Stratification system with dual human endogenous retroviruses for predicting immunotherapy efficacy in metastatic clear-cell renal cell carcinoma by Li Xu, Stephane Oudard, Catherine Sautes-Fridman, Xiaoping Su, Gabriel G. Malouf, Virginie Verkarre, Salma Kotti, Fangrong Yan, Yann-Alexandre Vano, Wolf Herve Fridman, Cheng-Ming Sun, Xiaofan Lu, Wenxuan Cheng

“…Notably, this ERV-based classification outperformed traditional transcriptomic signatures in predicting ICI efficacy and showed further improvement when combined with epigenetic DNA methylation markers.Conclusions Our findings introduce a dual ERV-based stratification system that effectively categorizes patient risk and predicts clinical outcomes for ccRCC patients undergoing ICI therapy. …”
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Alleviation of liver fibrosis by inhibiting a non-canonical ATF4-regulated enhancer program in hepatic stellate cells by Li-Xian Yang, Chuangye Qi, Si Lu, Xiang-Shi Ye, Parnaz Merikhian, Du-Yu Zhang, Tao Yao, Jiang-Sha Zhao, Ying Wu, Yongshi Jia, Bo Shan, Jinghai Chen, Xiaozhou Mou, Jia You, Wenbo Li, Yu-Xiong Feng

“…Here, we identify that ATF4, a master transcription factor in ER stress response, promotes liver fibrosis by facilitating a stress response-independent epigenetic program in hepatic stellate cells (HSCs). …”
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scCamAge: A context-aware prediction engine for cellular age, aging-associated bioactivities, and morphometrics by Vishakha Gautam, Subhadeep Duari, Saveena Solanki, Mudit Gupta, Aayushi Mittal, Sakshi Arora, Anmol Aggarwal, Anmol Kumar Sharma, Sarthak Tyagi, Rathod Kunal Pankajbhai, Arushi Sharma, Sonam Chauhan, Shiva Satija, Suvendu Kumar, Sanjay Kumar Mohanty, Juhi Tayal, Nilesh Kumar Dixit, Debarka Sengupta, Anurag Mehta, Gaurav Ahuja

“…We present scCamAge, an advanced context-aware multimodal prediction engine that co-leverages image-based cellular spatiotemporal features at single-cell resolution alongside cellular morphometrics and aging-associated bioactivities such as genomic instability, mitochondrial dysfunction, vacuolar dynamics, reactive oxygen species levels, and epigenetic and proteasomal dysfunctions. scCamAge employed heterogeneous datasets comprising ∼1 million single yeast cells and was validated using pro-longevity drugs, genetic mutants, and stress-induced models. scCamAge also predicted a pro-longevity response in yeast cells under iterative thermal stress, confirmed using integrative omics analyses. …”
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Transcriptome-wide dynamics of m6A methylation in ISKNV and Siniperca chuatsi cells infected with ISKNV by Qijin Miao, Jing Jiang, Siyou Huang, Jie Gao, Qingqing Liu, Rui Zheng, Yiling Kang, Changjun Guo, Jianguo He, Junfeng Xie

“…N6-methyladenosine (m6A), recognized as a common epigenetic modification of RNA, plays an important regulatory role during viral infection. …”
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Aminoglycoside tolerance in Vibrio cholerae engages translational reprogramming associated with queuosine tRNA modification by Louna Fruchard, Anamaria Babosan, Andre Carvalho, Manon Lang, Blaise Li, Magalie Duchateau, Quentin Giai Gianetto, Mariette Matondo, Frederic Bonhomme, Isabelle Hatin, Hugo Arbes, Céline Fabret, Enora Corler, Guillaume Sanchez, Virginie Marchand, Yuri Motorin, Olivier Namy, Valérie de Crécy-Lagard, Didier Mazel, Zeynep Baharoglu

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FTO rs17817449 Variant Increases the Risk of Severe Obesity in a Brazilian Cohort: A Case-Control Study by Salum KCR, Assis ISS, Kopke ÚA, Palhinha L, Abreu GM, Gouvêa LW, Teixeira MR, Mattos FCC, Nogueira Neto JF, Felício RFM, Rosado EL, Zembrzuski VM, Campos Junior M, Maya-Monteiro CM, Cabello PH, Carneiro JRI, Bozza PT, Kohlrausch FB, da Fonseca ACP

