Genes Involved in the Transcriptional Regulation of Pluripotency Are Expressed in Malignant Tumors of the Uterine Cervix and Can Induce Tumorigenic Capacity in a Nontumorigenic Cel... by Graciela Ruiz, Heriberto A. Valencia-González, Delia Pérez-Montiel, Felipe Muñoz, Rodolfo Ocadiz-Delgado, Jorge Fernández-Retana, Carlos Pérez-Plasencia, Osbaldo Reséndis-Antonio, Patricio Gariglio, Alejandro García-Carrancá

“…When we performed a meta-analysis using microarray data from cervical cancer biopsies and normal tissues, we found that the expression of OSKM-N and some target genes allowed separating tumor and normal tissues between samples, which enhanced the importance of OSKM-N in the tumorigenesis. …”
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Contribution of cuproptosis and immune-related genes to idiopathic pulmonary fibrosis disease by Chengji Jin, Jia Li, Qiaoyu Li, Lipeng Zhang, Shaomao Zheng, Qiong Feng, Yongjie Li, Yu Zheng, Qiuli Nie, Jin Liang, Jing Wang, Jing Wang

“…Additionally, multiple bioinformatics analyses were employed to identify immune-related biomarkers associated with the diagnosis of IPF, offering valuable insights for future treatment strategies.MethodsFour microarray datasets were selected from the Gene Expression Omnibus (GEO) collection for screening. …”
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Prognostic significance of cell cycle-associated proteins p16, pRB, cyclin D1 and p53 in resected oropharyngeal carcinoma by Michaela Plath, Martina A. Broglie, Diana Förbs, Sandro J. Stoeckli, Wolfram Jochum

“…The objective of this study was to assess cell cycle proteins as potential surrogate markers for HR-HPV DNA testing to identify OPSCC with favorable prognosis after resection. Methods Tissue microarray cores of 313 surgically treated OPSCC were stained for p16INK4a, pRB, cyclin D1 and p53 using immunohistochemistry. …”
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Uridine-cytidine kinase 2 is correlated with immune, DNA damage repair and promotion of cancer stemness in pan-cancer by Jinlong Tian, Yanlei Li, Yu Tong, Yuan Zhang, Tingxiao Zhao, Yao Kang, Qing Bi

“…GEO is a famous public genomics database supporting freely disseminates microarray data. Finally, we analyzed the correlation between UCK2 and drug sensitivity.ResultsUCK2 expression was observed to be high in most cancers and was remarkably related to the prognosis of pan-cancers. …”
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Rosiglitazone Induces Mitochondrial Biogenesis in Differentiated Murine 3T3-L1 and C3H/10T1/2 Adipocytes by James X. Rong, Jean-Louis D. Klein, Yang Qiu, Mi Xie, Jennifer H. Johnson, K. Michelle Waters, Vivian Zhang, Jennifer A. Kashatus, Katja S. Remlinger, Nan Bing, Renae M. Crosby, Tymissha K. Jackson, Sam M. Witherspoon, John T. Moore, Terence E. Ryan, Sue D. Neill, Jay C. Strum

“…By systematically analyzing mitochondrial gene expression in two common murine adipocyte models, the current study aimed to further establish the direct role of RSG and capture temporal changes in gene transcription. Microarray profiling revealed that in fully differentiated 3T3-L1 and C3H/10T1/2 adipocytes treated with RSG or DMSO vehicle for 1, 2, 4, 7, 24, and 48 hrs, RSG overwhelmingly increased mitochondrial gene transcripts time dependently. …”
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Effect of Electroacupuncture on Hippocampal Functional Activity and Molecular Expression Profile in Rats with Vascular Cognitive Impairment by WANG Zeyu, DING Yanyi, DAI Yaling, YANG Minguang, HUANG Jia, ZHANG Shenghang

