METTL1-mediated m7G tRNA modification drives papillary thyroid cancer progression and metastasis by regulating the codon-specific translation of TNF-α by Weiwei Li, Ruiwang Xie, Huaying Chen, Junyu Lin, Minjie Zhong, Junsi Zhang, Shengkai Zheng, Cen Jiang, Xiangjin Chen, Sunwang Xu

“…Positive correlations between METTL1, WDR4, and TNF-α expression, which affect the proliferation and metastasis of PTC, were confirmed via analysis of microarrays containing PTC tissues. These results demonstrate the oncogenic role of METTL1-mediated m7G tRNA modification in regulating codon-specific translation efficiency in PTC and suggest that targeting METTL1 may be a promising therapeutic approach for overcoming PTC progression by inhibiting PTC cell proliferation and metastasis.…”
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Automated cell annotation and classification on histopathology for spatial biomarker discovery by Zhe Li, Seyed Hossein Mirjahanmardi, Rasoul Sali, Feyisope Eweje, Matthew Gopaulchan, Leon Kloker, Xiaoming Zhang, Guoxin Li, Yuming Jiang, Ruijiang Li

“…By co-registering H&E images with mIF of the same tissue section at the single-cell level, we create a dataset of 1,127,252 cells with high-quality annotations on tissue microarray cores. …”
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Differential BACH1 Expression in Basal-like Breast Tumors of Black Women Identified via Immunohistochemistry by N. M. Dowling, Galina Khramtsova, Olufunmilayo Olopade, Shabnam Samankan, Bok-Soon Lee, Jiyoung Lee

“…However, the clinical relevance of BACH1 expression in breast tumors remains poorly understood. Using a tissue microarray from a cohort of 130 patients, we assessed the expression of BACH1 and its known target gene, MCT1 (encoded by <i>SLC16A1</i>), through immunohistochemistry (IHC). …”
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TIM‐4 increases the proportion of CD4+CD25+FOXP3+ regulatory T cells in the pancreatic ductal adenocarcinoma microenvironment by inhibiting IL‐6 secretion by Ziyao Wang, Zerong Xie, Yu Mou, Ruiman Geng, Chen Chen, Nengwen Ke

“…Meanwhile, multiple fluorescent immunohistochemical staining was used to study the distribution characteristics of TIM‐4, and through tissue microarrays, we explored its correlation with patient prognosis. …”
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The impact of MITF expression on tumor-infiltrating lymphocytes in melanoma: Insights into immune microenvironment dynamics by Damir Vučinić, Matea Lekić, Gordana Žauhar, Gordana Zamolo

“…Archival formalin-fixed, paraffin-embedded tissue samples from 81 primary melanoma patients were analyzed via tissue microarray immunohistochemistry to assess MITF protein levels. …”
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Exploring the immune microenvironment in small bowel adenocarcinoma using digital image analysis. by Fatima Abdullahi Sidi, Victoria Bingham, Stephen McQuaid, Stephanie G Craig, Richard C Turkington, Jacqueline A James, Matthew P Humphries, Manuel Salto-Tellez

“…<h4>Methods</h4>25 patient samples in the form of formalin fixed, paraffin embedded (FFPE) tissue were obtained in tissue microarray (TMAs) format. …”
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Immunohistochemical study of histone protein 3 modification in pediatric osteosarcoma identifies reduced H3K27me3 as a marker of poor treatment response. by Sebastian Kondratowski, Danielle Cohen, Rebecca J Deyell, Ash Sandhu, Jonathan W Bush

“…We aimed to characterize the methylation and phosphorylation status in osteosarcoma using histone markers found in primary diagnostic biopsies and their paired metastases. We constructed two tissue microarray sets from 58 primary diagnostic samples and 54 temporally-separated but related metastatic or recurrent samples, with tissue blocks available from 2002-2022. …”
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Methylomics of breast cancer: Seeking epimarkers in peripheral blood of young subjects by Golnaz Khakpour, Mehrdad Noruzinia, Pantea Izadi, Fatemeh Karami, Mohammad Ahmadvand, Ramin Heshmat, Mahsa M Amoli, Javad Tavakkoly-Bazzaz

“…In this way, methylated DNA immunoprecipitation microarray (MeDIP-chip) was performed on DNA samples isolated from white blood cells of 30 breast cancer patients compared to 30 healthy controls. …”
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Genome-Wide Characterization and Expression Profiles of the Superoxide Dismutase Gene Family in Gossypium by Jingbo Zhang, Bo Li, Yang Yang, Wenran Hu, Fangyuan Chen, Lixia Xie, Ling Fan

“…Moreover, the tissue-specific expression profile reveals the functional divergence of SOD genes in different organs development of cotton. …”
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PIWI‐interacting RNA MIABEPIR regulates cerebral endothelial cell function via DAPK2 pathway in offspring following maternal immune activation by Shan‐Shan Li, Miao Guo, Yao Long, Yuang Cai, Ying Zhao, Shaoyuan Huang, Houzhi Yang, Yonggang Fan, Xu Chen, Xin Jin

“…Here, we identify a novel MIA‐associated brain endothelial piRNA (MIABEPIR) involved in regulating BMEC function and BBB integrity. RNA microarray analysis of foetal brain tissue from MIA‐exposed mice revealed significant changes in piRNA expression, including a marked upregulation of MIABEPIR upregulated piRNAs. …”
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Molecular Signatures of Recurrent Hepatocellular Carcinoma Secondary to Hepatitis C Virus following Liver Transplantation by Trina Das, Deborah L. Diamond, Matthew Yeh, Sajida Hassan, Janine T. Bryan, Jorge D. Reyes, James D. Perkins

