Duodenal Organoids From Metabolic Dysfunction-Associated Steatohepatitis Patients Exhibit Absorptive and Barrier Alterations by Alia Hadefi, Morgane Leprovots, Gilles Dinsart, Maryam Marefati, Marjorie Vermeersch, Daniel Monteyne, David Pérez-Morga, Anne Lefort, Frédérick Libert, Laurine Verset, Claire Liefferinckx, Christophe Moreno, Jacques Devière, Eric Trépo, Marie-Isabelle Garcia

“…Biopsies and patient-derived organoid transcriptomes were then analyzed to evaluate if specific intestinal pathways were differentially modulated in MASH subjects. …”
Get full text

Identifying and exploiting combinatorial synthetic lethality by characterizing adaptive kinome rewiring of EGFRvIII-driven glioblastoma by Benjamin Lin, Abigail K. Shelton, Erin Smithberger, Julia Ziebro, Kasey R. Skinner, Ryan E. Bash, Richard Kirkman, Allie Stamper, Madison Butler, Alex Flores, Steven P. Angus, Michael P. East, Timothy F. Cloughesy, David A. Nathanson, Michael E. Berens, Jann N. Sarkaria, Zev A. Binder, Donald M. O’Rourke, Timothy C. Howton, Brittany N. Lasseigne, Christopher D. Willey, Gary L. Johnson, Anita B. Hjelmeland, Frank B. Furnari, C. Ryan Miller

“…Further molecular interrogation of signature genes revealed that drug treatment induces an unexpected increase in Cdk6 protein, but not mRNA, despite live cell imaging and transcriptomic evidence indicating decreased proliferation. …”
Get full text

Multi-omics analysis reveals immunosuppression in oesophageal squamous cell carcinoma induced by creatine accumulation and HK3 deficiency by Yingzhen Gao, Siyu He, Xiaoyan Meng, Kun Zheng, Heyang Cui, Yikun Cheng, Xinyuan Shen, Yuanfang Zhai, Binbin Zou, Fang Wang, Hongyi Li, Pengzhou Kong, Yanqiang Wang, Xuefei Feng, Bin Yang, Ruifang Sun, Yongsheng Meng, Enwei Xu, Yanlin Guo, Ning Ding, Weimin Zhang, Xiaolong Cheng, Lunzhi Dai, Yongping Cui, Ling Zhang

“…Methods We performed metabolomic and proteomic analyses combined with previous genomic and transcriptomic data, identified multi-omics-linked molecular features, and constructed metabolic-immune interaction-based ESCC classifiers in a discovery cohort and an independent validation cohort. …”
Get full text

Building digital histology models of transcriptional tumor programs with generative deep learning for pathology-based precision medicine by Hanna M. Hieromnimon, James Dolezal, Kristina Doytcheva, Frederick M. Howard, Sara Kochanny, Zhenyu Zhang, Robert L. Grossman, Kevin Tanager, Cindy Wang, Jakob Nikolas Kather, Evgeny Izumchenko, Nicole A. Cipriani, Elana J. Fertig, Alexander T. Pearson, Samantha J. Riesenfeld

“…Molecular assays, like transcriptomics, provide an information-rich view of the tumor that can be leveraged to inform therapeutic selection. …”
Get full text

A Bread Wheat Line with the Substituted Wild Emmer Chromosome 4A Results in Fragment Deletions of Chromosome 4B and Weak Plants by Yu Qiu, Fei Lu, Bohao Yang, Xin Hu, Yanhao Zhao, Mingquan Ding, Lei Yang, Junkang Rong

“…These results demonstrate that 4B segmental deletions drive weak phenotypes in CASL4AL progeny, and provide experimental evidence for chromosome deletions induced in wild emmer chromosome substitution lines. …”
Get full text

