Comprehensive analysis of single-cell and bulk RNA sequencing data unveils antigen-presenting and processing fibroblasts and establishes a predictive model in gastric cancer by Chenggang Zhang, Fangqi Chen, Jie Li, Yixuan He, Juan Sun, Zicheng Zheng, Guanmo Liu, Yihua Wang, Weiming Kang, Xin Ye

“…The predictive model based on APPFRGs effectively predicts the prognosis and tumor immune status of GC.…”
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Membranous Overexpression of Fibronectin Predicts Microvascular Invasion and Poor Survival Outcomes in Patients with Hepatocellular Carcinoma by Yoon Jung Hwang, Hyejung Lee, Suk Kyun Hong, Su Jong Yu, Haeryoung Kim

“…Methods: Immunohistochemical analysis of FN was conducted using tissue microarrays from 258 surgically resected HCCs and matched nontumorous liver tissues. …”
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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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Prevalence of βIII-tubulin (TUBB3) expression in human normal tissues and cancers by Fermín Person, Waldemar Wilczak, Claudia Hube-Magg, Christoph Burdelski, Christina Möller-Koop, Ronald Simon, Mercedes Noriega, Guido Sauter, Stefan Steurer, Susanne Burdak-Rothkamm, Frank Jacobsen

“…To systematically investigate the epidemiology of TUBB3 expression in normal and neoplastic tissues, we used tissue microarrays for analyzing the immunohistochemically detectable expression of TUBB3 in 3911 tissue samples from 100 different tumor categories and 76 different normal tissue types. …”
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Placental and immune cell DNA methylation reference panel for bulk tissue cell composition estimation in epidemiological studies by Kyle A. Campbell, Justin A. Colacino, John Dou, Dana C. Dolinoy, Sung Kyun Park, Rita Loch-Caruso, Vasantha Padmanabhan, Kelly M. Bakulski

“…We collated new and existing cell type DNAm profiles quantified via Illumina EPIC or 450k microarrays. To estimate cell composition, we deconvoluted whole placental samples (n = 36) with robust partial correlation based on the top 30 hyper- and hypomethylated sites identified per cell type. …”
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Serum extracellular vesicles 3’tRF-ThrCGTand 3’tRF-mtlleGAT combined with tumor markers can serve as minimally invasive diagnostic predictors for colorectal cancer by Jiefei Peng, Jiefei Peng, Fan Bu, Fan Bu, Lei Duan, Lei Duan, Anna Song, Guojun Wang, Zhijun Zhang, Zhijun Zhang

“…Gene microarrays were screened for differentially expressed tRF-RNA. …”
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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

“…This research focused on the effects of miR-520a on the development of non-small-cell lung cancer (NSCLC) and the molecules involved. …”
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Endoplasmic reticulum protein ERp46 in renal cell carcinoma. by Wilhelmina C M Duivenvoorden, Athanasios Paschos, Sarah N Hopmans, Richard C Austin, Jehonathan H Pinthus

“…The objectives of this study were to investigate ERp46 in RCC, its expression, its effects on RCC growth in a mouse model and whether it interacts with AdipoR1. …”
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Personalized risk stratification in colorectal cancer via PIANOS system by Du Cai, Haoning Qi, Qiuxia Yang, Huayu Li, Chenghang Li, Chuling Hu, Baowen Gai, Xu Zhang, Yize Mao, Feng Gao, Xiaojian Wu

“…Developed using gene expression data from 562 patients and employing a rank-based k-Top Scoring Pairs (k-TSP) algorithm alongside resampling, PIANOS was rigorously validated in 15 cohorts comprising 3666 patients with CRC. It effectively differentiates high-risk from low-risk patients, outperforms 105 existing models, and demonstrates robust performance across technologies like microarrays and RNA sequencing. …”
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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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Wolbachia infections in Anopheles gambiae cells: transcriptomic characterization of a novel host-symbiont interaction. by Grant L Hughes, Xiaoxia Ren, Jose L Ramirez, Joyce M Sakamoto, Jason A Bailey, Anne E Jedlicka, Jason L Rasgon

“…We used Affymetrix GeneChip microarrays to investigate the effect of wAlbB and wRi infection on the transcriptome of cultured Anopheles Sua5B cells, and for a subset of genes used quantitative PCR to validate results in somatically-infected Anopheles mosquitoes. …”
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The transcription factor SOX18 regulates the expression of matrix metalloproteinase 7 and guidance molecules in human endothelial cells. by Martina Hoeth, Heide Niederleithner, Renate Hofer-Warbinek, Martin Bilban, Herbert Mayer, Ulrike Resch, Christof Lemberger, Oswald Wagner, Erhard Hofer, Peter Petzelbauer, Rainer de Martin

