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

“…This study integrates multi-omics data and machine learning approaches to systematically identify and validate key PANoptosis-related biomarkers in periodontitis.MethodsPeriodontitis-related microarray datasets (GSE16134 and GSE10334) were obtained from the GEO database, and PANoptosis-related genes were retrieved from GeneCards. …”
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Mapping the key players in Kawasaki disease; role of inflammatory genes and protein-protein interactions by Wael Hafez, Feras Al-Obeidat, Asrar Rashid, Afsheen Raza, Nouran Hamza, Nesma Ahmed, Marwa M. Abdeljawad, Raziya Kadwa, Abdelhameed Elmesery, Muneir Gador, Dina Khair, Gihan Zina, fatema Abdulaal, Mina Wassef Girgiss, Maha Abdelhadi, Ahmed Abdelrahman, Mahmad Anwar Ibrahim, Mohamed El Sherbiny

“…Methods: RNA sequencing and microarray genomic datasets were retrieved from the NCBI Gene Expression Omnibus (GEO). …”
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Peroxisome proliferator‐activated receptor gamma (PPARγ) is central to the initiation and propagation of human angiomyolipoma, suggesting its potential as a therapeutic target by Oren Pleniceanu, Racheli Shukrun, Dorit Omer, Einav Vax, Itamar Kanter, Klaudyna Dziedzic, Naomi Pode‐Shakked, Michal Mark‐Daniei, Sara Pri‐Chen, Yehudit Gnatek, Hadas Alfandary, Nira Varda‐Bloom, Dekel D Bar‐Lev, Naomi Bollag, Rachel Shtainfeld, Leah Armon, Achia Urbach, Tomer Kalisky, Arnon Nagler, Orit Harari‐Steinberg, Jack L Arbiser, Benjamin Dekel

“…Here, we establish a human AML‐xenograft (Xn) model in mice, recapitulating AML at the histological and molecular levels. Microarray analysis demonstrated tumor growth in vivo to involve robust PPARγ‐pathway activation. …”
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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

“…To check the in vivo therapeutic effect of PRG-A-04, SOD1G93A−Tg mice were injected with PRG-A-04; then behavioral test, histological analysis and microarray were performed. Results PRG-A-04 demonstrated favorable pharmacokinetics including high bioavailability and significant blood–brain barrier penetration. …”
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GATA6 immunohistochemistry and prognosis after surgical resection of pancreatic adenocarcinoma: results from the ESPAC-4 trial by R.C. Grant, K. Duan, R. Jackson, W. Greenhalf, E. Costello-Goldring, P. Ghaneh, C. Halloran, D. Palmer, T. Hackert, M. Büchler, S. Hutchinson, S. Ramotar, A. Dodd, J. Wilson, F. Notta, G. O’Kane, J. Knox, J. Neoptolemos, S. Gallinger, S.E. Fischer

“…Two pathologists independently assessed GATA6 protein expression by immunohistochemistry in tissue microarray cores, manually and with digital assistance. …”
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Single-cell and spatial proteo-transcriptomic profiling reveals immune infiltration heterogeneity associated with neuroendocrine features in small cell lung cancer by Ying Jin, Yuefeng Wu, Alexandre Reuben, Liang Zhu, Carl M. Gay, Qingzhe Wu, Xintong Zhou, Haomin Mo, Qi Zheng, Junyu Ren, Zhaoyuan Fang, Teng Peng, Nan Wang, Liang Ma, Lungevity PANSHI Initiative Consortium, Yun Fan, Hai Song, Jianjun Zhang, Ming Chen

“…We performed ultra-high-plex Digital Spatial Profiling on 132 tissue microarray cores from 44 treatment-naive limited-stage SCLC tumors. …”
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Hedgehog Signaling Inhibition by Smoothened Antagonist BMS-833923 Reduces Osteoblast Differentiation and Ectopic Bone Formation of Human Skeletal (Mesenchymal) Stem Cells by Nihal AlMuraikhi, Nuha Almasoud, Sarah Binhamdan, Ghaydaa Younis, Dalia Ali, Muthurangan Manikandan, Radhakrishnan Vishnubalaji, Muhammad Atteya, Abdulaziz Siyal, Musaad Alfayez, Abdullah Aldahmash, Moustapha Kassem, Nehad M. Alajez

“…Global gene expression profiling was performed using the Agilent® microarray platform. Effects on in vivo ectopic bone formation were assessed by implanting hMSC mixed with hydroxyapatite-tricalcium phosphate granules subcutaneously in 8-week-old female nude mice, and the amount of bone formed was assessed using quantitative histology. …”
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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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Genetic Alterations in Chromatin Regulatory Genes in Upper Tract Urothelial Carcinoma and Urothelial Bladder Cancer by Shuo Wang, Xuzhi Yan, Weihua Lan, Yapeng Wang, Ze Wang, Dali Tong, Yao Zhang, Qiang Ran, Haoyang Li, Junhao Jin, Haiyang Xiao, Jing Xu, Qian Yan, Dianzheng Zhang, Qiang Ma, Hualiang Xiao, Jun Qin, Luofu Wang, Jun Jiang, Qiuli Liu

