Harnessing multi-omics and artificial intelligence: revolutionizing prognosis and treatment in hepatocellular carcinoma by Zhen Wang, Zhen Wang, Zhen Wang, Gangchen Zhou, Gangchen Zhou, Rongchuan Cao, Rongchuan Cao, Guolin Zhang, Guolin Zhang, Yongxu Zhang, Yongxu Zhang, Mingyue Xiao, Longbi Liu, Longbi Liu, Xuesong Zhang

“…CS1 was associated with better overall survival, while CS2 exhibited higher mutation burden and immune suppression. …”
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Divergent WNT signaling and drug sensitivity profiles within hepatoblastoma tumors and organoids by Thomas A. Kluiver, Yuyan Lu, Stephanie A. Schubert, Lianne J. Kraaier, Femke Ringnalda, Philip Lijnzaad, Jeff DeMartino, Wouter L. Megchelenbrink, Vicky Amo-Addae, Selma Eising, Flavia W. de Faria, Daniel Münter, Marc van de Wetering, Kornelius Kerl, Evelien Duiker, Marius C. van den Heuvel, Vincent E. de Meijer, Ruben H. de Kleine, Jan J. Molenaar, Thanasis Margaritis, Hendrik G. Stunnenberg, Ronald R. de Krijger, József Zsiros, Hans Clevers, Weng Chuan Peng

“…To characterize this heterogeneity and identify novel targeted therapies, we perform comprehensive analysis of hepatoblastomas and tumor-derived organoids using single-cell RNA-seq/ATAC-seq, spatial transcriptomics, and high-throughput drug profiling. …”
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Single-cell landscape of immunological responses in patients with juvenile idiopathic arthritis by Yun Liu, Xiwen Luo, Liuqing Yang, Qiang Luo, Xiya Luo, Li Xu, Yating Wang, Yunfei An, Yupeng Cun, Xuemei Tang

“…Results showed disrupted interferon and acute inflammatory responses in most cell types of JIA patients, with particularly intense responses in systemic JIA (sJIA) patients versus non-sJIA patients. Pseudotime analysis of CD4+ T, CD8+ T, B, and myeloid cells revealed that the functions of each cytokine production, cytotoxicity, and the processing and presentation of antigens were progressively strengthened, while the regulation of nuclear factor kappa B (NF-κB)-related pathways was weaker in CD4+ T and CD8+ T cells than in non-JIA. …”
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Endoplasmic Reticulum-Targeted Phototherapy Remodels the Tumor Immunopeptidome to Enhance Immunogenic Cell Death and Adaptive Anti-Tumor Immunity by Weidong Xiao, Mingquan Gao, Banghui Mo, Xie Huang, Zaizhi Du, Shufeng Wang, Jianhong Chen, Shenglin Luo, Haiyan Xing

“…<b>Methods:</b> Laser activation of the ER-targeted photosensitizer ER-Cy-<i>po</i>NO₂ was performed to investigate its effects on tumor cell antigenicity. Transcriptomic analysis was carried out to assess gene expression changes. …”
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Redefining the role of IL-18 in post-surgical recovery and sepsis: a key mediator of inflammation resolution by Ioanna Papatheodorou, Gabriela Blažková, Veronika Bosáková, Zuzana Tomášiková, Erin Spearing, Robin Klieber, Pavel Ostašov, Julie Štíchová, Martina Dvončová, Alexandra Mýtniková, Jan Emmer, Kamila Bendíčková, Tomáš Tomáš, Vladimír Šrámek, Petros Kolovos, Monika Holubová, Martin Helán, Marcela Vlková, Jan Frič, Marcela Hortová-Kohoutková

“…Monocytes from ORT patients underwent immunophenotyping together with bulk transcriptomic analysis. We found that IL-18 strongly defines the recovery immune signature. …”
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WNT-induced association of Frizzled and LRP6 is not sufficient for the initiation of WNT/β-catenin signaling by Jan Hendrik Voss, Zsombor Koszegi, Yining Yan, Emily Shorter, Lukas Grätz, Johanna T. Lanner, Davide Calebiro, Gunnar Schulte

“…WNT-16B emerged as a ligand of particular interest, as it efficiently promoted FZD-LRP6 association but, unlike WNT-3A, did not lead to WNT/β-catenin signaling. Transcriptomic analysis further revealed distinct transcriptional fingerprints of WNT-3A and WNT-16B stimulation in HEK293 cells. …”
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Avelumab induces greater Fc-Fc receptor-dependent natural killer cell activation and dendritic cell crosstalk compared to durvalumab by Nicole Osborne, Amit Rupani, Vladimir Makarov, Timothy A. Chan, Raghvendra M. Srivastava

