Single-cell sequencing reveals antitumor characteristics of intratumoral immune cells in old mice by Xin Wang, Lei Lei, Lin Shi, Lianjun Zhang, Xiaobo Zhou, Xiaofeng Yang, Yanhong Su, Cangang Zhang, Kaili Ma, Huiqiang Zheng, Anjun Jiao, Haiyan Liu, Yujing Zou, Chenming Sun, Yuzhu Hou, Zhengtao Xiao, Baojun Zhang

“…Multiple bioinformatics methods were adopted to analyze the characteristics of the transcriptome between two groups. To explore the impacts of young and old CD8+ T cells on tumor growth, mice were treated with anti-CD8 antibody every 3 days starting 7 days after tumor inoculation. …”
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IL-6/GATA2/SERPINE1 pathway is implicated in regulating cellular senescence after acute kidney injury by Hongshuang Su, Xiaoxi Lin, Ayinuer Paredong, Ayinuer Paredong, Congcong Yao, Yan Zhang, Mengke Geng, Yuqian Guan, Lichao Gong, Feng Jiang, Qi Lv, Songtao Shou, Heng Jin

“…Additionally, a dual-luciferase reporter gene assay was conducted to validate the binding effect of SERPINE1 and GATA2.ResultsTranscriptome Analysis revealed that genes including GATA2 and SERPINE1 were downregulated in HK-2 cells following tocilizumab treatment. …”
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A small heat shock protein Fmp28 influences virulence by regulating Als3 expression via the cAMP-PKA signaling pathway in Candida albicans by Junjun Tan, Qiong Liu, Zhiping Liu, Yanli Cao, Xiaomin Yu, Qianjun Zhao, Niya Hu, Yanling Liu, Yuwei Wan, Yeming Zhang, Huizhen Tian, Lingbing Zeng, Xiaotian Huang

“…Deletion of Fmp28 significantly impaired growth, adhesion, biofilm formation, invasive growth, and virulence at physiological temperature (37°C), respectively. Transcriptome analysis identified Als3 as a key downstream target of Fmp28. …”
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Targeted inhibition of PDGFRA with avapritinib, markedly enhances lenvatinib efficacy in hepatocellular carcinoma in vitro and in vivo: clinical implications by Bixing Zhao, Yang Zhou, Niangmei Cheng, Xiaoyuan Zheng, Geng Chen, Xin Qi, Xiangzhi Zhang, Fei Wang, Qiuyu Zhuang, Yehuda G. Assaraf, Xiaolong Liu, Yingchao Wang, Yongyi Zeng

“…Methods We utilized CRISPR/Cas9 gene knockout screening combined with transcriptome sequencing of lenvatinib-resistant HCC cell lines to identify resistance-associated genes. …”
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Metabolomic and evolutionary integration unveils medicinal potential in six Corydalis species by Yun Gao, Xiangyu Zhou, Mengxiao Yan, Zhengwei Wang, Xin Zhong, Xiaochen Li, Junjie Zhu, Yu Kong, Wanrong Zhu, Ruolin Geng, Yaping Zhou, Qing Zhao, Yonghong Hu, Ping Xu

“…These discoveries significantly enhance our understanding of metabolic diversity in tuberous Corydalis, providing essential insights for the exploration of novel medicinal resources and facilitating targeted genetic improvements for therapeutic use.…”
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Dissecting the genetic architecture of yield-related traits by QTL mapping in maize by Hao Zhang, Hao Zhang, Ting Li, Zhenyu Zhang, Jie Wang, Haoxiang Yang, Jiachen Liu, Wanchao Zhu, Wanchao Zhu, Jiquan Xue, Jiquan Xue, Shutu Xu, Shutu Xu

“…Through integrated transcriptome data and interaction networks, 20 genes located in these QTLs were investigated as candidate genes. …”
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Effects of heterologously overexpressing Manihot esculenta Crantz MeNRT2.6 gene in Arabidopsis thaliana on nitrogen utilization efficiency by Min ZHAI, Yingjie CAO, Chenyu LIN, Pingjuan ZHAO, Wenbin LI, Xiaoling YU, Wenbin LIAO, Mengbin RUAN, Liangping ZOU, Zhuang LI

“…Heterologous overexpression of MeNRT2.6 in A. thaliana improved nitrogen use efficiency, providing valuable insights for developing nitrogen-efficient cassava germplasms.…”
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Rewiring of 3D chromatin topology orchestrates transcriptional reprogramming in muscle fiber-type specification and transformation by Baohua Tan, Linjun Hong, Liyao Xiao, Jiajin Wu, Geyan Lu, Shanshan Wang, Langqing Liu, Enqin Zheng, Gengyuan Cai, Zicong Li, Ting Gu, Zhenfang Wu

“…Here, we present an integrative analysis of the transcriptome, epigenome, and 3D genome architecture in the slow-twitch glycolytic extensor digitorum longus (EDL) and fast-twitch oxidative soleus (SOL) muscles of the pig (Sus scrofa). …”
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Multimodal CRISPR screens uncover DDX39B as a global repressor of A-to-I RNA editing by Tianzi Wei, Jiaxuan Li, Xiang Lei, Risheng Lin, Qingyan Wu, Zhenfeng Zhang, Shimin Shuai, Ruilin Tian

