Developing transcriptomic biomarkers for TAVO412 utilizing next generation sequencing analyses of preclinical tumor models by Ying Jin, Peng Chen, Huajun Zhou, Guangmao Mu, Simin Wu, Zhengxia Zha, Bin Ma, Chao Han, Mark L. Chiu, Mark L. Chiu

“…TAVO412 demonstrated strong in vivo tumor growth inhibition in 23 cell-line derived xenograft (CDX) models representing diverse cancer types, as well as in 9 patient-derived xenograft (PDX) lung tumor models.MethodsUsing preclinical CDX data, we established transcriptomic biomarkers based on gene expression profiles that were correlated with anti-tumor response or distinguished between responders and non-responders. …”
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Stryphnodendron adstringens have a modulatory effect on inflammatory cytokines markers of in vitro activated macrophages by Ivana Beatrice Mânica da Cruz, Cibele Ferreira Teixeira, Neida Luiza Pellenz, Moisés Henrique Mastella, Verônica Farina Azzolin, Euler Esteves Ribeiro, Fernanda Barbisan

“…Extracts at concentrations of 0.49 mg/mL and 0.99 mg/mL decreased the protein and gene expression of pro-inflammatory cytokines, exhibiting the opposite effect concerning IL-10. …”
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WNT3A promotes the cementogenic differentiation of dental pulp stem cells through the FOXO1 signaling pathway by Dongmei Cheng, Yang Bao, Xue Wang, Haidong Xiang, Tianyuan Guo, Yong Du, Zhiyong Zhang, Han Guo

“…Methods DPSC data set GSE138179 was retrieved from gene expression omnibus (GEO) database. Weighted gene co-expression network analysis (WGCNA) was employed to identify significant modules. …”
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Higher gut Bacteroidetes and Actinobacteria population in early pregnancy is associated with lower risk of gestational diabetes in the second trimester by Seyedeh Neda Mousavi, Navid Momeni, Hossein Chiti, Howra Mahmoodnasab, Mohammad Ahmadi, Siamak Heidarzadeh

“…The dominant phylum population was determined based on 16SrRNA gene expression. Results Mothers with lower Bacteroidetes and Actinobacteria population in the first trimester were more susceptible to GDM in the screening time (p < 0.001 and p < 0.001). …”
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Identification of prognostic biomarker of non-small cell lung cancer based on mitochondrial permeability transition-driven necrosis-related genes and determination of anti-tumor ef... by Zhifei Ma, Wen Chen, Aiping Zhang, Xiaokang Shen, Lin Zheng

“…This study aimed to identify MPTDN-related biomarkers for predicting prognosis and guiding treatment in NSCLC. Methods Gene expression profiles and clinical information of NSCLC were collected from public databases, and MPTDN-related genes were obtained from published article. …”
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USP5 stabilizes YTHDF1 to control cancer immune surveillance through mTORC1-mediated phosphorylation by Na Shao, Lei Xi, Yangfan Lv, Muhammad Idris, Lin Zhang, Ya Cao, Jingyi Xiang, Xi Xu, Belinda X. Ong, Qiongyi Zhang, Xu Peng, Xiaoyan Yue, Feng Xu, Chungang Liu

“…Deficiency in YTHDF1 or USP5 increases PD-L1 expression and suppresses immune-related gene expression, facilitating immune evasion. Combining USP5 inhibition with anti-PD-L1 therapy enhances anti-tumor immunity, suggesting USP5 as a potential biomarker for patient stratification. …”
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Identification and functional analysis of energy metabolism and pyroptosis-related genes in diabetic nephropathy by Shan He, Jian Ye, Yu Wang, Lu yang Xie, Si Yi Liu, Qin kai Chen

“…Methods: EMAPRDEGs were identified by querying the GeneCards and Gene Expression Omnibus (GEO) databases. Subsequent analyses included Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment, Gene Set Enrichment Analysis (GSEA), and Protein-Protein Interaction (PPI) network analysis. …”
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Mechanistic elucidation of human pancreatic acinar development using single-cell transcriptome analysis on a human iPSC differentiation model by Atsushi Mima, Azuma Kimura, Ryo Ito, Yu Hatano, Hiraku Tsujimoto, Shin-Ichi Mae, Junko Yamane, Wataru Fujibuchi, Norimitsu Uza, Taro Toyoda, Hiroshi Seno, Kenji Osafune

“…Furthermore, differential gene expression analysis revealed upregulated pathways, including cAMP-related signals, involved in the differentiation of hiPSC-derived pancreatic acinar lineage cells in vivo, and we found that a cAMP activator, forskolin, facilitates the differentiation from hiPSC-derived pancreatic endoderm into pancreatic acinar progenitor cells in our in vitro differentiation culture. …”
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Application of deep learning models on single-cell RNA sequencing analysis uncovers novel markers of double negative T cells by Tian Xu, Qin Xu, Ran Lu, David N. Oakland, Song Li, Liwu Li, Christopher M. Reilly, Xin M. Luo

“…However, advanced deep learning models such as Single Cell Variational Inference (scVI) have the capability to capture nonlinear gene expression patterns in the sequencing data. In this study, employing the deep learning methodology, we have revealed novel markers for splenic DNT cells in C57BL/6 mice which were validated with flow cytometry analysis. …”
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Antioxidant and Anti-Inflammatory Potential of Cymbopogon nardus Ethanol Extract on 3T3-L1 Cells by Rohmawaty E, Wiraswati HL, Zahra TA, Amalina SN, Ramadhanti J, Rosdianto AM, Laelalugina A, Nasution GTD, Kamisah Y

