Construction of a prognostic model for gastric cancer based on immune infiltration and microenvironment, and exploration of MEF2C gene function by Si-yu Wang, Yu-xin Wang, Lu-shun Guan, Ao Shen, Run-jie Huang, Shu-qiang Yuan, Yu-long Xiao, Li-shuai Wang, Dan Lei, Yin Zhao, Chuan Lin, Chang-ping Wang, Zhi-ping Yuan

“…Methods Transcriptome sequence data of GC was obtained from The Cancer Genome Atlas (TCGA), the Gene Expression Omnibus (GEO) and PRJEB25780 cohort for subsequent immune infiltration analysis, immune microenvironment analysis, consensus clustering analysis and feature selection for definition and classification of gene M and N. …”
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Single-cell multiomics reveal divergent effects of DNMT3A- and TET2-mutant clonal hematopoiesis in inflammatory response by Wazim Mohammed Ismail, Jenna A. Fernandez, Moritz Binder, Terra L. Lasho, Minsuk Kim, Susan M. Geyer, Amelia Mazzone, Christy M. Finke, Abhishek A. Mangaonkar, Jeong-Heon Lee, Liguo Wang, Kwan Hyun Kim, Vernadette A. Simon, Fariborz Rakhshan Rohakthar, Amik Munankarmy, Seul Kee Byeon, Susan M. Schwager, Jonathan J. Harrington, Melissa R. Snyder, Keith D. Robertson, Akhilesh Pandey, Eric D. Wieben, Nicholas Chia, Alexandre Gaspar-Maia, Mrinal M. Patnaik

“…Using single-cell multiomics sequencing, we identify cell-specific gene expression changes associated with DNMT3A mutations, along with significant epigenomic deregulation affecting enhancer accessibility, resulting in overexpression of interleukin-32 (IL-32), a proinflammatory cytokine that can result in inflammasome activation in monocytes and macrophages. …”
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Peptide P2 targeting Vibrio parahaemolyticus PirB toxins blocks the cytotoxic effects to shrimp Litopenaeus vannamei by Xin Zhang, Ting Chen, Chunhua Ren, Yanhong Wang, Xiao Jiang, Jiasheng Huang, Bo Ma, Boxiang Zhu, Jiayue Yin, Chaoqun Hu, Peng Luo

“…The receptor candidates for PirB were genome-wide identified and selected based on gene expression profiles, and the biological function of Lv-APN1 was confirmed through RNAi. …”
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Bridging animal models and humans: neuroimaging as intermediate phenotypes linking genetic or stress factors to anhedonia by Huiling Guo, Yao Xiao, Shuai Dong, Jingyu Yang, Pengfei Zhao, Tongtong Zhao, Aoling Cai, Lili Tang, Juan Liu, Hui Wang, Ruifang Hua, Rongxun Liu, Yange Wei, Dandan Sun, Zhongchun Liu, Mingrui Xia, Yong He, Yankun Wu, Tianmei Si, Fay Y. Womer, Fuqiang Xu, Yanqing Tang, Jie Wang, Weixiong Zhang, Xizhe Zhang, Fei Wang

“…In contrast, the stress animal-like subtype did not show changes in genetic risk scores but exhibited enriched risk gene expression in somatic and endocrine tissues, along with mitochondrial dysfunction in the antioxidant stress system. …”
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Multi-omics analysis reveals the interplay between intratumoral bacteria and glioma by Ting Li, Zhanyi Zhao, Meichang Peng, Lu Zhang, Cheng Wang, Feiyang Luo, Meiqin Zeng, Kaijian Sun, Zhencheng Fang, Yunhao Luo, Yugu Xie, Cui Lv, Jiaxuan Wang, Jian-Dong Huang, Hongwei Zhou, Haitao Sun

“…Our findings shed light on the intricate interplay between intratumoral bacteria and glioma.IMPORTANCEOur study adopted a multi-omics approach to unravel the impact of intratumoral microbes on neuron-related gene expression through bacteria-associated metabolites. …”
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Using multiomic integration to improve blood biomarkers of major depressive disorder: a case-control studyResearch in context by Amazigh Mokhtari, El Chérif Ibrahim, Arnaud Gloaguen, Claire-Cécile Barrot, David Cohen, Margot Derouin, Hortense Vachon, Guillaume Charbonnier, Béatrice Loriod, Charles Decraene, Ipek Yalcin, Cynthia Marie-Claire, Bruno Etain, Raoul Belzeaux, Andrée Delahaye-Duriez, Pierre-Eric Lutz

“…Methods: We characterised gene expression and two mechanisms of epigenomic regulation, DNA methylation (DNAm) and microRNAs (miRNAs), in blood samples from a cohort of individuals with MDD and healthy controls (n = 169). …”
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Liver transcriptome analysis reveals PSC-attributed gene set associated with fibrosis progression by Alena Laschtowitz, Eric L. Lindberg, Anna-Maria Liebhoff, Laura Anne Liebig, Christian Casar, Silja Steinmann, Adrien Guillot, Jun Xu, Dorothee Schwinge, Michael Trauner, Ansgar Wilhelm Lohse, Stefan Bonn, Norbert Hübner, Christoph Schramm