Genomic insights reveal community structure and phylogenetic associations of endohyphal bacteria and viruses in fungal endophytes by Efraín Escudero-Leyva, Michal Belle, Abolfazl DadkhahTehrani, James N. Culver, Marcelo Araya-Salas, Joseph P. Kutza, Natasha Goldson, Max Chavarría, Priscila Chaverri

“…This study integrates genomic and transcriptomic approaches to (1) characterize the diversity of endohyphal bacterial and viral communities in fungal endophytes isolated from Fagus grandifolia leaves, and (2) assess potential host specialization through phylogenetic signal analyses. …”
Get full text

DNA Hypomethylation Underlies Epigenetic Swapping between <i>AGO1</i> and <i>AGO1-V2</i> Isoforms in Tumors by Jean S. Fain, Camille Wangermez, Axelle Loriot, Claudia Denoue, Charles De Smet

“…This expression pattern classifies <i>AGO1-V2</i> into the group of “Cancer-Germline” (CG) genes. Analysis of transcriptomic and methylomic datasets provided evidence that transcriptional activation of <i>AGO1-V2</i> depends on DNA demethylation of its promoter region. …”
Get full text

Multi-omics reveals the polyethylene terephthalate carcinogenicity: Cancer progression and immune microenvironment by Kangping Yang, Xianhuan Zhou, Kai Wu, Jiaqiang Wu, Chunxia Huang, Liang Yang

“…Our findings not only delineate PET's role in tumorigenesis but also establish a computational-experimental framework for environmental toxicant evaluation. This work provides critical insights for developing prevention strategies against pollutant-driven malignancies, bridging molecular toxicology with clinical cancer biology.…”
Get full text

Human umbilical cord mesenchymal stem cells restore chemotherapy-induced premature ovarian failure by inhibiting ferroptosis in vitro ovarian culture system by Jiaqi Chen, Zhuoying He, Wenjuan Xu, Yumiao Kang, Fengyu Zhu, Heng Tang, Jianye Wang, Fei Zhong

“…This research contributes to evaluating the effectiveness of hUCMSCs in treating chemotherapy-induced POF by inhibiting ferroptosis in an in vitro ovarian culture system and provides a potential therapeutic strategy for chemotherapy-induced POF.…”
Get full text

Deubiquitination of DNM1L by USP3 triggers the development and metastasis of gallbladder carcinoma by Ruopeng Liang, Xiaoxue Zhang, Shitao Wu, Jing Liu, Yunpeng Zhai, Chaojie Lin, Zhenya Wang, Yi Zhang, Hao Chen, Rongtao Zhu

“…The metabolomics data from transcriptomics/metabolomics were analyzed to identify the differentially expressed genes/metabolites of DNM1L in GBC. …”
Get full text

CXCL12/CXCR4 axis mediates CD8 + T cell overactivation in the progression of viral myocarditis by Li Zhang, Keyu Liu, Xiuyun Duan, Shan Zhou, Hailin Jia, Yingnan You, Bo Han

“…Conclusions These findings provide deeper insights into the immune landscape of pediatric FM, uncovering a novel role of the CXCL12/CXCR4 axis in driving CD8+T cell responses in myocarditis. …”
Get full text

Lake Baikal amphipods and their genomes, great and small by P. B. Drozdova, E. V. Madyarova, A. N. Gurkov, A. E. Saranchina, E. V. Romanova, J. V. Petunina, T. E. Peretolchina, D. Y. Sherbakov, M. A. Timofeyev

“…The existing taxonomies of this group list over 350 species and subspecies, which, according to the molecular phylogenetic studies of marker genes, full transcriptomes and mitochondrial genomes, originated from at least two introductions into the lake. …”
Get full text

Complex immunotoxic effects of T-2 Toxin on the murine spleen and thymus: Oxidative damage, inflammasomes, apoptosis, and immunosuppression by Mingyan Chen, Yanfang Zhang, Yangbo Zhao, Kewei Cao, Ruiyan Niu, Dongguang Guo, Zilong Sun

