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

“…Additionally, evaluations of cisplatin sensitivity were performed, providing an in-depth analysis of influence of SNRPB on HCC. …”
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Comprehensive immunophenotyping of gastric adenocarcinoma identifies an inflamed class of tumors amenable to immunotherapies by Felip Vilardell, Xavier Matias-Guiu, Robert Montal, Mar Iglesias, Maria Santacana, María Ruiz, Genis Parra, Joel Veas Rodriguez, Miquel Piñol, Maria Alba Sorolla, Eva Parisi, Anabel Sorolla, Mario Bernabeu, Carles Aracil, Alfredo Escartin, Antonieta Salud

“…Prediction of response to immunotherapies of the discovered immunophenotypes was assessed in 1039 patients with cancer from external cohorts with available transcriptome data.Results Unsupervised clustering by gene expression identified a subgroup of GAC that includes 52% of the tumors, the so-called Inflamed class, characterized by high tumor immunogenicity and cytotoxicity, particularly in the tumor center at protein level, with enrichment of PIK3CA and ARID1A mutations and increased presence of exhausted CD8+ T cells as well as co-inhibitory receptors such as PD1, CTLA4, LAG3, and TIGIT. …”
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STING agonism overcomes STAT3-mediated immunosuppression and adaptive resistance to PARP inhibition in ovarian cancer by Changli Qian, Gordon J Freeman, Tao Jiang, Ursula Matulonis, Ziying Lin, Hye-Jung Kim, Anniina Färkkilä, Hua Yu, Xin Cheng, Panagiotis A Konstantinopoulos, Antons Martincuks, Joyce F Liu, Qiwei Wang, Liya Ding, Michael J Kearns, Shaozhen Xie, Inga-Maria Launonen, Thomas M Roberts, Jean J Zhao

“…This is mediated by enrichment of protumor TAMs propelled by PARPi-induced STAT3 activation in tumor cells. We also provide a new strategy to reshape the immunosuppressive TME with STING agonists and overcome PARPi resistance in ovarian cancer.…”
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Multiomics insights into BMI-related intratumoral microbiota in gastric cancer by Kang Liu, Zhengchen Jiang, Zhengchen Jiang, Yubo Ma, Ruihong Xia, Yingsong Zheng, Kailai Yin, Chuhong Pang, Li Yuan, Li Yuan, Xiangdong Cheng, Xiangdong Cheng, Zhuo Liu, Bo Zhang, Shi Wang

“…The genus Abiotrophia may promote gastric cancer development and progression by regulating eosinophils and the purine metabolism pathway, which provides a new idea for the precise treatment of gastric cancer.…”
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Substantia nigra related gene polymorphisms associated with antipsychotic-induced acute movement disorders: a genome-wide association study and multi-ancestry validation in schizop... by Zhe Lu, Yao-Yao Sun, Zhe-Wei Kang, Guo-Rui Zhao, Yu-Yanan Zhang, Jun-Yuan Sun, Rui Yuan, Wei-Hua Yue

“…Subsequent post-GWAS analyses included gene-based analyses, transcriptome-wide association studies (TWASs), and polygenic risk score (PRS) profiling. …”
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In vitro and in vivo activity of sodium houttuyfonate and sodium new houttuyfonate against Candida auris infection by affecting adhesion, aggregation, and biofilm formation abiliti... by Guangyuan Yang, Ruotong Yang, Xiaoxiao Zhu, Qianwen Xu, Xiaojia Niu, Chengui Miao, Wenfan Wei, Changzhong Wang, Tianming Wang, Daqiang Wu

“…First, our results showed that SH and SNH exhibit significantly inhibitory activity against fluconazole-resistant C. auris strains, but do not possess effective fungicidal activity. In addition, transcriptome and RT-qPCR studies revealed that SH and SNH can repress the expression of genes related to adhesion, aggregation, and biofilm formation. …”
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A Comparison Between High- and Low-Performing Lambs and Their Impact on the Meat Quality and Development Level Using a Multi-Omics Analysis of Rumen Microbe–Muscle–Liver Interactio... by Haibo Wang, Jinshun Zhan, Shengguo Zhao, Haoyun Jiang, Haobin Jia, Yue Pan, Xiaojun Zhong, Junhong Huo

“…Analysis of the muscle transcriptome indicated a significant correlation between the turquoise module and host phenotypes, particularly body weight. …”
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Lactobacillus plantarum-derived extracellular vesicles from dietary barley leaf supplementation attenuate Citrobacter rodentium infection and intestinal inflammation by Yu Feng, Qian Zhao, Yifan Zhao, Chen Ma, Meiling Tian, Xiaosong Hu, Fang Chen, Daotong Li

“…Conclusions Our work thus provides evidence for utilizing BL and L. plantarum-derived EVs to manage enteric infection-associated IBD.…”
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Type I-E* CRISPR-Cas of Klebsiella pneumoniae upregulates bacterial virulence by targeting endogenous histidine utilization system by Jieying Li, Yuxiao Liu, Jingsi Jiang, Fang Chen, Nan Zhang, Xun Kang, Lin Liu, Yingjuan Wang, Qianfeng Xia, Chuanlong Zhu, Dai Kuang

“…The bacterium harbors the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems, which provide adaptive immunity against invading foreign nucleic acids. …”
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Macrophage Membrane-Coated Liposomes Delivering Vonoprazan Disrupt Mitochondrial Oxidative Phosphorylation in Diffuse Large B-Cell Lymphoma by Wang W, Wang L, Fan Q, Xu J, Li Y, Xu J, Zhao B, Ge D, Xiong L, Wu Y, Zhu Y, Chen M

