Multiomics reveals tumor microenvironment remodeling in locally advanced gastric and gastroesophageal junction cancer following neoadjuvant immunotherapy and chemotherapy by Yong Liu, Xia Wang, Rui Liu, Le Zhang, Hongli Li, Ting Deng, Lijun Ma, Yanhui Zhang, Lan Su, Yi Ba, Zhi Ji, Jiaqi Xin, Duo Zuo, Xinze Lv, Shaohua Ge, Tingting Ding

“…However, the mechanisms of response and resistance remain largely undefined. A detailed multiomic investigation is essential to elucidate these mechanisms.Methods We performed whole-exome sequencing, whole-transcriptome sequencing, multiplex immunofluorescence and single-cell RNA sequencing on matched pretreatment and post-treatment samples from 30 patients enrolled in an investigator-initiated Phase 2 clinical trial (NCT04908566). …”
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Essential Role for endogenous siRNAs during meiosis in mouse oocytes. by Paula Stein, Nikolay V Rozhkov, Fan Li, Fabián L Cárdenas, Olga Davydenko, Lee E Vandivier, Brian D Gregory, Gregory J Hannon, Richard M Schultz

“…Both small RNA species silence gene expression post-transcriptionally in association with the ARGONAUTE (AGO) family of proteins. …”
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Differences in gene expression between high and low tolerance rainbow trout (Oncorhynchus mykiss) to acute thermal stress. by Leah A Turner, Anne A Easton, Moira M Ferguson, Roy G Danzmann

“…Understanding the mechanisms that underlie the adaptive response of ectotherms to rising temperatures is key to mitigate the effects of climate change. …”
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Microphysiological gut-on-chip enables extended in vitro development of Cryptosporidium hominis by Samantha Gunasekera, Benjamin Thierry, Brendon King, Paul Monis, Jillian M. Carr, Abha Chopra, Mark Watson, Mark O’Dea, Edward Cheah, Ramesh Ram, Peta L. Clode, Nawal Hijjawi, Una Ryan

“…Differences in the HCT-8 transcriptome with and without fluid shear stress, and the host-parasite interaction, were both assessed using bulk transcriptomics.ResultsTranscriptomic analysis of the HCT-8 cell line cultured within the gut-on-chip demonstrated a metabolic shift towards oxidative phosphorylation when compared to the same cell line cultured under static conditions. …”
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Novel regulators of PrPC biosynthesis revealed by genome-wide RNA interference. by Daniel Heinzer, Merve Avar, Daniel Patrick Pease, Ashutosh Dhingra, Jiang-An Yin, Elke Schaper, Berre Doğançay, Marc Emmenegger, Anna Spinelli, Kevin Maggi, Andra Chincisan, Simon Mead, Simone Hornemann, Peter Heutink, Adriano Aguzzi

“…Here we performed an arrayed whole-transcriptome RNA interference screen to identify modulators of PrPC expression. …”
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The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system. by Tobias Sahr, Christophe Rusniok, Francis Impens, Giulia Oliva, Odile Sismeiro, Jean-Yves Coppée, Carmen Buchrieser

“…The carbon storage regulator protein CsrA regulates cellular processes post-transcriptionally by binding to target-RNAs altering translation efficiency and/or their stability. …”
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Development and characterization of high-efficiency cell-adapted live attenuated vaccine candidate against African swine fever by Min Ho Kim, Ashan Subasinghe, Yongkwan Kim, Hyeok-Il Kwon, Yehjin Cho, Kiramage Chathuranga, Ji-Won Cha, Ji-Yoon Moon, Ji-Hyeon Hong, Jin Kim, Seung-Chul Lee, Niranjan Dodantenna, Nuwan Gamage, W. A. Gayan Chathuranga, Yeonji Kim, In-Joong Yoon, Joo Young Lee, In Pil Mo, Weonhwa Jheong, Sung-Sik Yoo, Jong-Soo Lee

