DNA Methylation and Transcriptome Profiling Reveal the Role of the Antioxidant Pathway and Lipid Metabolism in <i>Plectropomus leopardus</i> Skin Color Formation by Yang Liu, Linna Wang, Zhentong Li, Linlin Li, Tangtang Ding, Shuai Chen, Pengfei Duan, Xinyi Wang, Yishu Qiu, Xiaoyu Ding, Yongsheng Tian

“…To dissect the regulatory mechanisms underlying the red skin trait in <i>P. leopardus</i>, gene expression and DNA methylation modifications were compared between red and black skin tissues after astaxanthin treatment. …”
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Generation of Insulin-Producing Cells from Canine Adipose Tissue-Derived Mesenchymal Stem Cells by Takahiro Teshima, Keiji Okamoto, Kazuho Dairaku, Tomokazu Nagashima, Masaki Michishita, Ryohei Suzuki, Hirotaka Matsumoto, Hidekazu Koyama

“…Canine IPCs also showed gene expression typical for pancreatic beta cells and increased insulin secretion in response to glucose stimulation. …”
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Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize by Yi Luo, Hang Zhai, Xiu Zhong, Bo Yang, Yang Xu, Tianhong Liu, Qi Wang, Yang Zhou, Yan Mao, Yaxi Liu, Qi Tang, Yanli Lu, Yao Wang, Jie Xu

“…Conclusions In summary, we identified and characterized CNS in maize through genomic comparative analysis, which provides valuable insights into their potential regulatory effects on gene expression and phenotypic variation.…”
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DNMT3a Downregulation Ttriggered Upregulation of GABAA Receptor in the mPFC Promotes Paclitaxel‐Induced Pain and Anxiety in Male Mice by Lixia Tian, Xu‐Hui Li, Yu‐Long Zhao, Hui‐Yuan Yi, Xue‐Ru Liu, Rongrong Yao, Xue‐Mei Hou, Xuan Zhu, Fu‐Quan Huo, Tao Chen, Lingli Liang

“…Abstract Chemotherapeutic agents, such as paclitaxel (PTX), induce neuroplastic changes and alter gene expression in the prefrontal cortex (PFC), which may be associated with chemotherapy‐induced pain and negative emotions. …”
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ALKBH5, an m6A demethylase, attenuates tumor growth and inhibits metastasis in papillary thyroid carcinoma by Yong Zhuang, Qingyan Cai, Xin Hu, Huibin Huang

“…Here, we compared cancer tissues and paracancerous tissues from PTC patients, along with cultured cells expressing ALKBH5 (overexpression, silent gene expression, normal stable expression). Our primary objective was to investigate the impact of ALKBH5 on PTC. …”
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Complement Receptors C5aR and C5L2 Are Associated with Metabolic Profile, Sex Hormones, and Liver Enzymes in Obese Women Pre- and Postbariatric Surgery by Reza Rezvani, Jessica Smith, Marc Lapointe, Picard Marceau, Andre Tchernof, Katherine Cianflone

“…Fasting plasma (hormone, lipid, and enzyme analysis) and liver biopsies (RT-PCR gene expression) were obtained from 91 women during surgery. …”
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Endogenous 17β-estradiol regulates sexually dimorphic anxiety responses in zebrafish via the HPI axis and 5-HT/DA pathways by Hong Tao, Hong Tao, Ying–Ying Zhang, Ying–Ying Zhang, Yan–Jun Shen, Yan–Jun Shen, Qi–Liang Chen, Qi–Liang Chen, Zhi–Hao Liu, Zhi–Hao Liu

“…Conversely, E2 treatment in males (E2-M) increased E2 levels and anxiety responses, elevated plasma cortisol levels, and decreased brain 5-HT and DA content, with corresponding changes in gene expression. These findings strongly suggest that E2 positively regulates sexually dimorphic anxiety responses possibly by modulating plasma cortisol levels and the synthesis and action of 5-HT/DA in the brain.…”
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Hyperleukocytosis in a neuroblastoma patient after treatment with natural killer T cells expressing a GD2-specific chimeric antigen receptor and IL-15 by Xin Xu, Shantan Reddy, Saleh Bhar, Frederic D Bushman, Amy N Courtney, Gabriel A Barragán, Gengwen Tian, Erica J Di Pierro, Leonid S Metelitsa, Antonino Montalbano, Hangjin Yu, Claudia Martinez Amador, Nisha Ghatwai, Michael S Wood, Deborah Schady, Aoife M Roche, David de la Cerda, Donald Williams Parsons, Andras Heczey

