Cost-effective solutions for high-throughput enzymatic DNA methylation sequencing. by Amy Longtin, Marina M Watowich, Baptiste Sadoughi, Rachel M Petersen, Sarah F Brosnan, Kenneth Buetow, Qiuyin Cai, Cayo Biobank Research Unit, Michael D Gurven, James P Higham, Heather M Highland, Yi-Ting Huang, Hillard Kaplan, Thomas S Kraft, Yvonne A L Lim, Jirong Long, Amanda D Melin, Michael J Montague, Jamie Roberson, Kee Seong Ng, Michael L Platt, India A Schneider-Crease, Jonathan Stieglitz, Benjamin C Trumble, Vivek V Venkataraman, Ian J Wallace, Jie Wu, Noah Snyder-Mackler, Angela Jones, Alexander G Bick, Amanda J Lea

“…., assays that rely on microarrays, enzyme digests, or sequence capture to target a subset of the genome). …”
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Infiltration of CD3+ and CD8+ lymphocytes in association with inflammation and survival in pancreatic cancer. by Gerik W Tushoski-Alemán, Kelly M Herremans, Patrick W Underwood, Ashwin Akki, Andrea N Riner, Jose G Trevino, Song Han, Steven J Hughes

“…We aimed to quantitatively assess infiltrating CD3+ and CD8+ lymphocytes in a treatment-naïve patient cohort and assess associations with overall survival and microenvironment inflammatory proteins.<h4>Methods</h4>Tissue microarrays were immunohistochemically stained for CD3+ and CD8+ lymphocytes and quantitatively assessed using QuPath. …”
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Association of PD-1, LAG-3 and TIM-3 expression on intratumoral CD8 T-cells with response to atezolizumab in a Real-World-Evidence biomarker study for advanced urothelial carcinoma... by Carlos E. de Andrea, Marta Abengozar-Muela, José Ángel Arranz, Miguel Angel Climent, Javier Puente, Ángel Vizcay, Ligia Montero de la Fuente, José Miguel Jurado, Teresa Bonfill, Carmen Santander, José Carlos Villa, Eduardo Pujol, Adriana Carolina Rosero, Jenifer Gomez, Eva María Fernández, Carlos Álvarez Fernández, Ignacio Ramirez, Pablo Arnáiz, Álvaro López-Janeiro, Ignacio Melero, Miguel F. Sanmamed, José Luis Pérez-Gracia

“…We assessed with Multiplexed Quantitative Immunofluorescence the expression of CD8, PD-1, TIM-3 and LAG-3 on T-cells in the different compartments of the TME (tumor, stroma and whole tissue) in pre-treatment tissue microarrays. We studied associations between the expression of the markers and clinical efficacy. …”
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Quantifying intratumoral biomarker heterogeneity in tubo-ovarian high-grade serous carcinoma to optimize clinical translation by Aline Talhouk, Derek S. Chiu, Liliane Meunier, Kurosh Rahimi, Cécile Le Page, Monique Bernard, Diane Provencher, David G. Huntsman, Anne Marie Mes Masson, Martin Köbel

“…Markers were stained on tissue microarrays and scored using a continuous or categorical interpretation of staining patterns. …”
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Expression and prognostic significance of the m6A RNA methylation regulator HNRNPC in HNSCC by Yulin Zhang, Yixu Wang, Jilin Peng, Kun Zhao, Ling Li, Yuan Zhang, Ziyu Zhai, Sijie Yuan, Shichao Li, Shichao Li, Shichao Li, Fanglei Ye, Le Wang

“…Gene Expression Omnibus (GEO), normal and tumor tissue microarrays (TMA), and tumor tissue samples from patients with HNSCC were observed that a high level of HNRNPC expression was closely linked to a poor prognosis among patients. …”
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Transcriptome and Proteome Research in Veterinary Science: What Is Possible and What Questions Can Be Asked? by Robert Klopfleisch, Achim D. Gruber

“…This review gives an overview on the methods currently available for transcriptome analysis, that is, microarrays, Ref-Seq, quantitative PCR arrays and discusses their potentials and limitations. …”
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Increased secretory leukocyte protease inhibitor (SLPI) production by highly metastatic mouse breast cancer cells. by Kevin T Sayers, Alan D Brooks, Thomas J Sayers, Oleg Chertov

