First interspecific genetic linkage map for Castanea sativa x Castanea crenata revealed QTLs for resistance to Phytophthora cinnamomi. by Carmen Santos, Charles Dana Nelson, Tetyana Zhebentyayeva, Helena Machado, José Gomes-Laranjo, Rita Lourenço Costa

“…Results presented here extend the genomic resources of Castanea genus providing potential tools to assist the ongoing and future chestnut breeding programs.…”
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Functional analysis of lncRNAs in lipid metabolism of fat and lean line broiler embryonic livers by Huili Zhang, Xuanming Cao, Youdong Wang, Bohan Cheng, Li Leng, Peng Luan, Zhiping Cao, Yumao Li, Xue Bai

“…This study enhances the scientific understanding of lipid metabolism regulation in chicken livers and provides a theoretical foundation for genetically improving abdominal fat traits in broilers.…”
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Genome-Wide Identification and Expression Analysis of the <i>PsTPS</i> Gene Family in <i>Pisum sativum</i> by Hao Yuan, Baoxia Liu, Guwen Zhang, Zhijuan Feng, Bin Wang, Yuanpeng Bu, Yu Xu, Zhihong Sun, Na Liu, Yaming Gong

“…Phylogenetic analysis delineated evolutionary relationships, while gene structure analysis revealed compositional insights, and motif analysis provided functional insights. Cis-regulatory element identification predicted gene regulation patterns. …”
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Epstein-Barr virus hijacks histone demethylase machinery to drive epithelial malignancy progression through KDM5B upregulation by Ya-Qing Zhou, Jia-Xin Jiang, Shuai He, Yi-Qi Li, Xi-Xi Cheng, Shu-Qiang Liu, Pan-Pan Wei, Xin-Yuan Guan, Choon Kiat Ong, Vivien Ya-Fan Wang, Chun-Ling Luo, Jin-Xin Bei

“…Through integrative analyses of single-cell and bulk transcriptome data from epithelial tumor tissues and EBV-infected cells, we identified KDM5B as a critical histone-modifying factor consistently upregulated following EBV infection. …”
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Comparative genomics uncovers organellar genome structural divergence in Caryophyllales and reveals widespread non-coding transcription in Bougainvillea glabra organellar by Shuo Zhang, Shengxin Chang, Xinge Lin, Shisong Xu, Qingyun Leng, Haiyan Li, Hernán Ariel López, Junmei Yin, Zhiqiang Wu, Junhai Niu

“…In this study, the organellar genomes and transcriptome of Bougainvillea glabra (Nyctaginaceae) were sequenced and assembled using PacBio sequencing and strand-specific RNA sequencing, respectively. …”
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Enhanced differentiation of neural progenitor cells in Alzheimer’s disease into vulnerable immature neurons by Joonho Cho, Simsung Bae, Juyeong Jeon, Janis Transfeld, Changyeob Lee, Alexi Nott, Fan Gao, Jinsoo Seo

“…This phenomenon was also evident when neural progenitor cells (NPCs) were differentiated into neurons. Furthermore, transcriptomic analyses of NPCs and neurons confirmed altered expression of neurogenesis-related genes in APPswe NPCs. …”
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Splice-site mutation enhances the efficiency of CRISPR-mediated gene knockout and new germplasm creation in fish by Zhen Xu, Ma Zhuo, Leihui Wang, Shuo Yan, Shiyi Zhang, Ying Chen, Guang Xu, Chenxu Wang, Wenjing Tao, Deshou Wang

“…These results demonstrated that gRNAs targeting SS provided an alternative and effective option for gene mutation and new germplasm creation in fish.…”
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RNA-Seq Analysis of Mouse Hepatocytes AML12 Exposed to Neodymium Nitrate by Ning Wang, Jing Leng, Yaxin Han, Gonghua Tao, Jingqiu Sun, Cheng Dong, Kelei Qian, Xiuli Chang, Ping Xiao, Xinyu Hong

