Huifen Cao, Yufei Zhang, Fujian Yang, Chunlian Wang, Guihua Wang, Binghui Wang, Lu Xia, Jiabian Lian, Yong Diao, Philipp Kapranov
{"title":"Complex mechanisms of topoisomerase II poisons revealed by whole-genome analysis.","authors":"Huifen Cao, Yufei Zhang, Fujian Yang, Chunlian Wang, Guihua Wang, Binghui Wang, Lu Xia, Jiabian Lian, Yong Diao, Philipp Kapranov","doi":"10.1038/s42003-026-10129-8","DOIUrl":"https://doi.org/10.1038/s42003-026-10129-8","url":null,"abstract":"<p><p>Topoisomerase II (TOP2) represents a vital enzyme which functions by introducing transient DNA breaks to resolve topological issues in DNA and regulate gene expression. The potentially toxic nature of these DNA breaks made the drugs that stabilize them, TOP2 poisons, into highly successful anticancer agents, and research tools. However, despite decades-long widespread usage of these drugs, not much is known about differences in the genome-wide profiles of DNA breaks caused by them. Here, we generate high-resolution genome-wide maps of DNA breaks induced by seven different TOP2 poisons in a human cancer cell line using the SSiNGLe method developed by our group. We find multiple notable differences even between the drugs with highly similar chemical structures, indicating that each poison targets a specific subpopulation of catalytically engaged TOP2 enzymes bound to DNA. The preferential targeting observed may be partly explained by the distinct local sequence preferences identified for each TOP2 poison. However, our results also indicate that genomic context, chromatin environment, and the heterogeneity of TOP2 cleavage complexes likely contribute. Altogether, this study has potential significant implications for our understanding of the reasons behind the clinical differences among the drugs and the mechanisms of TOP2 function.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811807","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nisha Rajan Narattil, Sailendrakumar Kolatt Chandran, Mouna Maroun
{"title":"Oxytocin agonist TGOT differentially modulates synaptic plasticity and intrinsic excitability in a sex-specific manner in the juvenile rat hippocampus.","authors":"Nisha Rajan Narattil, Sailendrakumar Kolatt Chandran, Mouna Maroun","doi":"10.1038/s42003-026-10088-0","DOIUrl":"https://doi.org/10.1038/s42003-026-10088-0","url":null,"abstract":"<p><p>Oxytocin (OXT) regulates social behavior and cognition in the mammalian brain through its receptor, OXTR, which is widely expressed, including in the hippocampus. OXTR expression changes across development in a sex-dependent manner. We recently showed that blocking OXTR in hippocampal CA1 impairs long-term object location memory (OLM) in juvenile male rats. Here, we examine the effect of OXT in juvenile males and females using in vivo and ex vivo electrophysiology. Microinjection of the selective OXTR agonist Thr4,Gly7-oxytocin (TGOT) significantly impairs long-term potentiation (LTP) in the Schaffer collateral-CA1 pathway in juvenile males, but we find no effect in females. Whole-cell patch-clamp recordings show that TGOT increases spontaneous inhibitory postsynaptic currents (sIPSCs) in both sexes, while reducing spontaneous excitatory postsynaptic currents (sEPSCs) only in males. TGOT also reduces intrinsic excitability in juvenile males, whereas female excitability is unchanged. These findings reveal sex-specific effects of oxytocin on hippocampal synaptic plasticity and neuronal excitability during juvenile development. They highlight the importance of considering both sex and age as critical biological variables in studies of hippocampal function and neurodevelopmental disorders.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147811897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bo Liu, Di Kang, Jinjin Zhang, Yujie Wang, Rongrong Li, Changjun Lv, Nailiang Zhai, Xiaodong Song, Songzi Zhang, Hongbo Li
{"title":"HDAC8-mediated CAPZB desuccinylation enhances cytoskeleton remodeling to promote idiopathic pulmonary fibrosis.","authors":"Bo Liu, Di Kang, Jinjin Zhang, Yujie Wang, Rongrong Li, Changjun Lv, Nailiang Zhai, Xiaodong Song, Songzi Zhang, Hongbo Li","doi":"10.1038/s42003-026-10125-y","DOIUrl":"https://doi.org/10.1038/s42003-026-10125-y","url":null,"abstract":"<p><p>Idiopathic pulmonary fibrosis (IPF) is a chronic progressive lung disease of unknown etiology, characterized by progressive scarring and fibrosis of the lungs, leading to irreversible loss of lung function. Current mechanism studies have found that fibroblasts, as the main effector cells, exhibit abnormal differentiation and proliferation in pulmonary fibrosis, thereby promoting collagen secretion for extracellular matrix (ECM) deposition. Cytoskeletal remodeling is the basis for fibroblast-to-myofibroblast differentiation, however, the key proteins and regulatory mechanisms involved in this process are still unclear. Here, F-actin-capping