Gene networks for use in metabolomic data analysis of blood plasma from patients with postoperative delirium by V. A. Ivanisenko, N. V. Basov, A. A. Makarova, A. S. Venzel, A. D. Rogachev, P. S. Demenkov, T.  V. Ivanisenko, M. A. Kleshchev, E. V. Gaisler, G. B. Moroz, V. V. Plesko, Y. S. Sotnikova, Y. V. Patrushev, V. V. Lomivorotov, N. A. Kolchanov, A. G. Pokrovsky

“…Within this set, 47 are assumed to be regulators of gene expression, governing the transcription of enzymes pivotal to the metabolic cascade. …”
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Identification of common and specific fibrosis-related genes in three common chronic kidney diseases by Zhangning Fu, Xiaodong Geng, Chao Liu, Wanjun Shen, Zheyi Dong, Guannan Sun, Guangyan Cai, Xiangmei Chen, Quan Hong

“…Background Kidney fibrosis is the common final pathway of virtually all advanced forms of chronic kidney disease (CKD) including diabetic nephropathy (DN), IgA nephropathy (IgAN) and membranous nephropathy (MN), with complex mechanism. Comparative gene expression analysis among these types of CKD may shed light on its pathogenesis. …”
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Dynamics and regulatory roles of RNA m6A methylation in unbalanced genomes by Shuai Zhang, Ruixue Wang, Kun Luo, Shipeng Gu, Xinyu Liu, Junhan Wang, Ludan Zhang, Lin Sun

“…N6-methyladenosine (m6A) in eukaryotic RNA is an epigenetic modification that is critical for RNA metabolism, gene expression regulation, and the development of organisms. …”
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Melanin-like nanoparticles slow cyst growth in ADPKD by dual inhibition of oxidative stress and CREB by Yongzhan Sun, Quan Zou, Huizheng Yu, Xiaoping Yi, Xudan Dou, Yu Yang, Zhiheng Liu, Hong Yang, Junya Jia, Yupeng Chen, Shao-Kai Sun, Lirong Zhang

“…Mechanistically, we observed that MMPP directly binds to the bZIP DNA-binding domain of CREB, leading to competitive inhibition of CREB’s DNA binding ability and subsequent reduction in CREB target gene expression. In summary, our findings identify an intracellular target of MMPP and demonstrate its potential for treating ADPKD by simultaneously targeting oxidative stress and CREB transcriptional activity.…”
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Titin gene mutations enhance radiotherapy efficacy via modulation of tumour immune microenvironment in rectum adenocarcinoma by Hengchang Liu, Jialiang Liu, Xu Guan, Zhixun Zhao, Pu Cheng, Haipeng Chen, Zheng Jiang, Xishan Wang

“…Abstract Objective This study investigates the impact of Titin (TTN) gene mutations on radiotherapy sensitivity in rectum adenocarcinoma (READ) by examining changes in the tumour immune microenvironment. Methods Data on gene expression and mutations in READ were obtained from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. …”
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Personalized allele-specific antisense oligonucleotides for GNAO1-neurodevelopmental disorder by Inna Shomer, Nofar Mor, Shaul Raviv, Noga Budick-Harmelin, Tanya Matchevich, Sharon Avkin-Nachum, Yoach Rais, Rebecca Haffner-Krausz, Ariela Haimovich, Aviv Ziv, Reut Fluss, Bruria Ben-Ze’ev, Gali Heimer, Denis N. Silachev, Vladimir L. Katanaev, Dan Dominissini

“…We show that reduction of mutated GNAO1 in vitro by knockout or by ASO has a beneficial functional outcome, which can be measured by cAMP accumulation and gene expression changes. We established a Gnao1-E246K mouse model that shows a neurological phenotype, which partially recapitulates the human condition. …”
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NEK4: prediction of available drug targets and common genetic linkages in bipolar disorder and major depressive disorder by Bin Gong, Chenxu Xiao, Yu Feng, Yu Feng, Jing Shen

“…The SMR approach, combined with expression quantitative trait loci (eQTL) data, was then applied to assess causal associations between these genetic variants and gene expression, aiming to identify genetic markers and potential drug targets associated with BD and MDD. …”
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Fhl1, a new spatially specific protein, regulates vein graft neointimal hyperplasia by Chaoqun Wang, Jiantao Chen, Zicong Feng, Bohao Jian, Suiqing Huang, Kangni Feng, Haoliang Liu, Zhuoming Zhou, Ziyin Ye, Jing Lu, Mengya Liang, Zhongkai Wu