“…ASFV-MEC-01 conferred 100% protection against challenge with lethal parental ASFV, which correlated with high ASFV-specific humoral and cellular immune responses. Additionally, ASFV-MEC-01 was not detected in blood until 28 days post-inoculation. …”
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Analysis of Alternative Splicing Events and Identification of Key Genes in <i>Brassica napus</i> Leaves Infected by <i>Leptosphaeria biglobosa</i> by Xinning Ma, Lin Yuan, Jiuru Huangfu, Mengjiao Yan, Chen Guo, Lili Zhao, Hongxia Sun, Xiaoqing Jia, Ziqin Li, Haiyan Huangfu

“…Here, we used the Illumina Novaseq sequencing platform to conduct transcriptome sequencing on canola (<i>Brassica napus</i>) leaves infected with the blackleg pathogen (<i>Leptosphaeria biglobosa</i> strain nm⁻¹) at 0 h, 72 h, 120 h, and 168 h post-inoculation to investigate the mechanism of AS coordination with transcriptional regulation in canola’s response to blackleg disease. …”
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Stabilization of Transcription Factor, HIF-1α by Prolylhydroxylase 1 Knockout Reduces Cardiac Injury After Myocardial Infarction in Mice by Mahesh Thirunavukkarasu, Seetur R. Pradeep, Babatunde Oriowo, Sue Ting Lim, Monica Maloney, Shayan Ahmed, Nicole Taylor, David M. Russell, Pavayee Socrates, Ethan Batko, Matan Berkovsky, John Alexander Palesty, Nilanjana Maulik

“…Hypoxia-inducible factor (HIF) is crucial in regulating signal responses mediated by hypoxia. HIF regulates the transcription of many genes involved in the response to hypoxia and ischemic insult. …”
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Transcriptional and cytokine signatures of Mycobacterium abscessus complex pulmonary disease during disease progression and treatment. by Ayesa Syenina, Yi Hern Tan, Danny Jian Hang Tng, Sandy Xue Qi Sim, Valerie Shyn Yun Chew, Jia Xin Yee, Eugenia Ziying Ong, Eng Eong Ooi, Jenny Guek Hong Low, Dorothy Hui Lin Ng

“…A major clinical challenge lies in distinguishing infection-related symptoms from underlying lung disease and identifying reliable prognosticators to guide treatment decisions and monitoring therapeutic response.<h4>Methodology/principal findings</h4>To address the gaps in clinically relevant indicators, we profiled whole blood transcriptome and 45 plasma proteins of MABC-PD patients across different disease and treatment phases. …”
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RBM47 functions as an anti-oncogene by regulating expression and alternative splicing of cell proliferation and apoptosis associated genes in colorectal cancer cells by Guangshi Liu, Tao Li, Peng Li, Suyan Wei, Kamuran Abulizi

“…Abstract Transcriptional and post-transcriptional regulation mediated by RNA binding proteins (RBPs) have essential influence on the progression of colorectal cancer (CRC), while the underlying mechanisms need to be clarified. …”
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FGF21 and its underlying adipose tissue-liver axis inform cardiometabolic burden and improvement in obesity after metabolic surgeryResearch in context by Marie Patt, Isabel Karkossa, Laura Krieg, Lucas Massier, Kassem Makki, Shirin Tabei, Thomas Karlas, Arne Dietrich, Martin Gericke, Michael Stumvoll, Matthias Blüher, Martin von Bergen, Kristin Schubert, Peter Kovacs, Rima M. Chakaroun

“…Relationships between FGF21 levels, AT histology, transcriptomes and proteomes, cardiometabolic risk factors, and post-surgery metabolic adjustments were assessed using univariate and multivariate analyses, causal mediation analysis, and network integration of AT transcriptomes and proteomes. …”
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Pro-repair macrophages driven by CGRP rescue white matter integrity following intracerebral hemorrhage by Huaping Huang, Yirui Kuang, Yang Chen, Yi Zhang, Jiayin Zhou, Xian Yu, Yonghe Zheng, Lingxin Cai, Wanglu Hu, Liansheng Gao, Haijian WU, Hui Ling, Xiao Dong, Hang Zhou, Xiaobo Yu, Yucong Peng, Gao Chen, Xiaoyu Wang, Wei Yan