“…We show a robust enhancement in NK-cell effector function, DC maturation, reciprocal NK:DC crosstalk and DC editing that is unique to avelumab treatment using multiple functional immune assays. By transcriptomic analysis, we show for the first time pivotal differences in gene sets involved in NK-cell effector function, DC maturation, immunoregulatory interactions, and cytokine production between innate immune cells treated with avelumab versus durvalumab. …”
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A microbiota-derived metabolite, 3-phenyllactic acid, prolongs healthspan by enhancing mitochondrial function and stress resilience via SKN-1/ATFS-1 in C. elegans by Juewon Kim, Yunju Jo, Gyumin Lim, Yosep Ji, Jong-Hwa Roh, Wan-Gi Kim, Hyon-Seung Yi, Dong Wook Choi, Donghyun Cho, Dongryeol Ryu

“…To elucidate the underlying mechanisms, we conduct transcriptomic profiling through RNA-seq analysis in C. elegans exposed to GTB1, a strain of Lactiplantibacillus plantarum or 3-phenyllactic acid (PLA), mimicking the presence of key candidate metabolites of GTB1 and evaluating healthspan. …”
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Choroid plexus organoids reveal mechanisms of Streptococcus suis translocation at the blood-cerebrospinal fluid barrier by Tiantong Zhao, Laura Pellegrini, Bart van der Hee, Jos Boekhorst, Aline Fernandes, Sylvia Brugman, Peter van Baarlen, Jerry M. Wells

“…S. suis was able to replicate at the same rate in CSF and laboratory S. suis culture medium but reached a lower final density. The analysis of transcriptomes in ChP organoids after S. suis infection indicated inflammatory responses, while the addition of Plg further suggested extracellular matrix (ECM) remodeling. …”
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Cannabidiol potentiates p53-driven autophagic cell death in non-small cell lung cancer following DNA damage: a novel synergistic approach beyond canonical pathways by Youngsic Jeon, Taejung Kim, Hyukjoon Kwon, Young Nyun Park, Tae-Hyung Kwon, Min Hong, Kyung-Chul Choi, Jungyeob Ham, Young-Joo Kim

“…To understand this synergistic effect, we conducted extensive transcriptomic and proteomic profiling, which showed that the combination of CBD and etoposide upregulated genes associated with autophagic cell death while downregulating key oncogenes known to drive tumor progression. …”
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Royal Jelly Enhances the Social Status of Submissive Rats by Restoring Balance to the Disturbed Gut–Brain Communication by Feng Zhu, Jinchun Xu, Tian Wang, Ruili Yang, Biao He, Hui-Li Wang, Yi Xu

“…At the genus level, both <i>Escherichia</i> and <i>Clostridium</i> displayed similar dynamics in relation to Proteobacteria, implying their involvement with the RJ-mediated dominance switching. Transcriptomic analysis in the medial prefrontal context showed that the expression of a broad range of genes was influenced by RJ intake, embodying various pathways related to neuronal transmission such as neuroactive ligan–receptor interaction, the synaptic vesicle cycle, etc. …”
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Repair of infarcted myocardium by skeletal muscle-derived mesenchymal stromal cells delivered by a bioprinted collagen patch by Rose Guesdon, Serena Santoro, Audrey Cras, Etienne Pagin, Didier Serteyn, Justine Ceusters, Fabien Guillemot, Albert Hagège, Philippe Menasché

“…To this end, mdMSC were embedded in a collagen bioprinted gel; the resulting epicardially-delivered patch significantly improved LV ejection fraction compared to a cell-free patch and sham-operated controls. Transcriptomic analysis revealed that this benefit was accompanied by a downregulation of fibrosis-, apoptosis-, and inflammation-related genes. …”
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Rare Copy Number Variants Reveal Critical Cell Types and Periods of Brain Development in Neurodevelopmental Disorders by Susmita Malwade, Carl M. Sellgren, Navneet A. Vasistha, Konstantin Khodosevich

“…Methods: We integrated >1 million single-cell transcriptomes from multiple datasets, capturing major brain regions and the entire timeline of human brain development. …”
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Lipopolysaccharide-Induced Transcriptional Changes in LBP-Deficient Rat and Its Possible Implications for Liver Dysregulation during Sepsis by Zhixiang He, Zichen Song, Leilei Meng, Wenhui Cheng, Fan Huang, Mao Zheng, Wenhui Xu, Rong Xiao, Haoshu Fang, Yaling Zhu

