Thymic dendritic cell-derived IL-27p28 promotes the establishment of functional bias against IFN-γ production in newly generated CD4+ T cells through STAT1-related epigenetic mecha... by Jie Zhang, Hui Tang, Haoming Wu, Xuewen Pang, Rong Jin, Yu Zhang

“…The newly generated CD4 single-positive (SP) T lymphocytes are featured by enhanced IL-4 but repressed IFN-γ production. …”
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Prediction of radiosensitivity in non-small cell lung cancer based on computed tomography and tumor genomics: a multiple real world cohort study by Peimeng You, Qiaxuan Li, Yu Lei, Chuhao Xu, Daipeng Xie, Lintong Yao, Jiaxin Yuan, Junyu Li, Haiyu Zhou

“…The tumor primary target area was delineated on a training set (n = 154) and segmented to obtain a radiogenomic single signature. The radiogenomic signature LCDigital-RT, which can predict radiosensitivity, was developed by combining transcriptome sequencing signature radiosensitivity index and validated on two independent external validation sets (n = 74) and (n = 160). …”
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Metabolic stress and early cell death in photoreceptor precursor cells following retinal transplantation by Raghavi Sudharsan, Natalia Dolgova, Jennifer Kwok, Alexa Gray, Yu Sato, Agustin Luz Madrigal, Praveen Joseph Susaimanickam, Emil Kriukov, Petr Baranov, John H. Wolfe, Gustavo D. Aguirre, David M. Gamm, William A. Beltran

“…Methods PRPCs derived from human embryonic stem cells (hESC)-based retinal organoids were subretinally transplanted into both normal and degenerated canine retinas to investigate the impact of host retinal degeneration on transplant survival and integration. Single-cell RNA sequencing (scRNAseq) was performed on transplanted PRPCs 3 days post-transplantation into normal canine retinas, as well as on host retinal cells to identify molecular pathways associated with early donor cell loss. …”
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Insights into the E2F target genes in breast cancer: associations of pathway genes with prognosis and immune cell filtration based on in silico and ex vivo analyses by Behnoosh Nikonezhad, Maryam Lotfian, Nadia Manavi, Atefeh Zamani, Mohammad Mahdevar

“…However, the exact role of E2F target genes in breast cancer (BC), as well as their influence on survival and immune response, remains poorly understood. …”
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Improved overall survival in an anti-PD-L1 treated cohort of newly diagnosed glioblastoma patients is associated with distinct immune, mutation, and gut microbiome features: a sing... by Shiao-Pei Weathers, Xiqi Li, Haifeng Zhu, Ashish V. Damania, Mark Knafl, Brian McKinley, Heather Lin, Rebecca A. Harrison, Nazanin K. Majd, Barbara J. O’Brien, Marta Penas-Prado, Monica Loghin, Carlos Kamiya-Matsuoka, W. K. Alfred Yung, Luisa M. Solis Soto, Dipen M. Maru, Ignacio Wistuba, Edwin R. Parra Cuentas, Sharia Hernandez, Andrew Futreal, Jennifer A. Wargo, Katja Schulze, Walter C. Darbonne, Nadim J. Ajami, Scott E. Woodman, John F. de Groot

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Fibrocartilage repair involves chronic cellular senescence in a rat model of bone marrow stimulation by Luke Childress, Landon B. Gatrell, Hong Wu, Elisabeth Ferreira, Intawat Nookaew, Ryan M. Porter

“…Repair tissue was characterized during the first months after marrow stimulation by histology as well as bulk and single cell transcriptomic analysis. …”
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Spatiotemporal profiling reveals the impact of caloric restriction in the aging mammalian brain by Zehao Zhang, Alexander Epstein, Chloe Schaefer, Abdulraouf Abdulraouf, Weirong Jiang, Wei Zhou, Junyue Cao

“…In this study, we profiled >500,000 cells from 36 control and CR mouse brains across three age groups with EasySci single-nucleus transcriptomics and performed imaging-free IRISeq spatial transcriptomics on twelve brain sections from CR and control aged mice. …”
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FPR3 orchestrates macrophage polarization in breast cancer: multi-omics dissection of prognostic relevance and therapeutic targeting by Ying Chen, Xin Tang, Liran Zhu, Yi Wang, Gaopeng Li, Wulin Yang

“…Methods A comprehensive analysis integrating bulk RNA-seq transcriptomics, methylomics, single-cell transcriptomics, and spatial single-cell transcriptomics data was conducted to elucidate the distinctive characteristics of FPRs in breast cancer. …”
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Targeting Hepatic Stellate Cells for the Prevention and Treatment of Liver Cirrhosis and Hepatocellular Carcinoma: Strategies and Clinical Translation by Hao Xiong, Jinsheng Guo

“…Recent advances in omics, particularly single-cell sequencing and spatial transcriptomics, hold promise for identifying new HSC targets for diagnosing and treating liver fibrosis/cirrhosis and liver cancer.…”
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DGE-ontology: A quick and simple gene set enrichment analysis and visualisation tool by Michal Bukowski, Benedykt Wladyka

“…The presented approach to data visualisation considerably facilitates communication of experimental results as well as inference from large omic data sets.…”
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Deciphering the interaction between the expression of LRP2 served as a mitochondrial metabolism-related gene and prognosis in colon cancer integrating multi-omics analysis by Jie Zhang, Ziyun Liu, Xiaoqing Ma, Zhenyu Shi, Jing Zhao, Yongjie Xie, Xiaobin Shang, Xia Zhang