“…Barnes maze test was used to evaluate the spatial learning and memory ability of rats; Y maze test was used to evaluate the spatial working memory ability of rats; small animal 7.0 T magnetic resonance resting brain functional imaging was used to analyze the changes of regional homogeneity (ReHo) of hippocampal functional activity; Agilent mRNA expression microarray was used to analyze the differential gene expression of the whole hippocampus genome.Results① Behavioral analysis results: compared with the sham operation group, the Barnes maze escape latency of the model group increased significantly (<italic>P</italic>&lt;0.05), the target quadrant duration percentage decreased significantly (<italic>P</italic>&lt;0.05), and the Y maze alternation rate decreased significantly (<italic>P</italic>&lt;0.05); compared with the model group, the Barnes maze escape latency of the electroacupuncture group decreased significantly (<italic>P</italic>&lt;0.05), the target quadrant duration percentage and the Y maze alternation rate increased significantly (<italic>P</italic>&lt;0.05). ② ReHo changes results: compared with the sham operation group, the ReHo of functional activitives of the bilateral prefrontal lobes, hippocampus and other brain regions in the model group decreased significantly (<italic>P</italic>&lt;0.005); compared with the model group, the ReHo of functional activities of the bilateral hippocampus, prefrontal lobes and piriform cortex in the model group increased significantly (<italic>P</italic>&lt;0.005). ③ Genomics results: a total of 705 genes with 2-fold differential expression of hippocampal mRNA between the model group and the sham operation group (<italic>P</italic>&lt;0.05), of which 195 genes (such as Sytl1, Trpv6, Klhl14, Npsr1, Myh3, Galnt3, Nr4a1, Bmp3, Egr2, etc.) were down-regulated, of which 510 genes (such as Insl6, Efcab1, Akr1b1, Tagln, Glrb, Akr1c13, Kcne1L, Ubap1, etc.) were up-regulated. …”
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The expression of BHLHE22 in endometrial carcinoma: Associations with mismatch repair protein expression status, tumor-infiltrating immune cells, programmed death-ligand 1 and clin... by Lin-Yu Chen, Hsing-Yu Chen, Hung-Cheng Lai, Shiou-Fu Lin, Kuo-Chang Wen, Darmawi, Phui-Ly Liew

“…Materials and methods: Immunohistochemistry on tissue microarray sections in primary EC to quantify BHLHE22, PD-L1, CD8 and CD68 was performed. …”
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PPARα suppresses growth of hepatocellular carcinoma in a high-fat diet context by reducing neutrophil extracellular trap release by Banglun Pan, Zhu Zhang, Dongjie Ye, Xiaoxia Zhang, Yuxin Yao, Yue Luo, Haijie Hong, Xinran Cai, Yanling Chen, Nanhong Tang

“…Methods: In this study, the molecular mechanism of NET release and the potential beneficial effects of PPARα agonists on the HCC microenvironment were explored through proteomics, metabolomics, tissue microarray, immunofluorescence, flow cytometry, western blot, and dual-luciferase reporter gene assays (n = 6 per group). …”
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The Characteristics Variation of Hepatic Progenitors after TGF-β1-Induced Transition and EGF-Induced Reversion by Ping Wang, Min Cong, Tianhui Liu, Aiting Yang, Guangyong Sun, Dong Zhang, Jian Huang, Shujie Sun, Jia Mao, Hong Ma, Jidong Jia, Hong You

“…The proliferation ability and differentiation potential of these cells were suppressed by TGF-β1, while EGF resumed these capacities to the level similar to the control cells. RNA microarray analysis showed that most of the genes with significant changes after TGF-β1 incubation were recovered by EGF. …”
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Deciphering hub genes and immune landscapes related to neutrophil extracellular traps in rheumatoid arthritis: insights from integrated bioinformatics analyses and experiments by Yang Li, Yang Li, Jian Liu, Jian Liu, Yue Sun, Yue Sun, Yuedi Hu, Yuedi Hu, Qiao Zhou, Qiao Zhou, Chengzhi Cong, Chengzhi Cong, Yiming Chen, Yiming Chen

“…Subsequently, three microarray datasets were collected for a training cohort and correlated with a bulk RNA-seq dataset associated with NETs. …”
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The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer by Yao Yi, Yao Yi, Yu Zhong, Yu Zhong, Lianhua Xie, Lianhua Xie, Shuxian Lu, Shuxian Lu, Yifeng Zhang, Yifeng Zhang

