Integrative single-cell and spatial transcriptomics uncover ELK4-mediated mechanisms in NDUFAB1+ tumor cells driving gastric cancer progression, metabolic reprogramming, and immune... by Yuwei Sun, Wenyang Nie, Zhikai Xiahou, Xiaojing Wang, Wenjia Liu, Zongkai Liu, Zhiheng Lin, Zhaidong Liu

“…ELK4 was identified as a key regulatory factor that markedly enhanced the proliferation, migratory capacity, and invasive potential of tumor cells, while changes in the TME were a driving force behind immune suppression and drug resistance. …”
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Association between transcriptomic metrics of exogenous antigen presentation and adaptive immunity with locoregional recurrence in localized estrogen receptor negative breast cance... by Timothy J. Robinson, Casey L. Liveringhouse, Christopher Wilson, Sam Friedman, Justyn Nakashima, Matthew N. Mills, Jacob D. Purcell, Nicholas B. Figura, Du Dongliang, Ram Thapa, Eric Welsh, Kamran A. Ahmed, G. Daniel Grass, Brooke L. Fridley, Roberto Diaz

“…Abstract Background Transcriptomic features of breast cancer locoregional recurrence (LRR) remain poorly understood. …”
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Modulation of gut microbiota by Gardeniae Fructus oil exerts TLR4/NF-κB/NLRP3 pathway-mediated antidepressant effects based on transcriptomics and fecal transplantation by Man Han, Man Han, Man Han, Yujing Zhou, Yujing Zhou, Yujing Zhou, Xinyu Gao, Xinyu Gao, Xinyu Gao, Xixi Cheng, Xixi Cheng, Xixi Cheng, Ling Deng, Ling Deng, Ling Deng, Shilin Ji, Shilin Ji, Shilin Ji, Zhengheng Li, Zhengheng Li, Zhengheng Li, Yu Cai, Yu Cai, Yu Cai, Chunchao Yan, Chunchao Yan, Chunchao Yan, Yunzhong Chen, Yunzhong Chen, Yunzhong Chen

“…The signaling pathways regulating the antidepressant properties of OGF were obtained by transcriptome sequencing analysis and validated at the protein level.ResultsCompared with the CON group, mice in the CUMS group showed significant depressive-like behavior, pathological damage to the hippocampus and colon tissues, significant decrease in levels of 5-HT, DA, and BDNF in the hippocampus, significant increase in levels of IL-1β, IL-6, TNF-α, DAO, and LPS in serum, significant decrease in colonic tight junction protein expression, and significant increase in protein expression of TLR4, p-NF-κB, NLRP3, ASC, and IL-1β in the hippocampus (P < 0.01); Compared with the CUMS group, the FMT group could effectively improve the above situation (P < 0.05, P < 0.01), whose therapeutic effect was second only to the OGF group (P < 0.01), while ABX + OGF group did not show obvious therapeutic effect.ConclusionOGF might exert antidepressant effects by modulating gut microbiota and mediating the hippocampal TLR4/NF-κB/NLRP3 pathway.…”
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Normal hearing function genetics: have you heard all about it? An integrated approach of genome-wide association studies and transcriptome-wide association studies in three Italian... by Aurora Santin, Aurora Santin, Giulia Pianigiani, Alessandro Gialluisi, Alessandro Gialluisi, Alessandro Pecori, Beatrice Spedicati, Beatrice Spedicati, Simona Costanzo, Mariarosaria Persichillo, Francesca Bracone, Giuseppe Giovanni Nardone, Paola Tesolin, Stefania Lenarduzzi, Anna Morgan, Amalia De Curtis, Wouter van der Valk, Wouter van der Valk, Francis Rousset, Marta Roccio, Marta Roccio, Heiko Locher, Heiko Locher, Licia Iacoviello, Licia Iacoviello, Maria Pina Concas, Giorgia Girotto, Giorgia Girotto

“…SnRNA-seq data analyses revealed a peculiar expression of the ASTN2 gene in the neuronal and dark cells populations, while for SLC1A6 no significant expression was detected. …”
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Transcriptomic and Metabolomic Joint Analysis Revealing Different Metabolic Pathways and Genes Dynamically Regulating Bitter Gourd (<i>Momordica charantia</i> L.) Fruit Growth and... by Boyin Qiu, Dazhong Li, Qianrong Zhang, Hui Lin, Yongping Li, Qingfang Wen, Haisheng Zhu