“…Spatial transcriptomics was performed on normal veins and 19‐day grafts to explore gene expression in neointimal regions. Immunohistochemical analysis identified neointima‐specific markers, while NIH progression was assessed in SD rats with four and a half LIM domains protein 1 (Fhl1) knockout and in human saphenous veins (HSV) with adenovirus‐mediated Fhl1 overexpression. …”
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Metabolomics, network pharmacology, and microbiome analyses uncover the mechanisms of the Chinese herbal formula for the improvement of meat quality in spent hens by Zhihua Li, Md. Abul Kalam Azad, Chengwen Meng, Xiangfeng Kong, Jue Gui, Wenchao Lin, Yadong Cui, Wei Lan, Qinghua He

“…The CHF supplementation increased the glutathione peroxidase level (P < 0.05) and upregulated gene expression related to the Nrf2 pathway (including HO-1, P < 0.05; Nrf2, P = 0.098; CAT, P = 0.060; GPX1, P = 0.063; and SOD2, P = 0.052) and lipid metabolism (including PPARγ, P < 0.05; SREBP1, P = 0.059; and CPT1A, P = 0.058). …”
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Modification and analysis of context-specific genome-scale metabolic models: methane-utilizing microbial chassis as a case study by M. A. Kulyashov, R. Hamilton, Y. Afshin, S. K. Kolmykov, T. S. Sokolova, T. M. Khlebodarova, M. G. Kalyuzhnaya, I. R. Akberdin

“…We optimized the previously reconstructed whole genome-scale metabolic network by adjusting the flux distribution using gene expression data. The outputs of the automatically reconstructed CS metabolic network were comparable to manually optimized iIA409 models for Ca-growth conditions. …”
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Surface functionalization of titanium implants with controlled-release glutathione conjugate for antioxidant and osteogenesis by Huichuan Xu, Kosuke Nozaki, Ziniu Yu, Nobuyuki Kawashima, Takeshi Ueno, Huaze Wu, Hao Wu, Noriyuki Wakabayashi

“…Runt-related transcription factor 2 (RUNX2), osteopontin (OPN) and osteocalcin (OCN) gene expression level were significantly up-regulated on VPA-GSH-treated Ti surfaces. …”
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The ABC transporter A7 modulates neuroinflammation via NLRP3 inflammasome in Alzheimer’s disease mice by Irene Santos-García, Pablo Bascuñana, Mirjam Brackhan, María Villa, Ivan Eiriz, Thomas Brüning, Jens Pahnke

“…Interestingly, microglia-specific ABCA7ko restored Aβ42 peptide levels and IBA1+ and GFAP+ and NLRP3-related gene expression to the original APPPS1 mouse levels. In primary glial cell cultures of APPPS1-hA7ko microglia and APPPS1 astrocytes from newborn pups, we observed that conditioned media from LPS-stimulated microglia was able to induce NLRP3 inflammasome expression and proinflammatory cytokine release in astrocytes. …”
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Microenvironment Influences on Human Umbilical Cord Mesenchymal Stem Cell-Based Bone Regeneration by Lingling E, Rongjian Lu, Jianwei Sun, Hongbo Li, Wen Xu, Helin Xing, Xing Wang, Tao Cheng, Shuo Zhang, Xiaocao Ma, Rong Zhang, Hongchen Liu

“…In the in vitro three-dimensional culture microenvironment, nHAC/PLA supported hUC-MSCs’ adhesion, proliferation, and differentiation; the microenvironment containing OMD or OMD and rhBMP-7 shortened cell proliferation progression and made osteogenic differentiation progression advance; rhBMP-7 significantly attenuated the inhibiting effect of OMD on hUC-MSCs’ proliferation and significantly enhanced the promoting effect of OMD on gene expression and protein secretion of osteogenic differentiation markers, calcium and phosphorous concentration, and mineralized matrix formation. …”
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Multi-omics and machine learning-driven CD8+ T cell heterogeneity score for head and neck squamous cell carcinoma by Di He, Zhan Yang, Tian Zhang, Yaxian Luo, Lianjie Peng, Jiatao Yan, Tao Qiu, Jingyu Zhang, Luying Qin, Zhichao Liu, Mouyuan Sun

