Decoding the epigenetic-immune nexus in hepatocellular carcinoma: a Mendelian randomization study reveals BTN3A2, S100A12 and TRIM27 as white blood cell regulators by Yang Qiu, Haiyan Zhang, Xiao Yu, Jielu Pan, Dinghong Xiao, Hongyu Miao, Ruiqing Wang, Nan Shen, Peimin Pu, Yinling Zhou, Zhidong Liu, Lin He, Lianjun Xing

“…The discovered methylation-immune axes provide mechanistic insights for developing combination therapies targeting epigenetic checkpoints to reverse immunosuppressive microenvironments in advanced HCC.…”
Get full text

Proteome-wide association studies using summary pQTL data of brain, CSF, and plasma identify 30 risk genes of Alzheimer’s disease dementia by Tingyang Hu, Qiang Liu, Qile Dai, Aron S. Buchman, David A. Bennett, Shinya Tasaki, Yanling Wang, Nicholas T. Seyfried, Philip L. De Jager, Michael P. Epstein, Jingjing Yang

“…Conclusions Our findings provide novel insights into the genetic mechanisms of AD dementia in brain, CSF, and plasma, and provide targets for developing new therapies. …”
Get full text

Prediction of radiosensitivity in non-small cell lung cancer based on computed tomography and tumor genomics: a multiple real world cohort study by Peimeng You, Qiaxuan Li, Yu Lei, Chuhao Xu, Daipeng Xie, Lintong Yao, Jiaxin Yuan, Junyu Li, Haiyu Zhou

“…At the same time, it provides a reference basis for evaluating radiation sensitivity from imaging, genetics, and other aspects.…”
Get full text

Investigation of high fecundity genes by nanopore sequencing in sheep (Ovis aries) pituitary by Xue Xiao, Zhibin Ji, Tong Wang, Dejie Zhu, Zhonghui Li, Xinming Xu, Fen Li

“…To explore the intrinsic molecular regulatory mechanisms and gene regulatory network of sheep reproductive traits, key genes affecting multiple fetal traits, such as ovulation number and litter size, were screened to provide a new reference for the study of reproduction traits in sheep. …”
Get full text

Integrative analysis of anti-breast CancerPotential of metabolites from Pseudomonas frederiksbergensis isolated from Taoerqi by Yuexing Ma, Yuexing Ma, Yuexing Ma, Yuexing Ma, Yuexing Ma, Haoyi Zheng, Haoyi Zheng, Haoyi Zheng, Simin Liu, Simin Liu, Simin Liu, En Yuan, Xin Qiao, Zhang Dai, Zhang Dai, Zhang Dai, Wenli Wu, Wenli Wu, Wenli Wu, Rongbin Pan, Rongbin Pan

“…Furthermore, a clinical risk assessment model was constructed using breast cancer transcriptome databases to explore the potential prognostic value of these targets.ResultsThe secondary metabolites from Pseudomonas frederiksbergensis exhibit significant anti-tumor effects and highlight their potential molecular mechanisms in breast cancer regulation.DiscussionThis study provides insights into the therapeutic potential of these metabolites and lays the groundwork for future preclinical and in vivo investigations.…”
Get full text

Sirtuin1 Suppresses Calcium Oxalate Nephropathy via Inhibition of Renal Proximal Tubular Cell Ferroptosis Through PGC‐1α‐mediated Transcriptional Coactivation by Chen Duan, Bo Li, Haoran Liu, Yangjun Zhang, Xiangyang Yao, Kai Liu, Xiaoliang Wu, Xiongmin Mao, Huahui Wu, Zhenzhen Xu, Yahua Zhong, Zhiquan Hu, Yan Gong, Hua Xu

“…In the present study, single‐cell transcriptome sequencing is performed on kidney samples from mice with CaOx nephrocalcinosis. …”
Get full text

Pangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice by Yongqing Qian, Zuwen Zhou, Tianmin Ouyang, Dongao Li, Ru Li, Ping Gan, Renfei Qiao, Yingying Tan, Mingchao Qian, Liezhao Liu, Jiana Li, Kun Lu, Jijing Luo, Ling-Ling Chen, Jia-Ming Song