“…Conclusion: This study provides the first comprehensive transcriptome database for Nd(NO₃)₃-induced liver injury, highlighting the involvement of ncRNAs in hepatotoxicity. …”
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Neoantigen-specific stimulation of tumor-infiltrating lymphocytes enables effective TCR isolation and expansion while preserving stem-like memory phenotypes by Yong Li, Steven A Rosenberg, Paul F Robbins, Zhiya Yu, Maria Parkhurst, Billel Gasmi, Nikolaos Zacharakis, Todd D Prickett, Jared J Gartner, Sri Krishna, Stephanie L Goff, Satyajit Ray, Frank J Lowery, Sivasish Sindiri, Alakesh Bera, Noam Levin, Sanghyun P Kim, Charles A Marquardt, Nolan R Vale, Lior Levy, Tiffany Benzine, Robert V Masi, Rafiqul Islam

“…Out of the 25 consecutive TIL samples, neoantigenic stimulation enabled the identification of 16 unique reactivities and 42 TCRs, while conventional TIL expansion identified 9 reactivities and 14 TCRs. Single-cell transcriptome analysis revealed that neoantigenic stimulation increased neoantigen-reactive TILs with stem-like memory phenotypes expressing IL-7R, CD62L, and KLF2. …”
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Integrated multi-omics analysis and machine learning identify G protein-coupled receptor-related signatures for diagnosis and clinical benefits in soft tissue sarcoma by Duo Wang, Duo Wang, Duo Wang, Jihao Tu, Jihao Tu, Jianfeng Liu, Jianfeng Liu, Yuting Piao, Yuting Piao, Yiming Zhao, Yiming Zhao, Ying Xiong, Ying Xiong, Jianing Wang, Jianing Wang, Xiaotian Zheng, Xiaotian Zheng, Bin Liu, Bin Liu

“…Moreover, the GPR-TME classifier as the prognosis model was constructed and further performed for immune infiltration, functional enrichment, somatic mutation, immunotherapy response prediction, and scRNA-seq analyses.ResultsWe identified 151 GPR-related genes at both the single-cell and bulk transcriptome levels, and identified a Stepglm[both]+Enet[alpha=0.6] model with seven GPR-related genes as the final diagnostic predictive model with high accuracy and translational relevance using a 127-combination machine learning computational framework, and the GPR-integrated diagnosis nomogram provided a quantitative tool in clinical practice. …”
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CSF3 enhances the innate immune responses to ALV-J infections via NF-κB and interferon pathways by Junliang Xia, Weiding Chen, Chengxun Xu, Meihuizi Wang, Guodong Mo, Xiquan Zhang

“…These results not only reveal the antiviral role of CSF3 but also provide new insights into the host's innate immune response to ALV. …”
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Metal-dependent cell death resistance contribute to lymph node metastasis of oral squamous cell carcinoma by Xuan-Hao Liu, Guang-Rui Wang, Nian-Nian Zhong, Zheng-Rui Zhu, Yao Xiao, Zheng Li, Lin-Lin Bu, Lin-Lin Bu, Bing Liu, Bing Liu

“…In addition, Epi_2 enriched multiple malignant-related pathways such as HEDGEHOG, NOTCH, and MYC. The spatial transcriptome and bulk RNA data verified that the proportion of Epi_2 in mPT was higher than that in nPT. …”
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CRISPR/Cas9-mediated knockout of SLC15A4 gene involved in the immune response in bovine rumen epithelial cells by Mao-cheng JIANG, Zi-xuan HU, Ke-xin WANG, Tian-yu YANG, Miao LIN, Kang ZHAN, Guo-qi ZHAO

“…In order to gain further insight into the potential function of SLC15A4, we utilized transcriptome data, which revealed a change in the genes between WT-BRECs and SLC15A4-KO. …”
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Sex-Dimorphic Differential Expression Profiles in the Brain of the Adult Chinese Soft-Shelled Turtle, <i>Pelodiscus sinensis</i> by Pan Liu, Yanchao Liu, Junxian Zhu, Chen Chen, Liqin Ji, Xiaoli Liu, Xiaoyou Hong, Chengqing Wei, Xinping Zhu, Qiaoqing Xu, Jiang Zhou, Wei Li