“…We report that the use of aAPCs instead of PBMCs for CAR-NKT restimulation contributed to a hyperproliferative state associated with distinct gene expression that possibly led to explosive lymphocyte expansion and uncontrolled toxicity in the patient. …”
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Selective expression and significance of ACKR2 in lung aerocytes by Alberto Mantovani, Gianluigi Condorelli, Raffaella Bonecchi, Massimo Locati, Marina Sironi, Roberta Carriero, Francesca Albano, Valeria Mollica Poeta, Lucia Zotti, Alessandra Castagna, Arianna Felicetta, Alessandro Mesaglio, Elisa Zaghen, Arianna Capucetti, Rachele Di Donato, Mattia Laffranchi, Matteo Massara, Silvano Sozzani

“…This study aims to explore the specific cell types expressing ACKR2 and their relative contributions to the protection against lung metastasis.Methods ACKR2 expression was studied by the generation of an inducible and conditional knockout (KO) mouse expressing two reporter genes, luciferase and TdTomato visible by In Vivo Imaging System, flow cytometry and immunofluorescence. Gene expression in lung endothelial cells (ECs) was investigated by RNA sequencing analysis. …”
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Identification of biomarkers for tumor regression grade in esophageal squamous cell carcinoma patients after neoadjuvant chemoradiotherapy by Zhifu Chen, Yan Wang, Jun Chen, Zijun Xu, Tingjuan Zhang, Lu Sun, Lihua Zhu, Liben Xu, Chaoyang Wu, Zhiyuan Qiu, Dianjun Wang, Ting Wu

“…The correlation between TRG groups, clinicopathologic characteristics, and prognosis was analyzed. Differential gene expression analysis was performed on ESCC patients before and after NCRT using the public database (GSE43519). …”
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Comprehensive analysis of H3K27me3 LOCKs under different DNA methylation contexts reveal epigenetic redistribution in tumorigenesis by Yuan Liang, Mengni Liu, Bingyuan Liu, Benjamin Ziman, Guanjie Peng, Qiong Mao, Xingzhe Wang, Lizhen Jiang, De-Chen Lin, Yueyuan Zheng

“…Our findings reveal that long LOCKs are predominantly associated with developmental processes, while short LOCKs are enriched in poised promoters and are most associated with low gene expression. Further analysis of LOCKs in different DNA methylation contexts shows that long LOCKs are primarily located in partially methylated domains (PMDs), particularly in short-PMDs, where they are most likely responsible for the low expressions of oncogenes. …”
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High expression of SULF1 is associated with adverse prognosis in breast cancer brain metastasis by Yitong Li, Tingting Feng, Qinghong Wang, Yue Wu, Jue Wang, Wenlong Zhang, Qi Kong

“…Methods Differential gene expression analysis (DEGs) for the datasets GSE43837 and GSE125989 from the GEO database was performed using online analysis tools such as GEO2R and Sangerbox. …”
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Transcriptome analysis reveals potential regulatory mechanism of genes and pathways following Aeromonas veronii infection and hypoxic stress in Chinese mitten crab, Eriocheir sinen... by Gang Jiang, Fengyuan Yan, Yuanfeng Xu, Jianlin Li, Wenrong Feng, Guo an Hua, Wen jing Li, Jun Zhou, Yongkai Tang

“…Under dual stress, protein synthesis and lipid metabolism were further repressed, and immune-related gene expression was markedly up-regulated. Notably, hypoxia and A. veronii infection exhibit a synergistic toxic effect on E. sinensis. …”
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Exposure to triphenyl phosphate during pregnancy: The role of gut-bile acids-liver axis on lipid metabolism in male offspring by Juntong Lin, Fuhui Yan, Longhui Liu, Ganzhong Liao, Yilei Xu, Qian Liu, Miaoliang Wu, Honghui Guo, Bai Zhi, Lianxian Guo, Xiaoshan Liu