protein subunit beta (CAPZB) was identified to be desuccinylated at three lysine residues (K57, K95, and K235). Gain- and loss-of-function studies in vitro and in vivo demonstrated that CAPZB regulates cytoskeletal remodeling and differentiation of fibroblasts to myofibroblasts by capping the barbed end of F-actin, and mutation of the modification site confirmed the inhibition of CAPZB function by desuccinylation. Further studies showed that histone deacetylase enzymes 8 (HDAC8) could interacts with CAPZB, and its pro-fibrotic role as a desuccinylase was verified. Our findings suggested that desuccinylation inhibited CAPZB function and promoted cytoskeletal remodeling, targeting the succinylation modification of CAPZB could potentially serve as a novel therapeutic approach for pulmonary fibrosis.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764817","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dilina Rusitanmu, Lijuan Li, Qianruo Wan, Jiwei Qi, Jie Han
{"title":"Population genomics reveals population structure, glacial divergence, and intertidal adaptation in the Chinese chiton (Liolophura sinensis).","authors":"Dilina Rusitanmu, Lijuan Li, Qianruo Wan, Jiwei Qi, Jie Han","doi":"10.1038/s42003-026-10149-4","DOIUrl":"https://doi.org/10.1038/s42003-026-10149-4","url":null,"abstract":"<p><p>Chitons (Mollusca: Polyplacophora) are a relatively primitive group within Aculifera that have retained their past life history and ecological traits. While chitons are recognized for their evolutionary significance and societal value (e.g., food, medicine, biomimetics), key aspects of their phylogeographic patterns and microevolutionary processes remain poorly understood, particularly regarding spatial dispersal and adaptation to the challenging intertidal zone environment. Here we show a population genomic analysis of the Chinese chiton (Liolophura sinensis), a species recently delineated from the Liolophura japonica species complex. Using high-depth resequencing of 68 individuals across nine populations, we identify distinct genetic substructure between the Taizhou and southern groups, with divergence dating back to approximately 19.0 thousand years ago, a timing that overlaps with late Pleistocene sea-level minima. A unidirectional gene flow pattern indicates ocean current-mediated larval dispersal, which is consistent with species-specific life history traits. Moreover, selection scans reveal significant enrichment of genes associated with immune responses, cellular homeostasis, and cytoskeleton dynamics, all traits that are potentially relevant for survival in wave-exposed rocky habitats. Our analyses identify strong population structure, recent divergence, and genomic regions potentially associated with local environmental variation, providing a foundational framework for future research on adaptation in marine intertidal species.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rebecca Nance-Richey, Leah Ackerman, Dylan Ammons, Ann M Chan, Valentina Stevenson, Gabriela Hery, Ian Hawkins, Ana Herrera, Alberto Riva, Yanping Zhang, Josephine Brown, Steven W Dow, Elizabeth A Maxwell, Judit Bertran, Josep Aisa, Marilia Takada, Michael Dark, Paulo Vilar Saavedra, Rowan J Milner
{"title":"Spatial transcriptomic mapping of canine osteosarcoma reveals immune microenvironment features linked to survival.","authors":"Rebecca Nance-Richey, Leah Ackerman, Dylan Ammons, Ann M Chan, Valentina Stevenson, Gabriela Hery, Ian Hawkins, Ana Herrera, Alberto Riva, Yanping Zhang, Josephine Brown, Steven W Dow, Elizabeth A Maxwell, Judit Bertran, Josep Aisa, Marilia Takada, Michael Dark, Paulo Vilar Saavedra, Rowan J Milner","doi":"10.1038/s42003-026-10152-9","DOIUrl":"https://doi.org/10.1038/s42003-026-10152-9","url":null,"abstract":"<p><p>Osteosarcoma (OSA) is the most common malignant bone tumor in dogs and serves as a translational model for human pediatric OSA due to shared molecular features. This aggressive and metastatic cancer exhibits significant heterogeneity, which has limited therapeutic advances. Spatial transcriptomics offers a powerful method to investigate intratumoral complexity and the tumor microenvironment. In this study, we used the 10x Genomics Visium platform to profile spatial gene expression in 14 fresh-frozen canine OSA (cOSA) tumor samples from 11 dogs, including primary, metastatic, and recurrent tumors. Samples were stratified by survival outcomes (short-, median-, and long-term). Spatially variable genes and conserved transcriptional clusters were identified, and integration with published single-cell cOSA data enabled deconvolution of cell type proportions and spatial co-localization. Analysis of 18,834 tissue spots revealed intra-tumoral subpopulations and spatial clustering patterns. Pathways related to immune clearance were spatially enriched in long-term survivors. Deconvolution uncovered co-localization of immune cells such as mast cells with osteoclasts, and T/NK cells with regulatory dendritic cells. This study maps the spatial transcriptomic landscape of cOSA, highlighting immune microenvironment features and spatial gene expression patterns associated with survival. These findings provide insights into OSA biology and may guide future therapeutic strategies in both canine and human patients.