Profiling of gastric cancer cell-surface markers to achieve tumour–normal discrimination by Henry Yang, Khek Yu Ho, Judith Toh, Michal Marek Hoppe, Teena Thakur, Kar Tong Tan, Brendan Pang, Sharmaine Ho, Rony Roy, Khay Guan Yeoh, Raghav Sundar, Anand Jeyasekharan

“…After validation with TCGA data (n=29 matched tumour and normal pairs), the following proteins were selected for mIHC analysis: CEACAM5, CEACAM6, CLDN4, CLDN7, and EpCAM. …”
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The significance of long chain non-coding RNA signature genes in the diagnosis and management of sepsis patients, and the development of a prediction model by Yong Bai, Jing Gao, Yuwen Yan, Xu Zhao

“…The purpose of this study was to determine the value of Long chain non-coding RNA (LncRNA) RP3_508I15.21, RP11_295G20.2, and LDLRAD4_AS1 in the diagnosis of adult sepsis patients and to develop a Nomogram prediction model.MethodsWe screened adult sepsis microarray datasets GSE57065 and GSE95233 from the GEO database and performed differentially expressed genes (DEGs), weighted gene co-expression network analysis (WGCNA), and machine learning methods to find the genes by random forest (Random Forest), least absolute shrinkage and selection operator (LASSO), and support vector machine (SVM), respectively, with GSE95233 as the training set and GSE57065 as the validation set. …”
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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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Long read whole genome sequencing-based discovery of structural variants and their role in aetiology of non-syndromic autism spectrum disorder in India by Jhanvi Shah, Debasrija Mondal, Deepika Jain, Priti Mhatre, Ketan Patel, Anand Iyer, Manoj Pandya, Bhargavi Menghani, Gayatri Dave, Jayesh Sheth, Frenny Sheth, Shweta Ramdas, Harsh Sheth

“…Short read sequencing (SRS) and chromosomal microarray (CMA) are unable to resolve these SVs due to their inherent technological limitations. …”
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A high-content small molecule screen identifies sensitivity of glioblastoma stem cells to inhibition of polo-like kinase 1. by Davide Danovi, Amos Folarin, Sabine Gogolok, Christine Ender, Ahmed M O Elbatsh, Pär G Engström, Stefan H Stricker, Sladjana Gagrica, Ana Georgian, Ding Yu, Kin Pong U, Kevin J Harvey, Patrizia Ferretti, Patrick J Paddison, Jane E Preston, N Joan Abbott, Paul Bertone, Austin Smith, Steven M Pollard

“…We used live-cell imaging and high content image analysis tools and identified JNJ-10198409 (J101) as an agent that induces mitotic arrest at prometaphase in GNS cells but not NS cells. Antibody microarrays and kinase profiling suggested that J101 responses are triggered by suppression of the active phosphorylated form of polo-like kinase 1 (Plk1) (phospho T210), with resultant spindle defects and arrest at prometaphase. …”
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Bioinformatics-based screening and validation of PANoptosis-related biomarkers in periodontitis by Qing Sun, Qing Sun, JinYue Hu, JinYue Hu, RuYue Wang, RuYue Wang, ShuiXiang Guo, ShuiXiang Guo, GeGe Zhang, GeGe Zhang, Ao Lu, Ao Lu, Xue Yang, Xue Yang, LiNa Wang, LiNa Wang

“…Subnetworks were identified using the MCODE plugin. Key genes were selected based on integration with rank-sum test results. …”
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Pan-cancer analysis identifies CD155 as a promising target for CAR-T cell therapy by Xiaohong Liu, Yue Sun, Boxu Lin, Hao Xiong, Xinyue Lu, Binghe Tan, Chenglin Zhang, Mingyao Liu, Juliang Qin, Na Zhang, Bing Du

“…Therefore, the exploration and rational selection of novel tumor targets is urgently needed. …”
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Immune-related gene characterization and biological mechanisms in major depressive disorder revealed based on transcriptomics and network pharmacology by Shasha Wu, Shasha Wu, Qing Jiang, Jinhui Wang, Jinhui Wang, Daming Wu, Yan Ren

“…Subsequently, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Cytoscape plugin CluGO, and Gene Set Enrichment Analysis (GSEA) were utilized to identify immune-related genes. The final selection of immune-related hub genes was determined through the least absolute shrinkage and selection operator (Lasso) regression analysis and PPI analysis. …”
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Machine learning-based integration identifies plasma cells-related gene signature ST6GAL1 in idiopathic pulmonary fibrosis by Fanjie Lin, Ken Lin, Donglei Li, Weiguo Kong, Jiayu Zhuang, Wei He, Xinguang Wei, Tianchi Xiao, Hao Zu, Zili Zhang, Wenju Lu

“…Moreover, the differentially expressed genes (DEGs) were obtained based on the bulk RNA-seq and microarray data. In addition, a machine learning-based integrative procedure for constructing a concordance plasma cells-related gene signature (PCRGS) was developed. …”
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Repurposing MDM2 inhibitor RG7388 for TP53-mutant NSCLC: a p53-independent pyroptotic mechanism via ROS/p-p38/NOXA/caspase-3/GSDME axis by Gaoyan Tang, Xuelei Cao, Jiaqi Chen, Fu Hui, Na Xu, Yiqing Jiang, Hongmin Lu, Haifeng Xiao, Xiuming Liang, Mingzhe Ma, Yu Qian, Dongli Liu, Zhenlu Wang, Shuzhen Liu, Guohua Yu, Lei Sun

