Recruitment of regulatory T cells is correlated with hypoxia-induced CXCR4 expression, and is associated with poor prognosis in basal-like breast cancers by Yan, M, Jene, N, Byrne, D, Millar, E, O'Toole, SA, McNeil, C, Bates, G, Harris, A, Banham, A, Sutherland, R, Fox, S

“…We hypothesised that immune suppression in this subtype may be due to T regulatory cells (Treg) recruitment driven by hypoxia-induced up-regulation of CXCR4 in Treg.Methods: Immunoperoxidase staining for FOXP3 and CXCL12 was performed on tissue microarrays from 491 breast cancers. The hypoxia-associated marker carbonic anhydrase IX (CA9) and double FOXP3/CXCR4 staining were performed on sections from a subset of these cancers including 10 basal-like and 11 luminal cancers matched for tumour grade.Results: High Treg infiltration correlated with tumour CXCL12 positivity (OR 1.89, 95% CI 1.22 to 2.94, P = 0.004) and basal phenotype (OR 3.14, 95% CI 1.08 to 9.17, P = 0.004) in univariate and multivariate analyses. …”

Inflammatory and myeloid-associated gene expression before and one day after infant vaccination with MVA85A correlates with induction of a T cell response by Matsumiya, M, Harris, SA, Satti, I, Stockdale, L, Tanner, R, O'Shea, M, Tameris, M, Mahomed, H, Hatherill, M, Scriba, T, Hanekom, W, McShane, H, Fletcher, H

“…Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis.Results: One day post-MVA85A, there is an induction of inflammatory pathways compared to placebo samples. …”

Inflammatory and myeloid-associated gene expression before and one day after infant vaccination with MVA85A correlates with induction of a T cell response. by Matsumiya, M, Harris, SA, Satti, I, Stockdale, L, Tanner, R, O'Shea, M, Tameris, M, Mahomed, H, Hatherill, M, Scriba, T, Hanekom, W, Mcshane, H, Fletcher, H

“…Gene expression analysis was performed at all three timepoints to identify early gene signatures predictive of the magnitude of the subsequent adaptive T cell response using the significance analysis of microarrays (SAM) statistical package and gene set enrichment analysis. …”

The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients. by Kelleher, M, Fruhwirth, G, Patel, G, Ofo, E, Festy, F, Barber, P, Ameer-Beg, S, Vojnovic, B, Gillett, C, Coolen, A, Kéri, G, Ellis, P, Ng, T

“…Analysis of protein expression and post-translational modifications such as phosphorylation and ubiquitination can be performed in cell lines and are remarkably efficiently in cancer tissue samples using tissue microarrays (TMAs). FRET assays can be performed to quantify protein-protein interactions within FFPE tissue, far beyond the spatial resolution conventionally associated with light or confocal laser microscopy. …”

Why some tumours trigger neovascularisation and others don’t: the story thus far by Adighibe, O, Leek, R, Fernandez-Mercado, M, Hu, J, Snell, C, Gatter, K, Harris, A, Pezzella, F

“…Methods Immunohistochemical staining for 35 angiogenesis- and hypoxia-related biomarkers were performed on a collection of 194 angiogenic and 73 non-angiogenic NSCLCs arranged on tissue microarrays. Sequencing of P53 was performed with frozen tissue samples of NSCLC. …”

Prognostic impact of CD34 and SMA in cancer‐associated fibroblasts in stage I–III NSCLC by Arik Bernard Schulze, Lars Henning Schmidt, Birthe Heitkötter, Sebastian Huss, Michael Mohr, Alessandro Marra, Ludger Hillejan, Dennis Görlich, Peter J. Barth, Jan Rehkämper, Georg Evers

“…All tissue samples were embedded on tissue microarrays (TMAs). Results Our analysis revealed an association for CD34+ CAFs with G1/2 tumors and adenocarcinoma histology. …”
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A gene signature can predict risk of MGUS progressing to multiple myeloma by Fumou Sun, Yan Cheng, Jun Ying, David Mery, Samer Al Hadidi, Visanu Wanchai, Eric R. Siegel, Hongwei Xu, Dongzheng Gai, Timothy Cody Ashby, Clyde Bailey, Jin-Ran Chen, Carolina Schinke, Sharmilan Thanendrarajan, Maurizio Zangari, Siegfried Janz, Bart Barlogie, Frits Van Rhee, Guido Tricot, John D. Shaughnessy, Fenghuang Zhan

