Genome-wide identification and functional characterization of LBD gene family in four Cymbidium species (Orchidaceae) and potential regulatory role of CsiLBD27 in floral developmen... by Yonglu Wei, Zengyu Lin, Jianpeng Jin, Wei Zhu, Jie Gao, Jie Li, Qi Xie, Chuqiao Lu, Genfa Zhu, Fengxi Yang

“…Promoter sequences of CymLBD genes revealed various cis-elements significant for light, hormonal, biotic, and abiotic stress responses. Transcriptomic analysis revealed tissue- and stage-specific expression of CymLBD genes in Cymbidium, and RT-qPCR and yeast one-hybrid assays indicated that CsiLBD27 may regulate floral patterning by directly binding to the CsiSEP3 promoter and activating its transcription. …”
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Enhancer Profiling Reveals a Protective Role of RXRα Against Calcium Oxalate‐Induced Crystal Deposition and Kidney Injury by Yu Yang, Xudan Dou, Yongzhan Sun, Mengyao Wang, Jing Wang, Xinyi Cao, Haijie Xie, Linguo Xie, Weiping Tian, Jing Nie, Yupeng Chen, Chunyu Liu, Lirong Zhang

“…Bioinformatic analysis pinpointing the RXRα as a central transcription factor (TF) modulating enhancer activity. …”
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Stratification system with dual human endogenous retroviruses for predicting immunotherapy efficacy in metastatic clear-cell renal cell carcinoma by Li Xu, Stephane Oudard, Catherine Sautes-Fridman, Xiaoping Su, Gabriel G. Malouf, Virginie Verkarre, Salma Kotti, Fangrong Yan, Yann-Alexandre Vano, Wolf Herve Fridman, Cheng-Ming Sun, Xiaofan Lu, Wenxuan Cheng

“…Beyond enhancing the predictive precision of existing transcriptomic models, this system paves the way for more targeted and individualized approaches in the realm of precision oncology.…”
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MiR-7 inhibits progression of glioblastoma by impairing autophagy resolution, energy metabolism and ECM remodeling by Marta Torrecilla-Parra, Virginia Pardo-Marqués, Antonio C. Fuentes-Fayos, Miguel E. G-García, Mario Fernández-de Frutos, José L. López-Aceituno, Cristina Puigdueta, Carmen Zamora, Ana Pérez-García, Juan F. Aranda, Rebeca Busto, Manuel D. Gahete, Raúl M. Luque, Cristina M. Ramírez

“…Methods Bioinformatics analysis was performed to identify miR-7 target genes potentially involved in the regulation of metabolism and cellular processes related to GBM. …”
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Lipid nanoparticles as a tool to dissect dendritic cell maturation pathways by Sofie Rennen, Victor Bosteels, Clint De Nolf, Sandra Maréchal, Jessica Vetters, Karo Van Lil, Greta Webb, Janne Swinnen, Evelien Van De Velde, Farzaneh Fayazpour, Ria Roelandt, Niels Vandamme, Kevin Verstaen, Stefaan C. De Smedt, Karine Breckpot, Stijn Vanhee, Philippe Gevaert, Eric Hoste, Bruno G. De Geest, Rein Verbeke, Ine Lentacker, Sophie Janssens

“…By using a lipid nanoparticle (LNP)-based approach and cellular indexing of transcriptomes and epitopes sequencing analysis, we designed a flow cytometry panel and transcriptional profiling tools to reliably annotate the two DC maturation states. …”
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Mechanism of Action of <i>Fusarium oxysporum</i> CCS043 Utilizing Allelochemicals for Rhizosphere Colonization and Enhanced Infection Activity in <i>Rehmannia glutinosa</i> by Feiyue Yuan, Fuxiang Qiu, Jiawei Xie, Yongxi Fan, Bao Zhang, Tingting Zhang, Zhongyi Zhang, Li Gu, Mingjie Li

“…In this study; the genome of <i>F. oxysporum</i> CCS043 from <i>R. glutinosa’s</i> rhizosphere microbiota was sequenced and assembled de novo; resulting in a 47.67 Mb genome comprising 16,423 protein-coding genes. Evolutionary analysis suggests that different <i>F. oxysporum</i> strains may adapt to the host rhizosphere microecosystem by acquiring varying numbers of specific genes while maintaining a constant number of core genes.The allelopathic effects of ferulic acid; verbascoside; and catalpol on <i>F. oxysporum</i> CCS043 were examined at the physiological and transcriptomic levels. …”
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The Role of L-Sorbose Metabolism in Enhancing Fitness and Virulence in Escherichia coli Under Acidic Conditions by Qiu T, Chen X, Deng X, Zhang G, Wen S, Wu J, Sun D, Li T, Yan B, Dai M, Zhong LL, Tian GB