“…This study constructed a macrophage membrane-coated liposomal formulation (MM-Lipid@Vpz) for the targeted delivery of vonoprazan to combat DLBCL, which enables the evasion of the reticuloendothelial system, ensuring enhanced specificity in tumor targeting.Methods: The vonoprazan was delivered by encapsulating liposomes with pre-isolated macrophage membranes, targeted to DLBCL cells and evaluated for changes in cell function. The cellular transcriptome was collected to analyze the mechanism of drug action. …”
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Expression analysis of glutathione S-transferase genes in Lasioderma serricorne (Coleoptera: Anobiidae) subjected to CO₂-enriched atmosphere by XU Kangkang, DING Tianbo, YAN Yi, LI Can, YANG Wenjia

“…However, when exposed to 50% lethal concentration (LC₅₀) of CO₂, the expression levels of LsGSTt1 and LsGSTs1 were significantly increased.In conclusion, the results suggest that LsGSTt1 and LsGSTs1 in L. serricorne might play important roles in defense responses challenged by CO₂ stress. This study provides the basis for clarifying the response mechanism of insects to CO₂ stress.…”
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CellMemory: hierarchical interpretation of out-of-distribution cells using bottlenecked transformer by Qifei Wang, He Zhu, Yiwen Hu, Yanjie Chen, Yuwei Wang, Guochao Li, Yun Li, Jinfeng Chen, Xuegong Zhang, James Zou, Manolis Kellis, Yue Li, Dianbo Liu, Lan Jiang

“…Without pre-training, CellMemory outperforms existing single-cell foundation models and accurately deciphers spatial transcriptomics at high resolution. Leveraging its robust representations, we further elucidate malignant cells and their founder cells across patients, providing reliable characterizations of the cellular changes caused by the disease.…”
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Application of “Systems Vaccinology” to Evaluate Inflammation and Reactogenicity of Adjuvanted Preventative Vaccines by David J. M. Lewis, Mark P. Lythgoe

“…Advances in “omics” technology (transcriptomics, proteomics, metabolomics, genomics/epigenomics, etc.) allied with statistical and bioinformatics tools are providing insights into basic mechanisms of vaccine and adjuvant efficacy or inflammation/reactogenicity. …”
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Causality-aware graph neural networks for functional stratification and phenotype prediction at scale by Charalampos P. Triantafyllidis, Ricardo Aguas

“…First, we leverage Prior Knowledge Networks (PKNs) to reconstruct gene networks from genomic and transcriptomic data. We demonstrate how this can be achieved through mathematical programming optimization and provide examples using comprehensive, established databases. …”
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Integrated Analysis of Single‐Cell and Bulk RNA‐Sequencing Defines N7‐Methylguanosine (m7G)‐Mediated Modifications' Role in Prognosis and the Tumor Immune Microenvironment in Hepat... by Jiahua Liang, Mingjian Ma, Borui Xu, Cheng Zhong, Guangyan Zeng, Huijiao Lu, Jiaming Lai, Jiancong Chen

“…Method Single‐cell RNA sequencing (scRNA‐seq) data was sourced from the GEO repository. Transcriptomic datasets were procured from TCGA, GEO, and ICGC databases. …”
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Berberine Extends Lifespan in <i>C. elegans</i> Through Multi-Target Synergistic Antioxidant Effects by Yingshuo Bei, Ting Wang, Shuwen Guan

“…These findings establish that berberine exerts multi-target anti-aging effects through coordinated activation of stress-responsive pathways and metabolic optimization, providing mechanistic insights for developing natural product-based geroprotective strategies.…”
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Regulatory Mechanisms of Phytohormones in Thiocyanate-Exposed Rice Plants: Integrating Multi-Omics Profiling with Mathematical Modeling by Yi Kang, Chengzhi Li, Xiaozhang Yu

“…Transcriptomic analysis revealed that a number of differentially expressed genes (DEGs) mapped in different phytohormone pathways in SCN⁻-treated rice seedlings, and their transcript abundances are tissue-specific. …”
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Neurotransmission Sex Dichotomy in the Rat Hypothalamic Paraventricular Nucleus in Healthy and Infantile Spasm Model by Dumitru Andrei Iacobas, Jana Veliskova, Tamar Chachua, Chian-Ru Chern, Kayla Vieira, Sanda Iacobas, Libor Velíšek

“…This study revealed substantial sex differences in the expression level, control, and inter-coordination of the investigated genes among the studied groups. The transcriptomic differences assist in providing a molecular explanation of the behavioral differences and development of infantile epilepsy spasm syndrome in the two sexes.…”
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Machine learning study on predicting depressive symptoms and genetic correlations in Parkinson’s disease by Haijun Zhang, Yifan Zhang, Guihua Li, Guihua Li

“…Furthermore, this study explores the biological functions and molecular mechanisms underlying shared transcriptomic proteins between PD and depression, providing insights into potential pathophysiological links between the two conditions.…”
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Bridging Ethnobotanical Knowledge and Multi-Omics Approaches for Plant-Derived Natural Product Discovery by Kekeletso H. Chele, Lizelle A. Piater, Justin J. J. van der Hooft, Fidele Tugizimana

“…For centuries, plant-derived natural products (NPs) have been fundamental to traditional medicine, providing essential therapeutic compounds. Ethnobotanical knowledge has historically guided NP discovery, leading to the identification of key pharmaceuticals such as aspirin, morphine, and artemisinin. …”
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