Machine learning on multiple epigenetic features reveals H3K27Ac as a driver of gene expression prediction across patients with glioblastoma. by Yusuke Suita, Hardy Bright, Yuan Pu, Merih Deniz Toruner, Jordan Idehen, Nikos Tapinos, Ritambhara Singh

“…In summary, while GSCs are known for their transcriptomic and phenotypic heterogeneity, we propose that they share a common epigenetic pattern of enhancer activation that defines their underlying transcriptomic expression pattern. …”
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Research Progress on the Mechanism of Ketamine in Neuropathic Pain Comorbid Depression by Li Q, Liu S, Qin B, Liu X

“…The mechanism of key brain regions, such as hippocampus and anterior cingulate cortex, is discussed in detail, and the antidepressant effect of ketamine is explored from the perspective of transcriptomics. Finally, this review integrates bioinformatics, molecular biology and other interdisciplinary approaches to elucidate the therapeutic effects and potential mechanisms of ketamine in treating neuropathic pain and depression comorbidity, providing a comprehensive theoretical basis, new directions for subsequent research and novel insights for the clinical application of ketamine.Keywords: ketamine, neuropathic pain, depression, specific brain regions…”
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Coding and non-coding RNA expression in NSC34 cells following TDP-43 depletion and mutant TDP-43 M337V expression by Ismail Gbadamosi, Sandra Binias, Bartłomiej Gielniewski, Ramiro Magno, Isabel Duarte, Ali Jawaid

“…Additionally, the inclusion of non-coding RNAs facilitates the construction of gene regulatory networks, providing insights into the interplay between coding and non-coding RNAs in gene expression regulation under TDP-43 loss-of-function or pathogenic mutation conditions.…”
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Modulating NPC1L1 to Potentiate PARP Inhibitor-Induced Ferroptosis and Immune Response in Triple-Negative Breast Cancer by Ge Li, Yuxia Yuan, Xinhua Wu, Lixian Wu

“…<b>Methods:</b> In this study, lipidomics and transcriptomics analyses were conducted to elucidate the mechanisms underlying PARP inhibitor-induced ferroptosis and immune modulation in triple-negative breast cancer (TNBC). …”
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Transglutaminase 2 Prevents Premature Senescence and Promotes Osteoblastic Differentiation of Mesenchymal Stem Cells through NRF2 Activation by Soo-Jin Lee, Ji-Woong Shin, Mee-Ae Kwon, Ki Baek Lee, Hyo-Jun Kim, Jin-Haeng Lee, Heun-Soo Kang, Jong Kwan Jun, Sung-Yup Cho, In-Gyu Kim

“…The role of TG2 in the regulation of antioxidant response was further supported by transcriptomic analysis of MSC. These results indicate that TG2 is a critical enzyme in eliciting antioxidant response in MSC through NRF2 activation, providing a target for optimizing MSC manufacturing processes to prevent premature senescence.…”
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Lactylation-related risk model for prognostication and therapeutic responsiveness in uterine corpus endometrial carcinoma by Yupeng Yin, Min Luo

“…This study introduces a lactylation-related risk model aimed at predicting UCEC prognosis and providing insights into treatment efficacy. Methods We analyzed transcriptomic data from The Cancer Genome Atlas (TCGA) for UCEC patients and identified two distinct lactylation-related patterns using consensus clustering. …”
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Advancing breast cancer circulating tumour cell research at the Institute of Oncology Ljubljana by Tanja Jesenko, Cvetka Grašič Kuhar, Živa Pišljar, Simona Miceska, Veronika Kloboves-Prevodnik, Maja Čemažar

“… Circulating tumour cells (CTCs) have become an important biomarker in breast cancer, providing an insight into disease progression and monitoring of therapeutic response. …”
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Differential retinal ganglion cell resilience to optic nerve injury across vertebrate species by Julie D. De Schutter, Anyi Zhang, Pieter-Jan Serneels, Lieve Moons, Luca Masin, Steven Bergmans

“…In this study, we compare RGC densities and survival rates following optic nerve crush (ONC) in three vertebrate models—mice, zebrafish, and killifish—under standardized experimental conditions. Transcriptomic analysis confirmed that, similar to RBPMS in mice, Rbpms2 serves as a pan-RGC marker in zebrafish and killifish. …”
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CCR2 restricts IFN-γ production by hippocampal CD8 TRM cells that impair learning and memory during recovery from WNV encephalitis by Shenjian Ai, Artem Arutyunov, Joshua Liu, Jeremy D. Hill, Xiaoping Jiang, Robyn S. Klein

“…Overall, these data implicate CCR2 signaling in the regulation of CD8 TRM phenotype, including antiviral specificity and IFN-γ expression, highlighing a neuroprotective role for CCR2 in limiting CD8 T cell-mediated neuroinflammation and cognitive deficits, providing insights into potential therapeutic targets for CNS infections.…”
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Bone Marrow Endothelial Progenitor Cells remodelling facilitates normal hematopoiesis during Acute Myeloid Leukemia Complete Remission by Tong Xing, Li-Juan Hu, Hong-Yan Zhao, Chen-Yuan Li, Zhen-Kun Wang, Meng-Zhu Shen, Zhong-Shi Lyu, Jing Wang, Yu Wang, Hao Jiang, Qian Jiang, Ying-Jun Chang, Xiao-Hui Zhang, Yuan Kong, Xiao-Jun Huang