“…CGRP, elevated in meninges and bone marrow post-ICH, drove macrophage polarization toward THBS + phenotypes. …”
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Machine Learning and Experimental Validation Reveal MYH11 as a Novel Prognostic Biomarker and Therapeutic Target in Bladder Cancer by Tan Z, Chen X, Fu S, Huang Y, Li H, Gong C, Lv D, Yang C, Wang J, Ding M, Wang H

“…Interestingly, high-risk patients showed a significantly lower response to PD-L1 treatment, with higher TIDE scores. …”
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Interferon regulates neural stem cell function at all ages by orchestrating mTOR and cell cycle by Damian Carvajal Ibañez, Maxim Skabkin, Jooa Hooli, Santiago Cerrizuela, Manuel Göpferich, Adrien Jolly, Katrin Volk, Marc Zumwinkel, Matilde Bertolini, Gianluca Figlia, Thomas Höfer, Guenter Kramer, Simon Anders, Aurelio A Teleman, Anna Marciniak‐Czochra, Ana Martin‐Villalba

“…Interferon orchestrates cell cycle and mTOR activity to post‐transcriptionally repress Sox2 and induces quiescence. …”
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Case Report: A rare pediatric case of B-cell lymphoblastic lymphoma presenting as an isolated renal mass with EWSR1::FLI1 translocation and germline CHEK2 variant by Katelyn P. Daniels, Kim E. Nichols, Arti S. Pandey, Gabriela Gheorghe, Sara Helmig, Kevin Garrett, Asim K. Bag, Hiroto Inaba, Raul Ribeiro

“…Given the unusual clinical presentation, somatic and germline genetic findings, and impossibility of measuring early response to therapy, the classical treatment of lymphoblastic lymphoma was modified. …”
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Complementing muscle regeneration—fibro-adipogenic progenitor and macrophage-mediated repair of elderly human skeletal muscle by Jonas Brorson, Lin Lin, Jakob Wang, Amanda Bæk, Tine Borum Billeskov, Frederik Forsberg Thybo, Jesper Just, János Haskó, Christen Ravn, Rehne L. Hansen, Mats Bue, Jens Otto Lunde Jørgensen, Yonglun Luo, Niels Jessen, Jean Farup

“…Here, we unravel the intricate dynamics of elderly human skeletal muscle regeneration by combining spatial, temporal, and single cell transcriptomics. Using spatial RNA sequencing (n = 3), we profile the expression of human protein-coding genes in elderly human skeletal muscle biopsies before as well as 2-, 8-, and 30-day post injury (NCT03754842). …”
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Trained human bone marrow mesenchymal stem cells restore tissue immuno-microenvironment in fulminant hepatic failure mice by Bingqi Li, Xiaofei Zeng, Jing Jiang, Qian Zhou, Li Tong, Xi Liang, Jiaojiao Xin, Xi Chen, Xiao Wu, Yuheng Kong, Shiwen Ma, Jinjin Luo, Wei Qiang, Bing Zhu, Xinhua Luo, Jun Li, Dongyan Shi

“…The therapeutic potential of T-hBMSC was evaluated through transplantation into FHF mice. Transcriptomic analysis was performed to elucidate the mechanism of liver regeneration post-transplantation of T-hBMSC. …”
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Identification and validation of hub genes related to neutrophil extracellular traps-mediated cell damage and immune recruitment during abdominal aortic aneurysm by Chuanlong Lu, Heng Wang, Maolin Qiao, Runze Chang, Jinshan Chen, Lizheng Li, Keyi Fan, Sheng Yan, Ruijing Zhang, Honglin Dong

“…Abstract Previous research has shown that the formation of Neutrophil Extracellular Traps (NETs), mediated by neutrophils, leads to an increase in inflammatory cell response and cellular tissue damage during Abdominal Aortic Aneurysm (AAA). …”
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Transcriptional profiling of Chlamydia trachomatis and its host in an ex vivo endocervical primary cell culture system using dual RNA sequencing by Olusola Olagoke, Siddharth Chittaranjan, Deborah Dean, Deborah Dean, Deborah Dean, Deborah Dean, Deborah Dean

“…Understanding host-pathogen interactions is challenging but dual RNA sequencing offers simultaneous transcriptome data for comprehensive interrogations into these interactions. …”
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