“…Functional enrichment analysis revealed that inflammatory response to LPS mediated by Ifng, Cxcl10, Serpine1, and Lbp was enhanced at 6 h, while lipid-related metabolism associated with C5, Cyp4a1, and Eci1 was enriched at 24 h after LPS administration in the WT samples. …”
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A Maternal Gene Regulator CPEB2 Is Involved in Mating-Induced Egg Maturation in the <i>Cnaphalocrocis medinalis</i> by Yi Duan, Yueran Xiao, Guo Cai, Kepeng Wang, Chenfan Zhao, Pengcheng Liu

“…Liposome-mediated RNA interference targeting <i>CmCPEB2</i> resulted in a 52% reduction in transcript abundance, leading to significant defects in ovarian maturation, diminished vitellogenin deposition, and a 36.7% decline in fecundity. The transcriptomic analysis of RNAi-treated ovaries identified 512 differentially expressed genes, with downregulated genes enriched in chorion formation and epithelial cell development. …”
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microRNA miR-142-3p Inhibits Breast Cancer Cell Invasiveness by Synchronous Targeting of WASL, Integrin Alpha V, and Additional Cytoskeletal Elements. by Alexander Schwickert, Esther Weghake, Kathrin Brüggemann, Annika Engbers, Benjamin F Brinkmann, Björn Kemper, Jochen Seggewiß, Christian Stock, Klaus Ebnet, Ludwig Kiesel, Christoph Riethmüller, Martin Götte

“…We aimed at investigating the role of miR-142-3p in breast cancer cell invasiveness. Supported by transcriptomic Affymetrix array analysis and confirmatory investigations at the mRNA and protein level, we demonstrate that overexpression of miR-142-3p in MDA-MB-231, MDA-MB-468 and MCF-7 breast cancer cells leads to downregulation of WASL (Wiskott-Aldrich syndrome-like, protein: N-WASP), Integrin-αV, RAC1, and CFL2, molecules implicated in cytoskeletal regulation and cell motility. …”
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FAK inhibition disrupts tumor growth, apoptosis, and transcriptional regulation in GI-NETs by Lara Toffoli, Angeliki Ditsiou, Luca Triboli, Victorine Hamm, Eva Moschioni, Francesca D’Este, Teresa Gagliano

“…Assays assessing viability and apoptosis were performed in both 2D and 3D culture conditions, while invasion and colony formation were assessed in 2D culture. …”
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Constitutive expression of full-length or partial of SOC1 genes for yield enhancement in tomato by Gharbia H. Danial, Gharbia H. Danial, Jirapa Jaikham, Guo-qing Song

“…Notably, compared to non-transgenic controls, all three constructs enhanced fruit yield per plant to varying degrees, including ZmSOC1 by 81-169%, GmSOC1 by 60-112%, and VcSOC1K by 52-88%, primarily through enhanced branching. At the transcriptomic level, comparative analysis of GmSOC1 revealed the broader impact of the transformed genes. …”
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SUMOylation-regulated genes in colon cancer: expression patterns and clinical implications by Wen Peng, Zirong Yang, Ru Yan, Lan Mu, Lan Li, Shan Jin, Shisheng Tan

“…Emerging evidence implicates SUMOylation-regulated genes as pivotal regulators of cancer-associated pathways, yet their prognostic potential and therapeutic implications in CRC remain unexplored. A comprehensive analysis of SUMOylation-regulated gene expression, clinical and prognostic value in CRC was performed using transcriptomic data from TCGA-COAD and GEO datasets. …”
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Skeletal muscle lncRNA profile associated with fatty acids in Nellore beef cattle by Bruna Maria Salatta, Maria Malane Magalhães Muniz, Larissa Fernanda Simielli Fonseca, Lucio Flavio Macedo Mota, Caio de Souza Teixeira, Gabriela Bonfá Frezarim, Marta Serna-García, Danielly Beraldo dos Santos Silva, Angélica Simone Cravo Pereira, Fernando Baldi, Lucia Galvão de Albuquerque

“…Longissimus thoracis muscle samples from 48 young bulls were used to quantify fatty acid (FA) (myristic, palmitic, stearic, oleic, linoleic, conjugated linoleic (CLA), α-linolenic and the groups of saturated fatty acids (SFA), monounsaturated (MUFA), polyunsaturated (PUFA), ω3, ω6, PUFA/SFA ratio and ω6/ω3) and to generate RNA-Sequencing data for transcriptomic analyses. The K-means analysis was used to classify the 48 animals into three clusters based on their FA patterns. …”
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