Revealing the role of natural killer cells in ankylosing spondylitis: identifying diagnostic biomarkers and therapeutic targets by Yuling Chen, Yan Li, Yuan Xu, Qing Lv, Yuanchun Ye, Jieruo Gu

“…This study integrated bioinformatics methods with experimental validation to explore the role of natural killer (NK) cells in AS.Methods Two microarray datasets, GSE25101 and GSE73754, were selected, and the scRNA-seq data were obtained from GSE194315 and Liu’s research. …”
Get full text

Integrative analysis of T cell-mediated tumor killing-related genes reveals KIF11 as a novel therapeutic target in esophageal squamous cell carcinoma by Xinxin Cheng, Huihui Zhao, Zhangwang Li, Liping Yan, Qingjie Min, Qingnan Wu, Qimin Zhan

“…Abstract Background Immune checkpoint inhibitors (ICIs) are emerging promising agents for the treatment of patients with esophageal squamous cell carcinoma (ESCC), however, there are only a small proportion respond to ICI therapy. Therefore, selecting candidate patients who will benefit the most from these drugs is critical. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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). …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

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. …”
Get full text

Adenosine Receptor 3 in Liver Cancer: Expression Variability, Epigenetic Modulation, and Enhanced Histone Deacetylase Inhibitor Effects by Louise Kaldjob-Heinrich, Sandro Nuciforo, Steffen Lemke, Aaron Stahl, Stefan Czemmel, Sepideh Babaei, Lauriane Blukacz, Marie-Anne Meier, Yizheng Zhang, Christian M. Schürch, Irene Gonzalez-Menendez, Pascal Woelffing, Nisar P. Malek, Veit Scheble, Sven Nahnsen, Manfred Claassen, Markus Templin, Hans Bösmüller, Markus H. Heim, Daniel Dauch, Michael Bitzer

“…However, further data are required to clarify ADORA3 expression patterns in liver cancer, mechanisms of action, and the potential for combination therapies to inform patient selection for future clinical trials. Methods: Patient-derived tissue microarrays and RNA-sequencing were employed to investigate ADORA3 expression. …”
Get full text

Identification and Cross-Platform Validation of Sparse Molecular Classifiers for Antibody-Mediated and T-Cell–Mediated Rejection After Kidney Transplantation by Jasper Callemeyn, Josué Manik Nava-Sedeño, Dany Anglicheau, Jack Beadle, Jan Hinrich Bräsen, Marian C. Clahsen-van Groningen, Iacopo Cristoferi, Henriette de Loor, Andreas Deutsch, Marie Essig, Wilfried Gwinner, Philip F. Halloran, Dennis A. Hesselink, Priyanka Koshy, Dirk Kuypers, Evelyne Lerut, Pierre Marquet, Robert C. Minnee, Candice Roufosse, Ben Sprangers, Amaryllis H. Van Craenenbroeck, Haralampos Hatzikirou, Maarten Naesens

“…Methods: In a discovery cohort of 224 kidney transplant biopsies, lasso regression was applied on microarray gene expression data to derive a molecular classifier for ABMR and TCMR, respectively. …”
Get full text

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. …”
Get full text

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

Get full text

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

“…In vitro and in vivo experiments have demonstrated that MRTX1719, a small molecule that selectively binds PRMT5/MTA complex, significantly inhibits the proliferation of MTAP‐deficient tumors and has a weak toxic effect on normal cells. …”
Get full text