Multi-omics data reveal that SAA1 + fibroblasts exacerbate periodontitis by regulating macrophage inflammation and chemotaxis by Li Li, Yuting Yang, Fang Dai, Libin Deng, Meixiu Jiang, Chenjiang He, Ting Long, Kaiqiang Yang, Xinbo Yang, Li Song

“…Methods Through integrative analysis of single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, and bulk transcriptome datasets from periodontal tissues, we systematically characterized the spatial architecture and intercellular communication networks within the inflammatory periodontal microenvironment, identifying a functionally serum amyloid A1 + fibroblasts (SAA1 + Fib) that critically drives disease progression. …”
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A three-component signaling system plays multiple roles in the pathogenicity of Xanthomonas citri subsp. citri by Xiaoyan Zhao, Xiaoyun Chen, Junjie Lei, Jiaying Feng, Yunyang Dong, Yu Shi, Linghui Xu, Junxia Wang

“…Transcriptome sequencing analysis and quantitative real-time PCR validation were performed to elucidate the underlying regulatory mechanisms. …”
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Entrectinib can induce nerve cell damage by inhibiting PI3K-AKT and TGF-β signaling pathways by Qingshan Tang, Jiachen Dong, Feng Zhang, Dan Zhao, Qi Yang, Jiayu Wen, Yuhao Sun, Jifu Wei, Zhixian Liu

“…Additionally, we Preliminary observed and validated whether THBS1 overexpression could rescue nerve cell damage and the abnormalities in PI3K-AKT and TGF-β signaling pathways.ResultsEntrectinib significantly inhibited the nerve cells proliferation and colony formation, and induced nerve cells apoptosis. Transcriptome sequencing analysis and qRT-PCR revealed that THBS1 was downregulated within entrectinib treatment. …”
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Tissue specific role of ABCA1 in lung cholesterol homeostasis under high-cholesterol diet by Jian Ma, Jian Ma, Zhongwen Gong, Hong Lu, Han Yang, Shengquan Wang, Qian Zhu, Hongya Liu, Yongjia Li, Yuemei Zhang, Xuemei Lian, Xuemei Lian

“…In CYP27A1(−/−) mice, hepatic lipid accumulation was more severe with further suppression of ABCA1, whereas ABCA1 expression in the lung remained elevated. Transcriptome analysis revealed that upregulated genes in lung tissue were significantly enriched in the inflammation-related nuclear factor kappa-B (NF-κB) signaling pathway. …”
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Identification and experimental validation of prognostic genes related to cytochrome c in breast cancer by Huimin Yu, Shihong Li, Jian Wu, Haobin Wang, Haobin Wang

“…Prognostic genes were identified through differential expression analysis, univariate Cox regression, and LASSO analysis. …”
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Seed Priming with 2,4-Epibrassionolide Enhances Seed Germination and Heat Tolerance in Rice by Regulating the Antioxidant System and Plant Hormone Signaling Pathways by Jingya Qian, Xu Mo, Yue Wang, Qiang Li

“…Additionally, exogenous EBR increases the levels of GA and IAA while decreasing the ABA content. According to a transcriptomic analysis, exogenous EBR can induce the expression of key genes involved in GA, IAA, and ABA hormone biosynthesis and metabolism, regulating GA-, IAA-, ABA-, and H₂O₂-mediated signaling pathways to promote the germination of rice seeds under heat stress. …”
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New perspectives on YTHDF2 O-GlcNAc modification in the pathogenesis of intervertebral disc degeneration by Liangjie Lu, Lijun Wang, Minjie Yang, Huihan Wang

“…Abstract This study investigates the potential molecular mechanisms by which O-GlcNAc modification of YTHDF2 regulates the cell cycle and participates in intervertebral disc degeneration (IDD). We employed transcriptome sequencing to identify genes involved in IDD and utilized bioinformatics analysis to predict key disease-related genes. …”
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Molecular mechanisms of cryoablation-mediated lung cancer suppression unveiled by non-coding RNA regulatory network profiling by Xiaofan Wang, Mohan Zhang, Dianna Liu, Shicheng Lin, Yuxin Zhang, Quanwang Li

“…Abstract While cryoablation demonstrates therapeutic potential for lung adenocarcinoma, the precise molecular mechanisms underlying its antitumor effects require further elucidation. …”
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The toxicity and mechanisms of pyrotinib on male reproductive system by Xiao Hu, Zhongjian Pan, Jie Yang, Peng Zheng, Jian Tan, Zhipeng Xu, Huaming Tang, Jianpeng Hu

“…Transcriptomic analysis identified 197 downregulated genes enriched in chromatin organization and mitotic processes, particularly cell cycle regulation. …”
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Potential radiosensitive germline biomarkers in the testes of wild mice after the Fukushima accident by Syun Tokita, Ryo Nakayama, Yohei Fujishima, Valerie Swee Ting Goh, Donovan Anderson, Ippei Uemura, Hikari Ikema, Jin Shibata, Yoh Kinoshita, Yoshinaka Shimizu, Hisashi Shinoda, Jun Goto, Maria Grazia Palmerini, Abdulla Mohamed Hatha, Takashi Satoh, Akifumi Nakata, Manabu Fukumoto, Tomisato Miura, Hideaki Yamashiro

“…Conversely, in the non‐breeding season, Fmo2 and Fmo2 (highly similar) were significantly upregulated in radiation‐exposed Fukushima mice. qPCR analysis results were consistent with transcriptome sequencing, detecting Lsp1 and Ptprk regulation in the testes of Fukushima mice. …”
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Mechanisms of skeletal muscle atrophy in type 2 diabetes mellitus by Jingyi Yang, Yingdong Wang, Yuzhe Xu, Xinqi Jia, Fangping Lu

