Communications Biology最新文献

{"title":"Time-dependent consolidation mechanisms of durable memory in spaced learning.","authors":"Yifeixue Yang, Ziyi Huang, Yun Yang, Mingxia Fan, Dazhi Yin","doi":"10.1038/s42003-025-07964-6","DOIUrl":"10.1038/s42003-025-07964-6","url":null,"abstract":"<p><p>Emerging studies suggest that time-dependent consolidation enables memory stabilization by promoting memory integration and hippocampal-cortical transfer. Compared to massed learning, how time-dependent consolidation contributes to forming durable memory and what neural signatures predict durable memory in spaced learning remain unclear. We recruited 48 participants who underwent either 3-day spaced learning or 1-day massed learning, and both resting-state and task-based fMRI data were collected in multiple delayed tests (i.e., immediate, 1-week, and 1-month). We use representational similarity analysis to assess neural integration and replay in the hippocampus and default mode network (DMN) subsystems. In contrast with massed learning, spaced learning induces higher neural pattern similarity during immediate retrieval only in DMN subsystems. Particularly, the neural pattern similarity in the dorsal-medial DMN (DMN_dm) and medial-temporal DMN subsystems predicts the durable memory defined by 1-month delay. Moreover, we find increased neural replay of durable memory in the DMN_dm for spaced learning and in the hippocampus for both spaced and massed learning. Our findings suggest that time-dependent consolidation promotes neural integration and replay in the cortex rather than in the hippocampus, which may underlie the formation of durable memory after spaced learning.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"535"},"PeriodicalIF":5.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11962080/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143763208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OPN3-mediated positive regulation of angiogenesis in HUVECs through VEGFR2 interaction.","authors":"Huanhuan Luo, Wei Zhang, Wen Zeng, Yu Wang, Jianglong Feng, Yinghua Lan, Xian Dong, Ting Liu, Yan Sun, Hongguang Lu","doi":"10.1038/s42003-025-07958-4","DOIUrl":"10.1038/s42003-025-07958-4","url":null,"abstract":"<p><p>Many rhodopsin-like G-protein-coupled receptors (Rh-GPCRs) are known to either promote or inhibit angiogenesis. Among these, Opsin 4 and Opsin 5 are specifically involved in vascular development within the eye. Opsin 3 (OPN3), another member of Rh-GPCRs, performs a variety of light-dependent and light-independent functions in extraocular tissue. However, its role in endothelial cells and angiogenesis remains unclear. Here, we found that OPN3 knockdown or knockout in zebrafish impairs embryonic angiogenesis and vascular development. Similarly, silencing OPN3 in human umbilical vein endothelial cells (HUVECs) inhibits cellular proliferation, migration, sprouting, and tube formation, while OPN3 overexpression promotes these cellular processes. Moreover, OPN3 regulates angiogenesis in HUVECs through the VEGFR2-AKT pathway, with OPN3 and VEGFR2 co-localizing at the plasma membrane and forming a physical complex. These findings provide new insights into the non-light-dependent functions of OPN3 in angiogenesis, expanding our understanding of its physiological roles and offering potential therapeutic strategies for angiogenesis-related diseases.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"529"},"PeriodicalIF":5.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958745/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Author Correction: 3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression.","authors":"Xiang Xu, Jingbo Gan, Zhaoya Gao, Ruifeng Li, Dandan Huang, Lin Lin, Yawen Luo, Qian Yang, Jingxuan Xu, Yaru Li, Qing Fang, Ting Peng, Yaqi Wang, Zihan Xu, An Huang, Haopeng Hong, Fuming Lei, Wensheng Huang, Jianjun Leng, Tingting Li, Xiaochen Bo, Hebing Chen, Cheng Li, Jin Gu","doi":"10.1038/s42003-025-07957-5","DOIUrl":"10.1038/s42003-025-07957-5","url":null,"abstract":"","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"525"},"PeriodicalIF":5.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751316","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Protein covariation networks for elucidating ferroptosis inducer mechanisms and potential synergistic drug targets.","authors":"Rina Kunishige, Yoshiyuki Noguchi, Naomi Okamoto, Lei Li, Akito Ono, Masayuki Murata, Fumi Kano","doi":"10.1038/s42003-025-07886-3","DOIUrl":"10.1038/s42003-025-07886-3","url":null,"abstract":"<p><p>In drug development, systematically characterizing a compound's mechanism of action (MoA), including its direct targets and effector proteins, is crucial yet challenging. Network-based approaches, unlike those focused solely on direct targets, effectively detect a wide range of cellular responses elicited by compounds. This study applied protein covariation network analysis, leveraging quantitative, morphological, and localization features from immunostained microscopic images, to elucidate the MoA of AX-53802, a novel ferroptosis inducer. From the candidate targets extracted through network analysis, GPX4 was verified as the direct target by validation experiments. Additionally, aggregates involving GPX4, TfR1, and F-actin were observed alongside iron reduction, suggesting a ferroptosis defense mechanism. Furthermore, combination therapies targeting GPX4 and FAK/Src were found to enhance cancer cell death, and MDM2, ezrin, and cortactin were identified as potential ferroptosis inhibitor targets. These findings highlight the effectiveness of network-based approaches in uncovering a compound's MoA and developing combination therapies for cancer.