“…CIBERSORT analysis was used to characterize the composition of immune cells within complex tissues based on gene expression data, typically derived from bulk RNA sequencing or microarray datasets. Therefore, we explored the immune microenvironment differences between TNBC and non-TNBC by leveraging the CIBERSORT algorithm. …”
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Ultrasound May Suppress Tumor Growth, Inhibit Inflammation, and Establish Tolerogenesis by Remodeling Innatome via Pathways of ROS, Immune Checkpoints, Cytokines, and Trained Immun... by Qian Yang, Ruijing Zhang, Peng Tang, Yu Sun, Candice Johnson, Jason Saredy, Susu Wu, Jiwei Wang, Yifan Lu, Fatma Saaoud, Ying Shao, Charles Drummer, Keman Xu, Daohai Yu, Rongshan Li, Shuping Ge, Xiaohua Jiang, Hong Wang, Xiaofeng Yang

“…The immune mechanisms underlying low-intensity ultrasound- (LIUS-) mediated suppression of inflammation and tumorigenesis remain poorly determined. Methods. We used microarray datasets from the NCBI GEO DataSet repository and conducted comprehensive data-mining analyses, where we examined the gene expression of 1376 innate immune regulators (innatome genes (IGs) in cells treated with LIUS. …”
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MicroRNAs Expression Profile in MN1-Altered Astroblastoma by Francesca Gianno, Evelina Miele, Claudia Sabato, Elisabetta Ferretti, Simone Minasi, Francesca Romana Buttarelli, Debora Salerno, Natalia Pediconi, Giuseppe Rubens Pascucci, Francesca Guerrieri, Andrea Ciolfi, Simone Pizzi, Maura Massimino, Veronica Biassoni, Elisabetta Schiavello, Marco Gessi, Sofia Asioli, Angela Mastronuzzi, Antonio d’Amati, Giuseppina Catanzaro, Elisabetta Viscardi, David Capper, Felice Giangaspero, Manila Antonelli

“…Subsequently, the methylation status of promoters of deregulated miRNAs was investigated through a methylation profiling microarray. Finally, bioinformatics analysis was conducted to explore the biological processes (BPs) and target genes of differentially expressed miRNAs. …”
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Delineation of the Genetic Architecture and Clinical Polymorphism of 3q29 Duplication Syndrome: A Review of the Literature and a Report of Two Novel Patients With Single‐Gene BDH1... by A. A. Kashevarova, M. E. Lopatkina, O. Yu. Vasilyeva, D. A. Fedotov, A. D. Lobanov, E. A. Fonova, I. Z. Zhalsanova, A. A. Zarubin, O. A. Salyukova, E. O. Belyaeva, V. V. Petrova, E. G. Ravzhaeva, A. A. Agafonova, A. D. Cheremnykh, N. B. Torkhova, S. L. Vovk, I. N. Lebedev

“…Methods Patients were investigated by performing a cytogenetic analysis of GTG‐banded metaphases, aCGH with the SurePrint G3 Human CGH Microarray 8×60K, qPCR, FISH, and WES. Results Here, we report five new patients with atypical duplications overlapping with the 3q29 duplication syndrome region and no other genetic findings. …”
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Non-coding RNAs secreted by renal cancer include piR_004153 that promotes migration of mesenchymal stromal cells by Joanna Bogusławska, Małgorzata Grzanka, Piotr Popławski, Weronika Zarychta-Wiśniewska, Anna Burdzinska, Karolina Hanusek, Helena Kossowska, Roksana Iwanicka-Nowicka, Alex Białas, Beata Rybicka, Anna Adamiok-Ostrowska, Joanna Życka-Krzesińska, Marta Koblowska, Leszek Pączek, Agnieszka Piekiełko-Witkowska

“…Expression of MSCs genes was evaluated using microarray and qPCR. TCGA data were analyzed to explore the expression of sncRNAs in RCC tumors. …”
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Inhibitory Effect of PRMT5/MTA Inhibitor on MTAP‐Deficient Glioma May Be Influenced by Surrounding Normal Cells by Yunjie Wang, Xiaohui Sun, Runchen Ma, Xiaofan Zhang, Shengmin Ji, Zhaofeng Liu, Gangqiang Yang, Hongbo Wang, Peng Zhang, Jianzhao Zhang, Jingwei Tian

