TSPAN4+ fibroblasts coordinate metastatic niche assembly through migrasome-driven metabolic reprogramming and stromal-immune crosstalk in pancreatic adenocarcinoma by Qingwen Hu, Qingwen Hu, Jiali Chen, Yang Liu, Yang Liu, Haiqing Chen, Haotian Lai, Lai Jiang, Xuancheng Zhou, Shengke Zhang, Jinbang Huang, Hao Chi, Bo Li, Xiaolin Zhong

“…This study explored migrasome-associated fibroblasts, especially TSPAN4 and ITGA5, as key regulators of pancreatic cancer metastasis, aiming to provide new ideas for therapeutic strategies targeting TME.MethodsWe employed single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics to analyze pancreatic cancer tissues. …”
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CYP1B1 Knockout in a Bovine Hepatocyte-like Cell Line (BFH12) Unveils Its Role in Liver Homeostasis and Aflatoxin B1-Induced Hepatotoxicity by Silvia Iori, Ludovica Montanucci, Caterina D’Onofrio, Maija Lahtela-Kakkonen, Lorena Lucatello, Anisa Bardhi, Andrea Barbarossa, Francesca Capolongo, Anna Zaghini, Marianna Pauletto, Mauro Dacasto, Mery Giantin

“…In this study, we generated a <i>CYP1B1</i> knockout (<i>CYP1B1</i>^KO) bovine hepatocyte-like cell line to indirectly investigate its role in liver function. Transcriptomic analysis revealed alterations in immune regulation, epithelial barrier integrity, and detoxification pathways, with concurrent compensatory <i>CYP1A1</i> upregulation. …”
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Saliva-derived exosomes regulate fibroblast metabolic reprogramming in skin wound healing by Sijia Song, Sijia Song, Sijia Song, Sijia Song, Rong Xiang, Rong Xiang, Rong Xiang, Rong Xiang, Siyu Chen, Siyu Chen, Siyu Chen, Siyu Chen, Jianbo Wu, Jianbo Wu, Jianbo Wu, Jianbo Wu, Wenxia Chen, Wenxia Chen, Wenxia Chen, Wenxia Chen, Xianyu Li, Xianyu Li, Xianyu Li, Xianyu Li

“…A rat full-thickness skin defect model and in vitro assays with human skin fibroblasts and HaCaT keratinocytes were employed to evaluate S-Exo effects on wound closure, ECM remodeling, and cellular metabolism. Transcriptomic profiling of wound tissues, targeted metabolomic analysis of fibroblasts, and proteomic evaluation of S-Exo cargo were performed to explore underlying mechanisms. …”
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Single-cell and spatiotemporal profile of ovulation in the mouse ovary. by Ruixu Huang, Caroline E Kratka, Jeffrey Pea, Cai McCann, Jack Nelson, John P Bryan, Luhan T Zhou, Daniela D Russo, Emily J Zaniker-Gomez, Achla H Gandhi, Alex K Shalek, Brian Cleary, Samouil L Farhi, Francesca E Duncan, Brittany A Goods

“…Taken together, our data provides a rich and comprehensive resource of murine ovulation that can be mined for discovery by the scientific community.…”
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CNTools: A computational toolbox for cellular neighborhood analysis from multiplexed images. by Yicheng Tao, Fan Feng, Xin Luo, Conrad V Reihsmann, Alexander L Hopkirk, Jean-Philippe Cartailler, Marcela Brissova, Stephen C J Parker, Diane C Saunders, Jie Liu

“…Therefore, it is critical to accurately and efficiently identify cellular neighborhoods from spatially-resolved single-cell transcriptomic data or single-cell resolution tissue imaging data. …”
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Chromosome-level genome assembly of Ampulex clypecomplana Chen & Li (Hymenoptera: Ampulicidae) by Dan Yue, Ziqi Wang, Zhizhi Liu, Chunhong Wang, Qiang Li, Li Ma

“…In this study, we employed ONT long-read sequencing, MGI-SEQ short-read sequencing, Hi-C sequencing and transcriptomic data to assemble the high-quality genome of A. clypecomplana. …”
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Fermentative factors shape transcriptional response of Lachancea thermotolerans and wine acidification by Javier Vicente, Santiago Benito, Domingo Marquina, Antonio Santos

“…This study evaluated how biotic and abiotic factors relevant to climate change influence both wine acidification and the transcriptomic response of L. thermotolerans. We assessed the effects of varying sugar concentrations, pH levels, and organic/inorganic nitrogen ratios, individually and combined. …”
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A spatial single-cell atlas of the claustro-insular region uncovers key regulators of neuronal identity and excitability by Leon Fodoulian, Madlaina Boillat, Marie Moulinier, Alan Carleton, Ivan Rodriguez

“…By combining single-cell RNA sequencing and spatial transcriptomics, we create a high-resolution atlas of this region in mice, uncovering distinct neuronal subtypes and unexpected complexity. …”
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Re-evaluating evidence for giant genomes in amoebae by Daniel Barzilay, João P. B. Alcino, Giulia M. Ribeiro, Alfredo L. P. Sousa, Daniel J. G. Lahr

