The miR-146a SNP Rs2910164 and miR-155 SNP rs767649 Are Risk Factors for Non-Small Cell Lung Cancer in the Iranian Population by Neda K. Dezfuli, Ian M. Adcock, Shamila D. Alipoor, Sharareh Seyfi, Babak Salimi, Maryam Mafi Golchin, Neda Dalil Roofchayee, Mohammad Varhram, Esmaeil Mortaz

“…MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression and may act as both tumor suppressors and as oncogenes. …”
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Comparative transcriptomics reveal stage-dependent parasitic adaptations in the myxozoan Sphaerospora molnari by Monika M. Wiśniewska, Jiří Kyslík, Gema Alama-Bermejo, Alena Lövy, Martin Kolísko, Astrid S. Holzer, Anush Kosakyan

“…Results We used parasite isolation protocols and comparative transcriptomics to study early proliferative and spore-forming stages of S. molnari, unveiling variation in gene expression between each stage. We discovered several apparent innovations in the S. molnari transcriptome, including proteins that are likely to function in the uptake of previously unknown key nutrients, immune evasion factors that may contribute to long-term survival in hosts, and proteins that likely improve adhesion to host cells that may have arisen from horizontal gene transfer. …”
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Epitranscriptome profiles reveal participation of the RNA methyltransferase gene OsMTA1 in rice seed germination and salt stress response by Yingbo Li, Ming Yin, Juan Wang, Xiuqin Zhao, Jianlong Xu, Wensheng Wang, Binying Fu

“…Further combined analysis of the m6A methylome and transcriptome revealed that the loss of function of OsMTA1 had a more complex impact on gene expression in osmta1-1. Several hypomethylated genes with a negative role in growth and development, such as OsHsfA7 and OsHDAC3, were highly up-regulated in the osmta1-1 mutant under the control condition. …”
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Exposure to Subclinical Doses of Fumonisins, Deoxynivalenol, and Zearalenone Affects Immune Response, Amino Acid Digestibility, and Intestinal Morphology in Broiler Chickens by Revathi Shanmugasundaram, Laharika Kappari, Mohammad Pilewar, Matthew K. Jones, Oluyinka A. Olukosi, Anthony Pokoo-Aikins, Todd J. Applegate, Anthony E. Glenn

“…Higher mycotoxin groups T2 to T6 had a reduction in the digestibility of amino acids methionine (<i>p</i> < 0.05), aspartate (<i>p</i> < 0.05), and serine (<i>p</i> < 0.05); a reduction in CD4+, CD8+ T-cell populations (<i>p</i> < 0.05) and an increase in T regulatory cell percentages in the spleen (<i>p</i> < 0.05); a decrease in splenic macrophage nitric oxide production and total IgA production (<i>p</i> < 0.05); and upregulated cytochrome P450-1A1 and 1A4 gene expression (<i>p</i> < 0.05). Birds fed the lower mycotoxin concentration groups, T7 and T8, did not have a significant effect on performance, intestinal health, and immune responses, suggesting that these concentrations pose the least negative effects in broiler chickens. …”
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Integrating bulk and single-cell RNA sequencing data: unveiling RNA methylation and autophagy-related signatures in chronic obstructive pulmonary disease patients by Shi-Xia Liao, Lan-Ying Zhang, Ling-Mei Shi, Huai-Yu Hu, Yan-Hui Gu, Ting-Hua Wang, Yao Ouyang, Peng-Peng Sun

“…We analyzed tissue-based bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq) datasets from COPD and non-COPD patients, sourced from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were identified between COPD and non-COPD samples, and protein–protein interaction networks were constructed. …”
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Molecular characterization of pregnancy-associated breast cancer and insights on timing from GEICAM-EMBARCAM study by Regina Peña-Enríquez, Begoña Bermejo, Marina Pollán, Alejandra Díaz-Chacón, Yolanda Jerez Gilarranz, José J Ponce Lorenzo, Antonio Fernández Aramburo, Blanca Cantos Sánchez de Ibargüen, Ana Santaballa Bertrán, Elena Galve-Calvo, Álvaro Jiménez-Arranz, Yolanda Fernández, María Eva Pérez, Susana De La Cruz, Antonio Anton-Torres, Fernando Moreno, María Jesús Vidal-Losada, María Helena López-Ceballos, Isabel Blancas, María José Echarri, Raúl Rincón, Rosalía Caballero, Ángel Guerrero-Zotano, Silvia Guil-Luna, Juan de la Haba-Rodríguez