“…Results: Differential gene expression analysis of the liver transcriptome from patients with PSC with advanced vs. early fibrosis revealed 431 genes associated with fibrosis development. …”
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miR-317 regulates the proliferation and apoptosis of duck follicle granulosa cells by targeting VIPR1 by Li Li, Qingwu Xin, Linli Zhang, Zhongwei Miao, Zhiming Zhu, Xiaopan Liu, Qiannan Cai, Wenli Shi, Bangzhe Zhao, Changtao Liu, Zhengkui Zhou, Azheng Liang, Qinlou Huang, Nenzhu Zheng

“…Fluorescence quantitative PCR revealed that, compared with that in the corresponding control groups, VIPR1 gene expression was significantly lower in the miR-317 mimic group (P < 0.05) but significantly higher in the miR-317 inhibitor group (P < 0.05). …”
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Cancer cells avoid ferroptosis induced by immune cells via fatty acid binding proteins by Maria Angelica Freitas-Cortez, Fatemeh Masrorpour, Hong Jiang, Iqbal Mahmud, Yue Lu, Ailing Huang, Lisa K. Duong, Qi Wang, Tiffany A. Voss, Claudia S. Kettlun Leyton, Bo Wei, Wai-Kin Chan, Kevin Lin, Jie Zhang, Efrosini Tsouko, Shonik Ganjoo, Hampartsoum B. Barsoumian, Thomas S. Riad, Yun Hu, Carola Leuschner, Nahum Puebla-Osorio, Jing Wang, Jian Hu, Michael A. Davies, Vinay K. Puduvalli, Cyrielle Billon, Thomas P. Burris, Philip L. Lorenzi, Boyi Gan, James W. Welsh

“…Furthermore, cancer cells increase Fabp7 expression in CD8+ T cells, disrupting circadian clock gene expression and triggering apoptosis through p53 stabilization. …”
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Genetic determinants of COVID-19 severity and mortality: ACE1 Alu 287 bp polymorphism and ACE1, ACE2, TMPRSS2 expression in hospitalized patients by João Locke Ferreira de Araújo, Átila Duque Rossi, Jessica Maciel de Almeida, Hugo José Alves, Isabela de Carvalho Leitão, Renata Eliane de Ávila, Anna Carla Pinto Castiñeiras, Jéssica da Silva Oliveira, Rafael Mello Galliez, Marlon Daniel Lima Tonini, Débora Souza Faffe, Shana Priscila Coutinho Barroso Barroso, Gustavo Gomes Resende, Cássia Cristina Alves Gonçalves, Terezinha Marta Pereira Pinto Castiñeiras, Amilcar Tanuri, Mauro Martins Teixeira, Renato Santana Aguiar, Cynthia Chester Cardoso, Renan Pedra de Souza

“…ACE1, ACE2, TMPRSS2, and B2M (reference gene) expression levels were evaluated in 40 cycles of quantitative PCR. …”
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Intrahepatic levels of microbiome-derived hippurate associates with improved metabolic dysfunction-associated steatotic liver disease by Maxime Deslande, Francesc Puig-Castellvi, Inés Castro-Dionicio, Romina Pacheco-Tapia, Violeta Raverdy, Robert Caiazzo, Guillaume Lassailly, Audrey Leloire, Petros Andrikopoulos, Yasmina Kahoul, Nawel Zaïbi, Bénédicte Toussaint, Frédérik Oger, Nicolas Gambardella, Philippe Lefebvre, Mehdi Derhourhi, Souhila Amanzougarene, Bart Staels, François Pattou, Philippe Froguel, Amélie Bonnefond, Marc-Emmanuel Dumas

“…Methods: We characterised liver biospies from 318 patients with obesity using RNAseq and metabolomics in liver and plasma to derive associations among hepatic hippurate, hepatic gene expression and MASLD and phenotypes. To test a potential beneficial role for hippurate in hepatic insulin resistance, we profile the metabolome of (IHH) using ultra-high-performance liquid chromatography coupled to high-resolution tandem mass spectrometry (UHPLC-MS/MS), and characterised intracellular triglyceride accumulation and glucose internalisation after a 24 h insulin exposure. …”
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LRH‐1/NR5A2 targets mitochondrial dynamics to reprogram type 1 diabetes macrophages and dendritic cells into an immune tolerance phenotype by Nadia Cobo‐Vuilleumier, Silvia Rodríguez‐Fernandez, Livia López‐Noriega, Petra I. Lorenzo, Jaime M. Franco, Christian C. Lachaud, Eugenia Martin Vazquez, Raquel Araujo Legido, Akaitz Dorronsoro, Raul López‐Férnandez‐Sobrino, Beatriz Fernández‐Santos, Carmen Espejo Serrano, Daniel Salas‐Lloret, Nila vanOverbeek, Mireia Ramos‐Rodriguez, Carmen Mateo‐Rodríguez, Lucia Hidalgo, Sandra Marin‐Canas, Rita Nano, Ana I. Arroba, Antonio Campos Caro, Alfred CO Vertegaal, Alejandro Martín‐Montalvo, Franz Martín, Manuel Aguilar‐Diosdado, Lorenzo Piemonti, Lorenzo Pasquali, Roman González Prieto, Maria Isabel García Sánchez, Decio L. Eizirik, Maria Asuncion Martínez‐Brocca, Marta Vives‐Pi, Benoit R. Gauthier