“…The precise molecular mechanisms enabling cancer cells to metastasize from the primary tumor to different tissue locations are still largely unknown. Secretion of some proteins by metastatic cells could facilitate metastasis formation. …”
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Spatially resolved proteomics surveys the chemo‐refractory proteins related to high‐grade serous ovarian cancer by Linyuan Fan, Yi Liu, Haichao Zhou, Yang Feng, Guangyi Jiang, Guixue Hou, Zhihan Cao, Zhiguo Zheng, Lu Sun, Hao Chen, Yuefei Zhang, Weiran Chen, Yun Xi, Benliang Cheng, Qinghai Yang, Yan Ren, Jianqing Zhu, Siqi Liu

“…Immunohistochemical validation of HGSC tissue microarrays confirmed the spatial proteomic localization of TFRC and PDLIM3, which are linked to tumour progression, while establishing their novel role as chemotherapy resistance biomarkers through this study, with broader predictive potential observed across additional targets in the discovery cohort. …”
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Effects of pregnancy on breast cancer immunology: immune biomarker and TIL quantification by Kristin Galas, Moritz Gleitsmann, Julia Rey, Christine Solbach, Isabell Witzel, Thomas Karn, Sabine Schmatloch, Christian Schem, Andreas Schneeweis, Bruno Sinn, Tanja Fehm, Carsten Denkert, Peter Fasching, Anne-Sophie Litmeyer, Frederik Marmé, Paul Jank, Volkmar Müller, Sabine Seiler, Elmar Stickeler, Olaf Ortmann, Marion van Mackelenbergh, Valentina Nekljudova, Johannes Holtschmidt, Sibylle Loibl

“…Further understanding of how pregnancy affects the tumor microenvironment (TME) is essential. We constructed Tissue Microarrays (TMA) of tumor specimens from 126 pregnant breast cancer (BC) patients and examined standard BC markers such as ER, PR, Ki67, HER2, tumor infiltrating lymphocytes (TILs), and immunomarkers HLA class I, HLA-G, PD-L1, TIGIT and Nectin-4. …”
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Graph of graphs analysis for multiplexed data with application to imaging mass cytometry. by Ya-Wei Eileen Lin, Tal Shnitzer, Ronen Talmon, Franz Villarroel-Espindola, Shruti Desai, Kurt Schalper, Yuval Kluger

“…Each slide is a spatial assay consisting of high-dimensional multivariate observations (m-dimensional feature space) collected at different spatial positions and capturing data from a single biological sample or even representative spots from multiple samples when using tissue microarrays. Often, each of these spatial assays could be characterized by several regions of interest (ROIs). …”
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Evaluation of the androgen receptor in patients with ERα-positive early breast cancer treated with adjuvant tamoxifen ± fluoxymesterone by James N. Ingle, Vera J. Suman, Malvika H. Solanki, Marie R. Passow, Jordan D. Campbell, Liewei Wang, Matthew P. Goetz

“…We sought to corroborate our preclinical findings that AR-agonists were efficacious in patients with ER-positive tumors that also expressed high levels of AR. Methods Tissue microarrays (TMAs) were prepared from primary tumor blocks from patients entered on a prospective randomized adjuvant trial of tamoxifen (Tam) alone or combined with fluoxymesterone (Flu), an AR-agonist, (NCCTG 89-30-52). …”
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Global gene expression analysis of murine limb development. by Leila Taher, Nicole M Collette, Deepa Murugesh, Evan Maxwell, Ivan Ovcharenko, Gabriela G Loots

“…We used whole-genome microarrays to identify genes with differential expression at 5 stages of limb development (E9.5 to 13.5), during fore- and hind-limb patterning. …”
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Adverse predictive value of ASPM on lung adenocarcinoma overall survival depended on chemotherapy status by Yan Zheng, Baichen Sun, Zhiling Qu