“…We have explored the use of gene expression profiling to risk-stratify MGUS and developed an optimized signature based on large samples with long-term follow-up. Microarrays of plasma cell mRNA from 334 MGUS with stable disease and 40 MGUS that progressed to MM within 10 years, was used to define a molecular signature of MGUS risk. …”
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Multimodal Lung Cancer Subtyping Using Deep Learning Neural Networks on Whole Slide Tissue Images and MALDI MSI by Charlotte Janßen, Tobias Boskamp, Jean Le’Clerc Arrastia, Daniel Otero Baguer, Lena Hauberg-Lotte, Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuß, Rita Casadonte, Jörg Kriegsmann, Peter Maaß

“…We trained the algorithm on six tissue microarrays (TMAs) with tumor samples from N = 232 patients and used 14 additional whole sections for validation and model selection. …”
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A Role for H₂O₂ and TRPM2 in the Induction of Cell Death: Studies in KGN Cells by Carsten Theo Hack, Theresa Buck, Konstantin Bagnjuk, Katja Eubler, Lars Kunz, Doris Mayr, Artur Mayerhofer

“…We studied expression and functionality of TRPM2 in KGN cells and examined GCT tissue microarrays (TMAs) to explore in vivo relevance. We employed live cell, calcium and mitochondrial imaging, viability assays, fluorescence activated cell sorting (FACS) analysis, Western blotting and immunohistochemistry. …”
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Resistance and aerobic training increases genome-wide DNA methylation in women with polycystic ovary syndrome by Cristiana Libardi Miranda Furtado, Megan Hansen, Gislaine Satyko Kogure, Victor Barbosa Ribeiro, Nathanael Taylor, Murilo Racy Soares, Rui Alberto Ferriani, Kenneth Ivan Aston, Timothy Jenkins, Rosana Maria dos Reis

“…Genome-wide leukocyte DNA methylation was analysed by Infinium Human MethylationEPIC 850K BeadChip microarrays (Illumina). Both resistance and aerobic exercise improved anthropometric indices, metabolic dysfunction, and hyperandrogenism in PCOS after the training programme, but no differences were observed between the two exercises. …”
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Quality Verification with a Cluster−Controlled Manufacturing System to Generate Monocyte−Derived Dendritic Cells by Haruhiko Kawaguchi, Takuya Sakamoto, Terutsugu Koya, Misa Togi, Ippei Date, Asuka Watanabe, Kenichi Yoshida, Tomohisa Kato, Yuka Nakamura, Yasuhito Ishigaki, Shigetaka Shimodaira

“…Additionally, cc−IL-4−DCs produced higher levels of IFN−γ, possessing the CTL induction. Furthermore, DNA microarrays revealed the upregulation of BCL2A1, a pro−survival gene. …”
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Integrating transcriptomics and machine learning for immunotherapy assessment in colorectal cancer by Jun Xiang, Shihao Liu, Zewen Chang, Jin Li, Yunxiao Liu, Hufei Wang, Hao Zhang, Chunlin Wang, Lei Yu, Qingchao Tang, Guiyu Wang

“…To elucidate variations in prognosis, clinical features, genomic alterations, and responses to immunotherapy in CRC, we employed a non-negative matrix factorization algorithm to categorize 2595 CRC samples of 27 microarrays from the Gene Expression Omnibus database. …”
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Frequent copy number variants in a cohort of Mexican-Mestizo individuals by Silvia Sánchez, Ulises Juárez, Julieta Domínguez, Bertha Molina, Rehotbevely Barrientos, Angélica Martínez-Hernández, Alessandra Carnevale, Patricia Grether-González, Dora Gilda Mayen, Camilo Villarroel, Esther Lieberman, Emiy Yokoyama, Victoria Del Castillo, Leda Torres, Sara Frias

“…CNVs are detected by microarrays of different densities and are generally visualized, and their frequencies analysed using the HapMap as default reference population. …”
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Differential Kinase Activation in Peripheral Blood Mononuclear Cells from Non-Small-Cell Lung Cancer Patients Treated with Nivolumab by Gaëlle Noé, Audrey Bellesoeur, Lisa Golmard, Audrey Thomas-Schoemann, Pascaline Boudou-Rouquette, Manuela Tiako Meyo, Alicja Puszkiel, Jennifer Arrondeau, Jérome Alexandre, François Goldwasser, Benoit Blanchet, Michel Vidal