“…Furthermore, immunohistochemical (IHC) analysis of an NSCLC tissue microarray confirmed a strong positive correlation between p-p38 and NOXA expression. …”
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PODO447: a novel antibody to a tumor-restricted epitope on the cancer antigen podocalyxin by Blake Gilks, Martin Köbel, Diana Canals Hernaez, Michael R Hughes, Pamela Dean, Peter Bergqvist, Ismael Samudio, Ola Blixt, Katharina Wiedemeyer, Yicong Li, Chris Bond, Eric Cruz, Calvin D Roskelley, Kelly M McNagny

“…Tumor specificity was assessed using primary normal tissue and an ovarian cancer tissue microarray (TMA). Mapping of the tumor-restricted epitope was performed using enzyme-treated human tumor cell lines and a glycan array.Results One mAb (PODO447) showed strong reactivity with a variety of Podxl+ tumor cell lines but not with normal primary human tissue including Podxl+ kidney podocytes and most vascular endothelia. …”
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Inhibition of SOD1 trimerization is a novel drug target for ALS disease by Tae-Gyun Woo, Jin Han, Yuju Kim, Young jun Hwang, Mua Lee, So-mi Kang, Soyoung Park, Yeongseon Ji, Yeon-Ho Chung, Songyoung Baek, Eunbyeol Shin, Minju-Kim, Hyewon Jang, Yun-Jeong Shin, Yonghoon Kwon, Bae-Hoon Kim, Bum-Joon Park

“…In vitro, PRG-A-04 selectively bound to the mutant form of SOD1, but not the wild type, and efficiently inhibited the aggregation caused by SOD1-G147P (a SOD1 trimer stabilizer). …”
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Improved epigenetic age prediction models by combining sex chromosome and autosomal markers by Zhong Wan, Peter Henneman, Huub C. J. Hoefsloot, Ate D. Kloosterman, Pernette J. Verschure

“…Results We employed random forest regression (RFR) to construct age prediction models with publicly available DNAm Infinium 450 K microarray data of sex chromosomes from human whole blood and buffy coat samples and assessed the RFR model performance based on the root-mean squared error (RMSE) and the mean absolute deviation (MAD) of cross-validation. …”
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Construction of a circRNA-miRNA-mRNA Regulatory Network for the Immune Regulation of Lung Adenocarcinoma by Hanyi Li, Xin Jin, Wei Li, Fan Ren, Tong Li, Xuanguang Li, Haochuan Yu, Dianxun Fu, Zuoqing Song, Song Xu

“…Methods and Materials We utilized microarray datasets from the GEO NCBI database (GSE101586) to identify differentially expressed circRNAs (DEcircRNAs) in LUAD. …”
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Study on the mechanisms and functions of lncRNAs in regulating carboplatin resistance in ovarian cancer cells by HONG Yi, CHEN Cuilan, YIN Fuqiang, LIU Xia

“…Based on expression profiling microarrays and RT-qPCR validation, lncRNA DAPK1-IT1, which was significantly down-regulated by more than 4-fold in both two carboplatin-resistant cell lines, was selected for functional verification. …”
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NF1 expression profiling in IDH-wildtype glioblastoma: genomic associations and survival outcomes by Michael Chang, Mohamed Sherief, Maria Ioannou, Viveka Chinnasamy, Lucy Chen, Michael Frost, Michelle Mattson-Hoss, Herb Sarnoff, David O. Kamson, Matthias Holdhoff, Debraj Mukherjee, Chetan Bettegowda, Jordina Rincon-Torroella, Victoria Croog, Peng Huang, Fausto J. Rodriguez, Calixto-Hope G. Lucas, Karisa C. Schreck

“…Methods We assembled a single-institution, retrospective cohort of 542 IDH-wildtype GBM with somatic next generation sequencing to investigate the frequency and nature of detected NF1 alterations. We selected 69 GBMs from which to build a tissue microarray (TMA) of 44 NF1-wildtype and 25 NF1-mutant cases. …”
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Spatially resolved analysis of the T cell immune contexture in lung cancer-associated brain metastases by Richa Gupta, Sarah B Goldberg, Kurt A Schalper, Harriet M Kluger, Lucia B Jilaveanu, Adebowale J Adeniran, Benjamin Y Lu, Adam Aguirre-Ducler, Nicole Gianino, Hailey Wyatt, Matthew Ribeiro, Veronica L Chiang, Joseph N Contessa

“…The signal for each marker was measured in marker-selected tissue compartments, and associations between marker levels, tumor location, and major clinicopathological variables were studied. …”
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Tumor immune microenvironment permissive to metastatic progression of ING4-deficient breast cancer. by Emily Tsutsumi, Anne M Macy, Janine LoBello, Karen T Hastings, Suwon Kim

“…To characterize the tumor immune microenvironment associated with ING4-deficient tumors, three approaches were employed in this study: First, tissue microarrays composed of 246 primary breast tumors including 97 ING4-deficient tumors were evaluated for the presence of selective immune markers, CD68, CD4, CD8, and PD-1, using immunohistochemical staining. …”
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Candidate gene biodosimetry markers of exposure to external ionizing radiation in human blood: A systematic review. by Jerome Lacombe, Chao Sima, Sally A Amundson, Frederic Zenhausern

“…Original English-language publications of microarray studies assessing radiation-induced changes in gene expression levels in human blood after external IR were included. …”
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Identification and external validation of tumor DNA methylation panel for the recurrence risk stratification of stage II colon cancer by Tanwei Yuan, Dominic Edelmann, Víctor Moreno, Elisabeth Georgii, Lisa Barros de Andrade e Sousa, Helena Pelin, Xiaofeng Jiang, Jakob Nikolas Kather, Katrin E. Tagscherer, Wilfried Roth, Melanie Bewerunge-Hudler, Alexander Brobeil, Matthias Kloor, Hendrik Bläker, Hermann Brenner, Michael Hoffmeister

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