“…This study analyzed the clinicopathological characteristics and gene expression profile of 33 PABC and 26 non-PABC patients using the nCounter BC360 Panel (NanoString). …”
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Characterization of the genomic landscape of canine diffuse large B-cell lymphoma reveals recurrent H3K27M mutations linked to progression-free survival by Anna Darlene van der Heiden, Raphaela Pensch, Sophie Agger, Heather L. Gardner, William Hendricks, Victoria Zismann, Shukmei Wong, Natalia Briones, Bryce Turner, Karin Forsberg-Nilsson, Cheryl London, Kerstin Lindblad-Toh, Maja Louise Arendt

“…In particular, we identified hotspot mutations in two histone genes, H3C8, and LOC119877878, resulting in H3K27M alterations predicted to dysregulate gene expression. Finally, a survival analysis revealed that H3K27M mutations in H3C8 were associated with increased hazard ratios for progression-free survival. …”
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Development and characterization of a chicory extract fermented by Akkermansia muciniphila: An in vitro study on its potential to modulate obesity-related inflammation by A. Chervet, R. Nehme, C. Defois-Fraysse, C. Decombat, C. Blavignac, C. Auxenfans, B. Evrard, S. Michel, E. Filaire, J.-Y. Berthon, A. Dreux-Zigha, L. Delort, F. Caldefie-Chézet

“…We found that C-Akm extract decreased ROS generation, TNF-α and Il-6 gene expression in polarized macrophages, INFγ and IL-17A secretion in LPS-stimulated PBMCs stimulated with LPS. …”
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Proteostasis Decline and Redox Imbalance in Age-Related Diseases: The Therapeutic Potential of NRF2 by Brigitta Buttari, Antonella Tramutola, Ana I. Rojo, Niki Chondrogianni, Sarmistha Saha, Alessandra Berry, Letizia Giona, Joana P. Miranda, Elisabetta Profumo, Sergio Davinelli, Andreas Daiber, Antonio Cuadrado, Fabio Di Domenico

“…As we age, the efficiency of the NRF2 pathway declines due to several factors including increased activity of its repressors, impaired NRF2-mediated antioxidant and cytoprotective gene expression, and potential epigenetic changes, though the precise mechanisms remain unclear. …”
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Human placental extract improves liver cirrhosis in mice with regulation of macrophages and senescent cells by Natsuki Ishikawa, Yusuke Watanabe, Yuichirou Maeda, Tomoaki Yoshida, Naruhiro Kimura, Hiroyuki Abe, Akira Sakamaki, Hiroteru Kamimura, Takeshi Yokoo, Kenya Kamimura, Atsunori Tsuchiya, Shuji Terai

“…The results showed that HPE strongly polarized macrophages to the M2 phenotype, especially in macrophage-rich regions in the liver. Gene expression pathway analysis using spatial transcriptomics also revealed the possibility of improving senescent cell-derived inflammation via mitochondrial function. …”
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Integrating Bulk and Single-Cell Transcriptomic Data to Identify Ferroptosis-Associated Inflammatory Gene in Alzheimer&rsquo;s Disease by Zhou H, Peng Y, Huo X, Li B, Liu H, Wang J, Zhang G

“…However, the cellular and molecular links between ferroptosis, immune inflammation, and the brain-peripheral blood axis in Alzheimer’s disease (AD) remain unclear.Methods: We integrated bulk RNA-seq data from AD brain tissue and peripheral blood and refined the screening of AD candidate genes through differential gene expression analysis, weighted gene co-expression network analysis (WGCNA), and other approaches. …”
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AaMYB61-like and AabHLH137 jointly regulate anthocyanin biosynthesis in Actinidia arguta by Zhe Song, Yukuo Li, Xu Zhan, Xiaohan Li, Lingshuai Ye, Miaomiao Lin, Ran Wang, Leiming Sun, Jinyong Chen, Jinbao Fang, Feng Wei, Xiujuan Qi

“…The RT-qPCR results revealed that transient overexpression of AaMYB61-like in A. arguta fruit at 90–100 DAFB significantly promoted anthocyanin biosynthesis, as did the gene expression levels of AaCHS, AaCHI, AaF3H, AaLDOX, and AaF3GT, whereas the result of VIGS revealed the opposite results in A. arguta fruit at 105–115 DAFB. …”
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Prognostic significance of p27 in colorectal cancer: a meta-analysis and bioinformatics analysis by Jing Zou, Dong Wang, Gaoping Yin, Kexiang Lu, Kaibin Chang, He Li

