Characterizing spatial immune architecture in metastatic melanoma using high-dimensional multiplex imaging by Joel Eliason, Santhoshi Krishnan, Yasunari Fukuda, Matias A. Bustos, Dan Winkowski, Sungnam Cho, Akshay Basi, Akshay Basi, Regan Baird, Elizabeth A. Grimm, Michael A. Davies, Dave S. B. Hoon, Arvind Rao, Arvind Rao, Arvind Rao, Arvind Rao, Jared K. Burks, Jared K. Burks, Suhendan Ekmekcioglu

“…Understanding how the spatial architecture of immune and inflammatory components changes across disease stages may reveal novel prognostic biomarkers and therapeutic targets.MethodsWe performed high-dimensional spatial profiling of two melanoma tissue microarrays (TMAs), representing Stage III (n = 157) and Stage IV (n = 248) metastatic tumors. …”
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HERV-derived epitopes represent new targets for T-cell-based immunotherapies in ovarian cancer by Qing Wang, Maha Ayyoub, Olivia Le Saux, Paola Bonaventura, Isabelle Treilleux, Nicolas Chopin, Clarisse Dubois, Virginie Mutez, Nicolas Chuvin, Yann Estornes, Jenny Valladeau-Guilemond, Stephane Depil, Nicolas Gadot, Marie Michelas, Audrey Page, Olivier Tabone, Marie Delles, Sarah Moran, Thibault Richard, Marjorie Lacourrège, Dina M Tawfik, Ema Etchegaray, Adrian Valente, Rasha E Boulos, Gabriel Jimenez Dominguez

“…The presence of HERV-K/HML-2 Gag antigen was then assessed by immunohistochemistry (IHC) on tumor microarrays from ovarian cancer samples and normal ovarian tissues. …”
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Effector T cells under hypoxia have an altered transcriptome similar to tumor-stressed T cells found in non-responsive melanoma patients by Ahmad A Tarhini, Zhihua Chen, Dongliang Du, Joshua Davis, Justin C Boucher, Katarzyna A Rejniak, Jose A Guevara-Patino, Timothy I Shaw, Alyssa Obermayer, Mate Z Nagy, Lourdes B Plaza-Rojas, Elena Kostenko, Anna L Austin, Awino Maureiq E Ojwang'

“…As T cell-based therapies often fail to work in solid tumors, this study aims to investigate the effects of hypoxia on T cell topo-distribution in the TME, gene expression association with T cell states, and clinical responses in melanoma.Methods To generate detailed information on tumor oxygenation and T cell accessibility, we used mathematical modeling of human melanoma tissue microarrays that incorporate oxygen supply from vessels, intratumoral diffusion, and cellular uptake. …”
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Vitamin K‐dependent gamma‐carboxyglutamic acid protein 1 promotes pancreatic ductal adenocarcinoma progression through stabilizing oncoprotein KRAS and tyrosine kinase receptor EGF... by Zheng Wu, Qing Ye, Shan Zhang, Li‐Peng Hu, Xiao‐Qi Wang, Lin‐Li Yao, Lei Zhu, Shu‐Yu Xiao, Zong‐Hao Duan, Xue‐Li Zhang, Shu‐Heng Jiang, Zhi‐Gang Zhang, De‐Jun Liu, Dong‐Xue Li, Xiao‐Mei Yang

“…Methods Analysis of pancreatic ductal adenocarcinoma (PDAC) datasets, including transcription profiles, clinical data, and tissue microarrays, was conducted to evaluate PRRG1 expression and its clinical relevance. …”
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The role of the aging process and related factor EMP1 in promoting progression of resectable pancreatic cancer by Junfeng Zhang, Jianyou Gu, Tao Zhang, Renpei Xia, Jianbo Li, Mingda Tan, Yongjun Yang, Jifeng Xiang, Bin Xie, Rong Tang, Wangge Li, Xianxing Wang, Shixiang Guo, Huaizhi Wang

“…We employed lentiviral vectors for both knockdown and overexpression of EMP1 in Panc02 cells, followed by the establishment of subcutaneous, pulmonary metastasis, and orthotopic pancreatic liver metastasis models in mice. Using tissue microarrays, we evaluated the expression of EMP1 and its downstream entities, and then conducted clinical correlation analysis. …”
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Identification of Tumor‐Specific Surface Proteins Enables Quantification of Extracellular Vesicle Subtypes for Early Detection of Pancreatic Ductal Adenocarcinoma by Chen Zhao, Zhili Wang, Hyoyong Kim, Hui Kong, Junseok Lee, Jacqueline Ziqian Yang, Anmin Wang, Ryan Y. Zhang, Yong Ju, Jina Kim, Bing Feng, Dejun Liu, Yating Zhang, Zhenfang Wang, Yandong Zhang, Shujing Guo, Dekang Gao, James S. Tomlinson, Renjun Pei, Jipeng Wan, Stephen J. Pandol, Myung‐Shin Sim, Sungyong You, Ding Ma, Shaohua Lu, Na Sun, Hsian‐Rong Tseng, Yazhen Zhu