“…Mechanistically, the transcriptome characteristics of leukemia-modified BM EPCs return to near-normal after CR. …”
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Single-cell RNA sequencing reveals a new mechanism of endothelial cell heterogeneity and healing in diabetic foot ulcers by Songyun Zhao, Hua Yu, Zihao Li, Wanying Chen, Kaibo Liu, Hao Dai, Gaoyi Wang, Zibing Zhang, Jiaheng Xie, Yucang He, Liqun Li

“…This study not only enhances the understanding of the pathogenesis ofDFU but also provides a scientific basis for the development ofnew therapeutic strategies.…”
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Single-cell spatial atlas of smoking-induced changes in human gingival tissues by Yong Zhang, Zongshan Shen, Jiayu Yang, Junxian Ren, Chi Zhang, Lingping Tan, Li Gao, Chuanjiang Zhao

“…Recent advances in spatial transcriptomics have enabled a deeper exploration of the periodontal tissue microenvironment at single-cell resolution, offering new opportunities to investigate these mechanisms. …”
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Cortical arealization of interneurons defines shared and distinct molecular programs in developing human and macaque brains by Xiangling Feng, Yingjie Gao, Fan Chu, Yuwen Shan, Meicheng Liu, Yaoyi Wang, Ying Zhu, Qing Lu, Mingfeng Li

“…Our integrative and comparative analyses reveal that less transcriptomic alteration is accompanied by interneuron migration within the ganglionic eminence subdivisions, in contrast to the dramatic changes observed in cortical tangential migration, which mostly characterize the transcriptomic specification for different destinations and for species divergence. …”
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Multi‐Omics Analysis Reveals Impacts of LincRNA Deletion on Yeast Protein Synthesis by Ling Qin, Yuyang Pan, Songlyu Xue, Zhibo Yan, Chufan Xiao, Xiufang Liu, Dan Yuan, Jin Hou, Mingtao Huang

“…This study highlights the significant potential of lincRNAs in modulating cellular metabolism, providing deep insights and strategies for the development of more efficient protein‐producing cell factories.…”
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SOX3 protein is associated with epithelial-mesenchymal transition (EMT) changes in human melanoma cell by Ana Paula Gomes dos Santos Miranda, Bruna Mendes Lima, Bárbara Andrade de Carvalho, Emanuele Tadeu Pozzolini, Diego Crimi de Castro, Fábio Eduardo dos Santos, Luciana de Oliveira Andrade, Jeremy W. Prokop, Adam Underwood, Helen Lima Del Puerto, Enio Ferreira

“…Methods Evaluation of SOX3 expression in single-cell transcriptomic data using the CZI CellxGene database. …”
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Genome-Wide Analysis of GmMYB S20 Transcription Factors Reveals Their Critical Role in Soybean Nodulation by Junchen Leng, Ruobing Xu, Yanshuang Liu, Tianshu Jiang, Haiying Hu, Zhaojun Ding, Shaojun Dai

“…Collectively, our findings identify <i>GmMYB62a</i> and <i>GmMYB62b</i> as critical molecular regulators of nodulation in soybean, providing promising targets for improving symbiotic nitrogen fixation efficiency in legume crops.…”
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Multiomics analysis unveils key biomarkers during dynamic progress of IAV infection in mice by Huan Lei, Huan Lei, Huan Lei, Yixi Xu, Yixi Xu, Yixi Xu, Hao Zhang, Hao Zhang, Hao Zhang, Bin Zhang, Wenjun Luo, Wenjun Luo, Wenjun Luo, Xiao Liu, Xiao Liu, Xiao Liu, Haijun Zhang, Haijun Zhang, Haijun Zhang, Jinming Yang, Jinming Yang, Jinming Yang, Wen Wen, Wen Wen, Wen Wen, Ping Wang, Ping Wang, Ping Wang, Shijun Xu, Shijun Xu, Shijun Xu

“…Additionally, we developed a serum-based influenza disease progression scoring system.DiscussionThis study provides new insights into the molecular mechanisms underlying influenza progression and identifies potential targets for therapeutic intervention. …”
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3D visualization of uterus and ovary: tissue clearing techniques and biomedical applications by Qiqi Liu, Zhuo Song, Simin Liu, Zirui Dong, Xi Zheng, Tak Yeung Leung, Xiaoyan Chen

“…Tissue clearing technologies provide a robust strategy for early diagnosis of uterine and ovarian pathologies. …”
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Hierarchical Regulatory Networks Reveal Conserved Drivers of Plant Drought Response at the Cell‐Type Level by Moyang Liu, Yuanyuan Xu, Yue Song, Dongying Fan, Junpeng Li, Zhen Zhang, Lujia Wang, Juan He, Cheng Chen, Chao Ma

“…In addition, the authors’ causal network analysis pinpoints critical regulatory drivers such as NLP7 and CIPK23, providing insights into the molecular mechanisms of drought adaptation. …”
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Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes by Yihan Wang, Daniel A. Armendariz, Lei Wang, Huan Zhao, Shiqi Xie, Gary C. Hon

“…Analysis of > 500,000 single-cell transcriptomes in two breast cancer cell lines shows that perturbation of BC-associated enhancers disrupts breast cancer gene programs. …”
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