Mesenchymal stromal cells promote the formation of lung cancer organoids via Kindlin-2 by Zhilin Sui, Xianxian Wu, Jiaxin Wang, ShihJye Tan, Chao Zhao, Zhentao Yu, Chuanyue Wu, Xiaoxiao Wang, Ling Guo

“…We evaluated whether LCOs co-cultured with fibroblast retained the original genetic mutations of their source tumors based on WES. RNA sequencing was used to analyze the differences in gene expression profiles between LCOs co-cultured with fibroblast and paracancerous organoids (POs). …”
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Gene signatures derived from transcriptomic-causal networks stratify colorectal cancer patients for effective targeted therapy by Akram Yazdani, Heinz-Josef Lenz, Gianluigi Pillonetto, Raul Mendez-Giraldez, Azam Yazdani, Hanna Sanoff, Reza Hadi, Esmat Samiei, Alan P. Venook, Mark J. Ratain, Naim Rashid, Benjamin G. Vincent, Xueping Qu, Yujia Wen, Michael Kosorok, William F. Symmans, John Paul Y. C. Shen, Michael S. Lee, Scott Kopetz, Andrew B. Nixon, Monica M. Bertagnolli, Charles M. Perou, Federico Innocenti

“…This integrative approach involved germline genotype and tumor RNA-seq data from 1165 metastatic CRC patients. …”
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Helicobacter pylori SlyD stabilizes TPT1 via hnRNPK and enhances OCT1-mediated CDX2 transcriptional activation to drive gastric intestinal metaplasia by Shuwen Zheng, Yingying Wang, Chuxuan Ni, Rui Guo, Xunan Qiu, Jijun Chen, Lu Wang, Xiaohu Sun, Moye Chen, Yunen Liu, Yuan Yuan, Yuehua Gong

“…Real-time qPCR and western blot were subsequently used to assess the expression levels of hnRNPK, TPT1, OCT1, and GIM markers. RNA sequencing was employed to identify differentially expressed genes associated with H. pylori SlyD infection. …”
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Single-cell profiling of SLC family transporters: uncovering the role of SLC7A1 in osteosarcoma by Yan Liao, Junkai Chen, Hao Yao, Ting Zheng, Jian Tu, Weidong Chen, ZeHao Guo, Yutong Zou, Lili Wen, Xianbiao Xie

“…Methods The single-cell sequencing data from GSE152048 and GSE162454, along with RNA-seq from the TARGET and GSE21257 cohorts, were utilized for the analysis in this study. …”
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Identification of a transcription factor AoMsn2 of the Hog1 signaling pathway contributes to fungal growth, development and pathogenicity in Arthrobotrys oligospora by Qianqian Liu, Kexin Jiang, Shipeng Duan, Na Zhao, Yanmei Shen, Lirong Zhu, Ke-Qin Zhang, Jinkui Yang

“…Methods: The function of AoMsn2 was characterized using targeted gene deletion, phenotypic experiments, real-time quantitative PCR, RNA sequencing, untargeted metabolomics, and yeast two-hybrid analysis. …”
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Integrated hepatic transcriptomics and metabolomics identify Pck1 as a key factor in the broad dysregulation induced by vehicle pollutants by Gajalakshmi Ramanathan, Yuqi Zhao, Rajat Gupta, Siri Langmo, May Bhetraratana, Fen Yin, Will Driscoll, Jerry Ricks, Allen Louie, James A. Stewart, Timothy R. Gould, Timothy V. Larson, Joel Kaufman, Michael E. Rosenfeld, Xia Yang, Jesus A. Araujo

“…As an example, while gene network analysis of DE livers identified phosphoenolpyruvate carboxykinase 1 (Pck1) as a key driver gene of DE response, DEP treatment of HepG2 cells resulted in increased mRNA expression of Pck1 and glucose production, the latter replicated in mouse primary hepatocytes. …”
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Acquired vulnerability against EGF receptor inhibition in gastric cancer promoted by class I histone deacetylase inhibitor entinostat by Tamara Zenz, Robert Jenke, Denys Oliinyk, Sandra Noske, René Thieme, Tim Kahl, Ines Gockel, Florian Meier-Rosar, Achim Aigner, Thomas RH Büch

