Transcriptome Changes in Three Brain Regions during Chronic Lithium Administration in the Rat Models of Mania and Depression by Dawid Szczepankiewicz, Piotr Celichowski, Paweł A. Kołodziejski, Ewa Pruszyńska-Oszmałek, Maciej Sassek, Przemysław Zakowicz, Ewa Banach, Wojciech Langwiński, Kosma Sakrajda, Joanna Nowakowska, Magdalena Socha, Ewelina Bukowska-Olech, Joanna Pawlak, Joanna Twarowska-Hauser, Leszek Nogowski, Janusz K. Rybakowski, Aleksandra Szczepankiewicz

“…Gene expression profile was done using SurePrint G3 Rat Gene Expression whole transcriptome microarrays. Data were analyzed using Gene Spring 14.9 software. …”
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Identification of a Biomarker Combination for Survival Stratification in pStage II/III Gastric Cancer after Curative Resection by Itaru Hashimoto, Yayoi Kimura, Naohide Oue, Yukihiko Hiroshima, Toru Aoyama, Yasushi Rino, Tomoyuki Yokose, Wataru Yasui, Yohei Miyagi, Takashi Oshima

“…Further, immunohistochemistry (IHC) using tumor microarrays (TMAs) in another cohort of patients was performed to identify an optimal biomarker combination for survival stratification in GC patients. …”
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Tyrosine Phosphoproteomics of Patient-Derived Xenografts Reveals Ephrin Type-B Receptor 4 Tyrosine Kinase as a Therapeutic Target in Pancreatic Cancer by Santosh Renuse, Vijay S. Madamsetty, Dong-Gi Mun, Anil K. Madugundu, Smrita Singh, Savita Udainiya, Kiran K. Mangalaparthi, Min-Sik Kim, Ren Liu, S. Ram Kumar, Valery Krasnoperov, Mark Truty, Rondell P. Graham, Parkash S. Gill, Debabrata Mukhopadhyay, Akhilesh Pandey

“…Immunohistochemistry-based validation using tissue microarrays from 346 patients with PDAC showed significant expression of EphB4 in >70% of patients. …”
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DYRK2 downregulation in colorectal cancer leads to epithelial–mesenchymal transition induction and chemoresistance by Chunrong Wu, Guiyin Sun, Fan Wang, Jiangyan Chen, Fangbiao Zhan, Xiaojuan Lian, Jie Wang, Fanbin Weng, Bo Li, Weijun Tang, Jin Quan, Debing Xiang

“…Initial analyses of The Cancer Genome Atlas database and clinical tissue microarrays revealed significant DYRK2 downregulation in CRC in a manner correlated with poor prognosis. …”
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Concordance between Three PD-L1 Immunohistochemical Assays in Head and Neck Squamous Cell Carcinoma (HNSCC) in a Multicenter Study by Elena Guerini Rocco, Albino Eccher, Ilaria Girolami, Paolo Graziano, Gabriella Fontanini, Elena Vigliar, Giancarlo Troncone, Massimo Barberis, Patrizia Morbini, Maurizio Martini

“…Harmonization studies comparing the different antibodies and immunohistochemistry platforms available for the evaluation of PD-L1 expression with Combined Positive Score (CPS) in HNSCC are strongly required. Tissue microarrays (TMA) constructed from formalin-fixed, paraffin-embedded (FFPE) tissue blocks of HNSCC tumor were stained with two commercial in-vitro diagnostic (IVD) PD-L1 immunohistochemical assays (22C3 pharmDx on Autostainer Link48 and Omnis platforms, and SP263) and were reviewed by seven trained pathologists to assess CPS. …”
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CD229 (Ly9) a Novel Biomarker for B-Cell Malignancies and Multiple Myeloma by Giovanna Roncador, Joan Puñet-Ortiz, Lorena Maestre, Luis Gerardo Rodríguez-Lobato, Scherezade Jiménez, Ana Isabel Reyes-García, Álvaro García-González, Juan F. García, Miguel Ángel Piris, Santiago Montes-Moreno, Manuel Rodríguez-Justo, Mari-Pau Mena, Carlos Fernández de Larrea, Pablo Engel