“…We identify 26,914 TEs responsive to cold stress from transcriptome data, indicating their potential significance in regulatory networks for this response. …”
Get full text

Genetic Basis and Exploration of Major Expressed QTL <i>qLA2-3</i> Underlying Leaf Angle in Maize by Yonghui He, Chenxi Wang, Xueyou Hu, Youle Han, Feng Lu, Huanhuan Liu, Xuecai Zhang, Zhitong Yin

“…Re-sequencing and transcriptome results revealed that five candidate genes may be involved in the regulation of LA. …”
Get full text

Pinoresinol Diglucoside Attenuates Nuclear Receptor Coactivator 4‐Mediated Ferritinophagy Associated with Cisplatin‐Induced Hearing Loss by Yin Chen, Cheng Cheng, Ao Li, Dengbin Ma, Siyu Li, Handong Wang, Song Gao, Dingding Liu, Panpan Song, Chenjie Yu, Xiaoyun Qian, Guoqiang Wan, Xia Gao

“…PDG partially restores hearing loss caused by cisplatin. Transcriptome sequencing identifies Suppressor of Cytokine Signaling 1 (SOCS1), which is significantly elevated in the cisplatin‐only group but significantly reduced after PDG application. …”
Get full text

Molecular dynamics of chemotactic signalling orchestrates dental pulp stem cell fibrosis during aging by Tianmeng Sun, Tianmeng Sun, Qing Zhong, Qing Zhong, Xiaoyi Yu, Xiaoyi Yu, Huanyu Luo, Huanyu Luo, Feilong Ren, Feilong Ren, Cangwei Liu, Peng Chen, Fabian Flores-Borja, Hongchen Sun, Zhengwen An, Zhengwen An

“…Leveraging single-cell transcriptome analysis from both our own and publicly available datasets, we identified Ccrl2+ macrophages as particularly vulnerable during the early stages of aging. …”
Get full text

Immunometabolism signature derived from on-treatment tumor specimens predicts immune checkpoint blockade response in metastatic melanoma by Shuzhao Chen, Shutong Liu, Jiangtao Song, Xiaojin Li, Huaze Liao, Shuiqin Chen, Yuanbin Song, Yun Wang, Yang Liang, Qianqian Huang, Weiran Lv

“…In conclusion, we identified and verified an immunometabolism signature that provides a theoretical basis for applying such signatures derived from on-treatment tumor samples to predict therapeutic responses to ICB therapies.…”
Get full text

Bioactive manganese-decorated titanium implants for osteoporotic bone regeneration by Lei Wang, Chaoxi Yan, Fan Wang, Qiang Wang, Degang Huang, Xin Yang, Tao Ma, Pingbo Chen, Congming Li, Zhouzhou Zhang, Guoyang Wan, Xing Yang

“…The mechanism of Mn-enhanced osteogenesis developed in this study could provide theoretical and practical insights for enhancing implant-to-bone osseointegration in osteoporotic bone defects.…”
Get full text

Combined systems approaches reveal highly plastic responses to antimicrobial peptide challenge in Escherichia coli. by Justyna Kozlowska, Louic S Vermeer, Geraint B Rogers, Nabila Rehnnuma, Sarah-Beth T A Amos, Garrit Koller, Michael McArthur, Kenneth D Bruce, A James Mason

“…Analysis of the ontological profiles generated from the transcriptomic analyses suggests this approach can accurately predict the antibacterial mode of action, providing a fresh, novel perspective for previous functional and biophysical studies.…”
Get full text

Absent in melanoma 2: a potent suppressor of retinal pigment epithelial-mesenchymal transition and experimental proliferative vitreoretinopathy by Yu Chen, Mingyuan Jiang, Liping Li, Shanshan Yang, Zuimeng Liu, Shiwen Lin, Wanxiao Wang, Jinyang Li, Feng Chen, Qiang Hou, Xiaoyin Ma, Ling Hou