“…The three PDAC EV‐specific surface proteins are identified using a bioinformatics framework and validated on PDAC cell lines and tissue microarrays. The resultant PDAC EV Score, derived from signals of the three PDAC EV subpopulations, demonstrates robust differentiation of PDAC patients from noncancer controls, with area under the receiver operating characteristic curves of 0.94 in the training (n = 124) and 0.93 in the validation (n = 136) cohorts. …”
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Malate initiates a proton-sensing pathway essential for pH regulation of inflammation by Yu-jia-nan Chen, Rong-chen Shi, Yuan-cai Xiang, Li Fan, Hong Tang, Gang He, Mei Zhou, Xin-zhe Feng, Jin-dong Tan, Pan Huang, Xiao Ye, Kun Zhao, Wen-yu Fu, Liu-li Li, Xu-ting Bian, Huan Chen, Feng Wang, Teng Wang, Chen-ke Zhang, Bing-hua Zhou, Wan Chen, Tao-tao Liang, Jing-tong Lv, Xia Kang, You-xing Shi, Ellen Kim, Yin-hua Qin, Aubryanna Hettinghouse, Kai-di Wang, Xiang-li Zhao, Ming-yu Yang, Yu-zhen Tang, Hai-long Piao, Lin Guo, Chuan-ju Liu, Hong-ming Miao, Kang-lai Tang

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Tumour extracellular vesicle surface Protein-mRNA integration assay for early detection of epithelial ovarian cancerResearch in context by Ying-Tzu Yen, Chen Zhao, Tian Gao, Jacqueline Ziqian Yang, Ning Kang, Jiahui Pu, Lei Qiu, Qixin Hu, Hyoyong Kim, Anmin Wang, Junseok Lee, Ryan Y. Zhang, Na Liu, Yue Ma, You-Ren Ji, Yong Ju, Lynn L. Zheng, James Lee-South, Vivian X. Zuo, Audrey Qian, Aaron Kwan, Yating Zhang, Shenghua Zhang, Zhili Wang, Jing Ren, Huaichao Liu, Zihan Wang, Yang Yue, Jina Kim, Jennifer Sun, Gabriella A. DiBernardo, Laura B. James-Allan, Ying Chen, Weipei Zhu, Guoyun Wang, Renjun Pei, Sanaz Memarzadeh, Sungyong You, Bobbie J. Rimel, Kate Lawrenson, Beth Y. Karlan, Myung Shin Sim, Shaohua Lu, Jipeng Wan, Na Sun, Hsian-Rong Tseng, Yazhen Zhu

“…., FRα, MSLN, and TROP2) were selected through a bioinformatic framework using multi-omics data and underwent rigorous validation using EOC cell lines and EOC tissue microarrays. We then explored the translational potential of the EOC EV SPRI Assay through a phase II case–control study. …”
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Integrated analyses of copy number variations and gene expression in lung adenocarcinoma. by Tzu-Pin Lu, Liang-Chuan Lai, Mong-Hsun Tsai, Pei-Chun Chen, Chung-Ping Hsu, Jang-Ming Lee, Chuhsing Kate Hsiao, Eric Y Chuang

“…Identification of prognostic biomarkers for lung cancer using gene expression microarrays poses a major challenge in that very few overlapping genes have been reported among different studies. …”
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LMX1B Activated Circular RNA GFRA1 Modulates the Tumorigenic Properties and Immune Escape of Prostate Cancer by Min Meng, Yi-chen Wu

“…In this study, circRNA microarrays using four pairs of PCa tissues were utilized to show that circGFRA1 was upregulated in PCa tumor tissues. …”
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Evaluating Biocompatibility: From Classical Techniques to State-of-the-Art Functional Proteomics by Ana Nuño-Soriano, Carlota Arias-Hidalgo, Enrique Montalvillo, Rafael Góngora, Ángela-Patricia Hernández, Pablo Juanes-Velasco, Manuel Fuentes

“…Biocompatibility remains a central issue for introducing biomaterials and nanomedicines into the clinic, requiring safety, functionality, toxicity prevention, and the control of foreign body reactions. …”
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MicroRNA-520a Suppresses Pathogenesis and Progression of Non-Small-Cell Lung Cancer through Targeting the RRM2/Wnt Axis by Yi Xie, Congyu Xue, Shuai Guo, Lei Yang