“…In this study, we used a new mAb against the cytoplasmic region of CD229 to study the expression of CD229 on normal tissues and B-cell malignancies, including multiple myeloma (MM), using tissue microarrays. We showed CD229 to be restricted to hematopoietic cells. …”
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Characterization of Mutational Status, Spheroid Formation, and Drug Response of a New Genomically-Stable Human Ovarian Clear Cell Carcinoma Cell Line, 105C by Bart Kolendowski, Yudith Ramos Valdes, Hal Hirte, Hiroaki Itamochi, Wonjae Lee, Mark Carey, Trevor G. Shepherd, Gabriel E. DiMattia

“…We provide an extensive characterization of ‘105C’, a cell line generated from an adenocarcinoma of the clear cell histotype using targeted next-generation sequencing, cytogenetic microarrays, along with analyses of AKT/mTOR signaling. …”
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Proteasome-Mediated Regulation of GATA2 Expression and Androgen Receptor Transcription in Benign Prostate Epithelial Cells by Waqas Azeem, Jan Roger Olsen, Margrete Reime Hellem, Yaping Hua, Kristo Marvyin, Xisong Ke, Anne Margrete Øyan, Karl-Henning Kalland

“…Luminal differentiation markers were assessed by RT-qPCR, Western blot and global gene expression microarrays. We utilized our previously established AR and androgen-dependent fluorescence reporter assay to investigate AR activity at the single-cell level. …”
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Metal-Assisted Chemical Etching for Anisotropic Deep Trenching of GaN Array by Qi Wang, Kehong Zhou, Shuai Zhao, Wen Yang, Hongsheng Zhang, Wensheng Yan, Yi Huang, Guodong Yuan

“…In this paper, we demonstrate a damage-free, rapid metal-assisted chemical etching (MacEtch) method and perform an anisotropic, deep trenching of a GaN array. Regular GaN microarrays are fabricated based on the proposed method, in which CuSO₄ and HF are adopted as etchants while ultraviolet light and Ni/Ag mask are applied to catalyze the etching process of GaN, reaching an etching rate of 100 nm/min. …”
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Azithromycin treatment modifies airway and blood gene expression networks in neutrophilic COPD by Katherine J. Baines, Thomas K. Wright, Peter G. Gibson, Heather Powell, Philip M. Hansbro, Jodie L. Simpson

“…Gene expression was defined using microarrays. Networks were analysed using the Search Tool for the Retrieval of Interacting Gene database. …”
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Tumour Stroma Ratio Assessment Using Digital Image Analysis Predicts Survival in Triple Negative and Luminal Breast Cancer by Ewan KA Millar, Lois H. Browne, Julia Beretov, Kirsty Lee, Jodi Lynch, Alexander Swarbrick, Peter H. Graham

“…Automated image analysis using QuPath software was applied to a cohort of 647 breast cancer patients (403 luminal and 244 TNBC) using digital H&E images of tissue microarrays (TMAs). Kaplan–Meier and Cox proportional hazards were used to ascertain relationships with overall survival (OS) and breast cancer specific survival (BCSS). …”
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Single-Cell Genomics: Enabling the Functional Elucidation of Infectious Diseases in Multi-Cell Genomes by Shweta Sahni, Partha Chattopadhyay, Kriti Khare, Rajesh Pandey

“…Since the time when detection of gene expression in single cells by microarrays to the Next Generation Sequencing (NGS) enabled Single Cell Genomics (SCG), it has played a pivotal role to understand and elucidate the functional role of cellular heterogeneity. …”
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Increased Expression and Altered Cellular Localization of Fibroblast Growth Factor Receptor-Like 1 (FGFRL1) Are Associated with Prostate Cancer Progression by Lan Yu, Mervi Toriseva, Syeda Afshan, Mario Cangiano, Vidal Fey, Andrew Erickson, Heikki Seikkula, Kalle Alanen, Pekka Taimen, Otto Ettala, Martti Nurmi, Peter J. Boström, Markku Kallajoki, Johanna Tuomela, Tuomas Mirtti, Inès J. Beumer, Matthias Nees, Pirkko Härkönen

“…FGFRL1 expression was studied by qRT-PCR and immunohistochemistry of patient tissue microarrays (TMAs) and correlated with clinical patient data. …”
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Clinicopathological characteristics, molecular landscape, and biomarker landscape for predicting the efficacy of PD-1/PD-L1 inhibitors in Chinese population with mismatch repair de... by Yu-Ting Ma, Yu-Ting Ma, Fang Hua, Xiu-Ming Zhong, Ying-Jie Xue, Jia Li, Yi-Cong Nie, Xue-Dong Zhang, Ji-Wei Ma, Cun-Hu Lin, Hao-Zhuang Zhang, Wei He, Dan Sha, Miao-Qing Zhao, Zhi-Gang Yao, Zhi-Gang Yao