“…We investigated the expression of LRP2 in COAD and its prognostic value utilizing single-cell sequencing and transcriptomics datasets, which was conducted preliminary validation at the patient samples and cellular levels as well. …”
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The suppressive role of GLS in radiosensitivity and irradiation-induced immune response in LUAD: integrating bioinformatics and experimental insights by Peicheng Jiang, Zhifeng Jiang, Su Li, Su Li, Ye-Xiong Li, Yuqiong Chen, Xinyan Li

“…However, the precise mechanisms through which GLS modulates radiosensitivity and irradiation-induced immune responses in lung adenocarcinoma (LUAD) and its clinical value remain to be fully elucidated.MethodsWe employed bulk RNA-seq and single-cell transcriptomics to explore the role of GLS expression in radiosensitivity and immune infiltration. …”
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Complementing muscle regeneration—fibro-adipogenic progenitor and macrophage-mediated repair of elderly human skeletal muscle by Jonas Brorson, Lin Lin, Jakob Wang, Amanda Bæk, Tine Borum Billeskov, Frederik Forsberg Thybo, Jesper Just, János Haskó, Christen Ravn, Rehne L. Hansen, Mats Bue, Jens Otto Lunde Jørgensen, Yonglun Luo, Niels Jessen, Jean Farup

“…Here, we unravel the intricate dynamics of elderly human skeletal muscle regeneration by combining spatial, temporal, and single cell transcriptomics. Using spatial RNA sequencing (n = 3), we profile the expression of human protein-coding genes in elderly human skeletal muscle biopsies before as well as 2-, 8-, and 30-day post injury (NCT03754842). …”
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Exercise and Ischemia-Activated Pathways in Limb Muscle Angiogenesis and Vascular Regeneration by Vihang A. Narkar

“…I also highlight future areas of exercise research (including metabolomics, single cell transcriptomics, and extracellular vesicle biology) to advance our understanding of how exercise induces vascular regeneration at the molecular level, and propose the idea of “exercise-mimicking” therapeutics for vascular recovery.…”
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Unveiling purine metabolism dysregulation orchestrated immunosuppression in advanced pancreatic cancer and concentrating on the central role of NT5E by Junqian Zhang, Xiaobo Zhang, Ruixin Wu, Chang-Sheng Dong

“…The by-products of purine metabolic reprogramming are extensively engaged in tumor immune modulation, influencing the functions and recruitment of immune cells and molding an immune microenvironment that is propitious for tumor growth.MethodsWe harnessed single-cell transcriptomics and spatial transcriptomics to concurrently analyze the purine metabolism (PM) features of the PC microenvironment. …”
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Microglial intervention in ischemic stroke: Roles and intervention strategies by Cuiling Ji, Lixinbei Sheng, Kaijun Han, Ping Yuan, Wei Li, Lu Chen, Yongyue Gao

“…Potential therapeutic agents include natural compounds found in drugs such as minocycline, as well as traditional Chinese medicines. Drugs that target these regulatory mechanisms, such as small molecule inhibitors and components of traditional Chinese medicines, along with emerging technologies such as single-cell RNA sequencing and spatial transcriptomics, offer new therapeutic strategies and clinical translational potential for ischemic stroke.…”
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Transcriptional progression during meiotic prophase I reveals sex-specific features and X chromosome dynamics in human fetal female germline. by Xueying Fan, Ioannis Moustakas, Vanessa Torrens-Juaneda, Qijing Lei, Geert Hamer, Leoni A Louwe, Gonneke S K Pilgram, Karoly Szuhai, Roberto Matorras, Cristina Eguizabal, Lucette van der Westerlaken, Hailiang Mei, Susana M Chuva de Sousa Lopes

“…Therefore, it remains unclear how the different stages of meiotic prophase I between human oogenesis and spermatogenesis compare. Analysis of single-cell transcriptomics data from human fetal germ cells (FGC) allowed us to identify the molecular signatures of female meiotic prophase I stages leptotene, zygotene, pachytene and diplotene. …”
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Fine Mapping Identifies Candidate Genes Associated with Swine Inflammation and Necrosis Syndrome by Katharina Gerhards, Sabrina Becker, Josef Kühling, Joel Mickan, Mirjam Lechner, Hermann Willems, Gerald Reiner

“…Inflammation is documented at different levels based on clinical signs, histopathology, clinical chemistry, metabolomics and transcriptomics. The influence of sow and boar, as well as a heritability of around 0.3, suggest a genetic component to the disease. …”
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Precision Medicine in Hematologic Malignancies: Evolving Concepts and Clinical Applications by Rita Khoury, Chris Raffoul, Christina Khater, Colette Hanna

“…However, advances in single-cell sequencing, spatial transcriptomics, drug repurposing, immunotherapies, pan-cancer trials, precision prevention, and AI-guided algorithms offer promising avenues to refine treatment and improve outcomes. …”
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The Δ40p53 isoform inhibits p53-dependent eRNA transcription and enables regulation by signal-specific transcription factors during p53 activation. by Cecilia B Levandowski, Taylor Jones, Margaret Gruca, Sivapriya Ramamoorthy, Robin D Dowell, Dylan J Taatjes

“…We circumvented this issue with a well-tested strategy that expressed Δ40p53:WTp53 as a single transcript, ensuring a 2:2 tetramer stoichiometry. …”
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