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764818","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Low-power differencing feature extracts spiking-band activities for high-performance intracortical brain-computer interfaces.","authors":"Guangxiang Xu, Chenbin Yu, Gengrong Shao, Gang Pan, Yueming Wang, Yaoyao Hao","doi":"10.1038/s42003-026-10144-9","DOIUrl":"https://doi.org/10.1038/s42003-026-10144-9","url":null,"abstract":"<p><p>Intracortical brain-computer interfaces (iBCIs) demand computationally efficient feature extraction methods to process high-bandwidth neural signals in resource-constrained implantable systems. We present the mean absolute of n-th difference (MAND), a feature extraction technique that utilizes optimized differencing operations to isolate spiking-band activity with minimal computational overhead. Through theoretical and empirical validation across multiple datasets encompassing human handwriting, primate reaching/grasping, and rodent cognitive tasks, MAND demonstrated superior performance compared to state-of-the-art features, significantly reducing velocity reconstruction error and improving classification accuracy. An extended MAND variant, incorporating a weighted sum of dual-differencing, achieved additional performance gains through enhanced spectral alignment with neural spiking activity. Hardware implementation on FPGA/MCU platforms confirmed MAND's exceptional efficiency - processing 10-second neural recordings in just 6 ms while consuming only 3 mW of power - representing orders-of-magnitude improvements in both speed and energy efficiency compared to conventional methods. These results establish MAND as a breakthrough solution that enables superior decoding performance with exceptional computational efficiency, paving the way for next-generation, fully implantable iBCI systems.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764838","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yan Liu, Jinjin Guo, Yueyang Lu, Weijie Shao, Bo Chang, Jialiang Luo, Zhuojun Zheng, Xiao Lu, Lin Yu, Ke Ma, Mingyong Wang, Daming Zuo, Jia Zhou
{"title":"Macrophage-derived MBL restrains coronavirus-induced pulmonary inflammation by modulating metabolic regulator PKM2-mediated NLRP3 activation.","authors":"Yan Liu, Jinjin Guo, Yueyang Lu, Weijie Shao, Bo Chang, Jialiang Luo, Zhuojun Zheng, Xiao Lu, Lin Yu, Ke Ma, Mingyong Wang, Daming Zuo, Jia Zhou","doi":"10.1038/s42003-026-10146-7","DOIUrl":"https://doi.org/10.1038/s42003-026-10146-7","url":null,"abstract":"<p><p>The precise mechanisms governing innate immune response to coronaviruses remain elusive. Our study reveals that mannose-binding lectin (MBL), a key pattern recognition molecule, exhibits significant upregulation in PBMCs from COVID-19 patients, with expression levels positively correlating with clinical severity. Through intranasal coronavirus MHV-A59 challenge in MBL-deficient mice, we demonstrate that macrophage-derived MBL attenuates viral pneumonia by limiting NLRP3 inflammasome hyperactivation. Mechanistically, MBL directly binds pyruvate kinase M2 (PKM2), an interaction significantly enhanced upon viral stimulation. Crucially, MBL competitively inhibits O-GlcNAcylation at PKM2 Thr405/Ser406 residues, thereby disrupting PKM2 tetramer-to-dimer transition and its subsequent nuclear translocation. The MBL-mediated metabolic reprogramming effectively dampens NLRP3 inflammasome activation, with wild-type mice exhibiting markedly reduced caspase-1 cleavage and IL-1β maturation relative to MBL-deficient mice following MHV-A59 infection. Genetic ablation of NLRP3 abolished the differential susceptibility between wild-type and MBL-deficient animals, confirming NLRP3 as the critical downstream effector. Pharmacological inhibition of either PKM2 or NLRP3 restored cytokine homeostasis in virus-infected MBL-deficient mice. These findings establish a previously unrecognized regulatory pathway in which macrophage-specific MBL fine-tunes antiviral immunity through the PKM2-NLRP3 axis. Our work provides crucial insights into the sophisticated interplay between innate immunity and cellular metabolism, laying the groundwork for developing host-directed therapies against coronaviruses.