study analyzes the immune microenvironment of ATC and Papillary Thyroid Cancer (PTC) using single-cell RNA sequencing (scRNA-seq).
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