Ultrasound May Suppress Tumor Growth, Inhibit Inflammation, and Establish Tolerogenesis by Remodeling Innatome via Pathways of ROS, Immune Checkpoints, Cytokines, and Trained Immun... by Qian Yang, Ruijing Zhang, Peng Tang, Yu Sun, Candice Johnson, Jason Saredy, Susu Wu, Jiwei Wang, Yifan Lu, Fatma Saaoud, Ying Shao, Charles Drummer, Keman Xu, Daohai Yu, Rongshan Li, Shuping Ge, Xiaohua Jiang, Hong Wang, Xiaofeng Yang

“…We used microarray datasets from the NCBI GEO DataSet repository and conducted comprehensive data-mining analyses, where we examined the gene expression of 1376 innate immune regulators (innatome genes (IGs) in cells treated with LIUS. …”
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MicroRNAs Expression Profile in MN1-Altered Astroblastoma by Francesca Gianno, Evelina Miele, Claudia Sabato, Elisabetta Ferretti, Simone Minasi, Francesca Romana Buttarelli, Debora Salerno, Natalia Pediconi, Giuseppe Rubens Pascucci, Francesca Guerrieri, Andrea Ciolfi, Simone Pizzi, Maura Massimino, Veronica Biassoni, Elisabetta Schiavello, Marco Gessi, Sofia Asioli, Angela Mastronuzzi, Antonio d’Amati, Giuseppina Catanzaro, Elisabetta Viscardi, David Capper, Felice Giangaspero, Manila Antonelli

“…MicroRNAs (miRNAs) are important gene expression regulators with strong implications in biological processes. …”
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Construction of a circadian rhythm-related gene signature for predicting the prognosis and immune infiltration of breast cancer by Lin Ni, Lin Ni, He Li, Yanqi Cui, Wanqiu Xiong, Shuming Chen, Hancong Huang, Zhiwei Wang, Hu Zhao, Hu Zhao, Hu Zhao, Bing Wang, Bing Wang, Bing Wang

“…ObjectivesIn this study, we constructed a model based on circadian rhythm associated genes (CRRGs) to predict prognosis and immune infiltration in patients with breast cancer (BC).Materials and methodsBy using TCGA and CGDB databases, we conducted a comprehensive analysis of circadian rhythm gene expression and clinicopathological data. Three different machine learning algorithms were used to screen out the characteristic circadian genes associated with BC prognosis. …”
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Neoadjuvant atezolizumab + chemotherapy for resectable NSCLC: 3-year clinical update of phase II clinical trial results and translational findings by Benjamin Izar, Justin F Gainor, Mark M Awad, Codruta Chiuzan, Anjali Saqi, Catherine A Shu, Katja Schulze, Brian S Henick, Naiyer A Rizvi, Samyukta Mallick, Yohanna Georgis, Peter D Koch, Stephanie Izard, Robert F Garofano, Cheryl V Wong, Jessica Grindheim, Joshua R Sonett, Alison M Taylor

“…Major pathological response (MPR, primary endpoint) was previously reported; here, we report 3-year disease-free survival (DFS), OS, and clinical characteristics of patients developing brain metastases (BM) with integrated data from tumor genomics, gene expression, and quantitative immunofluorescent measurement of immune markers.Results Of 30 enrolled patients, 29 were taken to the operating room. 26 underwent R0 resection, with 17 experiencing MPR (10 pCR). …”
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PCSK9-antibodies fail to block PCSK9-induced inflammation in macrophages and cannot recapitulate protective effects of PCSK9-deficiency in experimental myocardial infarction by Simon Rauterberg, Simon Rauterberg, Carmen Härdtner, Jennifer Hein, Paola Schrepf, Remi Peyronnet, Christoph Koentges, Tamara A. Vico, Carolin Ehlert, Bianca Dufner, Diana Lindner, Constantin von zur Mühlen, Dennis Wolf, Dirk Westermann, Ingo Hilgendorf, Alexander von Ehr