“…Kaio Cezar Rodrigues Salum,1,2 Izadora Sthephanie da Silva Assis,1,2 Úrsula de Almeida Kopke,3 Lohanna Palhinha,4 Gabriella de Medeiros Abreu,2,5 Laura Wendling Gouvêa,1,2 Myrela Ribeiro Teixeira,2,6,7 Fernanda Cristina C Mattos,5 José Firmino Nogueira Neto,8 Rafaela de Freitas Martins Felício,9,10 Eliane Lopes Rosado,5 Verônica Marques Zembrzuski,2 Mario Campos Junior,2 Clarissa Menezes Maya-Monteiro,4 Pedro Hernán Cabello,2 João Regis Ivar Carneiro,1 Patrícia Torres Bozza,4 Fabiana Barzotto Kohlrausch,6 Ana Carolina Proença da Fonseca2,4,11 1Medical Clinic Department, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; 2Human Genetics Laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil; 3Chester Medical School, University of Chester, Chester, UK; 4Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Rio de Janeiro, Brazil; 5Institute of Nutrition Josué de Castro, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil; 6Human Genetics Laboratory, Institute of Biology, Federal Fluminense University Niterói, Rio de Janeiro, Brazil; 7Postgraduate in Sciences and Biotechnology, Fluminense Federal University Niterói, Rio de Janeiro, Brazil; 8Department of Pathology and Laboratory, Rio de Janeiro State University, Rio de Janeiro, Brazil; 9Birth Defect Epidemiology laboratory, Oswaldo Cruz Institute, Rio de Janeiro, Brazil; 10Health Care Network for Congenital Anomalies of the Central Nervous System, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil; 11Genetics Laboratory, Grande Rio University, Rio de Janeiro, BrazilCorrespondence: Ana Carolina Proença da Fonseca, Laboratory of Immunopharmacology, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), 4365 Brasil Avenue, 108 Building – Office 44, Rio de Janeiro, 21040-360, Brazil, Tel +55(21)38658192, Email ana.proenca@ioc.fiocruz.br Kaio Cezar Rodrigues Salum, Human Genetics Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (Fiocruz), 4365 Brasil Avenue, Leônidas Deane Building – Office 611/615, Rio de Janeiro, 21040-360, Brazil, Tel +55 21 38658213, Fax +55 21 38658239, Email kaio.salum@hotmail.comPurpose: Obesity is a complex disease caused by a combination of genetic, environmental, and epigenetic factors, and is associated with an increased risk of chronic diseases. …”
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Association between METTL14 gene polymorphisms and risk of ovarian endometriosis by Zijun Zhou, Zijun Zhou, Youkun Jie, Xianyue Hu, Xianyue Hu, Guange Chen, Yanjing Bao, Yanjing Bao, Zhenbo OuYang, Liangzhi Wu, Tianyang Gao, Qiushi Zhang, Qiushi Zhang, Wenfeng Hua, Wenfeng Hua

“…Despite numerous studies indicating a correlation between epigenetic regulation and endometriosis, its precise genetic etiology remains elusive. …”
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Associations of HLA-G 3’UTR polymorphisms and increased HLA-G expression with gastric cancer susceptibility and prognosis by Ines Zemni, Daria Bortolotti, Sabrine Dhouioui, Sana Baroudi, Malek Ferjani, Inès Nasri, Yosr Zenzri, Md Ataur Rahman, Abdel Halim Harrath, Roberta Rizzo, Nadia Boujelbene, Inès Zidi

“…Background: Gastric cancer (GC) remains a serious health concern and is characterized by a multifactorial etiology involving both genetic and epigenetic factors. The aim of the current study was to examine the relationship between Human leukocyte antigen (HLA)-G 3’UTR polymorphisms and the expression of HLA-G in both tumor tissues and plasma samples from patients with GC in the Tunisian population. …”
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Patient-derived follicular lymphoma spheroids recapitulate lymph node signaling and immune profile uncovering galectin-9 as a novel immunotherapeutic target by Cèlia Dobaño-López, Juan García Valero, Ferran Araujo-Ayala, Ferran Nadeu, Fabien Gava, Carla Faria, Marine Norlund, Renaud Morin, Pascale Bernes-Lasserre, Fabian Arenas, Marta Grau, Cristina López, Irene López-Oreja, Neus Serrat, Ares Martínez-Farran, Lluís Hernández, Heribert Playa-Albinyana, Rubén Giménez, Silvia Beà, Elías Campo, Jean-Michel Lagarde, Armando López-Guillermo, Laura Magnano, Dolors Colomer, Christine Bezombes, Patricia Pérez-Galán