“…Methods: We investigated entinostat effects on EGFR and amphiregulin (AREG) expression in various cell line- and primary patient tumor-based in vitro, ex vivo and in vivo models, on the mRNA and protein level. Based on these results, a combined entinostat plus EGFR inhibitor erlotinib treatment in vitro and in vivo was studied. …”
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Haploinsufficiency of PDE2A causes in mice increased exploratory behavior associated with upregulation of neural nitric oxide synthase in the striatum by Ana Gabriela de Oliveira do Rêgo, Francesca D'Amico, Vincenza D’Angelo, Silvia Cardarelli, Debora Cutuli, Davide Decandia, Eugenia Landolfo, Laura Petrosini, Manuela Pellegrini, Marcello D’Amelio, Nicola Biagio Mercuri, Mauro Giorgi, Giuseppe Sancesario

“…HET mice exhibited greater tendency to explore novel environments in comparison to WT mice, but spatial working memory, anxiety, and sociability were similar in adult HET and WT mice.In HET mice, PDE2A mRNA, PDE2A protein expression, and cGMP hydrolyzing enzymatic activity were consistently reduced by about 50 %. …”
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A Comprehensive Dataset on Microbiome Dynamics in Rheumatoid Arthritis from a Large-Scale Cohort Study by Jing Li, Jun Xu, Jiayang Jin, Congmin Xu, Yuzhou Gan, Yifan Wang, Ruiling Feng, Wenqiang Fan, Yingni Li, Xiaozhen Zhao, Yucui Li, Shushi Gong, Linchong Su, Yueming Cai, Lianjie Shi, Xiaolin Sun, Yang Xiang, Qingwen Wang, Ru Li, Jinxia Zhao, Yulan Liu, Junjie Qin, Zhanguo Li, Jing He

“…This dataset is enriched with detailed clinical metadata, including patient profiles, treatment histories, and environmental factors, providing a comprehensive “disease exposome” for RA. By integrating 16S rRNA gene sequencing with demographic, clinical, and environmental data, we offer a valuable resource to explore the complex relationships between gut microbiota and RA progression. …”
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Epigenetic modifications and emerging therapeutic targets in cardiovascular aging and diseases by Yurou Qiu, Qing Xu, Peichen Xie, Chenshuang He, Qiuchan Li, Xin Yao, Yang Mao, Xiaoqian Wu, Tiejun Zhang

“…We also discuss the readers of these modifications, such as the 5-methylcytosine binding domain proteins, and the erasers ten-eleven translocation (TET) proteins. The emerging role of RNA methylation, particularly N6-methyladenosine (m6A), in cardiovascular pathogenesis is also discussed. …”
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Valerenic acid attenuates pathological myocardial hypertrophy by promoting the utilization of multiple substrates in the mitochondrial energy metabolism by Tiantian Liu, Xu Chen, Qianbin Sun, Junjun Li, Qiyan Wang, Peng Wei, Wei Wang, Chun Li, Yong Wang

“…Methods: The efficacy of VA on PMH was confirmed by in vivo and in vitro experiments and the underlying mechanism was investigated by molecular dynamics (MD) simulations and specific siRNA interference. Results: VA enhanced cardiomyocyte fatty acid oxidation (FAO), inhibited hyper-activated glycolysis, and improved the unbalanced pyruvate-lactate axis. …”
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Correlation analysis of DLG5 and PD-L1 expression in triple-negative breast cancer by Jingmin Che, Bo Chen, Xusheng Wang, Baoe Liu, Cuixiang Xu, Huxia Wang, Jingying Sun, Qing Feng, Xiangrong Zhao, Zhangjun Song

“…A combination of PD-L1 inhibitors and DLG5 RNA interference techniques was used, along with various methods including cell counting kit-8 (CCK-8), colony formation, wound healing, transwell migration, reverse transcription-quantitative real-time PCR (RT-qPCR), immunofluorescence, immunohistochemical staining (IHC), expression analysis from datasets and western blotting. …”
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Blueberry malvidin-3-galactoside modulated gut microbial dysbiosis and microbial TCA cycle KEGG pathway disrupted in a liver cancer model induced by HepG2 cells by Zhen Cheng, Jie Lin, Ningxuan Gao, Xiyun Sun, Xianjun Meng, Ruihai Liu, Yunen Liu, Weisheng Wang, Bin Li, Yuehua Wang