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"480"},"PeriodicalIF":5.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751411","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Siblicide between fertilized and unfertilized ovaries within the maize ear.","authors":"Cheng Huang, Zhi-Wei Wang, Yi-Hsuan Lin, Xiao-Gui Liang, Hui-Min Chen, Bo Hong, Xian-Min Chen, Ya-Ning Zhou, Zhen-Yuan Chen, Shuai Dong, Xin Wang, Si Shen, Shun-Li Zhou","doi":"10.1038/s42003-025-07784-8","DOIUrl":"10.1038/s42003-025-07784-8","url":null,"abstract":"<p><p>Evolutionarily, plants overproduce ovaries but selectively eliminate those inferiors to ensure competitive offspring to set. This sibling rivalry, reducing grain number, is detrimental agronomically. However, the interaction between early-fertilized and unfertilized ovaries in sequentially-pollinated panicles is unclear. Here, we fertilized the ovaries on half rows of maize ear (HP) while keeping the rest unfertilized to investigate their interaction. HP reduced the growth of unfertilized ovaries while promoting fertilized ovary (grain) development. ¹³C-isotope labeling of grains led to isotope signal detected in the unlabeled ovaries, validating their interactions. Transcriptionally, HP caused cell wall degradation and senescence of unfertilized ovaries, reducing their viability. These ovaries showed promoted auxin and jasmonic acid levels with activated auxin signaling but suppressed MAPK signaling. Conversely, HP grains activated MAPK signaling, sugar utilization, and cell proliferation. These findings demonstrate that grains suppress ovaries in ear to consolidate sugar utilization advantage for development, potentially through hormone and MAPK signaling.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"528"},"PeriodicalIF":5.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Nicotinic acetylcholine receptors regulate growth hormone in pituitary somatotrophs of tigers.","authors":"Lulu Liu, Shilong Yang, Longhui Chai, Shipei Zhang, Dan Liu, Haitao Xu, Yue Zhao, Shiyu Chen, Guangshun Jiang, Bin Li","doi":"10.1038/s42003-025-07980-6","DOIUrl":"10.1038/s42003-025-07980-6","url":null,"abstract":"<p><p>The Felidae exhibits remarkable diversity in body size, with lengths ranging from 50 to 370 cm and weights from 1.1 to 423 kg. However, the underlying mechanisms driving this variation remain poorly understood. Here, we focused on the Siberian tiger (Panthera tigris altaica), the largest of the six extant tiger subspecies, and revealed the surprising expression of nicotinic acetylcholine receptors (nAChRs) in pituitary somatotrophs, which are crucial for regulating growth hormone (GH) secretion. Single-nucleus RNA sequencing of Siberian tiger pituitary cells exhibited the coexpression of CHRNA3, CHRNB4, and CHRNA5 genes in somatotrophs, a finding confirmed by electrophysiological experiments demonstrating the formation of functional nAChRs. Activation of these receptors elevated intracellular Ca²⁺ levels, thereby enhancing GH secretion in somatotrophs. Notably, nAChRs were absent in the pituitary glands of mice, domestic cats, and rats, both in early life and adulthood, despite high acetylcholine levels during early life. These results suggest that nAChRs in Siberian tiger somatotrophs play a pivotal role in GH release, offering new insights into the molecular mechanisms regulating body size in these terrestrial giants.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"526"},"PeriodicalIF":5.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958662/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comprehensive multimodal and multiomic profiling reveals epigenetic and transcriptional reprogramming in lung tumors.","authors":"Peiyao Wu, Zhengzhi Liu, Lina Zheng, Yanmiao Du, Zirui Zhou, Wei Wang, Chang Lu","doi":"10.1038/s42003-025-07954-8","DOIUrl":"10.1038/s42003-025-07954-8","url":null,"abstract":"<p><p>Epigenomic mechanisms are critically involved in mediation of genetic and environmental factors that underlie cancer development. Histone modifications represent highly informative epigenomic marks that reveal activation and repression of gene activities and dysregulation of transcriptional control due to tumorigenesis. Here, we present a comprehensive epigenomic and transcriptomic mapping of 18 stage I and II tumor and 20 non-neoplastic tissues from non-small cell lung adenocarcinoma patients. Our profiling covers 5 histone marks including activating (H3K4me3, H3K4me1, and H3K27ac) and repressive (H3K27me3 and H3K9me3) marks and the transcriptome using only 20 mg of tissue per sample, enabled by low-input omic technologies. Using advanced integrative bioinformatic analysis, we uncover cancer-driving signaling cascade networks, changes in 3D genome modularity, differential expression and functionalities of transcription factors and noncoding RNAs. Many of these identified genes and regulatory molecules show no significant change in their expression or a single epigenomic modality, emphasizing the power of integrative multimodal and multiomic analysis using patient samples.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"527"},"PeriodicalIF":5.