Construction and validation of a chemokine-related gene signature associated with prognosis, clinical significance, and immune microenvironment characteristics in cervical cancer by Tianjiao Huang, Renshuang Cao, Cong Gao, Jie Luo, Zhiyu Zhou, Kun Ma

“…Conclusion This study presents a clinically applicable prognostic model based on chemokine-related genes, providing insights for risk stratification and therapeutic decision-making in CC. …”
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Comprehensive analysis of housekeeping genes, tissue-specific genes, and dynamic regulation across developmental stages in pearl millet by Wei Luo, Min Sun, Ailing Zhang, Chuang Lin, Yarong Jin, Xiaoshan Wang, Linkai Huang

“…We provided valuable options for transcript normalization and crucial targets for exploring gene function for the plant growth and development in pearl millet. …”
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Identification of potential pathogenic genes associated with the comorbidity of rheumatoid arthritis and renal fibrosis using bioinformatics and machine learning by Jiao Qiu, Yalin Xu, Luyuan Tong, Xingchun Yang, Xiao Wu

“…Abstract This study aimed to identify the potential pathogenic genes associated with the comorbidity of rheumatoid arthritis (RA) and renal fibrosis (RF). Transcriptomic data related to RA and RF were retrieved from the GEO database. …”
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Identification of RNA binding protein genes associated with colorectal cancer by bioinformatics analysis by Rong-Chao He, Haibo Wang, Jun He, Hou-Dong Wang, Zhong Shen

“…This research conducted a thorough examination of the prognostic and functional significance of RBP-related gene sets (RBPGs) in CRC by utilizing transcriptomic data from the cancer genome atlas (TCGA). …”
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Potential biomarkers and immune infiltration linking endometriosis with recurrent pregnancy loss based on bioinformatics and machine learning by Jianhui Chen, Qun Li, Xiaofang Liu, Fang Lin, Yaling Jing, Jiayan Yang, Lianfang Zhao

“…This study aims to investigate the potential biomarkers and immune infiltration in EMs and RPL, providing a basis for early detection and treatment of the two diseases.MethodsTwo RPL and six EMs transcriptomic datasets from the Gene Expression Omnibus (GEO) database were used for differential analysis via limma package, followed by weighted gene co-expression network analysis (WGCNA) for key modules screening. …”
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Multi-omics network toxicology reveals the role of benzo[a]pyrene in ovarian cancer: Integrating gut microbiota dynamics and Mendelian randomization by Jinfa Huang, Qian Yang, Lingling Zeng, Kaixian Deng

“…., upregulated BCL2L1/CASP3; downregulated ALB/MTOR; all p < 0.001), with prognostic implications (AHR HR = 1.17, p = 0.028; CYCS HR = 1.18, p = 3.5E-05). Single-cell transcriptomic data analysis (via scCancerExplorer) uncovered cell-type-specific enrichment patterns (e.g., AHR/EGF in endothelial/proliferative T cells). …”
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Identification of lipid metabolism-related genes in myocardial infarction: implications for diagnosis and therapy by Qiang Wang, Xian Wu, Bo Yu

“…Materials and methods Endothelial cell transcriptomes from MI patients and controls were downloaded from the Gene Expression Omnibus (GEO) database. …”
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Molecular landscape of sex- and modality-specific exercise adaptation in human skeletal muscle through large-scale multi-omics integration by Macsue Jacques, Shanie Landen, Adam P. Sharples, Andrew Garnham, Ralf Schittenhelm, Joel Steele, Aino Heikkinen, Elina Sillanpää, Miina Ollikainen, James Broatch, Navabeh Zarekookandeh, Ola Hanson, Ola Ekström, Olof Asplund, Séverine Lamon, Sarah E. Alexander, Cassandra Smith, Carlie Bauer, Mary N. Woessner, Itamar Levinger, Andrew E. Teschendorff, Linn Gillberg, Ida Blom, Jørn Wulff Helge, Nicholas R. Harvey, Larisa M. Haupt, Lyn R. Griffiths, Atul S. Deshmukh, Kirsi H. Pietiläinen, Päivi Piirilä, Robert A.E. Seaborne, Marie Klevjer, Anja Bye, Ulrik Wisløff, Bernadette Jones-Freeman, Nir Eynon