“…These findings reveal critical pathways through which T-2 impairs immune system functionality and provide a basis for developing targeted therapeutic strategies to mitigate its immunotoxic effects.…”
Get full text

Immune-Mediated Bidirectional Causality Between Inflammatory Bowel Disease and Chronic Periodontitis: Evidence from Mendelian Randomization and Integrative Bioinformatics Analysis by Zhijun Feng, Zihan Chen, Xiaoxu Wang, Meijuan Zhou, Shupeng Liu

“…<b>Conclusions</b>: Our findings provide genetic evidence supporting a bidirectional causal relationship between IBD and periodontitis. …”
Get full text

Citrullinated IGF2BP1 promotes rheumatoid synovial aggression via increasing the mRNA stability of SEMA3D by Yang Qin, Li Liu, Yanwen Zhang, Xiaowei Chen, Jiani Zhang, Sunwang Ling, Jianguang Wang, Xinyu Yang

“…In this study, a new citrullinated protein of IGF2BP1 is discovered, and the molecular mechanism of its citrullinated modification promoting the progression of RA disease is elucidated, which provides theoretical basis for the diagnosis and treatment of RA.…”
Get full text

BubR1 Controls Heart Development by Promoting Expression of Cardiogenesis Regulators by Renju Pun, Aradhana Thapa, Sylar R. Takafuji, Rexton M. Suzuki, Gabrielle F. Kay, Toni D. Howard, Michael H. Kim, Brian J. North

“…Finally, CellChat analysis provided details on the major signaling interactions that were either absent or hyperactive in the BubR1 knockout heart. …”
Get full text

The pre-mRNA splicing modulator pladienolide B inhibits Cryptococcus neoformans germination and growth by Sierra L. Love, Megan C. McKeon, Henrik Vollmer, Joshua C. Paulson, Nanami Oshimura, Olivia Valentine, Sébastien C. Ortiz, Christina M. Hull, Aaron A. Hoskins

“…This combination treatment resulted in significant reductions in fungal growth and prevented spore germination. Transcriptomic analysis revealed that PladB inhibits splicing in C. neoformans and results in widespread intron retention. …”
Get full text

Panoramic spatial enhanced resolution proteomics (PSERP) reveals tumor architecture and heterogeneity in gliomas by Ziyan Xu, Yunzhi Wang, Tao Xie, Rongkui Luo, Heng-Li Ni, Hang Xiang, Shaoshuai Tang, Subei Tan, Rundong Fang, Peng Ran, Qiao Zhang, Xiaomeng Xu, Sha Tian, Fuchu He, Wenjun Yang, Chen Ding

“…Through integrative analysis with single-cell transcriptomic data, we elucidated the cellular composition and cell–cell communications in a spatial context. …”
Get full text

Mechanism of Action of <i>Fusarium oxysporum</i> CCS043 Utilizing Allelochemicals for Rhizosphere Colonization and Enhanced Infection Activity in <i>Rehmannia glutinosa</i> by Feiyue Yuan, Fuxiang Qiu, Jiawei Xie, Yongxi Fan, Bao Zhang, Tingting Zhang, Zhongyi Zhang, Li Gu, Mingjie Li

“…This study provides a preliminary indication that the use of allelochemicals by <i>F. oxysporum</i> CCS043 can promote its own growth and proliferation and enhance infection activity. …”
Get full text

Identification of neutrophil extracellular trap-related biomarkers in ulcerative colitis based on bioinformatics and machine learning by Jiao Li, Yupei Liu, Zhiyi Sun, Suqi Zeng, Caisong Zheng

“…Finally, the expression of core genes in patients was validated using Quantitative real-time PCR (qRT-PCR), and potential therapeutic drugs for UC were explored through drug target databases.ResultDifferential analysis of transcriptomic sequencing data from UC samples identified 29 DEGs related to NETs. …”
Get full text