“…PamChip^® microarrays were used to explore the STK kinomic profile in PBMC from 28 NSCLC patients before nivolumab initiation (D0) and on day 14 (D14) of the first administration. …”
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Tumor Infiltration by OX40+ Cells Enhances the Prognostic Significance of CD16+ Cell Infiltration in Colorectal Cancer by Fabian Haak, Isabelle Obrecht, Nadia Tosti, Benjamin Weixler MD, Robert Mechera MD, Silvio Däster MD, Marco von Strauss MD, Tarik Delko MD, Giulio C. Spagnoli, Luigi Terracciano MD, Giuseppe Sconocchia, Markus von Flüe MD, Marko Kraljević MD, Raoul A. Droeser MD

“…Methods: Colorectal cancer infiltration by OX40 and CD16 expressing cells was investigated in 441 primary CRCs using tissue microarrays and specific antibodies, by immunohistochemistry. …”
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Loss of CDKN1A mRNA and Protein Expression Are Independent Predictors of Poor Outcome in Chromophobe Renal Cell Carcinoma Patients by Riuko Ohashi, Silvia Angori, Aashil A. Batavia, Niels J. Rupp, Yoichi Ajioka, Peter Schraml, Holger Moch

“…Genome-wide DNA copy-number alterations were analyzed by Affymetrix OncoScan^® CNV FFPE Microarrays in a second cohort of Swiss chRCC. In both cohorts, tumors with loss of chromosomes 2, 6, 10, 13, 17 and 21 had signs of tumor progression. …”
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Alterations of Fucosyltransferase Genes and Fucosylated Glycans in Gastric Epithelial Cells Infected with <i>Helicobacter pylori</i> by Ruyue Fan, Xiurui Han, Yanan Gong, Lihua He, Zhijing Xue, Yaming Yang, Lu Sun, Dongjie Fan, Yuanhai You, Fanliang Meng, Xiaomei Yan, Maojun Zhang, Jianzhong Zhang

“…In this study we used lectin microarrays to detect the expression of fucosylated glycans in gastric epithelial cells (GES-1) infected with <i>H. pylori</i> strains isolated from patients with different diseases including chronic gastritis, duodenal ulcers, and gastric cancer (each containing two strains) at 4 h. …”
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High expression of fibroblast‐activating protein is a prognostic marker in non‐small cell lung carcinoma by Naoki Yanagawa, Mayu Sugai, Shunsuke Shikanai, Ryo Sugimoto, Mitsumasa Osakabe, Noriyuki Uesugi, Hajime Saito, Makoto Maemondo, Tamotsu Sugai

“…Methods In total, 344 NSCLC tissues were examined. Tissue microarrays were constructed, and FAP expression was analyzed using immunohistochemistry. …”
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Immunohistochemical Expression of Vitamin D Receptor in Uterine Fibroids by Anna Markowska, Paweł Kurzawa, Wiesława Bednarek, Anna Gryboś, Marcin Mardas, Monika Krzyżaniak, Jan Majewski, Janina Markowska, Marian Gryboś, Jakub Żurawski

“…Our VDR expression studies were performed immunohistochemically with tissue microarrays (TMA) in three tissue groups: 98 uterine myoma tissues, 98 uterine tissues (tumor margin), and 12 tissues of normal uterine muscle (i.e., without fibroids). …”
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Loss of MMP-27 Predicts Mandibular Bone Invasion in Oral Squamous Cell Carcinoma by Jonas Eichberger, Florian Weber, Gerrit Spanier, Michael Gerken, Stephan Schreml, Daniela Schulz, Mathias Fiedler, Nils Ludwig, Richard Josef Bauer, Torsten Eugen Reichert, Tobias Ettl

“…Afterwards, the protein expression of bone-metabolizing MMP-27, TNFRSF11B (Osteoprotegerin, OPG), and TNFSF11 (RANKL) was investigated via Tissue Microarrays (TMAs) for their impact on mandibular bone invasion. …”
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