“…FL-PDLS recapitulates the most relevant B-cell transcriptional pathways present in FL-LN (proliferation, epigenetic regulation, mTOR, adaptive immune system, among others). …”
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Mapping naturally presented T cell antigens in medulloblastoma based on integrative multi-omics by Julia Velz, Lena K. Freudenmann, Gioele Medici, Marissa Dubbelaar, Malte Mohme, David R. Ghasemi, Jonas Scheid, Daniel J. Kowalewski, Angelica B. Patterson, Anna M. Zeitlberger, Katrin Lamszus, Manfred Westphal, Matthias Eyrich, Martina Messing-Jünger, Andreas Röhrig, Harald Reinhard, Kévin Beccaria, Rogeiro B. Craveiro, Beat M. Frey, Martin Sill, Sven Nahnsen, Marie Gauder, Konstantina Kapolou, Manuela Silginer, Tobias Weiss, Hans-Georg Wirsching, Patrick Roth, Michael Grotzer, Niklaus Krayenbühl, Oliver Bozinov, Luca Regli, Hans-Georg Rammensee, Elisabeth J. Rushing, Felix Sahm, Juliane S. Walz, Michael Weller, Marian C. Neidert

“…Integration of immunopeptidomics, transcriptomics, and epigenetic data leads to the identification of a large set of actionable targets that can be further used for the translation into the clinical setting by facilitating the informed design of immunotherapeutic approaches to children with medulloblastoma.…”
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Injectable Autocatalytic Hydrogel Triggers Pyroptosis to Stimulate Anticancer Immune Response for Preventing Postoperative Tumor Recurrence by Zhiping Rao, Yutong Zhu, Zhuang Chen, Yi Luo, Zuo Yang, Weijing Liu, Chaoqiang Qiao, Yuqiong Xia, Peng Yang, Dong‐Man Ye, Zhongliang Wang

“…The in vivo results show a 67% elimination of local tumor recurrence via treatment with DAC+CP@Gel, suggesting the successful integration of sustained drug release with autocatalysis and epigenetic modification. The results thus suggest great potential for pyroptosis‐based and injectable hydrogel‐aided strategies for preventing the postoperative recurrence of TNBC.…”
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LRP11 promotes stem-like T cells via MAPK13-mediated TCF1 phosphorylation, enhancing anti-PD1 immunotherapy by Zhishui Chen, Gang Chen, Li Chen, Xiangli Zhao, Lingjuan Sun, Zhibo Ma, Xiaosheng Tan, Yuhao Tu, Jingzeng Wang, Peixiang Lan

“…In contrast to the finding that TCF1 controls epigenetic and transcriptional reprogramming in tumor-infiltrating stem-like T cells, little is known about the regulation of TCF1. …”
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In vitro functional validation of anti-CD19 chimeric antigen receptor T cells expressing lysine-specific demethylase 1 short hairpin RNA for the treatment of diffuse large B cell l... by Zhi Guo, Zhi Guo, Mingxin He, Ning Liu, Yiqing Yang, Rui Sun, Jianxun Wang, Qiang Wang

“…CAR-T cell exhaustion is a major cause of relapse. Epigenetic modifications can regulate T cell activation, maturation and depletion; they can be applied to reduce T cell depletion, improve infiltration, and promote memory phenotype formation to reduce relapse after CAR-T cell therapy.PurposeWe propose to develop and validate in vitro the function of novel CAR-T cells for the treatment of DLBCL, which simultaneously express an anti-CD19 CAR with lysine-specific demethylase 1 (LSD1) short hairpin (sh)RNA to prevent depletion and prolong the survival of CAR-T cells.MethodsWe designed an shRNA sequence targeting LSD1 mRNA, and created a vector with the following elements: the U6 promoter driving expression of the LSD1 shRNA sequence, the EF1a promoter driving a second-generation anti-CD19 CAR sequence encoding an anti-CD19 single-chain variable fragment (FMC63), the CD8 hinge and transmembrane structural domains, the CD28 co-stimulatory structural domain, and the CD3ζ-activating structural domain. …”
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Dual specific STAT3/5 degraders effectively block acute myeloid leukemia and natural killer/T cell lymphoma by Daniel Pölöske, Helena Sorger, Anna Schönbichler, Elvin D. deAraujo, Heidi A. Neubauer, Anna Orlova, Sanna H. Timonen, Diaaeldin I. Abdallah, Aleksandr Ianevski, Heikki Kuusanmäki, Marta Surbek, Elisabeth Heyes, Thomas Eder, Christina Wagner, Tobias Suske, Martin L. Metzelder, Michael Bergmann, Maik Dahlhoff, Florian Grebien, Roman Fleck, Christine Pirker, Walter Berger, Emir Hadzijusufovic, Wolfgang R. Sperr, Lukas Kenner, Peter Valent, Tero Aittokallio, Marco Herling, Satu Mustjoki, Patrick T. Gunning, Richard Moriggl