“…Cardiac function was assessed via echocardiography and isolated working heart model experiments. Gene expression changes were evaluated using RNA sequencing, and inflammatory responses in bone marrow-derived macrophages (BMDMs) were analyzed in vitro.ResultsPCSK9 was expressed in murine heart tissue at levels comparable to the liver, despite minimal heart RNA expression. …”
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Downregulation of MerTK in circulating T cells of patients with non-proliferative diabetic retinopathy by Shimiao Bu, Shimiao Bu, Jiang-Yue Ling, Jiang-Yue Ling, Xiaojun Wu, Xiaojun Wu, Liting Zhang, Liting Zhang, Xiangyu Shi, Lang Huang, Zheng Zhao, Ying Yang, Zongqin Xiang, Yong U. Liu, Yong U. Liu, Yufeng Liu, Yuehong Zhang, Yuehong Zhang

“…ObjectiveTo explore the differential gene expression in peripheral blood immune cells of individuals with type 2 diabetes mellitus (DM), comparing those with and without non-proliferative diabetic retinopathy (NPDR).MethodsFrom a pool of 126 potential participants, 60 were selected for detailed analysis. …”
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Assessing the effects of a mixed Eimeria spp. challenge on performance, intestinal integrity, and the gut microbiome of broiler chickens by Danielle Graham, Victor M. Petrone-Garcia, Xochitl Hernandez-Velasco, Makenly E. Coles, Marco A. Juarez-Estrada, Juan D. Latorre, Jianmin Chai, Stephanie Shouse, Jiangchao Zhao, Aaron J. Forga, Roberto Senas-Cuesta, Lauren Laverty, Kristen Martin, Carolina Trujillo-Peralta, Ileana Loeza, Latasha S. Gray, Billy M. Hargis, Guillermo Tellez-Isaias

“…Additionally, at d24, FITC-d was used as a biomarker to evaluate intestinal permeability and ileal tissue sections were collected for histopathology and gene expression of tight junction proteins. Ileal and cecal contents were also collected to assess the impact of challenge on the microbiome. …”
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Invited review: Improved control of Johne's disease in dairy cattle through advancements in diagnostics, testing, and management of young stock by Larissa Martins, Karin Orsel, Razieh Eshraghisamani, Jose Miguel Hernández-Agudelo, A. Caroline Pereira, Waseem Shaukat, Ad P. Koets, John P. Bannantine, Caroline Ritter, David F. Kelton, Richard J. Whittington, Maarten F. Weber, Antonio Facciuolo, Navneet K. Dhand, Karsten Donat, Susanne Eisenberg, Miguel A. Salgado, John P. Kastelic, Jeroen De Buck, Herman W. Barkema

“…New diagnostics have been developed, including phage-based tests to detect viable MAP, as well as gene expression patterns and metabolomics to detect MAP-infected young stock. …”
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CD38 deficiency leads to a defective short-lived transcriptomic response to chronic graft-versus-host disease induction, involving purinergic signaling-related genes and distinct t... by Mercedes Zubiaur, Laura C. Terrón-Camero, Fernando Gordillo-González, Eduardo Andrés-León, Alicia Barroso-del Jesús, Luz María Canet-Antequera, María M. Pérez Sánchez-Cañete, África Martínez-Blanco, Marilú Domínguez-Pantoja, María Botia-Sánchez, Sonia Pérez-Cabrera, Nerea Bello-Iglesias, Antonio Alcina, Ana-Clara Abadía-Molina, Fuencisla Matesanz, Esther Zumaquero, Ramón Merino, Jaime Sancho

“…A second purinergic receptor transcriptomic profile, which included P2rx7 and P2rx4, showed a coordinated gene expression of the components of the NLRP3 inflammasome with its potential activators. …”
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An exploratory study of INPP4B, a biomarker of gemcitabine chemoresistance in pancreatic cancer by REN Jiaqiang, WU Shuai, SU Tong, LI Jie, HAN Liang, WU Zheng

