SEC61 translocon gamma subunit is correlated with glycolytic activity, epithelial mesenchymal transition and the immune suppressive phenotyp... by Zhou Changshuai, Cui Huanhuan, Yang Yuechao, Chen Lei, Feng Mingtao, Gao Yang, Li Deheng, Li Liangdong, Chen Xin, Li Xiaoqiu, Cao Yiqun

“…Remarkably, we identify a negative association between SEC61G expression levels and the infiltration of critical immune cell populations within the TME, along with correlations with immune checkpoint gene expression and tumor heterogeneity scores in LUAD. …”
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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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Integrated transcriptomic analysis reveals evolutionary and developmental characteristics of tendon ossification in teleost by Xu-Dong Wang, Fei-Long Shi, Jia-Jia Zhou, Zheng-Yu Xiao, Tan Tu, Xue-Mei Xiong, Chun-Hong Nie, Shi-Ming Wan, Ze-Xia Gao

“…Notably, a compensatory effect was observed in cell differentiation and gene expression in runx2b −/− zebrafish, suggesting that runx2b and the candidate genes, such as clec3bb, were involved in the gene network of IB development. …”
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Exploring the metabolic patterns and response mechanisms of bile acids during fasting: A study with poultry as an example by Jun Zhang, Yujie Gong, Yidan Zhu, Qingduo Zeng, Hao Zhang, Ruili Han, Yujie Guo, Donghua Li, Yadong Tian, Xiangtao Kang, Yawei Yang, Zhuanjian Li, Ruirui Jiang

“…The physiological and biochemical parameters and gene expression of multiple tissues of chickens at every critical time node were measured by ELISA and qPCR. …”
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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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Single-nucleotide polymorphisms in genes associated with the vitamin D pathway related to clinical and therapeutic outcomes of American tegumentary leishmaniasis by Iara Barreto Neves Oliveira, Ramon Vieira Nunes, Vanessa Rafaela Milhomem Cruz Leite, Camila Freire Araújo, Murilo Barros Silveira, Sebastião Alves Pinto, Lorena Andrade Lamounier, Clayton Luiz Borges, Edésio Martins, Iane de Oliveira Pires Porto, Rodrigo Saar Gomes, Fátima Ribeiro-Dias

“…In addition, some SNPs appear to influence the VDR and CYP27B1 (IL15 rs10519613 and IL15 rs3775597) and IL6 (VDR rs7975232) expressions in LCL and the IL17 expression in ML (IL15 rs3775597). Gene expression was also correlated with clinical parameters, such as number of lesions (CYP27B1 mRNA) and treatment failure (VDR mRNA). …”
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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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Identification of Three Significant Genes Associated with Immune Cells Infiltration in Dysfunctional Adipose Tissue-Induced Insulin-Resistance of Obese Patients via Comprehensive B... by Ming Zhai, Peipei Luan, Yefei Shi, Bo Li, Jianhua Kang, Fan Hu, Mingjie Li, Lei Du, Donglei Zhou, Weixia Jian, Wenhui Peng

“…In this study, we would like to explore the correlation of genes and immune cells infiltration in adipose tissue via comprehensive bioinformatics analyses and experimental validation in mice and human adipose tissue. Methods. Gene Expression Omnibus (GEO) datasets (GSE27951, GSE55200, and GSE26637) of insulin-resistant individuals or type 2 diabetes patients and normal controls were downloaded to get differently expressed genes (DEGs), and GO and KEGG pathway analyses were performed. …”
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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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Neoadjuvant anti-PD1 immunotherapy for surgically accessible recurrent glioblastoma: clinical and molecular outcomes of a stage 2 single-arm expansion cohort by J. Ricardo McFaline-Figueroa, Lu Sun, Gilbert C. Youssef, Raymond Huang, Gang Li, Jiyoon Kim, Eudocia Q. Lee, Lakshmi Nayak, Ugonma Chukwueke, Rameen Beroukhim, Tracy T. Batchelor, E. Antonio Chiocca, Richard G. Everson, Lisa Doherty, Jennifer Stefanik, Kathryn Partridge, Amanda Spearman, Alexa Myers, Catharina Westergaard, Alyssa Russ, Maria Lavallee, Anna Smokovich, Corey LaForest-Roys, Rachel Garcia Fox, Christine McCluskey, Wenya Linda Bi, Omar Arnaout, PierPaolo Peruzzi, G. Rees Cosgrove, Keith L. Ligon, Isabel Arrillaga-Romany, Jennifer L. Clarke, David A. Reardon, Timothy F. Cloughesy, Robert M. Prins, Patrick Y. Wen

“…Neoadjuvant pembrolizumab was associated with suppression of cell cycle/cancer proliferation genes and upregulation of T-cell/interferon-related gene expression. This signature was unique to patients treated with neoadjuvant pembrolizumab and was an independent positive risk factor for survival. …”
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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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The analysis of gene co-expression network and immune infiltration revealed biomarkers between triple-negative and non-triple negative breast cancer by Yao Yi, Yao Yi, Yu Zhong, Yu Zhong, Lianhua Xie, Lianhua Xie, Shuxian Lu, Shuxian Lu, Yifeng Zhang, Yifeng Zhang

“…CIBERSORT analysis was used to characterize the composition of immune cells within complex tissues based on gene expression data, typically derived from bulk RNA sequencing or microarray datasets. …”
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Identification of PET/CT radiomic signature for classification of locally recurrent rectal cancer: A network-based feature selection approach by Sara Dalmonte, Maria Adriana Cocozza, Dajana Cuicchi, Daniel Remondini, Lorenzo Faggioni, Paolo Castellucci, Andrea Farolfi, Emilia Fortunati, Alberta Cappelli, Riccardo Biondi, Arrigo Cattabriga, Gilberto Poggioli, Stefano Fanti, Gastone Castellani, Francesca Coppola, Nico Curti

“…Feature selection was performed using a novel approach derived from gene expression analysis, based on the DNetPRO algorithm. …”
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