Phylogenomics of East Asian lineage within subgenus Anguinum (Allium, Amaryllidaceae): insights into its taxonomic puzzles and phylogenetic conflicts by Rui-Yu Cheng, Yuan Wang, Bo-Ni Song, Jin-Bo Tan, Jia-Hui Sun, Song-Dong Zhou, Xing-Jin He, Deng-Feng Xie

“…In this study, we collected 102 samples, including 45 transcriptomes and 57 plastid genomes, covering multiple populations of all currently recognized taxa within the EAL and relatives. …”
Get full text

Recombinant serralysin metalloproteases D enhances the intracellular replication of infectious bovine rhinotracheitis virus by Longfei Yan, Yanran Li, Jiancheng Qi, Li Ren, Xueke Zhou, Liping Gou, Zhicai Zuo

“…Quantification of IBRV gB gene copy numbers using fluorescence quantification PCR (FQ-PCR) revealed that rSPD promotes viral replication during the intracellular stage, without affecting viral adsorption, entry, or directly interacting with viral particles. The transcriptomic analysis further demonstrated that rSPD suppresses innate immune responses while amplifying inflammatory pathways in IBRV-infected MDBK cells. …”
Get full text

Expression Pattern Analyzation and Regulation Genes Identification on the Purple Phenotype in the Different Tissues of the Purple Pak-choi and Zicaitai by Yating Zhu, Xia Wang, Xiuping Tu, Shujiang Zhang, Shifan Zhang, Hui Zhang, Rifei Sun, Xiuxiu Xu, Xinyu Gao, Guoliang Li, Fei Li

“…In conjunction with field identification, RNA-seq was used to sequence the transcriptomes of the purple expression sites of purple pak-choi, zicaitai, and their F₁. …”
Get full text

Newly identified c-di-GMP pathway putative EAL domain gene STM0343 regulates stress resistance and virulence in Salmonella enterica serovar Typhimurium by Kaifeng Chen, Lili Li, Nanwei Wang, Zhouping Zhou, Peng Pan, Chenggang Xu, Dage Sun, Jiayi Li, Changzhi Dai, Dai Kuang, Ming Liao, Jianmin Zhang

“…Typhimurium. We performed transcriptomic analysis and screened for a c-di-GMP pathway key gene STM0343, a putative EAL domain protein with an unknown function. …”
Get full text

Investigating immune cell infiltration and gene expression features in pterygium pathogenesis by Ji Yang, Ya-Nan Chen, Chen-Yan Fang, Yan Li, Hong-Qin Ke, Rui-Qin Guo, Ping Xiang, Yun-Ling Xiao, Li-Wei Zhang, Hai Liu

“…Clinical samples of pterygium and adjacent relaxed conjunctival tissue were collected for transcriptomic analysis using RNA sequencing combined with bioinformatics approaches. …”
Get full text

Combining single-cell analysis and molecular docking techniques to construct a prognostic model for colon adenocarcinoma and uncovering inhibin subunit βb as a novel therapeutic ta... by Qinqing Wu, Qinqing Wu, Lu Ye, Yuwei Wu, Mengyu Zhao, Mengyu Zhao, Jiaxin Lu, Yanping Yu, Yanping Yu, Yixiao Niu, Yixiao Niu, Luxiao Zhang, Peijun Zuo, Peijun Zuo

“…However, the specific biological link between anoikis and COAD, as well as its mechanisms in tumor progression, remains unclear, making it a potential new direction for therapeutic strategy research.MethodsWe employed transcriptomic data and clinical information from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to pinpoint differentially expressed anoikis-related genes (ARGs) in COAD. …”
Get full text

The CXCL16/CXCR6 axis is linked to immune effector cell-associated neurotoxicity in chimeric antigen receptor (CAR) T cell therapy by I-Na Lu, Louisa Müller-Miny, Carolin Krekeler, Phyllis Fung-Yi Cheung, Georgia Antonopoulou, Astrid Jeibmann, Andreas Schulte-Mecklenbeck, Kornelius Kerl, Simon Call, Christian Reicherts, Annalen Bleckmann, Matthias Stelljes, Georg Lenz, Heinz Wiendl, Gerd Meyer zu Hörste, Oliver M. Grauer

