The NR_109/FUBP1/c-Myc axis regulates TAM polarization and remodels the tumor microenvironment to promote cancer development by Baoen Shan, Cong Zhang, Guogui Sun, Hongtao Zhang, Xiaoya Li, Sisi Wei, Suli Dai, Huixia Wang, Lianmei Zhao

“…Long noncoding RNAs (lncRNAs) have been implicated in various physiological and pathological processes, yet the underlying mechanism on how lncRNAs manipulate the polarization states of TAMs is still unclear and remains to be further investigated.Methods Microarray analyses were employed to characterize the lncRNA profile involved in THP-1-induced M0, M1 and M2-like macrophage. …”
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Identifying critical modules and biomarkers of intervertebral disc degeneration by using weighted gene co‐expression network by Daqian Zhou, Tao Liu, Yongliang Mei, Jiale Lv, Kang Cheng, Weiye Cai, Silong Gao, Daru Guo, Xianping Xie, Zongchao Liu

“…Additionally, we predicted miRNAs involved in hub gene co‐regulation and analyzed miRNA microarray data from GSE116726 to identify four differentially expressed miRNAs. …”
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PARP9-PARP13-PARP14 axis tunes colorectal cancer response to radiotherapy by Rimvile Prokarenkaite, Karolina Kuodyte, Greta Gudoityte, Elzbieta Budginaite, Daniel Naumovas, Egle Strainiene, Kristijonas Velickevicius, Audrius Dulskas, Ernestas Sileika, Jonas Venius, Virginijus Tunaitis, Augustas Pivoriunas, Vytaute Starkuviene, Vaidotas Stankevicius, Kestutis Suziedelis

“…The transcriptomes of nonirradiated and irradiated cells were analyzed using microarrays. Gene set enrichment analysis was conducted to determine the pathways in which PARP13 is engaged. …”
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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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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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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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Berberine Improves Inflammatory Responses of Diabetes Mellitus in Zucker Diabetic Fatty Rats and Insulin-Resistant HepG2 Cells through the PPM1B Pathway by Yang Sheng Wu, Zhe Ming Li, Yi Tao Chen, Shi Jie Dai, Xiao Jie Zhou, Yuan Xiao Yang, Jian Shu Lou, Li Ting Ji, Yu Ting Bao, Ling Xuan, Lu Ning Lin, Chang Yu Li

“…Berberine (BBR), a natural compound extracted from a Chinese herb, has been shown to effectively attenuate insulin resistance (IR) and inflammation in the clinic. …”
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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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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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Oncolytic adenovirus decreases the proportion of TIM-3+ subset of tumor-infiltrating CD8+ T cells with correlation to improved survival in patients with cancer by Matti Kankainen, Timo Joensuu, Akseli Hemminki, Juuso Juhila, Siri Tähtinen, Otto Hemminki, Anna Kanerva, Kristian Taipale, Ilkka Liikanen, Minna Oksanen, Dafne C A Quixabeira, Saru Basnet

“…Meanwhile, less is known about their effects on immune checkpoints, the main targets for passive immunotherapy of cancer. …”
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Differential expression pattern of CC chemokine receptor 7 guides precision treatment of hepatocellular carcinoma by Jie Qin, Qianyi Gong, Cheng Zhou, Jietian Xu, Yifei Cheng, Weiyue Xu, Di Zhu, Yiming Liu, Yuye Zhang, Yanru Wang, Lingling Gao, Lanfang Li, Wulei Hou, Qian Li, Binbin Liu, Yazhen Zhu, Zuoyun Wang, Jieyi Shi, Shuangjian Qiu, Chunmin Liang

“…In this study, the complex tumor microenvironment was identified by using tissue microarray (TMA), spatial transcriptomes and single-cell sequencing. …”
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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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Decoding chromosomal instability insights in CRC by integrating omics and patient-derived organoids by Federica Papaccio, Manuel Cabeza-Segura, Blanca García-Micó, Francisco Gimeno-Valiente, Sheila Zúñiga-Trejos, Valentina Gambardella, María Fernanda Gutiérrez‐Bravo, Carolina Martinez‐Ciarpaglini, Pilar Rentero‐Garrido, Tania Fleitas, Susana Roselló, Juan Antonio Carbonell-Asins, Marisol Huerta, David Moro-Valdezate, Desamparados Roda, Noelia Tarazona, Manuel M. Sánchez del Pino, Andrés Cervantes, Josefa Castillo

“…From a clinical perspective, a better knowledge of these tumour’s biology will help to guide therapeutic strategies more effectively. Methods We used high-density chromosomal microarray analysis to evaluate CIN level of patient-derived organoids (PDOs) and their original mCRC tissues. …”
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Variations in salivary microbiome and metabolites are associated with immunotherapy efficacy in patients with advanced NSCLC by DanHui Huang, YueHua Chen, Cui Li, Shuang Yang, LiShan Lin, XiaoNan Zhang, XiaoFang Su, LaiYu Liu, Haijin Zhao, Tingyue Luo, Shaoxi Cai, QianNan Ren, Hangming Dong

“…Besides, in vitro experiments and tumor tissue microarray, including 70 NSCLC patients, were utilized to further explore the potential mechanism linking the oral microbiome and immunotherapy efficacy. …”
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LAPTM4B enhances the stemness of CD133+ liver cancer stem-like cells via WNT/β-catenin signaling by Jiahong Wang, Jianping Liao, Ye Cheng, Meirong Chen, Aimin Huang

“…Therefore, we investigated the effects of LAPTM4B on the stemness regulation of cluster of differentiation 133 (CD133)+ liver cancer stem-like cells (CSLCs). …”
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Aldo-keto reductase family 1 member B10 prevents esophageal squamous cell carcinoma from reactive carbonyl species-induced cell death and promotes its progression by Shau-Hsuan Li, Wan-Ting Huang, Yen-Hao Chen, Hung-I Lu, Chien-Ming Lo, Hsin-Ting Tsai, Chang-Han Chen

“…Furthermore, the identified signaling pathway and its biological effects were investigated in ESCC cell lines in vitro and 4-nitroquinoline 1-oxide (4-NQO)-induced-ESCC murine model in vivo. …”
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