“…Summary: We investigated the molecular mechanisms of exercise adaptations in human muscle by integrating genome, methylome, transcriptome, and proteome data from over 1,000 participants (2,340 muscle samples). …”
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Mature tertiary lymphoid structures linked to HPV status and anti-PD-1 based chemoimmunotherapy response in head and neck squamous cell carcinoma by Lizao Zhang, Siqi Ren, Tianjun Lan, Ventin Marco, Niu Liu, Bin Wei, Yunsheng Chen, Jiaying Wu, Qunxing Li, Fan Wu, Peichia Lu, Jiahao Miao, Hsinyu Lin, Xinhui Wang, Jianglong Zhong, Jinsong Li, Song Fan

“…By analyzing TCGA-HNSC transcriptomic data and pathology slides, we identified an immune subtype enriched in TLSs, predominantly in HPV-positive tumors, which correlated with favorable immunotherapy response. …”
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Divergent combinations of enhancers encode spatial gene expression by Danni Hong, Muya Shu, Jiamao Liu, Lifang Liu, Hao Cheng, Ming Zhu, Yi Du, Bo Xu, Di Hu, Zhiyong Liu, Yannan Zhao, Jianwu Dai, Falong Lu, Jialiang Huang

“…Abstract Spatial transcriptomics and epigenomics have enabled mapping gene regulation in the tissue context. …”
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Inhibiting microtubule polymerization with EAPB02303, a prodrug activated by catechol-O-methyl transferase, enhances paclitaxel effect in pancreatic cancer models by Kévin Bigot, Cindy Patinote, Véronique Garambois, Adrien Chouchou, Stéphanie Gayraud-Paniagua, Nadia Vie, Yann Maggipinto, Elias Smyej, Mathilde Robin, Margot Machu, Marine Bruciamacchie, Pierre-Emmanuel Colombo, Corinne Bousquet, Muriel Mathonnet, Ela Levy-Augé, Diego Tosi, Pierre-Antoine Bonnet, Céline Gongora, Carine Deleuze-Masquéfa, Christel Larbouret

“…Moreover, EAPB02303 had a synergistic effect when combined with paclitaxel (the standard-of-care agent in PDAC) providing the rationale to continue the development of EAPB02303 combination strategies for the treatment of catechol-O-methyltransferase-overexpressing PDAC.…”
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Delayed Starch Degradation Triggers Chromoplast Structural Aberration to Inhibit Carotenoid Cleavage: A Novel Mechanism for Flower Color Deepening in <i>Osmanthus fragrans</i> by Xiangling Zeng, Yunfei Tan, Xin Wen, Qiang He, Hui Wu, Jingjing Zou, Jie Yang, Xuan Cai, Hongguo Chen

“…This study uses the Jingui cultivar ‘Jinqiu Gui’ (JQG) and its bud mutation cultivar ‘Huolian Jindan’ (HLJD) as materials, combining genome resequencing, ultrastructural observation, targeted metabolomics, and transcriptomic analysis to elucidate the molecular and cellular mechanisms underlying flower color variation. …”
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Thiacloprid exposure disrupts the gut-liver axis and induces liver dysfunction in the Reeves' turtles (Mauremys reevesii) by Shuqin Lin, Yunjuan Xiao, Siyu Li, Liyan Tang, Haitao Shi, Meiling Hong, Li Ding

“…Our findings demonstrate that THI impairs the intestinal barrier and causes liver dysfunction and damage in turtles, providing new insights into evaluating the toxic effects of thiacloprid on aquatic organisms.…”
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High-starchy carbohydrate diet aggravates NAFLD by increasing fatty acids influx mediated by NOX2 by Yuqi Gao, Rui Hua, Kezheng Peng, Yuemiao Yin, Chenye Zeng, Yannan Guo, Yida Wang, Liyuan Li, Xue Li, Ying Qiu, Zhao Wang