“…By analyzing the gene expression related to CD8+ T cells, we have differentiated HNSCC into cold and hot tumor subtypes, uncovering disparities in clinical prognosis and responses to immunotherapy. …”
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Low Expression of FFAR2 in Peripheral White Blood Cells May Be a Genetic Marker for Early Diagnosis of Acute Myocardial Infarction by Jianjun Ruan, Heyu Meng, Xue Wang, Weiwei Chen, Xiaomin Tian, Fanbo Meng

“…Furthermore, the relationship between gene expression and clinical data was also analyzed and compared. …”
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Skatole Alleviates Osteoarthritis by Reprogramming Macrophage Polarization and Protecting Chondrocytes by Weiyun Wang, Yaru Chu, Yunkun Lu, Jie Xu, Weixuan Zhao, Zhuo Liang, Xueqiang Guo, Lingling Xi, Tao Han, Yaping Shen, Wenjuan Song, Yanhua Tang, Mengnan Wen, Zhuang Qian, Lei Wang, Zhenlin Fan, Guangdong Zhou, Wenjie Ren

“…The CUT&Tag assay results indicated that the downstream transcription factor p65 of NFκB can directly bind to gene loci related to inflammation, oxidative phosphorylation, and glutathione metabolism, thereby modulating gene expression. This regulatory process is inhibited by skatole. …”
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Targeting SRSF1 improves cancer immunotherapy by dually acting on CD8+T and tumor cells by Gui-Qi Zhu, Zheng Tang, Tian-Hao Chu, Biao Wang, Shi-Ping Chen, Chen-Yang Tao, Jia-Liang Cai, Rui Yang, Wei-Feng Qu, Yi Wang, Qian-Fu Zhao, Run Huang, Meng-Xin Tian, Yuan Fang, Jun Gao, Xiao-Ling Wu, Jian Zhou, Wei-Ren Liu, Zhi Dai, Ying-Hong Shi, Jia Fan

“…Abstract Serine arginine-rich splicing factor 1 (SRSF1) is a key oncogenic splicing factor in various cancers, promoting abnormal gene expression through post-translational regulation. …”
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Ultrasound May Suppress Tumor Growth, Inhibit Inflammation, and Establish Tolerogenesis by Remodeling Innatome via Pathways of ROS, Immune Checkpoints, Cytokines, and Trained Immun... by Qian Yang, Ruijing Zhang, Peng Tang, Yu Sun, Candice Johnson, Jason Saredy, Susu Wu, Jiwei Wang, Yifan Lu, Fatma Saaoud, Ying Shao, Charles Drummer, Keman Xu, Daohai Yu, Rongshan Li, Shuping Ge, Xiaohua Jiang, Hong Wang, Xiaofeng Yang

“…We used microarray datasets from the NCBI GEO DataSet repository and conducted comprehensive data-mining analyses, where we examined the gene expression of 1376 innate immune regulators (innatome genes (IGs) in cells treated with LIUS. …”
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MicroRNAs Expression Profile in MN1-Altered Astroblastoma by Francesca Gianno, Evelina Miele, Claudia Sabato, Elisabetta Ferretti, Simone Minasi, Francesca Romana Buttarelli, Debora Salerno, Natalia Pediconi, Giuseppe Rubens Pascucci, Francesca Guerrieri, Andrea Ciolfi, Simone Pizzi, Maura Massimino, Veronica Biassoni, Elisabetta Schiavello, Marco Gessi, Sofia Asioli, Angela Mastronuzzi, Antonio d’Amati, Giuseppina Catanzaro, Elisabetta Viscardi, David Capper, Felice Giangaspero, Manila Antonelli

“…MicroRNAs (miRNAs) are important gene expression regulators with strong implications in biological processes. …”
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Construction of a circadian rhythm-related gene signature for predicting the prognosis and immune infiltration of breast cancer by Lin Ni, Lin Ni, He Li, Yanqi Cui, Wanqiu Xiong, Shuming Chen, Hancong Huang, Zhiwei Wang, Hu Zhao, Hu Zhao, Hu Zhao, Bing Wang, Bing Wang, Bing Wang

“…ObjectivesIn this study, we constructed a model based on circadian rhythm associated genes (CRRGs) to predict prognosis and immune infiltration in patients with breast cancer (BC).Materials and methodsBy using TCGA and CGDB databases, we conducted a comprehensive analysis of circadian rhythm gene expression and clinicopathological data. Three different machine learning algorithms were used to screen out the characteristic circadian genes associated with BC prognosis. …”
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