“…Second-generation high-throughput RNA-seq sequencing was conducted on these resistant cells, and bioinformatics analysis was employed to identify four pancreatic cancer genes from the Gene Expression Omnibus (GEO) datasets (GSE106336, GSE110580, GSE35141, and GSE140077). …”
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ERRα promotes glycolytic metabolism and targets the NLRP3/caspase-1/GSDMD pathway to regulate pyroptosis in endometrial cancer by Pingping Su, Xiaodan Mao, Jincheng Ma, Lixiang Huang, Lirui Yu, Shuting Tang, Mingzhi Zhuang, Zhonglei Lu, Kelvin Stefan Osafo, Yuan Ren, Xinrui Wang, Xite Lin, Leyi Huang, Xiaoli Huang, Elena Ioana Braicu, Jalid Sehouli, Pengming Sun

“…In addition, the expression of ERRα-related pyroptosis genes was analyzed using The Cancer Genome Atlas and Gene Expression Omnibus database. Results Triggered by a hypoxic microenvironment, highly expressed ERRα could bind to the promoter of NLRP3 and inhibit caspase-1/GSDMD signaling, which reduced inflammasome activation and increased pyroptosis resistance, thereby resulting in the resistance of cancer cells to cisplatin. …”
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Analysis of Genetic Variation in CD40 and CD40L: Relationship with mRNA Relative Expression and Soluble Proteins in Acute Coronary Syndrome by D. E. Martínez-Fernández, J. R. Padilla-Gutiérrez, F. Casillas-Muñoz, Emmanuel Valdés-Alvarado, Brenda Parra-Reyna, Maricela Aceves-Ramírez, J. F. Muñoz-Valle, U. Zalapa Flores, J. C. Chávez Herrera, Y. Valle

“…CD40 and CD40L expressions at the mRNA level were quantified using TaqMan Gene Expression Assays. Soluble protein isoforms were measured by enzyme-linked immunosorbent assay. …”
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Soluble and cell-based markers of immune checkpoint inhibitor-associated nephritis by Sandra M Herrmann, Riley Fadden, Ryan J Sullivan, Kerry L Reynolds, Harish Seethapathy, Meghan E Sise, Shruti Gupta, Alexandra-Chloe Villani, Qiyu Wang, Daiana Moreno, Destiny Harden, R Neal Smith, Ivy A Rosales, Robert B Colvin, Sarah Chute, Lynn D Cornell, Nancy J Yang, Sara Barmettler, Sophia Wells, Jocelyn Farmer

“…By peripheral blood flow cytometry analysis, lower absolute CD8+T cells, CD45RA+CD8+ T cells, memory CD27+B cells, and expansion of plasmablasts were prominent features of ICI-nephritis compared with ICI-treated controls. Gene expressions for IL2RA, IL-2 signaling, and T cell receptor signaling in the kidney tissue with ICI-nephritis were significantly higher compared with controls.Conclusion Elevated sIL-2R level and flow cytometric markers of both B and T cell dysregulation may aid the diagnosis of ICI-nephritis.…”
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Transcriptomic Profiling and Tumor Microenvironment Classification Reveal Unique and Dynamic Immune Biology in HIV-Associated Kaposi Sarcoma by Jihua Yang, Ayse Ece Cali Daylan, Aleksei Shevkoplias, Ekaterina Postovalova, Meng Wang, Andrey Tyshevich, Matthew Lee, Hiba Narvel, Ksenia Zornikova, Nara Shin, Nikita Kotlov, Luca Paoluzzi, Changcheng Zhu, Balazs Halmos, Xingxing Zang, Haiying Cheng

“…Notably, HIV-negative KS samples showed alterations in NK cell-mediated immunity and cytotoxic response pathways, whereas HIV-positive samples exhibited changes in growth regulation and protein kinase activity pathways at the time of initial diagnosis. The gene expression of immune checkpoints, including CD274 (PD-L1) and PDCD1LC2 (PD-L2), was comparable between HIV-positive and HIV-negative KS samples at diagnosis. …”
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Intestinal butyric acid-mediated disruption of gut hormone secretion and lipid metabolism in vasopressin receptor-deficient mice by Kazuki Harada, Eiji Wada, Yuri Osuga, Kie Shimizu, Reiko Uenoyama, Masami Yokota Hirai, Fumihiko Maekawa, Masao Miyazaki, Yukiko K. Hayashi, Kazuaki Nakamura, Takashi Tsuboi