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958746/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751317","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of drug-resistant individual cells within tumors by semi-supervised transfer learning from bulk to single-cell transcriptome.","authors":"Kaishun Huang, Hui Liu","doi":"10.1038/s42003-025-07959-3","DOIUrl":"10.1038/s42003-025-07959-3","url":null,"abstract":"<p><p>The presence of pre-existing or acquired drug-resistant cells within the tumor often leads to tumor relapse and metastasis. Single-cell RNA sequencing (scRNA-seq) enables elucidation of the subtle differences in drug responsiveness among distinct cell subpopulations within tumors. A few methods have employed scRNA-seq data to predict the drug response of individual cells to date, but their performance is far from satisfactory. In this study, we propose SSDA4Drug, a semi-supervised few-shot transfer learning method for inferring drug-resistant cancer cells. SSDA4Drug extracts pharmacogenomic features from both bulk and single-cell transcriptomic data using semi-supervised adversarial domain adaptation. This allows us to transfer knowledge of drug sensitivity from bulk-level cell lines to single cells. We conduct extensive performance evaluation experiments across multiple independent scRNA-seq datasets, demonstrating SSDA4Drug's superior performance over current state-of-the-art methods. Remarkably, with only one or two labeled target-domain samples, SSDA4Drug significantly boosts the predictive performance of single-cell drug responses. Moreover, SSDA4Drug accurately recapitulates the temporally dynamic changes of drug responses during continuous drug exposure of tumor cells, and successfully identifies reversible drug-responsive states in lung cancer cells, which initially acquire resistance through drug exposure but later restore sensitivity during drug holidays. Also, our predicted drug responses consistently align with the developmental patterns of drug sensitivity observed along the evolutionary trajectory of oral squamous cell carcinoma cells. In addition, our derived SHAP values and integrated gradients effectively pinpoint the key genes involved in drug resistance in prostate cancer cells. These findings highlight the exceptional performance of our method in determining single-cell drug responses. This powerful tool holds the potential for identifying drug-resistant tumor cell subpopulations, paving the way for advancements in precision medicine and novel drug development.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"530"},"PeriodicalIF":5.2,"publicationDate":"2025-03-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11958800/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A GTP-driven central carbon metabolism in the cellulolytic bacterium Ruminiclostridium cellulolyticum.","authors":"Nian Liu, Nicolas Vita, Marion Holmière, Séverine Gagnot, Gaël Brasseur, Pascale de Philip, Sandrine Pagès, Stéphanie Perret, Henri-Pierre Fierobe","doi":"10.1038/s42003-025-07971-7","DOIUrl":"10.1038/s42003-025-07971-7","url":null,"abstract":"<p><p>In Ruminiclostridium cellulolyticum, the hexokinase and galactokinase were formerly shown to strongly prefer GTP over ATP, whereas the phosphofructokinase is PPi-dependent, suggesting an unconventional central carbon metabolism in this anaerobic bacterium. Herein, the characterization of all other kinases of this pivotal pathway led to the identification of their preferred NTP/NDP. The kinases involved in the first reactions, primarily functioning as NTP-consuming enzymes, appear to be GTP-dependent. In contrast, the enzymes catalyzing the downstream steps that mainly generate NTP, show no marked preference. Consequently, its central carbon metabolism appears essentially driven by GTP, whose cellular content nears that of ATP. Interestingly, in vivo reciprocal exchange of the GTP-dependent hexokinase in R. cellulolyticum by the ATP-dependent glucokinase from Escherichia coli and vice versa generates modified strains that still catabolize glucose and glucose disaccharides. Altogether our data suggest an unexpected diversity and flexibility in the functioning of this central pathway in bacteria.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"523"},"PeriodicalIF":5.2,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11955521/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reference-informed evaluation of batch correction for single-cell omics data with overcorrection awareness.","authors":"Xiaoyue Hu, He Li, Ming Chen, Junbin Qian, Hangjin Jiang","doi":"10.1038/s42003-025-07947-7","DOIUrl":"10.1038/s42003-025-07947-7","url":null,"abstract":"<p><p>Batch effect correction (BEC) is fundamental to integrate multiple single-cell RNA sequencing datasets, and its success is critical to empower in-depth interrogation for biological insights. However, no simple metric is available to evaluate BEC performance with sensitivity to data overcorrection, which erases true biological variations and leads to false biological discoveries. Here, we propose RBET, a reference-informed statistical framework for evaluating the success of BEC. Using extensive simulations and six real data examples including scRNA-seq and scATAC-seq datasets with different numbers of batches, batch effect sizes and numbers of cell types, we demonstrate that RBET evaluates the performance of BEC methods more fairly with biologically meaningful insights from data, while other methods may lead to false results. Moreover, RBET is computationally efficient, sensitive to overcorrection and robust to large batch effect sizes. Thus, RBET provides a robust guideline on selecting case-specific BEC method, and the concept of RBET is extendable to other modalities.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"521"},"PeriodicalIF":5.2,"publicationDate":"2025-03-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11954866/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}