“…In addition, through gene set enrichment analysis (GSEA), we screened out two genes, LIM homeobox protein 1 (<i>LHX1</i>) and fibroblast growth factor 7 (<i>FGF7</i>), which are related to both growth and sex differentiation, and through protein interaction analysis of these genes, we screened out eight genes, including <i>LHX1</i>, <i>FGF7</i>, <i>GHR</i>, fibroblast growth factor 4 (<i>FGF4</i>), <i>EGFR</i>, <i>BMP3</i>, GLI family zinc finger 2 (<i>GLI2</i>), and neuronal differentiation 1 (<i>NEUROD1</i>), and verified the expression levels of these eight genes in the brain of the <i>P. sinensis</i> by real-time quantitative PCR (qRT-PCR), which supported the reliability and accuracy of our transcriptome analysis. Our study provides a solid foundation for analyzing the mechanisms of sexual-dimorphic growth of <i>P. sinensis</i> and even other turtles.…”
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scRL: Utilizing Reinforcement Learning to Evaluate Fate Decisions in Single-Cell Data by Zeyu Fu, Chunlin Chen, Song Wang, Junping Wang, Shilei Chen

“…Single-cell RNA sequencing now profiles whole transcriptomes for hundreds of thousands of cells, yet existing trajectory-inference tools rarely pinpoint where and when fate decisions are made. …”
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Signalomics for molecular tumor boards and precision oncology of breast and gynecological cancers by Tatiana V Denisenko, Anna E Ivanova, Alexey Koval, Denis N Silachev, Lee Jia, Gennadiy T Sukhikh, Vladimir L Katanaev

“…Using transcriptional reporters introduced in primary tumor cells, this approach identifies the pathways overactivated in a given tumor and validates their sensitivity to targeted therapies, providing actionable insights for personalized treatment strategies. …”
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Gata3 drives miR-21-5p transcription to mitigate hyperoxia-induced lung injury, independent of CpG Island methylation by Yingcong Ren, Song Qin, Ping Yuan, Qianxia Huang, Ma Huang, Yuanzhi Shi, Miao Chen

“…Bioinformatic analyses and GEO transcriptomic data revealed a positive correlation between Gata3 and miR-21-5p levels. …”
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Radiotherapy and immune microenvironment crosstalk in pancreatic cancer: a comprehensive review of current insights and future directions by Yucheng Xu, Jingjing Chen, Jingjing Chen, Yudong Qiu, Juan Du, Juan Du

“…These effects may transform immunologically “cold” tumors into “hot” ones, providing a rationale for combination strategies with immunotherapy. …”
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Characterization of full-length long noncoding RNAs and identification of virus-responsive lncRNAs in Sogatella furcifera by Yawen Ban, Yawen Ban, Ting Cui, Ting Cui, Lifei Zhao, Lifei Zhao, Xue Li, Xue Li, Qing Bai, Qing Bai, Qingfa Wu, Qingfa Wu

“…By integrating PacBio single-molecule real-time (SMRT) sequencing with publicly available Iso-Seq datasets, we reconstructed a high-confidence, full-length transcriptome and identified 1,211 lncRNAs spanning 1,174 loci. …”
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Targeting N4‐acetylcytidine suppresses hepatocellular carcinoma progression by repressing eEF2‐mediated HMGB2 mRNA translation by Hailing Liu, Lei Xu, Shiwei Yue, Hongfei Su, Xing Chen, Qiumeng Liu, Hui Li, Huifang Liang, Xiaoping Chen, Jiefeng He, Zeyang Ding, Bixiang Zhang

“…Conclusions Our study identified a novel oncogenic epi‐transcriptome axis involving NAT10‐ac4C/eEF2‐HMGB2, which plays a pivotal role in regulating HCC growth and metastasis. …”
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