“…Correlation analysis revealed that 11 DEMs were positively correlated with four traits except for arbutin, while eight DEGs were related to all traits, including six significantly positive and two significantly negative correlations. …”
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Transcriptome-wide analysis reveals potential roles of CFD and ANGPTL4 in fibroblasts regulating B cell lineage for extracellular matrix-driven clustering and novel avenues for imm... by Hongwei Wang, Yu-nan Zhu, Sifan Zhang, Kexin Liu, Rong Huang, Zhigao Li, Lan Mei, Yingpu Li

“…However, the compositional patterns of ECM in breast cancer and their underlying biological functions remain elusive. Methods Transcriptome and genome data of breast cancer patients from TCGA database was downloaded. …”
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Comparative transcriptome-based identification and expression analysis of ATP-binding cassette (ABC) transporters reveals a likely role in the transport of β-caryophyllene and resp... by Haibin Wang, Chen Zong, Yibo Bai, Shuilin Yuan, Yan Li, Tiantian Han, Huanhuan Xu, Chunmei Hu, Xilin Hou, Ying Li

“…The RNA-seq and qRT-PCR results showed that eight ABC genes were expressed in a tissue- and development-specific manner, while their abundance apparently varied when plants were exposed to different treatment conditions. …”
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Tumor-agnostic transcriptome-based classifier identifies spatial infiltration patterns of CD8+T cells in the tumor microenvironment and predicts clinical outcome in early-phase and... by Cláudia S Ferreira, Konstanty Korski, Michael A Cannarile, Irina Klaman, Petra C Schwalie, Iakov I Davydov, Andreas Roller, Martha L Serrano-Serrano, Astrid Heller, Nicolas Staedler, Gabriele Dietmann, Alberto Valdeolivas

“…Melanoma and kidney cancers were among the strongest inflamed indications, while CD8-desert phenotypes were most abundant in liver metastases across all tumor types. …”
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Diurnal rhythms in durum wheat triggered by Rhopalosiphum padi (bird cherry-oat aphid) by Yoshiahu Goldstein, Jinlong Han, Daniel Kunk, Albert Batushansky, Vamsi Nalam, Vered Tzin

“…Under control conditions, 15,366 out of the 66,559 genes in the tetraploid wheat cultivar Svevo, representing approximately 25% of the transcriptome, exhibited diurnal rhythmicity. Upon aphid infestation, 5,682 genes lost their rhythmicity, while 5,203 genes began to exhibit diurnal rhythmicity. …”
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Pharmacoinformational, basic and clinical studies of 7-hydroxymatairesinol in the context of searching for effective and safe therapeutic approaches to the treatment of mastopathy by А. N. Rubashkina, I. Yu. Torshin, O. A. Gromova

“…An assessment of the transcriptomic effects of 7(OH)MR in breast cancer cells showed significant dose-dependent effects on the transcription of 3468 of 12700 genes. …”
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Mapping the molecular signature of ABA-regulated gene expression in germinating barley embryos by Ewa Sybilska, Bahareh Sadat Haddadi, Luis A. J. Mur, Manfred Beckmann, Szymon Hryhorowicz, Joanna Suszynska-Zajczyk, Monika Knaur, Andrzej Pławski, Agata Daszkowska-Golec

“…Abstract Background Abscisic acid (ABA) regulates key plant processes, including seed germination, dormancy, and abiotic stress responses. While its physiological role in germination is well-documented, the molecular mechanisms are still poorly understood. …”
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Preharvest Application of Exogenous 2,4-Epibrassinolide and Melatonin Enhances the Maturity and Flue-Cured Quality of Tobacco Leaves by Kesu Wei, Jiayi Tang, Lei Yang, Shaopeng Chen, Zhijun Cheng, Yijun Yang, Chen Xu, Shengjiang Wu, Yuhang Zhao, Hongmei Di, Ling Li, Dongyang Sun, Jianwei Li, Bo Sun

“…The levels of conventional chemical components were improved, enhancing the overall coordination of the tobacco. Transcriptome analysis revealed that EBR treatment down-regulated the chlorophyll biosynthetic genes <i>hemA</i>, <i>MgPEC</i>, and <i>ChlD</i>, while up-regulating the chlorophyll degradation genes <i>CHL2</i>, <i>SGR</i>, and <i>PAOs</i>. …”
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Optimizing Cost-Effective gene expression phenotyping approaches in cattle using 3′ mRNA sequencing by Ruwaa I. Mohamed, Taylor B. Ault-Seay, Sonia J. Moisá, Jonathan E. Beever, Agustín G. Ríus, Troy N. Rowan