“…We employed single-cell RNA sequencing (scRNA-seq) and flow cytometry to profile immune cell populations and performed multi-modal spatial transcriptomics and immunofluorescence on postmortem choroid plexus and brain tissue from a patient with fatal grade 4 ICANS. …”
Get full text

Integrated spatial multi‐omics profiling of Fusobacterium nucleatum in breast cancer unveils its role in tumour microenvironment modulation and cancer progression by Feng Zhao, Rui An, Yilei Ma, Shaobo Yu, Yuzhen Gao, Yanzhong Wang, Haitao Yu, Xinyou Xie, Jun Zhang

“…Integrative spatial multi‐omics and co‐culture transcriptomic analyses highlighted the MAPK signalling pathways as key altered pathways. …”
Get full text

Bikaverin as a molecular weapon: enhancing Fusarium oxysporum pathogenicity in bananas via rhizosphere microbiome manipulation by Honglin Lu, Suxia Guo, Yongbao Yang, Zhihao Zhao, Qingbiao Xie, Qiong Wu, Changjun Sun, Hongli Luo, Bang An, Qiannan Wang

“…Future research should focus on elucidating the molecular mechanisms underlying bikaverin-mediated microbial interactions, using integrated approaches such as transcriptomics and metabolomics. Together, these findings provide a foundation for novel approaches to combat banana wilt disease and enhance crop resistance. …”
Get full text

Exogenous prostaglandin D2 as a modulator in bovine endometritis: implications for reducing antibiotic use in dairy cattle by Xiaolin Yang, Xiaolin Yang, Shuangyi Zhang, Shuangyi Zhang, Bo Liu, Bo Liu, Lili Guo, Lili Guo, Pengfei Gong, Pengfei Gong, Pengfei Gong, Jingze Wu, Jingze Wu, Yi Zhao, Yi Zhao, Wei Mao, Wei Mao, Jinshan Cao, Jinshan Cao

“…We used bovine bone marrow-derived macrophages (BMDMs) and bovine endometrial tissue to investigate the specific genes and molecular mechanisms involved in E. coli-induced bovine endometritis.Methods and resultsTranscriptomic data show that E. coli infection significantly upregulated 2,141 genes and downregulated 2,381 genes in bovine BMDMs. …”
Get full text

SARS-CoV-2 infection induces hyaluronan production in vitro and hyaluronan levels in COVID-19 patients relate to morbidity and long-term lung impairment: a prospective cohort study by Urban Hellman, Ebba Rosendal, Joakim Lehrstrand, Johan Henriksson, Tove Björsell, Alfred Wennemo, Max Hahn, Björn Österberg, Luiza Dorofte, Emma Nilsson, Mattias N. E. Forsell, Anna Smed-Sörensen, Anna Lange, Mats G. Karlsson, Clas Ahlm, Anders Blomberg, Sara Cajander, Ulf Ahlgren, Alicia Lind, Johan Normark, Anna K. Överby, Annasara Lenman

“…In vitro 3D-lung models, differentiated from primary human bronchial epithelial cells, were used to study the effects of SARS-CoV-2 infection on HA metabolism, and transcriptomic analyses revealed a dysregulation of HA synthases and hyaluronidases, both contributing to increased HA in apical secretions. …”
Get full text

CCT196969 inhibits TNBC by targeting the HDAC5/RXRA/ASNS axis to down-regulate asparagine synthesis by Qiong Yuan, Qi Wang, Jun Li, Liyang Yin, Shu Liu, Xuyu Zu, Yingying Shen

“…Conclusions This study reveals a previously unrecognized anti-TNBC mechanism of CCT196969 through the HDAC5/RXRA/ASNS axis. This provides potential candidate targets for the treatment of TNBC and a theoretical basis for the clinical treatment of TNBC patients with CCT196969.…”
Get full text

Mitochondria-associated programmed cell death: elucidating prognostic biomarkers, immune checkpoints, and therapeutic avenues in multiple myeloma by Gongzhizi Gao, Jiyu Miao, Yachun Jia, Aili He, Aili He, Aili He