“…This study investigates the expression and prognostic value of ASPM, focusing on its role in chemotherapy outcomes.Methods We analyzed the prognostic relevance of ASPM using bioinformatics, immunohistochemical staining of LUAD tissue microarrays, and proteomics data. Further, in vitro experiments were conducted to evaluate the effects of ASPM overexpression on cell proliferation and sensitivity to cisplatin.Results Bioinformatics analysis revealed that ASPM’s prognostic significance differed between transcriptomic and proteomic datasets. …”
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Prognostic significance of cytotoxic-T-lymphocytes to immunosuppressive lymphocytes ratio (CIL) in laryngeal squamous cell carcinoma by Duo Zhang, Yu Heng, Qiu-yan Jin, Di Tang, Xiao-ke Zhu, Li-ming Lu, Chun-ping Wu, Lei Tao

“…Two cohorts were included in this study: The training cohort (N = 75) consisted of tumor tissue microarrays from LSCC patients in our department, and the validation cohort (N = 116) utilized bulk RNA-seq data from the TCGA database. …”
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A Transcriptomic Signature of Mouse Liver Progenitor Cells by Adam M. Passman, Jasmine Low, Roslyn London, Janina E. E. Tirnitz-Parker, Atsushi Miyajima, Minoru Tanaka, Helene Strick-Marchand, Gretchen J. Darlington, Megan Finch-Edmondson, Scott Ochsner, Cornelia Zhu, James Whelan, Bernard A. Callus, George C. T. Yeoh

“…A transcriptomic meta-analysis of over 400 microarrays was undertaken to compare LPC lines against datasets of muscle and embryonic stem cell lines, embryonic and developed liver (DL), and HCC. …”
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Prognostic value of B7-H3 expression in metastatic renal cell carcinoma and its impact on immunotherapy response by Faruk Recep Özalp, Kutsal Yörükoğlu, Eda Çalışkan Yıldırım, Mehmet Uzun, Hüseyin Salih Semiz

“…Methods Immunohistochemical analysis of B7-H3 expression was performed in 84 metastatic RCC patients. Tissue microarrays and separate sections of formalin-fixed paraffin-embedded tissue were used for immunohistochemical staining. …”
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Gene Expression Analysis and Validation of a Novel Biomarker Signature for Early-Stage Lung Adenocarcinoma by Sanjan S. Sarang, Catherine M. Cahill, Jack T. Rogers

“…This study aimed to identify a novel biomarker signature of early-stage LUAD utilizing gene expression analysis of human lung tissue samples. Using 22 pairs of LUAD and matched normal lung microarrays, 229 differentially expressed genes were identified. …”
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Expression profiling the temperature-dependent amphibian response to infection by Batrachochytrium dendrobatidis. by Laia Ribas, Ming-Shi Li, Benjamin J Doddington, Jacques Robert, Judith A Seidel, J Simon Kroll, Lyle B Zimmerman, Nicholas C Grassly, Trenton W J Garner, Matthew C Fisher

“…Using temporal expression-profiling by microarrays and qRT-PCR, we characterise this response in the main amphibian lymphoid tissue, the spleen. …”
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RPS21 Enhances hepatocellular carcinoma development through GPX4 stabilization by Siyuan Wu, Gaochao Wang, Likai Gu, Yinjie Zhang, Zhihuai Wang

“…Mutation analysis via the cBioPortal showed that primarily amplifications in RPS21 are associated with a poorer prognosis. Tissue microarrays confirmed higher RPS21 levels in tumor samples, which were associated with more advanced clinical stages and grades. …”
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Sarcomatoid areas of urothelial carcinoma are enriched for CD163‐positive antigen‐presenting cells by Burles A Johnson III, Vamsi Parimi, Sonia Kamanda, David C Corney, Woonyoung Choi, Jean Hoffman‐Censits, Max Kates, David J McConkey, Noah M Hahn, Andres Matoso

“…The objective of this study was to identify differences between the sarcomatoid and CUC tumor microenvironment components that may drive this aggressive phenotype. Using tissue microarrays from eight patient tumors with mixed CUC and SUC, we examined paired CUC, mixed urothelial carcinoma (UC) regions, and SUC using the Nanostring Digital Spatial Profiling platform. …”
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