“…The rapidly declining cost of next-generation sequencing presents opportunities for population-level molecular phenotyping. While the cost of whole transcriptome sequencing has declined recently, its required sequencing depth still makes it an expensive choice for wide-scale molecular phenotyping. …”
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Sex-specific differences in preclinical models of advanced chronic liver disease and portal hypertension by Peio Aristu-Zabalza, María Andrés-Rozas, Zoe Boyer-Díaz, David P. Al-Adra, Douglas Maya-Miles, Sergi Guixé-Muntet, Anabel Fernández-Iglesias, Jordi Gracia-Sancho

“…In the BDL model, females had more fenestrae and porosity, and less fibrosis. Transcriptomic analysis revealed that TAA males had dysregulated metabolic pathways, while females had deregulated genes in hormone signaling. …”
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Multi-Omics Analysis Provides New Insights into the Interplay Between Gut Microbiota, Fatty Acid Metabolism, and Immune Response in Cultured and Wild <i>Coilia nasus</i> from the Y... by Chang Yang, Kai Liu, Yanmin Deng, Qianhui Wang, Shiqian Cao, Qunlan Zhou

“…However, the shear force, water-holding capacity, and total n-6 PUFA content were lower in wild <i>C. nasus</i>. Transcriptome analysis revealed distinct gene expression patterns: wild <i>C. nasus</i> upregulated immune-related genes, while cultured <i>C. nasus</i> downregulated genes related to fatty acid metabolism. …”
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Targeting PDCD4 in cancer and atrial fibrillation: mechanistic insights from integrated multi-omics and single-cell analysis by Juledezi Hailati, Zhiqiang Liu, Lei Zhang, Muhuyati Wulasihan

“…BackgroundAtrial fibrillation (AF) is a complicated and varied cardiovascular disorder with inadequate understanding of its molecular underpinnings. While Programmed cell death factor 4 (PDCD4) has been associated in several illnesses, its particular significance in AF remains unknown. …”
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Moderate Septoria apocyni infection enhances flavonoid and mineral elements accumulation in Apocynum venetum leaves by Panpan Shang, Yanglu Ran, Xinchun Ge, Li Wang, Meiting Bai, Jiming Yang, Yonghe Cai, Tingyu Duan

“…This study employed transcriptomics technology to elucidate the molecular mechanisms underlying the response of A. venetum to spot blight, while simultaneously investigating flavonoid and mineral elements content of the leaves. …”
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Characterizing age-related features for assessing biological age and characteristics in Xinjiang Brown cattle by Jiahao Wang, Menghua Zhang, Qingyao Zhao, Siqian Chen, Yongjie Tang, Quanzhen Chen, Lei Xu, Dan Wang, Xiaoping Guo, Kai Xing, Yachun Wang, ChuduanWang, Xixia Huang, Ying Yu

“…Results A total of 1140 genes were identified as exhibiting a linear change in expression with age, while 697 genes showed non-linear changes, mainly enriched in immune and disease-related pathways. …”
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Diversity and Novelty of Venom Peptides in Vermivorous Cone Snails, Subgenus <i>Rhizoconus</i> (Gastropoda: Mollusca) by Christine Marie C. Florece, Quentin Kaas, Neda Barghi, Arturo O. Lluisma

“…In this study, we report the first venom gland transcriptomes from two species in the <i>Rhizoconus</i> clade, <i>Conus capitaneus</i> and <i>Conus mustelinus</i>, and a new <i>Conus miles</i> transcriptome from a specimen collected in the Philippines. …”
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Multi-omics joint analysis reveals the mechanism of flower color and fragrance variation in Lilium cernuum by Shaopeng Chen, Zhiqun Chen, Qianqian Zhuang, Hewen Chen

“…IntroductionLilium cernuum, a fragrant purple-red wild lily endemic to Northeast Asia, represents both ecological significance (as a key protected species) and horticultural value. While its white variant (L. cernuum var. album) exhibits distinct flower color and fragrance traits, the molecular mechanisms underlying these variations remain poorly understood. …”
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