“…Virulence was further tested using a Galleria mellonella infection model.Results: Deletion of sorD caused severe growth defects, loss of virulence factors (flagella and fimbriae), disrupted PMF, and oxidative stress accumulation under acidic conditions. Transcriptomic analysis revealed dysregulation of energy metabolism pathways and downregulation of virulence-associated genes in the ΔsorD mutant. …”
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GPD2 inhibition impairs coagulation function via ROS/NF-κB/P2Y12 pathway by Jiajie Chen, Guifeng Xu, Zhipeng Xie, Shaoxia Xie, Wenwei Luo, Shilong Zhong, Weihua Lai

“…Transcriptomic studies indicated that GPD2 gene (cg03230175) methylation affects mitochondrial function, nuclear factor kappa B (NF-κB) signaling pathway, reactive oxygen species metabolic process, and G protein-coupled receptor (GPCR) ligand binding. …”
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Restorative Effects of Synbiotics on Colonic Ultrastructure and Oxidative Stress in Dogs with Chronic Enteropathy by Dipak Kumar Sahoo, Tracey Stewart, Emily M. Lindgreen, Bhakti Patel, Ashish Patel, Jigneshkumar N. Trivedi, Valerie Parker, Adam J. Rudinsky, Jenessa A. Winston, Agnes Bourgois-Mochel, Jonathan P. Mochel, Karin Allenspach, Romy M. Heilmann, Albert E. Jergens

“…To explore potential signaling pathways that might modulate MITO and ER stress, a transcriptomic analysis was also performed. The degree of mucosal ultrastructural pathology differed among individual dogs before and after treatment. …”
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BRAF V600E mutation associated with papillary high-grade serous ovarian cystadenocarcinoma in a 22q11.2DS patient by Maria Antonietta Castaldi, Nadia Petrillo, Carmine Selleri, Monica Ianniello, Anna Maria Della Corte, Eloisa Evangelista, Luigia De Falco, Roberto Sirica, Marika Casillo, Alessia Caleo, Alessandro Caputo, Pio Zeppa, Salvatore Giovanni Castaldi, Pasqualina Scala, Bianca Serio, Giovanni Savarese, Valentina Giudice

“…Chromosome 22 abnormalities, including del(22q) and duplications, are genetic multisystemic disorders, most commonly affecting cardiovascular, immune, and gastrointestinal systems, while tumors are rarely reported. Methods: In this case report, we described a patient with 22q11.2 deletion syndrome who developed a papillary high-grade serous ovarian cystadenocarcinoma, and targeted- and whole-exome sequencing for genomic alterations identification and RNA-sequencing for transcriptomics analysis were performed. …”
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Host taxonomy and environment shapes insectivore viromes and viral spillover risks in Southwestern China by Ji-Hu Yang, Chun-Feng Luo, Rong Xiang, Jiu-Meng Min, Zong-Ti Shao, Yi-Lin Zhao, Lu Chen, Lin Huang, Yun Zhang, Shun-Shuai Liu, Yu-Qiong Li, En-Nian Pu, Wen-Qiang Shi, Hai-Feng Pan, Wei-Jun Chen, Chun-Hong Du, Jia-Fu Jiang

“…Cross-species transmission was predominantly observed in viruses carried by shrews, while moles may play a pivotal role in facilitating viral transmission among insectivores. …”
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IL-17A as a Key Mediator of Pulmonary-Intestinal Immune Interactions in a Mouse Model of Asthma and Colitis by Wu C, Hu X, Mo Z, Meng Y, Du Y, Duan Y, Zeng Z, Shan J, Li J, Zhang N, Ma Y, Wang H, Liu C, Zhang G, Foster PS, Xu H, Li F, Yang M

“…Additionally, we observed a reduction in mucus production, particularly in the airways, highlighting IL-17A’s direct role in mucin regulation. Transcriptomic analysis confirmed that IL-17A blockade downregulated several immune-related pathways in colon tissues, further supporting its central role in mediating multi-organ inflammation.Conclusion: These findings indicate that IL-17A represents a systemic immunomodulator, which orchestrates compartmentalized immune responses along the lung-gut axis. …”
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Basophil-derived exosomes exacerbate systemic lupus erythematosus by regulating B-cell proliferation via miR-24550 by Jiaxuan Chen, Shuzhen Liao, Jiaqi Lun, Xing Lu, Bitang Huang, Xiaoxian Liu, Xiaowei Xu, Lawei Yang, Fengbiao Guo, Liuyong You, Haiyan Xiao, Hua-Feng Liu, Qingjun Pan