“…Tumors were subtyped based on the expression of CK5 and GATA3. Results of tissue microarray of 78 muscle‐invasive bladder cancer (MIBC) samples were used as prognostic factors of different subtypes of MIBC. …”
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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

“…The objective of this study was to investigate the pathogenesis of MDD and to explore its association with the immune system by identifying hub biomarkers using bioinformatics analyses and examining immune infiltrates in human autopsy samples.MethodsGene microarray data were obtained from the Gene Expression Omnibus (GEO) datasets GSE32280, GSE76826, GSE98793, and GSE39653. …”
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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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CLU, FOS, and CXCL8 as diagnostic biomarkers for heart failure progression post-acute myocardial infarction: an integrated RNA-Seq and multi-machine learning study by Jingjing Wei, Peng Yu, Peng Yu, Yucai Hu, Lijie Qiao, Lijie Qiao, Bin Li, Bin Li, Haitao Li, Shiyang Xie, Zhengwei Dong, Aolong Wang, Yilin Zhang, Xinlu Wang, Yongxia Wang, Mingjun Zhu

“…We aimed to identify PBMCs-related critical genes as diagnostic biomarkers for HFpAMI and analyze the immune infiltration patterns.MethodsDifferential expression genes (DEGs) from PBMCs microarray data of AMI with or without HF were identified. …”
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Cancer-associated fibroblast-derived fibulin-5 promotes epithelial–mesenchymal transition in diffuse-type gastric cancer via cAMP response element-binding protein pathway, showing... by Jinju Choi, Yoonjin Kwak, Miree Park, Jeong Yeon Jo, Jun Hyuk Kang, Kook Myeong-Cherl, Hang-Rae Kim, Gwanghun Kim, Seong-Ho Kong, Do-Joong Park, Hye Seung Lee, Hyuk-Joon Lee, Jung Mogg Kim, Sang Gyun Kim, Han-Kwang Yang, Ji Kon Ryu, Soo-Jeong Cho

“…For validation, we used tissue microarray blocks of gastric cancers with immunohistochemical staining, single-cell RNA sequencing, primary cultures of cancer-associated fibroblasts (CAFs) and organoids, and a co-culture system involving CAFs and cancer cells. …”
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Mechanisms of ag85a/b DNA vaccine conferred immunotherapy and recovery from Mycobacterium tuberculosis‐induced injury by Nan Wang, Yan Liang, Qianqian Ma, Jie Mi, Yong Xue, Yourong Yang, Lan Wang, Xueqiong Wu

“…The gene expression profiles were analyzed using gene microarray technology to obtain differentially expressed (DE) genes. …”
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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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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

“…Methods Differential expressed lncRNAs were screened using expression profiling microarrays in two pairs of carboplatin-resistant and sensitive OC cells (HeyA8-CBP/HeyA8 and SKOV3-CBP/SKOV3). …”
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Spatial transcriptomics and multi-omics reveal relapse and resistance mechanisms of EndMT-derived CAFs mediated by TNC and FLNC in glioblastoma by Li Ji, Die Xia, Yu Zhou, Yaling Hu, Zhenkun Yang, Ying Yin, Jingjing Wang, Bo Zhang, Lingli Gong, Koukou Li, Jian Zou, Mei Wang

“…Methods Spatial transcriptome (ST) sequencing was conducted on the tissue microarray encompassing primary and recurrent glioma samples in order to characterize the cellular composition. …”
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N6-Methyladenosine modification of circDcbld2 in Kupffer cells promotes hepatic fibrosis via targeting miR-144-3p/Et-1 axis by Sai Zhu, Xin Chen, Lijiao Sun, Xiaofeng Li, Yu Chen, Liangyun Li, Xiaoguo Suo, Chuanhui Xu, Minglu Ji, Jianan Wang, Hua Wang, Lei Zhang, Xiaoming Meng, Cheng Huang, Jun Li

“…In this study, the expression levels of circRNAs, microRNAs, and messenger RNAs (mRNAs) in KCs from a mouse model of HF mice were investigated using microarray and circRNA-Seq analyses. circDcbld2 was identified as a candidate circRNA in HF, as evidenced by its up-regulation in KCs. …”
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Clinical application of sparse canonical correlation analysis to detect genetic associations with cortical thickness in Alzheimer’s disease by Bo-Hyun Kim, Sang Won Seo, Sang Won Seo, Sang Won Seo, Yu Hyun Park, JiHyun Kim, Hee Jin Kim, Hee Jin Kim, Hee Jin Kim, Hyemin Jang, Hyemin Jang, Hyemin Jang, Hyemin Jang, Jihwan Yun, Jihwan Yun, Jihwan Yun, Jihwan Yun, Mansu Kim, Jun Pyo Kim, Jun Pyo Kim, Jun Pyo Kim

“…We also investigated the role of the SNPs in neurological outcomes, including neurodegeneration and cognitive dysfunction.MethodsWe recruited 1125 Korean participants who underwent neuropsychological testing, brain magnetic resonance imaging, positron emission tomography, and microarray genotyping. We performed group-wise SCCA in Aβ negative (−) and Aβ positive (+) groups. …”
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