“…Differentially expressed miRNAs between tumor tissues and normal tissues were screened using microarrays, and miR-520a was screened to be significantly poorly expressed in tumor samples. …”
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Inhibition of PDK modulates radiotherapy resistance in gastric cancer by Qi Zhang, Wanjia Qiao, Xiaoyu Liu, Jun Lu, Farooq Benish, Shuping Li, Xiaojun Liu

“…Abstract To explore the effect of sodium dichloroacetate (DCA), a pyruvate dehydrogenase kinase (PDK) inhibitor, on the progression of gastric cancer and resistance to radiotherapy, we analyzed histopathological microarrays from 60 gastric cancer and paracancerous tissues to determine PDK expression and its prognostic significance. 5-Ethynyl-2′-deoxyuridine (EdU) incorporation assay and Transwell migration assay were used to investigate the effects of PDK inhibition on gastric cancer cell proliferation and migration. …”
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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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Role of laboratory biomarkers in monitoring and prediction of the effectiveness of treatment of rheumatic diseases using genetically engineered drugs by Elena Nikolayevna Aleksandrova, A A Novikov, E L Nasonov

“…Molecular and cellular biomarkers (antibodies, indicators of acute inflammation, cytokines, chemokines, growth factors, endothelial activation markers, immunoglobulins, cryoglobulins, T- and B-cell subpopulations, products of bone and cartilage metabolism, genetic and metabolic markers) that allow one to conduct immunological monitoring and prediction of the effectiveness of RD therapy using tumor necrosis factor α inhibitors (infliximab, adalimumab, golimumab, etanercept), anti-B-cell drugs (rituximab, belimumab), interleukin-6 receptor antagonist (tocilizumab), and T-cell costimulation blocker (abatacept) have been detected in blood, synovial fluid, urine, and bioptates of the affected tissues. In addition to the conventional uniplex immunodiagnostics techniques, multiplex analysis of marker, which is based on genetic, transcriptomic and proteomic technologies using DNA and protein microarrays, polymerase chain reaction, and flow cytometry, is becoming increasingly widespread. …”
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MicroRNA-206: a potential circulating biomarker candidate for amyotrophic lateral sclerosis. by Janne M Toivonen, Raquel Manzano, Sara Oliván, Pilar Zaragoza, Alberto García-Redondo, Rosario Osta

“…Besides their important regulatory role in variety of biological processes, miRNAs can also be released into the circulation by pathologically affected tissues and display remarkable stability in body fluids. …”
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Serum LncRNAs Profiles Serve as Novel Potential Biomarkers for the Diagnosis of HBV-Positive Hepatocellular Carcinoma. by Kang Wang, Wei Xing Guo, Nan Li, Chun Fang Gao, Jie Shi, Yu Fu Tang, Feng Shen, Meng Chao Wu, Shan Rong Liu, Shu Qun Cheng

“…<h4>Methods</h4>lncRNA microarrays were utilized to measure the differential expression of lncRNAs between tumor tissues and corresponding non-tumor tissues in HBV-positive hapatocellular carcinoma. uc001ncr and AX800134 were selected as candidate lncRNAs and detected in three independent cohorts containing a total of 684 participants (healthy individuals and chronic HBV patients and HBV-positive HCC patients) who were recruited between March 2011 and December 2012. …”
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Gene signature based on degradome-related genes can predict distal metastasis in cervical cancer patients by Jorge Fernandez-Retana, Horacio Zamudio-Meza, Miguel Rodriguez-Morales, Abraham Pedroza-Torres, David Isla-Ortiz, Luis Herrera, Nadia Jacobo-Herrera, Oscar Peralta-Zaragoza, César López-Camarillo, Fermin Morales-Gonzalez, David Cantu de Leon, Carlos Pérez-Plasencia

“…Proteases comprising the degradome given its ability to promote cell growth, migration, and invasion of tissues play an important role during tumor development and progression. …”
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Revealing new mouse epicardial cell markers through transcriptomics. by Lars Bochmann, Padmini Sarathchandra, Federica Mori, Enrique Lara-Pezzi, Domenico Lazzaro, Nadia Rosenthal

“…<h4>Conclusion</h4>This study presents the description of the murine epicardial transcriptome obtained from snap frozen tissues, providing essential information for further analysis of this important cardiac cell layer.…”
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FGFR1-induced epithelial to mesenchymal transition through MAPK/PLCγ/COX-2-mediated mechanisms. by Darren C Tomlinson, Euan W Baxter, Paul M Loadman, Mark A Hull, Margaret A Knowles

“…For epithelial cells to invade surrounding tissues and metastasise, an epithelial-mesenchymal transition (EMT) is required. …”
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