“…Methods We first analyzed whether there were MTAP‐expressing normal intracerebral cells around MTAP‐deficient glioma tissues by paraffin‐embedded tissue microarray of human glioma specimens. Then, in vivo and in vitro models of MTAP‐deficient gliomas coexisting with neurons or glial cells were constructed for evaluating the effectiveness of the anti‐tumor effects of MRTX1719 in this setting. …”
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Integrating melt electrospinning writing and microfluidics to engineer a human cardiac microenvironment for high-fidelity drug screening by Yu-hong Wang, Ting-ting Liu, Yan-ping Guo, Shuo-ji Zhu, Zi-ming Liao, Jia-mei Song, Xi-ming Zhu, Jia-liang Liang, Moussa Ide Nasser, Nan-bo Liu, De-hua Chang, Ping Zhu, Bin Yao

“…Taken together, these results highlight the ability of our myocardial microarray platform to accurately reflect clinical behaviour, underscoring its potential as a powerful pre-clinical tool for assessing drug response and toxicity.…”
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Novel biomarkers: the RUNX family as prognostic predictors in colorectal cancer by Yingting Liu, Yingting Liu, Yingting Liu, Junjun Chen, Junjun Chen, Junjun Chen, An Li, An Li, An Li, Yue Wu, Yue Wu, Yue Wu, Junwei Ge, Junwei Ge, Junwei Ge, Maoling Yuan, Maoling Yuan, Maoling Yuan, Bin Xu, Bin Xu, Bin Xu, Xiao Zheng, Xiao Zheng, Xiao Zheng, Lujun Chen, Lujun Chen, Lujun Chen, Jingting Jiang, Jingting Jiang, Jingting Jiang

“…Our study of human colorectal cancer tissue microarray (TMA) also revealed positive and statistically significant correlations between the expressions of RUNX1, RUNX2, and RUNX3 in both CD8+T cells and CD103+CD8+T cells. …”
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Whole blood ratio of CDK1/CX3CR1 mRNA expression combined to lactate refines the prediction of ICU mortality in septic patients in the Sepsis-3 era: a proof-of-concept study by Marie-Angélique Cazalis, Marie-Angélique Cazalis, Louis Kreitmann, Louis Kreitmann, Guillaume Monneret, Guillaume Monneret, Alexandre Pachot, Alexandre Pachot, Karen Brengel-Pesce, Karen Brengel-Pesce, Jean-François Llitjos, Jean-François Llitjos, Jean-François Llitjos

“…We aimed to: (a) identify and validate an mRNA biomarker signature whose association with all-cause intensive care unit (ICU) mortality is consistent at several timepoints; and (b) evaluate how this mRNA signature could be used in association with lactate levels for predictive and prognostic enrichment in sepsis.MethodsWe conducted a gene expression analysis study at two timepoints (day 1 and day 2–3 following ICU admission) using microarray data from adult septic patients to identify candidate biomarkers predictive of all-cause ICU mortality. …”
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A diagnostic host-specific transcriptome response for Mycoplasma pneumoniae pneumonia to guide pediatric patient treatment by Sandra Viz-Lasheras, Alberto Gómez-Carballa, Xabier Bello, Irene Rivero-Calle, Ana Isabel Dacosta, Myrsini Kaforou, Dominic Habgood-Coote, Aubrey J. Cunnington, Marieke Emonts, Jethro A. Herberg, Victoria J. Wright, Enitan D. Carrol, Stephane C. Paulus, Werner Zenz, Daniela S. Kohlfürst, Nina Schweintzger, Michiel Van der Flier, Ronald de Groot, Luregn J. Schlapbach, Philipp Agyeman, Andrew J. Pollard, Colin Fink, Taco T. Kuijpers, Suzanne Anderson, Ulrich Von Both, Marko Pokorn, Dace Zavadska, María Tsolia, Henriëtte A. Moll, Clementien Vermont, Michael Levin, Federico Martinón-Torres, Antonio Salas, On behalf of EUCLIDS, PERFORM, and DIAMONDS consortia

“…Using a LASSO regression simulation approach and blood microarray data from 107 children with pneumonia (including 30 M. pneumoniae) we identify eight different transcriptomic signatures, ranging from 3-10 transcripts, that differentiate mycoplasma pneumonia from other bacterial/viral pneumonias with high accuracy (AUC: 0.84–0.95). …”
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