Revealing pathogenesis-associated metabolites in Histoplasma capsulatum through comprehensive metabolic profiling by Adrian Heckart, Jean-Christophe Cocuron, Stephanie C. Ray, Chad A. Rappleye, Ana P. Alonso

“…While Histoplasma is a unique example of a true intra-phagosomal pathogen, insights into its pathogenesis may still inform the study of other intracellular pathogens.…”
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Molecular mechanisms of ageing in cancer development and therapeutic response: Translational implications for precision oncology by Laiba Husain

“…The integration of ageing biology into precision oncology frameworks presents opportunities for developing age‐informed therapeutic protocols that optimize efficacy while minimizing toxicity. Emerging technologies, including artificial intelligence‐driven molecular analysis and advanced imaging techniques, enable more precise characterization of ageing‐cancer interactions at the cellular and tissue levels. …”
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Integrative bioinformatics and machine learning identify iron metabolism genes MAP4, GPT, and HIRIP3 as diagnostic biomarkers and therapeutic targets in Alzheimer’s disease by Xiaoqiong An, Xiangguang Zeng, Zhenzhen Yi, Manni Cao, Yijia Wang, Wenfeng Yu, Wenfeng Yu, Zhenkui Ren, Zhenkui Ren

“…In APP/PS1 mice, MAP4 decreased, while GPT and HIRIP3 increased.DiscussionThis analysis highlights these genes as diagnostic biomarkers and therapeutic targets, connecting iron balance, neuroinflammation, and metabolic problems in AD. …”
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Dehydroleucodine exerts an antiproliferative effect on human Burkitt’s lymphoma Daudi cells via SLC7A11-mediated ferroptosis by Rui Shen, Fang Cheng, Rui Guo, Wenjing Wang, Xiaolong Yang, Yemiao Chen, Yaokai Chen

“…We evaluated DhL’s effects on cell cycle progression, apoptosis, and ferroptosis pathways using cell viability assays, flow cytometry, transcriptomic analysis, and validation experiments.ResultsDhL demonstrated robust and specific anti-proliferative effects against BL Daudi cells. …”
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Artificial intelligence-assisted RNA-binding protein signature for prognostic stratification and therapeutic guidance in breast cancer by Yunxia Zhao, Li Li, Shuqi Yuan, Zixin Meng, Jiayi Xu, Zhaogen Cai, Yijing Zhang, Xiaonan Zhang, Tao Wang

“…Low AIRS scores predicted better responses to immune checkpoint inhibitors, while drug sensitivity analysis highlighted panobinostat and paclitaxel as potential therapies for high-risk patients.ConclusionsThe AIRS model offers a robust tool for BC prognosis and treatment stratification, integrating genomic, transcriptomic, and single-cell data. …”
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Development and pan-cancer validation of an epigenetics-based random survival forest model for prognosis prediction and drug response in OS by Chaoyi Yin, Kede Chi, Zhiqing Chen, Shabin Zhuang, Yongsheng Ye, Binshan Zhang, Cailiang Cai

“…Risk stratification analysis revealed distinct therapeutic response patterns, with low-risk groups showing enhanced sensitivity to traditional chemotherapy drugs while high-risk groups responded better to targeted therapies.ConclusionOur epigenetics-based model demonstrates excellent prognostic accuracy (AUC>0.997 in internal validation, 0.832–0.929 in external cohorts) and provides a practical tool for treatment stratification. …”
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Probiotic <i>Lactobacillus johnsonii</i> Reduces Intestinal Inflammation and Rebalances Splenic Treg/Th17 Responses in Dextran Sulfate Sodium-Induced Colitis by Hao-Yu Liu, Shicheng Li, Kennedy Jerry Ogamune, Peng Yuan, Xinyu Shi, Wael Ennab, Abdelkareem A. Ahmed, In Ho Kim, Ping Hu, Demin Cai

“…Transcriptomic analysis of the spleen revealed that N5 mediated the downregulation of inflammatory pathways, including the IL-17 and TNF signaling pathways, as well as the HIF-1 signaling pathway, and modulated the metabolic pathway of oxidative phosphorylation. …”
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Integrative genomic and bioinformatic prioritization of drug repurposing candidates for prostate cancer by Lalu Muhammad Irham, Wirawan Adikusuma, Arief Rahman Afief, Sabiah Khairi, Rockie Chong, Syarifatul Mufidah, Rahmat Dani Satria, Eko Mugiyanto, Darmawi Darmawi, Danang Prasetyaning Amukti, Brilliant Citra Wirsahada, Petrina Theda Philothra, Indra Jaya

“…Molecular docking analysis further supported these findings, revealing that estradiol-benzoate and estradiol-cypionate have strong predicted binding affinities for ESR2, while selumetinib robustly interacts with MAP2K1. …”
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Computational Insights into the Polypharmacological Landscape of BCR-ABL Inhibitors: Emphasis on Imatinib and Nilotinib by Rima Hajjo, Dima A. Sabbah, Raghad Alhaded, Aye Alquabe’h, Sanaa K. Bardaweel