“…The Pristane-Mcpt8 flox/flox, CAGGCre−ERTM mice were analyzed for basophil-derived exosome accumulation in the spleen and kidneys, and the effects on immune cell proliferation and plasma cell-plasmablast balance were assessed. Transcriptomic analysis was conducted on basophil-derived exosomes to identify key non-coding RNAs. …”
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SNRPB/CCNB1 axis promotes hepatocellular carcinoma progression and cisplatin resistance through enhancing lipid metabolism reprogramming by Xin Jin, Xigan He, Runze Huang, Qinyu Liu, Lei Wang, Xuanci Bai, Yibin Wu, Yixiu Wang, Ziting Jiang, Yi Shi, Gautam Sethi, Lu Wang, Weiping Zhu

“…Knockdown of SNRPB suppressed HCC cell proliferation and migration, while promoting apoptosis. Mechanistically, SNRPB regulated CCNB1 expression via FOXM1-mediated transcription, and SNRPB overexpression enhanced lipid metabolism and cisplatin resistance. …”
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Single-cell sequencing and machine learning reveal the role of dioxin-interacting genes in HCC prognosis and immune microenvironment by Senyan Wang, Qi Liu, Xiaoyan Sun, Minghui Hou, Wenjuan Wei, Hao Song, Jing Xu, Danyang Lu, Jing Fu, Xiaofang Zhao, Hongyang Wang

“…High-risk patients exhibited increased cell proliferation and aggressive tumor traits, while low-risk patients showed better metabolic stability and immune surveillance. …”
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Polystyrene microplastics induce nephrotoxicity through DDIT4-mediated autophagy and apoptosis by Yujiao Wang, Anxiu Zhang, Ting Liang, Long Chen, Shuqi Feng, Zhuoyuan Zhao, Ziye Jing, Jieping Lv, Jun Xie, Bingrui Zhou

“…Furthermore, enhanced autophagy and apoptosis were observed in nephron progenitor cells (NPCs), as evidenced by a 3.5-fold increase in LC3-II expression and a 1.5-fold increase in cleaved caspase-3 levels. Transcriptomic analysis identified DNA damage-inducible transcript 4 (DDIT4) as a key mediator, linking PS-MP exposure to the inhibition of mTOR signaling. …”
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Adaptation for Staphylococcus aureus to hosts via insertion mutation in the accessory gene regulator agrC gene: decreased virulence and enhanced persistence capacity by Jiawei Chen, Yun Wu, Ying Zhu, Li Zhang, Yingchun Xu, Yali Liu

“…Conversely, 23B exhibited enhanced biofilm formation, greater adherence to A549 cells, and increased persistence in the face of vancomycin and daptomycin treatment. Transcriptomic analysis revealed that 23B upregulated surface protein-encoding genes while simultaneously reducing the expression levels of virulence factors, highlighting the intricate regulatory adjustments facilitating its persistence and reducing pathogenic potential. …”
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Notch signaling regulates the responses of lipopolysaccharide-stimulated macrophages in the presence of immune complexes. by Wipawee Wongchana, Pornrat Kongkavitoon, Pattarin Tangtanatakul, Chutamath Sittplangkoon, Patcharavadee Butta, Supatta Chawalitpong, Thitiporn Pattarakankul, Barbara A Osborne, Tanapat Palaga

“…Defects in NF-κB p50 nuclear localization were observed in GSI-treated macrophages and in Rbpj-/- macrophages, suggesting cross-regulation between the Notch and NF-κB pathways. Transcriptomic analysis revealed that Notch signaling regulates the transcription of genes involved in the cell cycle, macrophage activation, leukocyte migration and cytokine production in LPS/IC-stimulated macrophages. …”
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Lack of IFN-γ response of human uterine myometrium-derived MSCs significantly improve multiple IBD parameters compared to bone marrow MSCs: Implications for anti-TNFα-refractory pa... by Li-Tzu Wang, Hsiu-Huan Wang, Shih-Sheng Jiang, Chia-Chih Chang, Pei-Ju Hsu, Ko-Jiunn Liu, Huey-Kang Sytwu, B. Linju Yen, Men-Luh Yen

“…We found that UtMSC but not BMMSC treatment significantly reversed disease parameters by improving microbiome and reducing mesenteric lymph node IFN-γ and IL-17A-secreting T cells. Transcriptomic analysis revealed UtMSCs had reduced MHC II pathway activation compared to BMMSCs. …”
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Diabetes exacerbates SARS-CoV-2 replication through ineffective pulmonary interferon responses, delayed cell-mediated immunity, and disruption of leptin signaling by Côme J. Thieulent, Côme J. Thieulent, Udeni B. R. Balasuriya, Udeni B. R. Balasuriya, Anna Tseng, Nicholas A. Crossland, Nicholas A. Crossland, Nicholas A. Crossland, Jacqueline M. Stephens, Wellesley Dittmar, Wellesley Dittmar, Jaroslaw Staszkiewicz, Juergen A. Richt, Mariano Carossino, Mariano Carossino

“…These data shed light on the alteration of the innate immune pathway in the lung using in-depth transcriptomic analysis and on adaptive immune responses to SARS-CoV-2 under T2DM conditions. …”
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