“…While the whole genome of the historically relevant Amoeba proteus has not yet been fully sequenced, we provide here a statistical analysis using protein-coding genes from transcriptomic data, suggesting that the genome size is consistent with this range, far smaller than previously claimed. …”
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The molecular subtyping and precision medicine in triple-negative breast cancer---based on Fudan TNBC classification by Lijuan Weng, Jianliang Zhou, Shenchao Guo, Nong Xu, Ruishuang Ma

“…Based on genomics, transcriptomics and metabolomics, the multi-omics analysis further clarifies TNBC subtyping, which provides a greater understanding of tumour heterogeneity and targeted therapy sensitivity. …”
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Opportunities for predictive proteogenomic biomarkers of drug treatment sensitivity in epithelial ovarian cancer by Trudy J. Philips, Britt K. Erickson, Stefani N. Thomas

“…Proteogenomics is the integration of genomics, transcriptomics, epigenomics and proteomics data. This review paper provides novel insight into the role of proteogenomics as an analytical approach to identify predictive biomarkers of drug treatment response in epithelial ovarian cancer. …”
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Tacrolimus (FK506) promotes placentation and maternal-fetal tolerance through modulating FASN-CEACAM1 pathway by Xinhang Meng, Minfeng Shi, Jinfeng Qian, Yujie Luo, Liyuan Cui, Dajin Li, Songcun Wang

“…Based on the integrated metabolomics and transcriptomics analyses, the present study provided the cellular and molecular cues evidently showing that FK506 had positive effects on the placentation and maternal-fetal tolerance through modulating FASN-CEACAM1 pathway. …”
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Unraveling heterogeneity and treatment of asthma through integrating multi-omics data by Wei Zhang, Yu Zhang, Lifei Li, Rongchang Chen, Fei Shi, Fei Shi

“…Integrating multi-omics and clinical data will provide more insights into the key pathogenic mechanism in asthma heterogeneity and reshape the strategies for asthma management and treatment.…”
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Malignant Hepatoblast‐Like Cells Sustain Stemness via IGF2‐Dependent Cholesterol Accumulation in Hepatoblastoma by Miao Ding, Siwei Mao, Han Wu, Sijia Fang, Ni Zhen, Tianshu Chen, Jiabei Zhu, Xiaochen Tang, Xiaoyang Wang, Fenyong Sun, Guoqing Zhu, Qiuhui Pan, Ji Ma

“…Single‐cell sequencing provides an in‐depth exploration at the single‐cell level and offers a deep understanding of tumor heterogeneity. …”
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Response strategies to acute and chronic environmental stress in the arctic breeding Lapland longspur (Calcarius lapponicus) by Zhou Wu, Matthew M. Hindle, Valerie R. Bishop, Angus M. A. Reid, Katarzyna Miedzinska, Jonathan H. Pérez, Jesse S. Krause, John C. Wingfield, Simone L. Meddle, Jacqueline Smith

“…The genome assembly and gene expression profiles provide comprehensive resources for future studies. …”
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Integrated multi-omics reveals flavonoid-dominated defense strategies in Coptis chinensis under Fusarium root rot infection by Kaidi Yu, Yuying Yang, Yuqing Duan, Jinwen You, Jie Guo

“…To dissect its defense mechanisms, we conducted integrated transcriptomic and metabolomic analyses on resistant (R), early-stage infected (S-ES), and late-stage infected (S-LS) plants Our findings reveal a disease severity-dependent escalation in flavonoid metabolism. …”
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Splicing junction-based classifier for the detection of abnormal constitutive activation of the KEAP1-NRF2 system by Raúl N. Mateos, Wira Winardi, Kenichi Chiba, Ai Okada, Ayako Suzuki, Yoichiro Mitsuishi, Yuichi Shiraishi

“…This shows the classifier’s potential to analyze hundreds of thousands of transcriptomes, highlighting its utility in broad-scale genomic studies and provides a new perspective on utilizing splicing aberrations caused by overexpression as diagnostic markers, offering potential improvements in diagnosis and treatment strategies.…”
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Spatiotemporal and single-cell atlases to dissect regional specific cell types of the developing ovary by Zheng-Hui Zhao, Tie-Gang Meng, Xue-Ying Chen, Fei Gao, Heide Schatten, Xiang-Hong Ou, Qing-Yuan Sun

“…Here, we combine spatial transcriptomics and single-cell RNA sequencing to build a spatiotemporal developmental atlas of ovaries from the fetal stage through adulthood. …”
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Peripheral substance P induces deficits in hippocampal synaptic plasticity and memory by Sun Yong Kim, Kyeong-No Yoon, Jungeun Ji, Min-Gyun Kim, Seung Ah Choi, Gunhyuk Park, Won-Woo Lee, Jin Ho Chung, Sang Jeong Kim, Joon-Yong An, Dong Hun Lee, Yong-Seok Lee

“…Targeting peripheral SP or its receptor may provide a therapeutic avenue for cognitive dysfunction associated with peripheral inflammation.…”
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The relationship between the skin microecology and the skin barrier by LIN Tianyi, CHEN Jiaoquan, OU Shanshan, WU Weihong, ZOU Hui, CHEN Ziyan, PENG Liqian, CHEN Quan, LI Huaping, ZHU Huilan

“…With the development of metagenomics sequencing and spatial transcriptomics, the door to the "microscopic world" of the skin surface has gradually been opened, and the "inhabitants" on the "habitat" of the skin have gradually become well-known. …”
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