“…However, the precise roles of mitochondria-related genes (MRGs) and PCD-related genes (PCDRGs) in MM prognosis remain unclear.MethodsTranscriptomic data from MM patients and healthy controls were analyzed to identify differentially expressed genes (DEGs). …”
Get full text

BACH1 deficiency improves placental angiogenesis via SLC25A51-mediated mitochondrial NAD+ transport in intrahepatic cholestasis of pregnancy by Shengpeng Li, Weiying Zhu, Zhixuan Xing, Dan Chen, Huimin Zhao, Yanli Zhang, Wenlong Zhang, Jiaojiao Sun, Yaxian Wu, Ling Ai, Qingfeng Pang

“…Specifically, pharmacological inhibition of BACH1 could provide a targeted therapeutic strategy for placental angiogenesis associated with ICP. …”
Get full text

Co-regulation and synteny of GFM2 and NSA2 links ribosomal function in mitochondria and the cytosol with chronic kidney disease by Minjie Zhang, Christer Hogstrand, Paola Pontrelli, Afshan N Malik

“…In the current paper, we show that NSA2 expression is co-regulated with the GTP-dependent ribosome recycling factor mitochondrial 2 (GFM2) and provide a molecular link between cytosolic and mitochondrial ribosomal biogenesis with mitochondrial dysfunction in chronic kidney disease (CKD). …”
Get full text

Pathogenic KCNH2-G53S variant in the PAS domain influences the electrophysiological phenotype in long QT syndrome type 2 by Dasom Mun, Ji-Young Kang, Malgeum Park, Gyeongseo Yoo, Nuri Yun, YouMi Hwang, YouMi Hwang, Boyoung Joung

“…KCNH2G53S hiPSC-CMs expressed less KCNH2 than normal CMs. Transcriptomic analysis of KCNH2G53S hiPSC-CMs revealed 3,857 differentially expressed genes, highlighting significant changes in pathways related to LQT2 development. …”
Get full text

Tumor tissue-of-origin classification using miRNA-mRNA-lncRNA interaction networks and machine learning methods by Ankita Lawarde, Ankita Lawarde, Masuma Khatun, Prakash Lingasamy, Prakash Lingasamy, Andres Salumets, Andres Salumets, Andres Salumets, Vijayachitra Modhukur, Vijayachitra Modhukur

“…Our comparative analysis demonstrated that models based on miRNA outperformed those using mRNA or lncRNA classifiers.DiscussionOur integrated framework provides a biologically grounded, interpretable, and highly accurate approach for tumor tissue-of-origin classification. …”
Get full text

Target oxidative stress-induced disulfidptosis: novel therapeutic avenues in Parkinson’s disease by Junshi Zhang, Tingting Liu, Haojie Wu, Jianshe Wei, Qiumin Qu

“…By identifying novel diagnostic biomarkers (e.g., DED-ORGs) and therapeutic targets (e.g., LRPPRC), our findings provide a mechanistic framework for PD management and lay the groundwork for future therapeutic development.…”
Get full text

Combinatorial functionomics identifies HDAC6-dependent molecular vulnerability of radioresistant head and neck cancer by Sharon Pei Yi Chan, Celestia Pei Xuan Yeo, Boon Hao Hong, Evelyn Mui Cheng Tan, Chaw Yee Beh, Eugenia Li Ling Yeo, Dennis Jun Jie Poon, Pek Lim Chu, Khee Chee Soo, Melvin Lee Kiang Chua, Edward Kai-Hua Chow

“…Regulatory roles of HDAC6/SP1 axis were investigated using immunoprecipitation, gel shift and ChIP-qPCR assays. Comparative transcriptomic analyses were employed to determine the prognostic significance of targeting HDAC6. …”
Get full text

Bile acids enhance fat metabolism and skeletal muscle development in Zhijiang duck by modulating gut microbiota by Liang Chen, Zhizhong Zhang, Wei Deng, Guitao Jiang, Deming Xie, Aizhi Cao

“…In contrast, the genera Christensenellaceae_R_7_group and Sutterella exhibited negative correlations with PPARα. These findings provide new insights into the role of BA in promoting growth performance and skeletal muscle development in Zhijiang ducks fed a high-fat diet, with this effect potentially linked to changes in the gut microbiota.…”
Get full text