“…Additionally, human Paneth cell-related gene expressions negatively correlated with that of V1 receptor genes. …”
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Astaxanthin mitigates doxorubicin-induced cardiotoxicity via inhibiting ferroptosis and autophagy: a study based on bioinformatic analysis and in vivo/vitro experiments by Bowen Yin, Jingyi Ren, Xuanyi Liu, Yadong Zhang, Jinshi Zuo, Rui Wen, Huanting Pei, Miaomiao Lu, Siqi Zhu, Zhenao Zhang, Ziyi Wang, Yanyi Zhai, Yuxia Ma

“…This has substantial practical significance for the clinical application of DOX.MethodsBioinformatic analyses were conducted using transcriptomic data from the gene expression omnibus (GEO) database to identify key mechanisms underlying DIC. …”
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Transcriptomic profiles of monocyte-derived macrophages exposed to SARS-CoV-2 VOCs reveal immune-evasion escape driven by delta by Alessia Gallo, Josè Camilla Sammartino, Roberta Vazzana, Roberto Giambruno, Claudia Carcione, Nicola Cuscino, Salvatore Castelbuono, Vitale Miceli, Matteo Bulati, Daniele Lilleri, Irene Cassaniti, Pier Giulio Conaldi, Fausto Baldanti

“…Methods We analysed the gene expression profiles of monocyte-derived macrophages (MDM) isolated from whole blood of healthy participants exposed to the 5 different SARS-CoV-2 VOC: D614G, Alpha (B.1.1.7), Gamma (P1), Delta (B.1.617.2), and Omicron BA.1 (B.1.1.529), and to the HCoV-OC43 strain, a coronavirus already present in the population before the SARS-CoV-2 pandemic. …”
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An anoikis-related signature predicts prognosis and immunotherapy response in gastrointestinal cancers by Ruyi Liu, Ruyi Liu, Ruyi Liu, Ruyi Liu, Ruyi Liu, Yuchen Liu, Yuchen Liu, Yuchen Liu, Yuchen Liu, Yuchen Liu, Weicheng Huang, Weicheng Huang, Weicheng Huang, Weicheng Huang, Weicheng Huang, Pengxiang Chen, Pengxiang Chen, Pengxiang Chen, Pengxiang Chen, Pengxiang Chen, Yufeng Cheng, Yufeng Cheng, Yufeng Cheng, Yufeng Cheng, Yufeng Cheng

“…We aimed to explore the roles of anoikis-related genes (ARGs) in the GI cancer prognosis.MethodsWe extracted RNA sequencing and clinical data from The Cancer Genome Atlas and Gene Expression Omnibu databases for patients with esophageal cancer, gastric cancer, colon cancer and rectal cancer and identified ARGs from GeneCards and Harmonizome. …”
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Cloning, Characterization and Expression Regulation in Response to High-Temperature Stress of TRAF7 Gene in the Sea Cucumber Apostichopus japonicus by Yanfeng ZHAO, Meijie LIAO, Jianlong GE, Jinjin WANG, Yingeng WANG, Xiaojun RONG, Bin LI, Yanting TAN

“…Its structural features and distribution in the genome were analyzed, and gene expression was examined in different tissues and under high-temperature stress. …”
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Comparative evaluation of ACetic - MEthanol high salt dissociation approach for single-cell transcriptomics of frozen human tissues by Marina Utkina, Anastasia Shcherbakova, Ruslan Deviatiiarov, Ruslan Deviatiiarov, Ruslan Deviatiiarov, Alina Ryabova, Marina Loguinova, Valentin Trofimov, Anna Kuznetsova, Mikhail Petropavlovskiy, Rustam Salimkhanov, Denis Maksimov, Eugene Albert, Alexandra Golubeva, Walaa Asaad, Lilia Urusova, Ekaterina Bondarenko, Anastasia Lapshina, Alexandra Shutova, Dmitry Beltsevich, Oleg Gusev, Oleg Gusev, Oleg Gusev, Oleg Gusev, Larisa Dzeranova, Galina Melnichenko, Ildar Minniakhmetov, Ivan Dedov, Natalya Mokrysheva, Sergey Popov

“…We compared the ability of enzymatic, ACME HS, and nuclei isolation methods to preserve major cell types, gene expression, and standard quality parameters across 41 tissue samples. …”
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