“…Moreover, the large amounts of ROS produced by NOX2 further exacerbated insulin resistance and increased lipolysis in perirenal white adipose tissue (periWAT), thereby providing fatty acids for hepatic lipid synthesis. …”
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Flow-Cytometric Quantification of Urine Kidney Epithelial Cells Specifically Reflects Tubular Damage in Acute Kidney Diseases by Leonie Wagner, Jacob Kujat, Valerie Langhans, Luka Prskalo, Diana Metzke, Emil Grothgar, Paul Freund, Nina Goerlich, Hannah Brand, Sara Timm, Matthias Ochs, Andreas Grützkau, Sabine Baumgart, Christopher M. Skopnik, Adrian Schreiber, Falk Hiepe, Gabriela Riemekasten, Philipp Enghard, Jan Klocke

“…We developed a protocol for the flow cytometric quantification of CD10/CD13+ proximal TECs (PTECs) and CD227/CD326+ distal TECs (DTECs) in urine by aligning urinary single-cell transcriptomes and TEC surface proteins using Cellular Indexing of Transcriptome and Epitope Sequencing (CITE-Seq). …”
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Identification of Glycolysis-Related Genes in MAFLD and Their Immune Infiltration Implications: A Multi-Omics Analysis with Experimental Validation by Jiawei Chen, Siqi Yang, Diwen Shou, Bo Liu, Shaohan Li, Tongtong Luo, Huiting Chen, Chen Huang, Yongjian Zhou

“…<b>Methods</b>: Integrative multi-omics analysis was performed on bulk RNA-seq, single-cell RNA-seq, and spatial transcriptomic datasets from MAFLD patients and controls. …”
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Gain of bipolar disorder-related lncRNA AP1AR-DT in mice induces depressive and anxiety-like behaviors by reducing Negr1-mediated excitatory synaptic transmission by Shufen Li, Hongyu Ni, Yaping Wang, Xiaohui Wu, Jianqiang Bi, Haiyan Ou, Zhongwei Li, Junjiao Ping, Zhongju Wang, Renhao Chen, Qiong Yang, Meijun Jiang, Liping Cao, Tingyun Jiang, Siqiang Ren, Cunyou Zhao

“…Conclusions The epigenetic and pathophysiological mechanism linking AP1AR-DT to the modulation of depressive and anxiety-like behaviors and excitatory synaptic function provides etiological implications for bipolar disorder.…”
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Molecular mechanisms of efferocytosis imbalance in the idiopathic pulmonary fibrosis microenvironment: from gene screening to dynamic regulation analysis by Qian Jin, Yi Kang, Wenwen Jin, Ying Liu, Qian Chen, Jian Liu, Yali Guo, Yuguang Wang

“…Additionally, the CIBERSORT algorithm was used to analyze immune infiltration levels, and transcriptomic validation of the hub genes was conducted in animal experiments. …”
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Decitabine promotes the differentiation of poorly differentiated gastric cancer cells and enhances the sensitivity of NK cell cytotoxicity via TNF-α by Man Lv, Yue Wang, Ziyin Yuan, Lina Zhai, Haroon Iqbal, Uzair Ur-Rehman, Xin Ning, Huiying Wei, Jun Xin, Zihui Jin, Zhou Yi, Baichuan Wang, Wangkai Chen, Run Xiao

“…In summary, DAC effectively reduces the malignant characteristics of the PDGC cells by promoting their transition towards a higher state of differentiation and enhancing their sensitivity to NK cell-mediated killing, providing new insights for the mechanisms of the antitumor effects of DAC.…”
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Molecular Adaptations and Quality Enhancements in a Hybrid (<i>Erythroculter ilishaeformis</i> ♀ × <i>Ancherythroculter nigrocauda</i> ♂) Cultured in Saline–Alkali Water by Lang Zhang, Qiuying Qin, Qing Li, Yali Yu, Ziwei Song, Li He, Yanhong Sun, Liting Ye, Guiying Wang, Jing Xu

“…This study elucidates molecular mechanisms of fish acclimation to SA environments, providing insights for sustainable aquaculture development and breeding of stress-tolerant species in SA regions.…”
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