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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Multiomics analysis reveals the involvement of NET1 in tumour immune regulation and malignant progression by Jian Pang, Xiaoyan Huang, Ya Gao, Xinyu Guan, Lejia Xiong, Lun Li, Nana Yin, Mei Dai, Tong Han, Wenjun Yi

“…The prognostic value of NET1 in triple-negative breast cancer (TNBC) was further validated using real-world and Gene Expression Omnibus (GEO) data. Finally, through both in vivo and in vitro experiments, we confirmed that the overexpression of NET1 contributed to the malignant progression of TNBC cells, and we explored the potential mechanism by which NET1 regulates malignant biological behaviour through cellular experiments. …”
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A hepatocellular carcinoma model with and without parenchymal liver damage that integrates technical and pathophysiological advantages for therapy testing by Karina Benderski, Paul Schneider, Panayiotis Kordeves, Michael Fichter, Jenny Schunke, Federica De Lorenzi, Feyza Durak, Barbara Schrörs, Özlem Akilli, Fabian Kiessling, Matthias Bros, Mustafa Diken, Stephan Grabbe, Jörn M. Schattenberg, Twan Lammers, Alexandros Marios Sofias, Leonard Kaps

“…Dt81Hepa1–6 cells displayed similar gene expression as human HCC. After intrasplenic injection, all mice developed multifocal disease. …”
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Disruption of tumor-intrinsic PGAM5 increases anti-PD-1 efficacy through the CCL2 signaling pathway by Yan Li, Hong Wang, Xiaoyang Li, Yuan He, Huiquan Liu, Dong Han, Ting Mei, Yixuan Li, Zilong Xu, Xiaoying Wei, Jianguo Wang, Peijie Zhou, Yuwen Wang, Ziye Li, Junhao Ning, Anlin Wang, Jingjing Cheng, Dong Qian

“…We aim to explore whether the regulation of tumor-intrinsic PGAM5 on mitochondria affects tumor-infiltrating immune cells in the microenvironment and whether tumor-intrinsic PGAM5 can be a therapeutic target to enhance the immunotherapy efficacy of hepatocellular carcinoma (HCC).Methods We analyzed the correlation of PGAM5 expression and immune cells infiltration using Gene Expression Omnibus (GEO) and The Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) data sets based on cibersort algorithm and tumor-tissue arrays from two independent cohorts. …”
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Mechanosensor YAP mediates bone remodeling via NF-κB p65 induced osteoclastogenesis during orthodontic tooth movement by Jie Deng, Yu-Ning Zhang, Ru-Shui Bai, Ting-Ting Yu, Yi Zhao, Hao Liu, Yun-Fan Zhang, Tian-Min Xu, Bing Han

“…In addition, RNA-sequencing highlighted increased nuclear factor kappa B (NF-κB) signaling, mineral absorption, and osteoclast differentiation at day-1 and 3. Moreover, gene expression analysis showed similar trends for NF-κB p65, YAP1, and TEA domain 1 (TEAD1) during this time. …”
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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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Intestine-derived fibroblast growth factor 19 alleviates lipopolysaccharide-induced liver injury by regulating bile acid homeostasis and directly improving oxidative stress by Xiaomeng Tang, Jingjing Ning, Yilin Zhao, Shuyun Feng, Lujing Shao, Tiantian Liu, Huijie Miao, Yucai Zhang, Chunxia Wang

“…Liver bile acid profiles and the gene expression involved in bile acid homeostasis were investigated in the mice groups. …”
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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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Acute stress triggers sex-dependent rapid alterations in the human small intestine microbiota composition by Bruno K. Rodiño-Janeiro, Bruno K. Rodiño-Janeiro, Olfat Khannous-Lleiffe, Olfat Khannous-Lleiffe, Marc Pigrau, Marc Pigrau, Marc Pigrau, Jesse R. Willis, Jesse R. Willis, Eloísa Salvo-Romero, Eloísa Salvo-Romero, Eloísa Salvo-Romero, Adoración Nieto, Adoración Nieto, Elba Expósito, Elba Expósito, Elba Expósito, Marina Fortea, Marina Fortea, Cristina Pardo-Camacho, Cristina Pardo-Camacho, Cristina Pardo-Camacho, Mercé Albert-Bayo, Mercé Albert-Bayo, Ana María González-Castro, Ana María González-Castro, Ana María González-Castro, Ana María González-Castro, Danila Guagnozzi, Danila Guagnozzi, Danila Guagnozzi, Danila Guagnozzi, Cristina Martínez, Cristina Martínez, Cristina Martínez, Beatriz Lobo, Beatriz Lobo, Beatriz Lobo, Beatriz Lobo, María Vicario, María Vicario, Javier Santos, Javier Santos, Javier Santos, Javier Santos, Toni Gabaldón, Toni Gabaldón, Toni Gabaldón, Toni Gabaldón, Carmen Alonso-Cotoner, Carmen Alonso-Cotoner, Carmen Alonso-Cotoner, Carmen Alonso-Cotoner

“…Microbiota alterations significantly correlated with changes in psychological responses, hormones, and gene expression in the intestinal mucosal. Cold pain stress was also associated with activation of autonomic, hormonal and psychological response, with no differences between sexes.ConclusionsAcute stress elicits rapid alterations in bacterial composition in the jejunum of healthy subjects and these changes are more pronounced in females. …”
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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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Evaluation of Inflammation-Related Proteins in Multiple Sclerosis Disease with Relapses and Remissions by Nisa Hocaoğlu, Nur Damla Korkmaz, Birsen Elibol, Zehra Cemre Karakayalı, Şule Terzioğlu-Uşak, Azize Esra Gürsoy

“…After RNA isolation and cDNA conversion, NLRP3, ASC, NLRX1, IL-1&#946;, and IL-18 gene expressions were measured in real time-polymerase chain reaction. …”
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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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Mechanisms of Rhodopsin-Related Inherited Retinal Degeneration and Pharmacological Treatment Strategies by Maria Azam, Beata Jastrzebska

“…Mutations in various genes expressed in the retina are associated with RP. …”
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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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Antiaging properties of chlorogenic acid through protein and gene biomarkers in human skin fibroblast cells as photoaging model by Ermi Girsang, Chrismis N. Ginting, I Nyoman Ehrich Lister, Wahyu Widowati, Afif Yati, Hanna Sari Widya Kusuma, Rizal Azis

“…CA at 25 μg/mL resulted in the most significant down-regulation of MMP-1, CASP-3, and CASP-8 genes’ expression (3.27, 1.25, and 3.59, respectively). …”
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