“…Structural clustering, cheminformatics analysis, and transcriptomic profiling using the Connectivity Map were employed to evaluate structural relationships, target profiles, and gene expression signatures associated with non-oncology indications. …”
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Functional Characterization of <i>TNFα</i> in the Starry Flounder (<i>Platichthys stellatus</i>) and Its Potential as an Immunostimulant by Min-Young Sohn, Gyoungsik Kang, Kyung-Ho Kim, Ha-Jeong Son, Chan-Il Park

“…In this study, we identified and characterized the <i>TNFα</i> gene in the starry flounder (<i>Platichthys stellatus</i>) through transcriptomic analysis. The deduced protein contained a conserved TNF domain and transmembrane region, and phylogenetic analysis confirmed its homology with other teleost TNFα proteins. …”
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TNFα activation of the PLEKHA5-FCRLA axis disturbs lipid metabolism, leading to the progression of cutaneous malignant melanoma by Kexin Yan, Wei Zhang, Wenqi Chu, Jinliang Qi, Hao Song, Xiulian Xu

“…A lipid metabolism-related predictive model was constructed in The Cancer Genome Atlas-skin cutaneous melanoma (TCGA-SKCM) using univariate Cox regression analysis, non-negative matrix factorization (NMF) clustering analysis, Weighted correlation network analysis (WGCNA), least absolute shrinkage and selection operator regression (LASSO) analysis, and outcomes-related genes were identified. …”
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Comparative Study of PPARγ Targets in Human Extravillous and Villous Cytotrophoblasts by Fulin Liu, Christine Rouault, Mickael Guesnon, Wencan Zhu, Karine Clément, Séverine A. Degrelle, Thierry Fournier

“…Differentially expressed genes (DEGs) were filtered and submitted for gene ontology (GO) annotation and pathway analysis with ClueGO. The online tool STRING was used to predict PPARγ and DEG protein interactions, while iRegulon was used to predict the binding sites for PPARγ and DEG promoters. …”
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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

“…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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Expression and prognostic value of SEC13 across multiple tumour types and its association with the regulation by Pulsatilla chinensis: a multi-omics and Mendelian Randomization Stu... by Huaqing Leng, Xin Luan, Ming Li

“…This study aims to explore the potential role of SEC13 across various types of cancer, with a particular focus on its value as a diagnostic and prognostic marker, using Mendelian randomization analysis. Methods In this study, we conducted a comprehensive analysis of SEC13 expression using data from TCGA and GTEx, and explored associated pathways through gene set enrichment analysis. …”
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Transcriptional Profiling of Testis Development in Pre-Sexually-Mature Hezuo Pig by Zunqiang Yan, Qiaoli Yang, Pengfei Wang, Shuangbao Gun

“…In this research, we performed 10× Genomics scRNA-seq to conduct an unbiased single-cell transcriptomic analysis in Hezuo pig (HZP) testis at one month of age during prepuberty. …”
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Identification of Anticancer Target Combinations to Treat Pancreatic Cancer and Its Associated Cachexia Using Constraint-Based Modeling by Feng-Sheng Wang, Ching-Kai Wu, Kuang-Tse Huang

“…These enhancements enabled the reconstruction of cell-specific GSMMs for PDAC and PDAC-CX, and their respective healthy counterparts, based on transcriptomic datasets. Medium-independent metabolic biomarkers were identified through Parsimonious Metabolite Flow Variability Analysis and differential expression analysis across five nutritional conditions. …”
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Changes in phytohormone levels and gene expression of potato plants in response to potato virus Y and a nonvector insect by GE Yang, ZHONG Jian, ZHANG Yadong, HE Xiaoli, LIU Lining, Asim MUNAWAR, MAO Lijuan, ZHU Zengrong, XU Yi, ZHOU Wenwu

“…In order to investigate whether PVY infection changed the physiological responses of potato plant to P. operculella, we studied performances of P. operculella on PVY-infected and non-infected healthy plants, and carried out the phytohormone analysis and comparative transcriptomic analysis for potato leaves which were affected by PVY infection and herbiory stimuli (dealing with the oral secretions of potato tuber moth), or co-stressed treatment. …”
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Identification, expression profiling and potential functional roles of nuclear receptors in the social aphid Pseudoregma bambucicola by Jianjun Lu, Xiaolei Huang

“…Results This study identified 21 NR genes based on the genomic data of P. bambucicola and analyzed the duplication and loss events of these genes through phylogenetic analysis. Additionally, differential expression of NR genes was analyzed using transcriptomic data. …”
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Cell-in-cell associated lncRNA signature predicts prognosis and immunotherapy response in gastric cancer by Junzuo Lin, Liancheng Wu, Zhengfei Zhao

“…High-risk patients exhibited an immunosuppressive tumor microenvironment (TME), characterized by elevated Tregs (P &lt;0.05) and M2 macrophages (P &lt;0.05), correlating with poor response to immune checkpoint inhibitors (TIDE score, P &lt;0.001). Drug sensitivity analysis revealed low-risk patients responded better to gefitinib/entinostat, while high-risk patients benefited from dasatinib/foretinib. …”
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Developments in Toxicity Testing with Duckweeds by Paul Ziegler

“…Improved modern biomarker analysis can help to both better understand the mechanisms underlying toxicity and facilitate the identification of unknown toxins.…”
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