“…In addition, we used Gene Expression Profiling Interactive Analysis (GEPIA), University of Alabama at Birmingham’s Cancer Data Analysis Portal (UALCAN), and the Human Protein Atlas (HPA) to validate our results.ResultsThrough an extensive examination of four prominent databases, a total of 21 original articles encompassing a cohort of 3,378 patients were identified. …”
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Upregulated SAE1 Drives Tumorigenesis and Is Associated with Poor Clinical Outcomes in Breast Cancer by Hong Liu, Jing Wang, Yunhai Li, Feng Luo, Lei Xing

“…Bioinformatics analysis was applied to analyze SAE1 expression in BC and normal breast tissues, its relationship with clinicopathologic characteristics and prognosis in BC patients, and data from the Cancer Genome Atlas database and Gene Expression Omnibus dataset. We performed immunohistochemistry to analyze SAE1 expression in BC tissues and para-cancer tissues in 79 breast cancer patients. …”
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Comprehensive analysis of metabolomics and transcriptomics reveals varied tepal pigmentation across Gloriosa varieties by Yue Sun, Pinli Hu, Yanan Jiang, Zhenzhen Wang, Jiaxing Chang, Yiwei Zhou, Haojing Shao

“…In this study, we employed sophisticated colorimetry, Ultra Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS), and transcriptome sequencing to investigate the phenotypic expression of tepal colors, the composition of carotenoids and anthocyanins, and the differential gene expression in four Gloriosa varieties during their full bloom phase. …”
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Identification of a 5-Gene-Based Scoring System by WGCNA and LASSO to Predict Prognosis for Rectal Cancer Patients by He Huang, Shilei Xu, Aidong Chen, Fen Li, Jiezhong Wu, Xusheng Tu, Kunpeng Hu

“…Sequencing (or microarray) data and clinicopathological details of patients with RC were retrieved from The Cancer Genome Atlas (TCGA-READ) or the Gene Expression Omnibus (GSE123390, GSE56699) database. …”
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Endothelial and neuronal engagement by AAV-BR1 gene therapy alleviates neurological symptoms and lipid deposition in a mouse model of Niemann-Pick type C2 by Charlotte Laurfelt Munch Rasmussen, Signe Frost Frederiksen, Christian Würtz Heegaard, Maj Schneider Thomsen, Eva Hede, Bartosz Laczek, Jakob Körbelin, Daniel Wüstner, Louiza Bohn Thomsen, Markus Schwaninger, Ole N. Jensen, Torben Moos, Annette Burkhart

“…Post-mortem analyses included gene expression analyses, verification of neurodegeneration in Purkinje cells, determination of NPC2 transduction in the CNS, assessment of gliosis, quantification of gangliosides, and co-detection of cholesterol with NPC2 in degenerating neurons. …”
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Bone Defect Repair Using a Bone Substitute Supported by Mesenchymal Stem Cells Derived from the Umbilical Cord by Michal Kosinski, Anna Figiel-Dabrowska, Wioletta Lech, Lukasz Wieprzowski, Ryszard Strzalkowski, Damian Strzemecki, Lukasz Cheda, Jacek Lenart, Krystyna Domanska-Janik, Anna Sarnowska

“…During the culture on the 1st, 7th, 14th, and 21st day (day in vitro (DIV)), we analyzed viability (confocal microscopy) and adhesion capability (electron microscopy) of WJ-MSC on Bio-Oss scaffolds, gene expression (qPCR), and secretion of proteins (Luminex). …”
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Identifying disulfidptosis-related biomarkers in epilepsy based on integrated bioinformatics and experimental analyses by Sijun Li, Lanfeng Sun, Hongmi Huang, Xing Wei, Yuling Lu, Kai Qian, Yuan Wu

“…Disulfidptosis, a proposed novel cell death mechanism, is thought to play a part in the pathogenesis of epilepsy, but the exact role is unclear. The gene expression omnibus series (GSE) 33000 and GSE63808 datasets were used to search for differentially expressed disulfidptosis-related molecules (DE-DRMs). …”
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Mycochemistry, antioxidant, anticancer activity, and molecular docking of compounds of F12 of ethyl acetate extract of Astraeus asiaticus with BcL2 and Caspase 3 by Swapan Kumar Ghosh, Koushik Pandey, Madhuparna Ghosh, Pradip Kumar Sur

“…The mechanism of anticancer effect of F12 (AAEAE) on cancer cell lines included induction of apoptosis, LDH leakage, and up regulation of gene expression levels of Caspase 3, Caspase 9, P53, and down regulation of BcL2 of all three cell lines. …”
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