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764813","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"PreStoi allows accurate prediction of protein complex stoichiometry by integrating AlphaFold3 and template information.","authors":"Jian Liu, Pawan Neupane, Jianlin Cheng","doi":"10.1038/s42003-026-10126-x","DOIUrl":"10.1038/s42003-026-10126-x","url":null,"abstract":"<p><p>Protein complexes carry out many essential functions in cells, but predicting their structures requires knowing their stoichiometry, meaning how many copies of each subunit are present. This information is often unavailable, making stoichiometry prediction crucial for complexes with unknown stoichiometry. Despite its importance, few computational methods address this challenge. Here we show that combining AlphaFold3 structure prediction with information from related known protein complexes enables accurate prediction of protein complex stoichiometry. Our method generates plausible subunit combinations, builds structural models for them using AlphaFold3, ranks them using AlphaFold3 scores, and further refines predictions with template-based information when available. In the 16th community-wide Critical Assessment of Techniques for Protein Structure Prediction, our method identifies the correct stoichiometry as the top prediction for 71.4% of targets and among the top three predictions for 92.9% of targets, outperforming other methods overall. This demonstrates the complementary strengths of AlphaFold3- and template-based predictions and highlights the applicability of our approach to uncharacterized protein complexes lacking stoichiometry data.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764763","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Minji Son, Inwoong Song, Prajitha Pradeep, Bomi Chang, Matthew J Girgenti, Cha Young Kim, Jae Cheol Jeong, Boyoung Lee
{"title":"Cannabidiol modulates spontaneous recovery through distinct and conserved transcriptomic signatures in mPFC subregions.","authors":"Minji Son, Inwoong Song, Prajitha Pradeep, Bomi Chang, Matthew J Girgenti, Cha Young Kim, Jae Cheol Jeong, Boyoung Lee","doi":"10.1038/s42003-026-10111-4","DOIUrl":"https://doi.org/10.1038/s42003-026-10111-4","url":null,"abstract":"<p><p>Cannabidiol (CBD) has shown therapeutic potential for post-traumatic stress disorder (PTSD) by reducing spontaneous recovery (SR), yet the underlying mechanisms remain unclear. We examined the effects of CBD on SR in male and female mice and found greater behavioral efficacy in males. To uncover the molecular basis of these effects, we performed transcriptomic profiling of the prelimbic (PL) and infralimbic (IL) subregions of the medial prefrontal cortex (mPFC). We identified distinct and overlapping SR-associated gene sets in each subregion, and CBD shifted the expression of a significant subset of these genes toward non-stressed control levels, including genes involved in retrograde endocannabinoid signaling. Cross-species comparisons with human PTSD transcriptomic datasets revealed conserved gene alterations within each subregion, suggesting shared molecular signatures between mouse SR and human PTSD. These findings highlight region-specific and conserved pathways through which CBD may exert therapeutic effects and provide mechanistic insight to advance CBD-based interventions for PTSD-associated spontaneous recovery.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Dailos Hernández-Brito, Fernando Hiraldo, Jaume Izquierdo-Palma, José L Tella, Martina Carrete
{"title":"Context-dependent plant-bird interactions shape polychory across the antagonism-mutualism continuum.","authors":"Dailos Hernández-Brito, Fernando Hiraldo, Jaume Izquierdo-Palma, José L Tella, Martina Carrete","doi":"10.1038/s42003-026-10142-x","DOIUrl":"https://doi.org/10.1038/s42003-026-10142-x","url":null,"abstract":"<p><p>Animals feeding on plants may benefit them through seed dispersal or harm them through seed predation, causing net interaction outcomes along an antagonism-mutualism continuum that remains poorly understood. We systematically monitored 6,012 foraging visits of 25 bird species interacting with 40 plant species over a full annual cycle. Interaction outcomes (seed predation, fruit defleshing, and seed dispersal) and dispersal mechanisms (endozoochory, stomatochory, and epizoochory) were shaped by fruit traits, bird feeding strategies, and fruit-to-bird size ratios. However, nearly all bird species (and 10% of individual foraging visits) combined multiple interaction outcomes, seed predators often acting as effective non-endozoochorous dispersers. This flexibility generated polychory in 50% of plant species, while 47.5% were dispersed by birds solely through stomatochory or epizoochory, mechanisms overlooked by classical dispersal syndromes. Our findings portray birds as dynamic, context-dependent agents of seed fate, highlight the need to integrate trait-based and behavioural perspectives in seed dispersal ecology.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":" ","pages":""},"PeriodicalIF":5.1,"publicationDate":"2026-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147764677","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}