“…Pathway enrichment analysis of differentially expressed genes was performed based on transcriptome sequencing data, focusing on apoptosis, ERS, and ubiquitin-proteasome pathways. …”
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A novel cardiomyopathy phenotype linked to a CHD7 missense variant by In Young Park, Chih-Wei Hsu, Karim Bouazoune, Christina E. Espindola, Madeline Hannah McLaughlin Armond, Cristian Coarfa, Sandra L. Grimm, James F. Martin, Donna M. Martin, Cheryl Lyn Walker

“…Notably, Chd7 fs/T720A mice died before postnatal day 2, indicating the Chd7 T720A allele is hypomorphic. Micro-CT analysis at E18.5 revealed that heterozygous mice primarily exhibited hypertrophic cardiomyopathy (HCM), while homozygous mice developed both HCM and dilated cardiomyopathy (DCM). …”
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(p)ppGpp imposes graded transcriptional changes to impair motility and promote antibiotic tolerance in biofilms by Florian Engelhardt, Kathryn Turnbull, Melisa Gür, Mathias Müsken, Matthias Preusse, Susanne Häussler, Mohammad Roghanian

“…Transcriptomic analysis reveals that (p)ppGpp ensures proportionate cellular responses to stress by imposing a layer-by-layer regulation of gene expression. …”
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Intermittent Supplementation with Far-Red Light Accelerates Leaf and Bud Development and Increases Yield in Lettuce by Yanke Liu, Rong Ye, Xinying Gao, Rongcheng Lin, Yang Li

“…This was validated by analyzing phytohormone content and the expression of genes related to hormone metabolism and transport at the tip of the lettuce stems. Transcriptome analysis revealed that the differences in gene expression between treatments were primarily concentrated in genes related to signaling, hormone metabolism, and transport. …”
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PADI4 expression in baseline circulating tumour cells acts as a prognostic biomarker in oral squamous cell carcinoma by Anshika Chauhan, Geeta S. Boora, Arindam Maitra, Rijuneeta Gupta, Jaimanti Bakshi, Sushmita Ghoshal, Arnab Pal

“…While exploring gene expression in CTCs, we performed whole transcriptome analysis of paired primary tumour and CTCs isolated from Oral Squamous Cell Carcinoma (OSCC) patients. …”
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Scorpion venom peptides enhance immunity and survival in Litopenaeus vannamei through antibacterial action against Vibrio parahaemolyticus by Ling Zeng, Yulin Sun, Hualin Zhang, Xiangxi Yi, Ran Du, Ziming Chen, Qi Wang

“…Furthermore, intestinal transcriptome profiling was performed to identify the activated immune pathways.ResultsAll peptides exhibited membrane-targeting activity: BmKn2-7 showed superior outer membrane penetration and depolarization, while BmKn1 was more effective in inner membrane disruption and ROS induction. …”
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Injectable and Assembled Calcium Sulfate/Magnesium Silicate 3D Scaffold Promotes Bone Repair by In Situ Osteoinduction by Wei Zhu, Tianhao Zhao, Han Wang, Guangli Liu, Yixin Bian, Qi Wang, Wei Xia, Siyi Cai, Xisheng Weng

“…In vivo efficacy was assessed in a rabbit model of ONFH to evaluate bone repair. (3) Results: The Mg@Ca scaffold demonstrated excellent biocompatibility and supported h-BMSC proliferation and differentiation, with significant up-regulation of <i>COL1A1</i> and <i>BGLAP</i>. Transcriptome analysis revealed activation of the PI3K-Akt signaling pathway, critical for osteogenesis. …”
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Impaired hippocampal neurogenesis associated with regulatory ceRNA network in a mouse model of postoperative cognitive dysfunction by Jingrun Lin, Xiaoqiu Zhu, Xuan Li, Yu Hong, Yaohui Liang, Siqi Chen, Chenzhuo Feng, Lin Cao

“…Surgery significantly reduced the rate of spontaneous alternations in the Y-maze (F1, 28 = 16.94, P < 0.001) and the recognition index in novel object recognition test (F1, 28 = 6.839, P < 0.05) in aging mice, but had no effect on young mice. Transcriptome analysis revealed that aging and surgery downregulated multiple neurogenesis-related genes in the hippocampus. …”
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Construction and Evaluation of a Rat Model of Abnormal Uterine Bleeding by LIAN Hui, JIANG Yanling, LIU Jia, ZHANG Yuli, XIE Wei, XUE Xiaoou, LI Jian

“…The samples were subjected to HE staining, serum sex hormone ELISA, immunohistochemistry, TUNEL apoptosis staining, Western blotting, transcriptome sequencing, and bioinformatics analysis for comprehensive evaluation of the AUB rat model.ResultsThe AUB rats exhibited uterine bleeding, endometrial detachment and injury, incomplete uterine restoration, inflammatory cell infiltration in the endometrium, enhanced tissue apoptosis, and structural damage of the stroma, glands, and vasculature. …”
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Decoding post-transcriptional gene expression controls in trypanosomatids using machine learning [version 2; peer review: 2 approved] by David Horn, Michele Tinti

“…Codon usage bias has a major impact on mRNA abundance in all three trypanosomatids, while analysis of T. brucei proteomics data yielded results consistent with the view that this is due to differential translation elongation rates. …”
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