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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Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function. by Wenbo Tang, Matthew Kowgier, Daan W Loth, María Soler Artigas, Bonnie R Joubert, Emily Hodge, Sina A Gharib, Albert V Smith, Ingo Ruczinski, Vilmundur Gudnason, Rasika A Mathias, Tamara B Harris, Nadia N Hansel, Lenore J Launer, Kathleen C Barnes, Joyanna G Hansen, Eva Albrecht, Melinda C Aldrich, Michael Allerhand, R Graham Barr, Guy G Brusselle, David J Couper, Ivan Curjuric, Gail Davies, Ian J Deary, Josée Dupuis, Tove Fall, Millennia Foy, Nora Franceschini, Wei Gao, Sven Gläser, Xiangjun Gu, Dana B Hancock, Joachim Heinrich, Albert Hofman, Medea Imboden, Erik Ingelsson, Alan James, Stefan Karrasch, Beate Koch, Stephen B Kritchevsky, Ashish Kumar, Lies Lahousse, Guo Li, Lars Lind, Cecilia Lindgren, Yongmei Liu, Kurt Lohman, Thomas Lumley, Wendy L McArdle, Bernd Meibohm, Andrew P Morris, Alanna C Morrison, Bill Musk, Kari E North, Lyle J Palmer, Nicole M Probst-Hensch, Bruce M Psaty, Fernando Rivadeneira, Jerome I Rotter, Holger Schulz, Lewis J Smith, Akshay Sood, John M Starr, David P Strachan, Alexander Teumer, André G Uitterlinden, Henry Völzke, Arend Voorman, Louise V Wain, Martin T Wells, Jemma B Wilk, O Dale Williams, Susan R Heckbert, Bruno H Stricker, Stephanie J London, Myriam Fornage, Martin D Tobin, George T O'Connor, Ian P Hall, Patricia A Cassano

“…Publicly available microarray data confirmed differential expression of all three genes in lung samples from COPD patients compared with controls. …”
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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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A novel polypeptide encoded by circSPIRE1 promotes prostate cancer proliferation and migration by restraining the ubiquitin-dependent degradation of LRP5 by Jintao Hu, Juanyi Shi, Junjie Wang, Yunfei Xiao, Degeng Kong, Mingchao Gao, Tianlong Luo, Shizhong Xu, Zhihan Yuan, Xinyi Ma, Xueseng Dong, Jingang Huang, Cheng Liu, Kewei Xu

“…This study characterizes a novel circRNA-encoded protein, rtSPIRE1, and investigates its mechanistic role in prostate cancer proliferation and migration, as well as its diagnostic and therapeutic potential. Methods RNA microarray identified circSPIRE1 in prostate cancer tissues. …”
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Exploring the role of ferroptosis in pemphigus: identification of diagnostic markers and regulatory mechanisms by Jing Mao, Jianping Lan, Zheyu Zhuang, Ying Chen, Ying Chen, Yushan Ou, Xinhong Su, Xueting Zeng, Fuchen Huang, Zequn Tong, Xiaoqing Lv, Xiaoqing Lv, Xiaoqing Lv, Hui Ke, Zhenlan Wu, Ying Zou, Bo Cheng, Bo Cheng, Bo Cheng, Chao Ji, Chao Ji, Chao Ji, Ting Gong

“…Additionally, we processed the GSE53873 microarray dataset, which includes 19 pemphigus samples and 5 controls. …”
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circKCNQ5 promotes the proliferation of DNA-methyltransferase 3A R882 mutated acute myeloid leukemia cells by elevating high-mobility group box 1 expression by Yijian Chen, Xiaodan Zhu, Chuanming Lin, Rong Xu, Pengxiang Xu, Liuyan Xin, Lin Li, Liqun Zhang

“…Background Patients with acute myeloid leukemia (AML) harboring the DNA-methyltransferase 3 A (DNMT3A) R882 mutation (DR882MUT) usually have a high recurrence rate and poor prognosis. circKCNQ5 levels were aberrantly elevated in patients with AML according to the microarray platform. Therefore, the purpose of this study is to investigate the effect and mechanism of circKCNQ5 on DR882MUT AML cell proliferation.Methods A DR882MUT cell line model was established. circKCNQ5 expression in AML cells expressing wild-type DNMT3A (DNMT3A-WT) or DR882MUT was analyzed using RT-qPCR. …”
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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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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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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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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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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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