“…Two groups of patients were selected, one including patients with HCV who developed HCC recurrence (HCC-R) ≤3 years from LT and the second group including patients with HCV who did not have recurrent HCC (HCC-NR). Microarray analysis containing more than 29,000 known genes was performed on formalin-fixed-paraffin-embedded (FFPE) liver tissue from explanted livers. …”
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Haplotype Analysis of Interleukin-8 Gene Polymorphisms in Chronic and Aggressive Periodontitis by Petra Borilova Linhartova, Jan Vokurka, Hana Poskerova, Antonin Fassmann, Lydie Izakovicova Holla

“…Subgingival bacterial colonization was investigated by the DNA-microarray detection kit in a subgroup of subjects (N=247). …”
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Identification and Characterization of Cyprinid Herpesvirus-3 (CyHV-3) Encoded MicroRNAs. by Owen H Donohoe, Kathy Henshilwood, Keith Way, Roya Hakimjavadi, David M Stone, Dermot Walls

“…MiRNAs from the two confirmed pre-miRNAs were also detected in gill tissue from CyHV-3-infected carp. We also present evidence that one confirmed miRNA can regulate the expression of a putative CyHV-3-encoded dUTPase. …”
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Comparison of effects of p53 null and gain-of-function mutations on salivary tumors in MMTV-Hras transgenic mice. by Dadi Jiang, Catherine I Dumur, H Davis Massey, Viswanathan Ramakrishnan, Mark A Subler, Jolene J Windle

“…Salivary tumors from these mice were characterized with regard to age of tumor onset, tumor growth rates, cell cycle distribution, apoptotic levels, tumor histopathology, as well as response to doxorubicin treatment. Microarray analysis was also performed to profile gene expression. …”
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Early-stage immunoexpression of inflammatory, angiogenic, and survival markers in tongue epithelium of mice exposed to hookah smoke. by Aldini Beuting Pereira, Arieli Carini Michels, Sarah Freygang Mendes Pilati, Filipe Modolo, Ana Paula Camargo Martins, Caroline Busatta Vaz De Paula, Seigo Nagashima, Lúcia Noronha, Ana Clara Prado Fonseca, Ariane Jéssica Torres Turmina, Heloisa Franco De Meira, Luisa Gabriela Carneiro Ramos, Thaís Grupp Da Rosa, Thais Maria Dos Santos Eckhardt, Sérgio Aparecido Ignácio, Luciana Reis Azevedo Alanis, Paulo Henrique Couto Souza, Rodrigo Nunes Rached, Bruno Correia Jham, Everdan Carneiro, Emanuela Carla Dos Santos, Aline Cristina Batista Rodrigues Johann

“…Tongues were embedded in paraffin. A tissue microarray was constructed, and immunohistochemistry was performed for Cyclooxygenase 2, NF-kappa B, Vascular Endothelial Growth Factor Receptor 1, and terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL) for apoptotic analysis. …”
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miR-4780 Derived from N2-Like Neutrophil Exosome Aggravates Epithelial-Mesenchymal Transition and Angiogenesis in Colorectal Cancer by Liang Wang, Yuqiang Shan, Sixin Zheng, Jiangtao Li, Peng Cui

“…In our results, we found that neutrophils were enriched in CRC tumor tissue and that CD11b expression correlated with tumor site and serous membrane invasion. …”
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Integrative bioinformatics analysis and experimental validation of key biomarkers driving the progression of cirrhotic portal hypertension by Meilin Li, Lilin Jiang, Yunrui Ru, Zhonghua Lu, Peng Gu

“…The aim of this study was to identify hub genes for predicting persistent progression of portal hypertension in patients with liver cirrhosis. Methods Related microarray datasets were obtained from the Gene Expression Omnibus database. …”
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Identification and validation of hub gene TNFAIP6 of fibroblast-like synoviocytes in rheumatoid arthritis by LEI Lei, LYU Yuxin, ZHANG Jing

“…Methods‍　‍Four independent synovial tissue microarray transcriptome sequencing datasets and one single cell sequencing dataset were downloaded from the Gene Expression Omnibus (GEO) database, and the hub gene of RA fibroblast-like synovial cells was identified by differential gene analysis, weighted gene co-expression network analysis (WGCNA) and single-cell sequencing data analysis. …”
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EsoDetect: computational validation and algorithm development of a novel diagnostic and prognostic tool for dysplasia in Barrett’s esophagus by Migla Miskinyte, Benilde Pondeca, José B. Pereira-Leal, Joana Cardoso

“…Specifically, for the diagnostic application, three RNAseq datasets were employed, while for the prognostic application, nine microarray datasets were identified, and 25 previously described genes were validated. …”
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The proteomics of colorectal cancer: identification of a protein signature associated with prognosis. by Donna O'Dwyer, Lynda D Ralton, Aisling O'Shea, Graeme I Murray

“…Fifteen proteins that showed increased expression were validated by immunohistochemistry using a well characterised colorectal cancer tissue microarray containing 515 primary colorectal cancer, 224 lymph node metastasis and 50 normal colonic mucosal samples. …”
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