“…Here, we present two complementary CRISPR-based genetic screening platforms: CREDITS (CRISPR-based RNA editing regulator screening), which enables genome-scale identification of editing regulators using an RNA recorder-based reporter system, and scCREDIT-seq (single-cell CRISPR-based RNA editing sequencing), which provides multiplexed single-cell characterization of transcriptome and editome changes for pooled perturbations. …”
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Single-cell network biology enabling cell-type-resolved disease genetics by Junha Cha, Insuk Lee

“…Abstract Gene network models provide a foundation for graph theory approaches, aiding in the novel discovery of drug targets, disease genes, and genetic mechanisms for various biological functions. …”
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Allelic expression of deleterious protein-coding variants across human tissues. by Kimberly R Kukurba, Rui Zhang, Xin Li, Kevin S Smith, David A Knowles, Meng How Tan, Robert Piskol, Monkol Lek, Michael Snyder, Daniel G Macarthur, Jin Billy Li, Stephen B Montgomery

“…Personal exome and genome sequencing provides access to loss-of-function and rare deleterious alleles whose interpretation is expected to provide insight into individual disease burden. …”
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The control effect and induced disease resistance mechanism of Bacillus tequilensis on wheat powdery mildew by Qiuyan Bi, Fen Lu, Jie Wu, Xiangyu Liu, Xiuying Han, Jianjiang Zhao

“…The field control effect was 83.21–100.00 %. Transcriptome sequencing analysis revealed 1,472 significantly upregulated genes and 1,995 downregulated genes. …”
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Genetic prioritisation of candidate drug targets for glaucoma through multi-trait and multi-omics integration by Jianqi Chen, Yangjiani Li, Yingting Zhu, Zhidong Li, Shitong Huang, Wenzhi Huang, Yuyao Ling, Jingying Liang, Yunxia Leng, Yehong Zhuo

“…Conclusions This study provides novel insights into glaucoma pathophysiology and promotes pharmaceutical target innovation.…”
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Identification of hub programmed cell death-related genes and immune infiltration in Crohn’s disease using bioinformatics by Biyao Wang, Biyao Wang, Hailing Liu, Hailing Liu, Qin Guo, Qin Guo, Xiang Gao, Xiang Gao, Kang Chao, Kang Chao, Qingfan Yang, Qingfan Yang

“…These genes regulate immune cell function and their expression levels are closely related to immune cell infiltration. These findings provide novel insights into the mechanisms underlying CD pathogenesis. …”
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CRISPR/dCas-mediated counter-silencing: reprogramming dCas proteins into antagonists of xenogeneic silencers by Johanna Wiechert, Biel Badia Roigé, Doris Dohmen-Olma, Hindra, Xiafei Zhang, Roberto G. Stella, Marie A. Elliot, Julia Frunzke

“…The strongest effect was observed when targeting the Lsr2 nucleation site. Genome-wide transcriptome profiling revealed high specificity with minimal off-target effects. …”
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Long noncoding RNA as an emerging regulator of endoderm differentiation: progress and perspectives by Jie Yang, Donghui Zhang, Wei Jiang

“…By consolidating current knowledge, we aim to provide a clearer perspective on how lncRNAs contribute to endoderm differentiation in different manners.…”
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Unveiling RNA Editing by ADAR and APOBEC Protein Gene Families by Alexander Modestov, Anton Buzdin, Maria Suntsova

“…RNA editing is a crucial post-transcriptional modification that alters the transcriptome and proteome and affects many cellular processes, including splicing, microRNA specificity, stability of RNA molecules, and protein structure. …”
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Construction and Validation of an Oxidative Phosphorylation Signature in High-Grade Glioma and Potential Inhibitors Screening by Hanwen Lu, Wenpeng Zhao, Bingchang Zhang, Yuanyuan Xie, Jiawei He, Huiying Yang, Zhanxiang Wang

“…In this study, we conducted a comprehensive analysis of transcriptome data to identify differentially expressed genes related to oxidative phosphorylation in glioma. …”
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Fluo-Cast-Bright: a deep learning pipeline for the non-invasive prediction of chromatin structure and developmental potential in live oocytes by Xiangyu Zhang, Claudia Baumann, Rabindranath De La Fuente

“…Fluo-Cast-Bright provides fast and non-invasive selection of meiotically competent oocytes for downstream research and clinical applications.…”
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The m6A Methylation Profile Identified That <i>OsHMT9.1</i> Deregulates Chromium Toxicity in Rice (<i>Oryza sativa</i> L.) Through Negative Regulatory Functions by Yushan Hou, Xuejiao Kong, Jingwen Li, Changsheng Liu, Shuo Wang, Shupeng Xie, Jingguo Wang, Hualong Liu, Lei Lei, Hongliang Zheng, Wei Xin, Detang Zou, Zhonghua Wei, Luomiao Yang

“…These results suggest that knocking out <i>OsHMT9.1</i> can promote Cr detoxification in rice by modulating the balance between Cr and other trace elements. These findings provide new insights into the molecular regulation and stress response of rice under Cr stress through transcriptome m6A methylation patterns.…”
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