“…The present study demonstrated that AIM2 functions as a potent suppressor of RPE cell proliferation and EMT to maintain retinal homeostasis. Transcriptome analysis using RNA-sequencing (RNA-Seq) revealed that AIM2 was significantly downregulated in primary human RPE (phRPE) cells undergoing EMT and proliferation. …”
Get full text

Label-free isolation of lipid-rich Saccharomyces cerevisiae mutant by high-throughput flow-mode Raman-activated cell sorting and multi-omics analysis for uncovering the mechanism o... by Xiaotong Ji, Xixian Wang, Wenjun Zhou, Lin Chen, Tianzhong Liu, Jian Xu, Bo Ma

“…Consequently, S. cerevisiae has the potential to sustainably produce palmitoleic acid through fermentation, provided that the issue of promoting its lipid content is addressed. …”
Get full text

Unraveling the Multilayered Regulatory Networks of miRNAs and PhasiRNAs in <i>Ginkgo biloba</i> by Qixuan Wei, Ang Xu, Anqi Zhao, Lisha Shi, Qi Wang, Xiaoming Yang, Meiling Ming, Liangjiao Xue, Fuliang Cao, Fangfang Fu

“…We conducted an in-depth analysis of deep sequencing data from the gymnosperm <i>Ginkgo biloba</i>, encompassing sRNA, transcriptome, and degradome libraries. Our analysis identified a total of 746 miRNAs and 654 phasiRNA precursor (PHAS) loci, with 526 (80%) of the PHAS loci predicted to be triggered by 515 miRNAs (69%). …”
Get full text

Novel_circ_0004013 targeting miR-29a-3p affects age-related hearing loss in miR-29a mouse model by RNA-seq analysis by Mulan Li, Bingqian Li, Shuli Wang, Pengcheng Liu, Zhen Liu, Tihua Zheng, Ruishuang Geng, Bo Li, Qingyin Zheng, Peng Ma

“…In this study, we analyzed the circRNA expression profiles of 2-month-old miR-29a+/+ mice and miR-29a−/− mice by transcriptome sequencing to investigate the role of circRNAs in ARHL. …”
Get full text

Molecular markers of reduced behavioral sensitivity to transfluthrin in Anopheles gambiae s.s. from Western Kenya by Stephen Okeyo, Dieunel Derilus, Lucy Mackenzie Impoinvil, Nsa Dada, Diana Omoke, Helga Saizonou, Cynthia Awuor Odhiambo, Nicola Mulder, Gerald Juma, Benard W. Kulohoma, John E. Gimnig, Luc S. Djogbénou, Audrey Lenhart, Eric Ochomo

“…Here, we employed whole transcriptome analysis to investigate the molecular mechanisms underlying reduced behavioral sensitivity to transfluthrin in two pyrethroid-resistant populations of Anopheles gambiae s.s. …”
Get full text

Adaptive mechanisms to hypoxia and hyperoxia in juvenile turbot, Scophthalmus maximus by Yi Chen, Yuntian Zhang, Rongwei Zhang, Hongsheng Deng, Xiangyu Meng, Kotoya Inaba, Tatsu Osato, Xiaoran Zhao, Xiaoran Zhao, Yuzhe Han, Yuzhe Han, Tongjun Ren, Tongjun Ren

“…The study aimed to explore the adaptive mechanisms of turbot under hypoxic and hyperoxic conditions, using microbiome, transcriptome, and hematological analyses over a 40-day period. …”
Get full text

Expression Analysis of the ABF Gene Family in <i>Actinidia chinensis</i> Under Drought Stress and the Response Mechanism to Abscisic Acid by Haoyu Wang, Yinqiang Zi, Xu Rong, Qian Zhang, Lili Nie, Jie Wang, Hailin Ren, Hanyao Zhang, Xiaozhen Liu

“…The correlation coefficients of the results with the transcriptome data were all above 0.70, and the expression level of ABA increased under drought treatment. …”
Get full text