“…Target bile acids (BAs) metabolites analysis revealed a significant increased levels of primary BAs cholic acid (CA), but decreased levels of chenodeoxycholic acid (CDCA), and decreased levels of the secondary BAs deoxycholic acid (DCA), hyodeoxycholic acid (HDCA), ursodeoxycholic acid (UDCA), and lithocholic acid (LCA) in TPhP treatment group. Measurements of gene expression along the gut-BAs-liver axis showed that the TPhP treatment group had an increase in cholesterol-7alpha-hydroxylase (CYP7A1) and a decrease in apical sodium-dependent bile acid transporter (ASBT), with only the low-dose group exhibiting an increase in carbohydrate response element binding protein (ChREBP). …”
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Disparate and shared transcriptomic signatures associated with cortical atrophy in genetic behavioral variant frontotemporal degeneration by Ting Shen, Jacob W. Vogel, Vivianna M. Van Deerlin, EunRan Suh, Laynie Dratch, Jeffrey S. Phillips, Lauren Massimo, Edward B. Lee, David J. Irwin, Corey T. McMillan

“…Conclusions Overall, this integrative transcriptomic approach identified several new shared and disparate genes associated with regional vulnerability with increased biological interpretation including overlap with synaptic density maps and pathologically-specific gene expression. These findings illuminated the intricate molecular underpinnings contributing to the heterogeneous nature of disease distribution in bvFTD with distinct genetic backgrounds.…”
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Immunoregulatory programs in anti‐N‐methyl‐D‐aspartate receptor encephalitis identified by single‐cell multi‐omics analysis by Xinhui Li, Yicong Xu, Weixing Zhang, Zihao Chen, Dongjie Peng, Wenxu Ren, Zhongjie Tang, Huilu Li, Jin Xu, Yaqing Shu

“…Methods Peripheral blood mononuclear cells (PBMCs) from patients in the acute phase of anti‐NMDARE and healthy controls were sequenced using single‐cell joint profiling of transcriptome and chromatin accessibility. Differential gene expression analysis, transcription factor activity profiling, and cell‐cell communication modeling were performed to elucidate the immune mechanisms underlying the disease. …”
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The control effect and induced disease resistance mechanism of Bacillus tequilensis on wheat powdery mildew by Qiuyan Bi, Fen Lu, Jie Wu, Xiangyu Liu, Xiuying Han, Jianjiang Zhao

“…Using transcriptome technology, we determined the differences in wheat gene expression in after treatment with B. tequilensis and verified the main molecular mechanism of B. tequilensis-induced resistance. …”
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Molecular and pharmacological heterogeneity of ETV6::RUNX1 acute lymphoblastic leukemia by Zhenhua Li, Huanbin Zhao, Wenjian Yang, Maud Maillard, Satoshi Yoshimura, Yu-Chih Hsiao, Xin Huang, Yoshihiro Gocho, Lauren Rowland, Anthony Brown, Landon Choi, Kristine R. Crews, Charles G. Mullighan, Samuel W. Brady, Cheng Cheng, Ti-Cheng Chang, Gang Wu, Mignon L. Loh, Allen Eng Juh Yeoh, Federico Antillon-Klussmann, Sima Jeha, Hiroto Inaba, Jiyang Yu, Ching-Hon Pui, Seth E. Karol, William E. Evans, Jun J. Yang

“…Re-introducing PAX5 in ETV6::RUNX1 ALL of the C2 subtype converts its gene expression and drug resistance profile to C1, with partial blockade of G1 to S transition mediated by CDK6 expression. …”
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Optimization of chemical transfection in airway epithelial cell lines by Tony J. F. Guo, Wan Yi Liang, Gurpreet K. Singhera, Jasmine Memar Vaghri, Janice M. Leung, Del R. Dorscheid

“…Abstract Background Chemical transfection is a widely employed technique in airway epithelium research, enabling the study of gene expression changes and effects. Additionally, it has been explored for its potential application in delivering gene therapies. …”
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Comprehensive Analysis of Programmed Cell Death-Related Genes in Diagnosis and Synovitis During Osteoarthritis Development: Based on Bulk and Single-Cell RNA Sequencing Data by Zhou J, Jiao S, Huang J, Dai T, Xu Y, Xia D, Feng Z, Chen J, Li Z, Hu L, Meng Q

“…Diverse programmed cell death (PCD) pathways are closely linked to the pathogenesis of OA, but few studies have explored the relationship between PCD-related genes and synovitis.Methods: The transcriptome expression profiles of OA synovial samples were obtained from the Gene Expression Omnibus (GEO) database. Using machine learning algorithms, Hub PCD-related differentially expressed genes (Hub PCD-DEGs) were identified. …”
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