“…<h4>Methodology/principal findings</h4>SOX18 was expressed in HUVEC using a recombinant adenoviral vector and the altered gene expression profile was analyzed using microarrays. Expression of several regulated candidate SOX18 target genes was verified by real-time PCR. …”
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Epigenomic modifications predict active promoters and gene structure in Toxoplasma gondii. by Mathieu Gissot, Krystyna A Kelly, James W Ajioka, John M Greally, Kami Kim

“…Initial studies suggest that epigenetic phenomena, including histone modifications and chromatin remodeling, have a profound effect upon gene expression and expression of virulence traits. …”
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Epithelial and stromal microRNA signatures of columnar cell hyperplasia linking Let-7c to precancerous and cancerous breast cancer cell proliferation. by Sofie Björner, Paul A Fitzpatrick, Yaoyong Li, Craig Allred, Anthony Howell, Anita Ringberg, Håkan Olsson, Crispin J Miller, Håkan Axelson, Göran Landberg

“…Here we have defined novel epithelial as well as stromal miRNA signatures from columnar cell hyperplasia lesions compared to normal terminal duct lobular units by using microdissection and miRNA microarrays. Let-7c were among the identified downregulated epithelial miRNAs and its functions were delineated in unique CCH derived cells and breast cancer cell line MCF-7 suggesting anti-proliferative traits potentially due to effects on Myb and ERα. …”
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Prognostic Significance of Tissue Inhibitor of Metalloproteinase-1 in Breast Cancer by Arunee Dechaphunkul, Monlika Phukaoloun, Kanet Kanjanapradit, Kathryn Graham, Sunita Ghosh, Cheryl Santos, John R. Mackey

“…Primary breast cancers from women with early stage disease treated with standard adjuvant therapy were analyzed by gene expression microarrays and immunohistochemistry for TIMP-1. Results. …”
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The Impact of Antenatal and Postnatal Factors on the Development of the Pulmonary Microvasculature in Preterm Infants by Raluca Chirculescu, Ruxandra Viorica Stănculescu, Paul Cristian Bălănescu, Gheorghe Peltecu

“…After selecting the cases from the autopsy database, two lung tissue microarrays were created. Histological slides were stained using the hematoxylin and eosin technique to precisely capture the microscopic details. …”
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Associations Between Follicular Fluid Biomarkers and IVF/ICSI Outcomes in Normo-Ovulatory Women—A Systematic Review by Soha Albeitawi, Saif-Ulislam Bani-Mousa, Baraa Jarrar, Ibrahim Aloqaily, Nour Al-Shlool, Ghaida Alsheyab, Ahmad Kassab, Baha’a Qawasmi, Abdalrahman Awaisheh

“…We parsed PubMed, Scopus, and Google Scholar for research on the effects of different FF biomarkers on IVF/ICSI outcomes in normo-ovulatory women. …”
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Lactobacilli-host interactions inhibit Staphylococcus aureus and Escherichia coli-induced cell death and invasion in a cellular model of infection by Despoina Eugenia Kiousi, Maria Panopoulou, Aglaia Pappa, Alex Galanis

“…Dual RNA-seq and protein microarrays were used to determine expression changes in L125 and host cells during co-incubation. …”
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Low density of intratumoral M1-macrophage infiltration may correlate with worse prognosis in low-grade early-stage uterine endometrioid carcinoma by Michiko Nagamine, Hiroshi Ogi, Maki Hirai, Ikoi Omatsu, Sanzo Moriwaki, Saya Shibata, Satoru Yasukawa, Kaori Yoriki, Motohiro Kojima, Taisuke Mori, Kyoko Itoh, Eiichi Konishi

“…Multiplex immunohistochemistry was performed on tissue microarrays constructed from formalin-fixed paraffin-embedded tissue blocks of primary surgical specimens and, when available, recurrent lesions. …”
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STING agonist-based treatment promotes vascular normalization and tertiary lymphoid structure formation in the therapeutic melanoma microenvironment by Walter J Storkus, Ronald J Fecek, Manoj Chelvanambi, Jennifer L Taylor

“…TLS formation in ADU S-100-treated mice was associated with the development of a highly oligoclonal TIL repertoire enriched in expanded T cell clonotypes unique to the TME and not detected in the periphery.Conclusions Our data support the premise that i.t. delivery of low-dose STING agonist promotes VN and a proinflammatory TME supportive of TLS formation, enrichment in the TIL repertoire and tumor growth control.…”
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