“…Cell subpopulations were then treated or not with BL001, a pharmacological agonist of LRH‐1/NR5A2, and processed for: (1) Cell surface marker profiling, (2) cytokine secretome profiling, (3) autologous T‐cell proliferation, (4) RNAseq and (5) proteomic analysis. BL001‐target gene expression levels were confirmed by quantitative PCR. …”
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Exogenous dopamine application ameliorates chilling injury and preserves quality of kiwifruit during cold storage by Morteza Soleimani Aghdam, Zeinab Asle-Mohammadi, Amin Ebrahimi, Farhang Razavi

“…By 150 µM dopamine application, higher SUMO E3 ligase (SIZ1) and target of rapamycin (TOR) genes expression accompanied by lower poly(ADP-Ribose) polymerase 1 (PARP1) and sucrose non-fermenting 1-related kinase 1 (SnRK1) genes expression was associated with higher salicylic acid, ATP, NADPH and proline accumulation in kiwifruits during storage at 1 °C for 120 days. …”
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Upregulation of p53 by tannic acid treatment suppresses the proliferation of human colorectal carcinoma by Karakurt Serdar, Kandir Sinan, Gökçek-Saraç Çiğdem

“…Tannic acid has been found to modulate enzyme, protein, and gene expressions of NQO1 in different levels and the upregulation of protein/gene expressions of p53 (p < 0.001), which leads the cells to trigger apoptosis. …”
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Integrative analysis of ATAC-seq and RNA-seq for cells infected by human T-cell leukemia virus type 1. by Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Norihiro Takenouchi, Masanori Nakagawa, Ki-Ryang Koh, Chiho Onishi, Hiromitsu Tanaka, Akihiro Fujimoto, Jun-Ichirou Yasunaga, Masao Matsuoka

“…Further, by focusing on systematically selected genes near the open chromatin regions, we quantified the difference between the infected CD4+ cells in ATL cases and healthy CD4+T cells in terms of the correlation between the chromatin structures and the gene expressions. Based on a further analysis of chromatin accessibility, we detected TLL1 (Tolloid Like 1) as one of the key genes that exhibit unique gene expressions in ATL cases. …”
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Glucagon-Like Peptide-1 Receptor Agonist Liraglutide Ameliorates the Development of Periodontitis by Noritaka Sawada, Kei Adachi, Nobuhisa Nakamura, Megumi Miyabe, Mizuho Ito, Shuichiro Kobayashi, Shin-ichi Miyajima, Yuki Suzuki, Takeshi Kikuchi, Makoto Mizutani, Taku Toriumi, Masaki Honda, Akio Mitani, Tatsuaki Matsubara, Keiko Naruse

“…Periodontitis was evaluated by histological staining, gene expressions of inflammatory cytokines in gingiva, and microcomputed tomography. …”
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Metabolic Alteration in Hepatocellular Carcinoma: Mechanism of Lipid Accumulation in Well-Differentiated Hepatocellular Carcinoma by Hideo Suzuki, Motoyuki Kohjima, Masatake Tanaka, Takeshi Goya, Shinji Itoh, Tomoharu Yoshizumi, Masaki Mori, Mariko Tsuda, Motoi Takahashi, Miho Kurokawa, Koji Imoto, Shigeki Tashiro, Akifumi Kuwano, Masaki Kato, Seiji Okada, Makoto Nakamuta, Yoshihiro Ogawa

“…Besides, the metabolomics was evaluated and integrated to gene expressions in nonalcoholic steatohepatitis (NASH)-HCC model mice. …”
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What is known and unknown about the role of neuroendocrine genes Ptprn and Ptprn2 by Stanko S. Stojilkovic, Srdjan J. Sokanovic, Stephanie Constantin

“…The protein tyrosine phosphatase receptors N and N2 are encoded by the Ptprn and Ptprn2 genes expressed in neuroendocrine cells of the hypothalamus, pituitary gland, and diffuse neuroendocrine system, including the pancreas, lung, and intestine. …”
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Drought Adaptation and Responses of Stipa krylovii Vary Among Different Regions: Evidence From Growth, Physiology, and RNA‐Seq Transcriptome Analysis by Ziqing Gong, Zehang Qu, Yulin Liu, Tao Wang, Baijie Fan, Anzhi Ren, Yubao Gao, Nianxi Zhao

“…By Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis on gene expressions of individuals from each treatment, unique enriched pathways were found under heavy drought. (2) The decrease in the number of tillers with the increasing drought was much lower for individuals from the western region than those from the other two regions. …”
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Decompensation of β-Cells in Diabetes: When Pancreatic β-Cells Are on ICE(R) by Roberto Salvi, Amar Abderrahmani

“…The seminal function of ICER is to negatively regulate the production and secretion of insulin by repressing the genes expression. This is part of adaptive response required for proper β-cells function in response to environmental factors. …”
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