“…In this study, feces samples from the same batch of mice were collected to explore the regulatory mechanism of M3G on intestinal microbiota and microbial TCA cycle metabolism KEGG pathway in HCC mice based on 16S rRNA sequencing and metagenomics. Our results showed that blueberry M3G increased the microbial diversity and regulated the structure of intestinal microbiota in mice, such as increasing the abundance of Clostridia (butyric acid-producing bacteria), Oscillospira and Ruminococcus, and reducing the abundance of pathogenic Erysipelotrichi. …”
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Identification and validation of glycolysis-related diagnostic signatures in diabetic nephropathy: a study based on integrative machine learning and single-cell sequence by Xiaoyin Wu, Xiaoyin Wu, Buyu Guo, Buyu Guo, Xingyu Chang, Xingyu Chang, Yuxuan Yang, Yuxuan Yang, Qianqian Liu, Qianqian Liu, Jiahui Liu, Jiahui Liu, Yichen Yang, Yichen Yang, Kang Zhang, Yumei Ma, Songbo Fu, Songbo Fu, Songbo Fu

“…The diagnostic efficacy was evaluated by decision curve and calibration curve. Single-cell RNA sequence data was used to identify cell subtypes and interactive signals. …”
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Enhancing diagnostic outcomes in kidney genetic disorders: the KidGen national kidney genomics study protocol by Amali Mallawaarachchi, Hugh McCarthy, Thomas A. Forbes, Kushani Jayasinghe, Chirag Patel, Stephen I. Alexander, Tiffany Boughtwood, Jeffrey Braithwaite, Aron Chakera, Sam Crafter, Ira W. Deveson, Randall Faull, Trudie Harris, Lilian Johnstone, Matthew Jose, Anna Leaver, Melissa H. Little, Daniel MacArthur, Tessa Mattiske, Christine Mincham, Kathy Nicholls, Catherine Quinlan, Michael C. J. Quinn, Gopala Rangan, Jessica Ryan, Cas Simons, Ian Smyth, Madhivanan Sundaram, Peter Trnka, Laura Wedd, Erik Biros, Zornitza Stark, Andrew Mallett

“…These include re-analysing existing data and/or undergoing advanced genomic testing methods, including short and long-read whole-genome sequencing, RNA sequencing, and functional genomics strategies using mouse modelling or kidney organoids. …”
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New evidence on the nephrotoxicity of fine particulate matter: Potential toxic components from different emission sources by Fu-Jen Cheng, Chien-Er Huang, Pei-Shih Chen, Yu-Lun Tseng, Chung-Shin Yuan, Ching-Shu Lai

“…Exposure to PM2.5 water extract increased the mRNA levels of tumor necrosis factor-α, interleukin-6, and nitrite production in RAW264.7 macrophages. …”
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Phase II trial of nab-paclitaxel plus ramucirumab in combination with nivolumab for unresectable advanced or recurrent gastric cancer after progression on first-line treatment incl... by Hidekazu Hirano, Naoki Takahashi, Yusuke Amanuma, Nobumi Suzuki, Daisuke Takahari, Takeshi Kawakami, Chie Kudo-Saito, Kengo Nagashima, Narikazu Boku, Ken Kato, Hirokazu Shoji

“…., flow cytometry, DNA sequencing [DNAseq]/RNA sequencing [RNAseq]). Recruitment started in November 2022. …”
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Deciphering the Differences Between Epstein–Barr Virus‐Associated and Negative Gastric Cancer in the Prospect of CDKN2A Genomic Alterations and Lymphoid Infiltration by Fuda Xie, Bonan Chen, Yang Lyu, Peiyao Yu, Canbin Fang, Kam Tong Leung, Shouyu Wang, Dazhi Xu, Jun Yu, Kwok Wai Lo, Ka Fai To, Wei Kang

“…Methods GC samples were stained by immunohistochemistry, fluorescent and EBV‐encoded small RNA in situ hybridization to identify CD8 expression, CDKN2A genomic alteration, and EBV existence. …”
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Kinetics of IgM, IgA, IgG to SARS-CoV-2 in children with COVID-19 in Lviv region in different periods of the infectious process depending on the severity of the course and age by Maria Stasiv

“…Diagnosis verification relied on clinical manifestations of the disease, with the detection of SARS-CoV-2 RNA from nasal mucus using the PCR method. The values of IgA, IgM, and IgG to S and N proteins of SARS-CoV-2, determined by the ELISA method at different times of the infectious process in 380 blood serum samples, were analyzed. …”
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USP22 inhibits microglial M1 polarization by regulating the PU.1/NLRP3 inflammasome pathway by Ming-chen Yu, Xiao-lin Li, Ming-liang Ning, Zhen-zhong Yan, Wan-tao Yu

“…Methods: The BV-2 mouse microglia line was cultured in vitro, and plasmid and siRNA transfection was performed to overexpress or knockdown USP22. …”
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