“…We found that both AML/NKCL cells hijack STAT3/5 signaling through either upstream activating mutations in kinases, activating mutations in STAT3, mutational loss of negative STAT regulators, or genetic gains in anti‐apoptotic, pro‐proliferative, or epigenetic‐modifying STAT3/5 targets. This emphasizes a vicious cycle for proliferation and survival through STAT3/5. …”
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Proteomic analysis to explore potential mechanism underlying pseudomale sperm defect in Cynoglossus semilaevis by Xihong Li, Lu Li, Zhongkai Cui, Ming Li, Xuexue Sun, Zhijie Li, Zhangfan Chen, Lanqing Ding, Dongdong Xu, Wenteng Xu

“…Pseudomales could only produce Z-type sperm, of which the inheritance epigenetic pattern makes their offspring tend to be pseudomales. …”
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Hepatitis B Virus-KMT2B Integration Drives Hepatic Oncogenic Processes in a Human Gene-edited Induced Pluripotent Stem Cells-derived ModelSummary by Jun Tsuchiya, Masato Miyoshi, Sei Kakinuma, Fukiko Kawai-Kitahata, Akihide Kamiya, Taro Shimizu, Ayako Sato, Keiya Watakabe, Tomohiro Mochida, Kento Inada, Rion Kamimae, Shun Kaneko, Miyako Murakawa, Sayuri Nitta, Mina Nakagawa, Mamoru Watanabe, Yasuhiro Asahina, Ryuichi Okamoto

“…Comprehensive transcriptional and epigenetic analyses revealed enhanced expression of cell cycle-related genes in hepatic cells with HBV-KMT2B integration based on perturbation of histone 3 lysine 4 tri-methylation (H3K4me3), mimicking that in the original HCC sample. …”
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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

“…Over the last few years, identifying molecular biomarkers of MDD has proven challenging, reflecting interactions among multiple environmental and genetic factors. Recently, epigenetic processes have been proposed as mediators of such interactions, with the potential for biomarker development. …”
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Targeting BRD4 ameliorates experimental emphysema by disrupting super-enhancer in polarized alveolar macrophage by Difei Li, Xing Shi, Yuqiong Yang, Yao Deng, Dandan Chen, Shuyu Chen, Jinyong Wang, Guanxi Wen, Zhenyu Liang, Fengyan Wang, Jiaqi Gao, Yuanyuan Liu, Danna Wang, Ruifang Liang, Haizhao Xu, Rongchang Chen, Shanze Chen, Lingwei Wang

“…Bromodomain-containing protein 4 (BRD4), an epigenetic reader that specifically binds to histones, plays a crucial role in inflammatory diseases by regulating macrophage polarization. …”
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Genetic evidence for the causal effects of air pollution on the risk of respiratory diseases by Yanjuan Wu, Yuting Zhang, Jingcun Wang, Qiming Gan, Xiaofen Su, Sun Zhang, Yutong Ding, Xinyan Yang, Nuofu Zhang, Kang Wu

“…In this study, Mendelian randomization (MR) analysis was used to explore the causal and epigenetic relationships between various air pollutants and common respiratory diseases. …”
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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

“…Fabp7 decreases the transcription of ferroptosis-inducing genes like Lpcat3 and increases the transcription of ferroptosis-protective genes such as Bmal1 through epigenetic reprogramming. Lipidomic profiling revealed that Fabp7 increases triglycerides and monounsaturated fatty acids (MUFAs), which impede lipid peroxidation and ROS generation. …”
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