“…We analyzed 374 patients with bladder urothelial carcinoma (BUC) and 232 patients with upper tract urothelial carcinoma (UTUC) using tissue microarrays, immunohistochemistry, and targeted next-generation sequencing. …”
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CSPG4 Expression in GIST Is Associated with Better Prognosis and Strong Cytotoxic Immune Response by Alexandre de Nonneville, Pascal Finetti, Maelle Picard, Audrey Monneur, Maria Abbondanza Pantaleo, Annalisa Astolfi, Jerzy Ostrowski, Daniel Birnbaum, Emilie Mamessier, François Bertucci

“…We analyzed CSPG4 mRNA expression data of 309 clinical GIST samples profiled using DNA microarrays and searched for correlations with clinicopathological and immune features. …”
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Germline PRKACA amplification-associated primary pigmented nodular adrenocortical disease: a case report and literature review by Wang-Rong Yang, Xing-Huan Liang, Ying-Fen Qin, Hai-Yan Yang, Shu-Zhan He, Zhen-Xing Huang, Yu-Ping Liu, Zuo-Jie Luo

“…PPNAD was pathologically diagnosed after unilateral adrenalectomy. Chromosome microarrays and whole exon sequencing analyses of the peripheral blood, as well as testing of sectioned adrenal tissue, showed a rise in the copy number of the duplication-containing PRKACA gene on chromosome 19p13.13p13.12, a de novo but not heritable gene defect that causes disease. …”
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Bioinformatics gene analysis of potential biomarkers and therapeutic targets of osteoarthritis associated myelodysplastic syndrome by Peicheng Xin, Ming Li, Jing Dong, Hongbo Zhu, Jie Li

“…Objective: Osteoarthritis (OA) and Myelodysplastic syndrome (MDS) are diseases caused by the same immune disorder with unclear etiology and many similarities in clinical manifestations; however, the specific mechanisms between osteoarthritis and myelodysplastic syndrome are unclear.Methods: The expression profile microarrays of osteoarthritis and myelodysplastic syndrome were searched in the GEO database, the intersection of their differential genes was taken, Venn diagrams were constructed to find common pathogenic genes, bioinformatics analysis signaling pathway analysis was performed on the obtained genes, and protein-protein interaction networks were constructed to find hub genes in order to establish diagnostic models for each disease and explore the immune infiltration of hub genes.Results: 52 co-pathogenic genes were screened for association with immune regulation, immune response, and inflammation. …”
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BCL11A Expression in Non-Small Cell Lung Cancers by Ewa Kątnik, Agnieszka Gomułkiewicz, Aleksandra Piotrowska, Jędrzej Grzegrzółka, Alicja Kmiecik, Katarzyna Ratajczak-Wielgomas, Anna Urbaniak, Natalia Glatzel-Plucińska, Piotr Błasiak, Piotr Dzięgiel

“…The localization and the level of BCL11A protein were examined using immunohistochemistry (IHC) on 259 cases of NSCLC, and 116 NMLT samples were prepared as tissue microarrays and using immunofluorescence (IF) in the following cell lines: NCI-H1703, A549 and IMR-90. …”
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The Stem Cell Expression Profile of Odontogenic Tumors and Cysts: A Systematic Review and Meta-Analysis by Eleni-Marina Kalogirou, Georgios Lekakis, Aristodimos Petroulias, Konstantinos Chavdoulas, Vasileios L. Zogopoulos, Ioannis Michalopoulos, Konstantinos I. Tosios

“…Results: 29 studies reported the expression of stem cell markers, e.g., SOX2, OCT4, NANOG, CD44, ALDH1, BMI1, and CD105, in various odontogenic lesions, through immunohistochemistry/immunofluorescence, polymerase chain reaction, flow cytometry, microarrays, and RNA-sequencing. Low, moderate, and high RoBs were observed in seven, nine, and thirteen studies, respectively. …”
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AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes by Young-Ji Na, Yonglae Cho, Ju Han Kim

“…The AnsNGS also connects those genes harbouring variants and the corresponding expression probes for downstream analysis using expression microarrays. Here, we demonstrate its ability to identify disease-related variants in the human genome.ConclusionsThe AnsNGS can give a key insight into which of these variants is already known to be involved in a disease-related phenotype or located in or near a known regulatory site. …”
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