“…Additionally, the effects of the extract on the gene expression of hypoxia-inducible factor 1α (HIF-1α) in menadione-induced 3T3-L1 cells, as well as interleukin-6 (IL-6) and cyclooxygenase-2 (COX-2) in lipopolysaccharide (LPS)-induced 3T3-L1 cells, were investigated.Results: Phytochemical screening revealed the presence of phenolics, tannins, alkaloids, and flavonoids in the ethanolic extracts. …”
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RETRACTED ARTICLE: NR3C2 affects the proliferation and invasiveness of colon cancer cells through the Wnt/β-Catenin signaling pathway by Ke Nie, Zhong-Jiang He, Ling-Jun Kong

“…Single-cell data from colon cancer samples in the GEO (Gene Expression Omnibus) database further investigated the mechanism of the lower survival associated with NR3C2 dysregulation. …”
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Role of Aging in Ulcerative Colitis Pathogenesis: A Focus on ETS1 as a Promising Biomarker by Ni M, Peng W, Wang X, Li J

“…In this study, we explored the role of aging-related genes (ARGs) in UC pathogenesis and diagnosis prediction.Methods: Gene expression data were obtained from four independent datasets (GSE75214, GSE87466, GSE94648, and GSE169568) in the GEO database, and ARGs were derived from multiple public databases. …”
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Network pharmacology and experimental verification to investigate the mechanism of isoliquiritigenin for the treatment of Alzheimer’s disease by Waimao Gao, Guang Yang, Xinjuan Liu, Kaifan Hu, Jie Pan, Xingyu Wang, Yan Zhao, Ying Xu

“…Subsequently, the receiver operating characteristic (ROC) curve analysis and the assessment of hub gene expression levels between AD and healthy individuals were used to estimate a possible link between target genes in AD. …”
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Heterochrony in orthodenticle expression is associated with ommatidial size variation between Drosophila species by Montserrat Torres-Oliva, Elisa Buchberger, Alexandra D. Buffry, Maike Kittelmann, Genoveva Guerrero, Lauren Sumner-Rooney, Pedro Gaspar, Georg C. Bullinger, Javier Figueras Jimenez, Fernando Casares, Saad Arif, Nico Posnien, Maria D. S. Nunes, Alistair P. McGregor, Isabel Almudi

“…Results Here, we used a combination of fine-scale mapping and gene expression analysis to further investigate positional candidate genes on the X chromosome. …”
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Age-related changes in DNA methylation in a sample of elderly Brazilians by Hayley Welsh, Caio M. P. F. Batalha, Weili Li, Nadja C. Souza-Pinto, Yeda A. O. Duarte, Michel S. Naslavsky, Esteban J. Parra

“…Abstract Background Age-related changes in DNA methylation (DNAm) play a critical role in regulating gene expression. However, most epigenome-wide association studies have predominantly focused on individuals of European descent. …”
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Comparison of phenotypic and genetic traits of ESBL-producing UPEC strains causing recurrent or single episode UTI in postmenopausal women by Michelle Kalu, Peter Jorth, Annie Wong-Beringer

“…Presence of hlyA, ompT, and fimH genes were confirmed by colony PCR, and qRT-PCR was performed using extracted RNA from a subset of 18 strains (12 recurrent; 6 single episode) grown in Luria-Bertani media and isolated from infected BECs to characterize gene expression. Bladder cell line 5637 was infected with study strains at MOI 15 for 2 h, treated with amikacin for 2 h to remove extracellular bacteria, then lysed to enumerate intracellular CFU counts. …”
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MicroRNA-541-3p/Rac2 signaling bridges radiation-induced lung injury and repair by Jiandong Zhang, Lei Ma, Limin He, Quanxiao Xu, Yan Ding, Lidong Wang

“…Flow cytometry, polymerase chain reaction, and western blotting were used to analyze cell necroptosis, target gene expression, and target protein expression, respectively. …”
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Impact of copper stress in the intestinal barriers and gut microbiota of Chinese stripe-necked turtle (Mauremys sinensis) by Zeeshan Ali, Ijaz Khan, Muhammad Shahid Iqbal, Haitao Shi, Li Ding, Meiling Hong

“…This study investigates the effects of copper on the intestinal health of Chinese stripe-necked turtle, focusing on histomorphology, mucosal barrier function, gene expression, and gut microbiota. Copper stress caused intestinal damage, characterized by shortened villi, inflammatory cell infiltration, and reduced epithelial layer thickness, as well as decreased acidic mucins, increased villi edema and inflammation. …”
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CAV1 promotes epithelial-to-mesenchymal transition (EMT) and chronic renal allograft interstitial fibrosis by activating the ferroptosis pathway by Qianguang Han, Bin Ni, Wei Bao, Junqi Zhang, Ming Zheng, Jinxu Miu, Zijie Wang, Jingwen Yuan, Jun Tao, Zhijian Han, Min Gu, Xiaobing Ju, Ruoyun Tan

“…However, the mechanism by which ferroptosis contributes to the onset and progression of CAD remains unclear.MethodsThis study analyzed transcriptome data from renal transplant biopsy samples in the Gene Expression Omnibus (GEO), through clinical samples, animal models, and cell experiments, this study investigated the mechanism by which Caveolin-1 (CAV1) promotes CAD through the regulation of the ferroptosis pathway.ResultsThe elevated levels of CAV1 were found to positively correlate with CAD incidence. …”
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Identification of a distinctive immunogenomic gene signature in stage-matched colorectal cancer by Pankaj Ahluwalia, Ashis K. Mondal, Ashutosh Vashisht, Harmanpreet Singh, Ahmet Alptekin, Kalyani Ballur, Nivin Omar, Meenakshi Ahluwalia, Kimya Jones, Amanda Barrett, Vamsi Kota, Ravindra Kolhe

“…Orthogonal analyses included single-cell profiling, differential gene expression, immune cell deconvolution, neoantigen prediction, and biological pathway assessment. …”
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