Yee Song Chong, Sheila Ruixia Ang, Sreedharan Sajikumar
{"title":"Beyond boundaries: extended temporal flexibility in synaptic tagging and capture.","authors":"Yee Song Chong, Sheila Ruixia Ang, Sreedharan Sajikumar","doi":"10.1038/s42003-025-07998-w","DOIUrl":"10.1038/s42003-025-07998-w","url":null,"abstract":"<p><p>Synaptic tagging and capture (STC) is a mechanism that enables the formation of associative synaptic plasticity by marking activated synapses with \"tags\" to capture plasticity-related products (PRPs) essential for plasticity stabilization. Experimental evidence using long-term potentiation (LTP), a widely studied cellular correlate of memory, shows that the duration of synaptic tags varies, lasting up to 90 minutes in ex vivo hippocampal slices but shorter in in vivo conditions, likely due to higher metabolic activity. In this study, we investigate the time window for tag-PRP interactions in STC using a strong-before-weak paradigm, where protein synthesis-dependent late-LTP precedes protein synthesis-independent early-LTP at various intervals. Surprisingly, successful STC is observed even with a 9-hour interval in the strong-before-weak paradigm, suggesting a broader temporal flexibility for tag-PRP interactions than previously understood. This unexpected finding offers alternative explanations for associative memory formation by cataloguing memory events, allowing weaker memories to be strengthened when preceded by stronger ones.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"553"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968991/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779348","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}
Insuck Baek, Seunghyun Lim, Visna Weerarathne, Dongho Lee, Jacob Botkin, Silvas Kirubakaran, Sunchung Park, Moon S Kim, Lyndel W Meinhardt, Ezekiel Ahn
{"title":"Spatial patterning of chloroplasts and stomata in developing cacao leaves.","authors":"Insuck Baek, Seunghyun Lim, Visna Weerarathne, Dongho Lee, Jacob Botkin, Silvas Kirubakaran, Sunchung Park, Moon S Kim, Lyndel W Meinhardt, Ezekiel Ahn","doi":"10.1038/s42003-025-08019-6","DOIUrl":"10.1038/s42003-025-08019-6","url":null,"abstract":"<p><p>Leaf development and the coordinated formation of its key components is a fundamental process driving plant growth and adaptation. In tropical species like cacao, flush growth, a period of rapid leaf expansion, is particularly dependent on the optimized spatial patterns of chloroplasts and stomata. In this study, we investigated the patterns in cacao leaves during growth Stage C, a phase marked by rapid chlorophyll accumulation. Microscopic image data revealed significant acropetal variations in the size and density of chloroplast clusters and stomata, with the largest values found near the leaf base, mirroring the leaf greenness gradient. These findings suggest a coordinated developmental sequence between chloroplasts, stomata, and leaf ontogeny. A Support Vector Machine (SVM) model successfully classified distinct leaf regions based on these morphological features (>80% accuracy), highlighting the potential of machine learning applications in this area. Our results provide novel insights into the spatial coordination of chloroplast and stomatal development during cacao leaf maturation, offering a foundation for future research on flush growth optimization. To the best of our knowledge, this is the first report that combines microscopic data and machine learning analysis to investigate the leaf developmental process at stage C in cacao.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"554"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11968909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779354","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}
Alessandro Sammarco, Giorgia Guerra, Katharina M Eyme, Kelly Kennewick, Yu Qiao, Joelle El Hokayem, Kevin J Williams, Baolong Su, Cagri Cakici, Hayk Mnatsakanyan, Valentina Zappulli, Steven J Bensinger, Christian E Badr
{"title":"Targeting SCD triggers lipotoxicity of cancer cells and enhances anti-tumor immunity in breast cancer brain metastasis mouse models.","authors":"Alessandro Sammarco, Giorgia Guerra, Katharina M Eyme, Kelly Kennewick, Yu Qiao, Joelle El Hokayem, Kevin J Williams, Baolong Su, Cagri Cakici, Hayk Mnatsakanyan, Valentina Zappulli, Steven J Bensinger, Christian E Badr","doi":"10.1038/s42003-025-07977-1","DOIUrl":"10.1038/s42003-025-07977-1","url":null,"abstract":"<p><p>Breast cancer brain metastases (BCBM) are incurable, and new therapies are urgently needed. BCBM upregulates stearoyl-CoA desaturase (SCD), an enzyme that catalyzes the synthesis of monounsaturated fatty acids, suggesting a potential metabolic vulnerability. Here, we test the effect of a brain-penetrant, clinical-stage SCD inhibitor (SCDi) on breast cancer cells and mouse models of BCBM. We show that SCDi markedly reshapes the lipidome of breast cancer cells, resulting in endoplasmic reticulum stress, DNA damage, impaired DNA damage repair, and cytotoxicity. Importantly, SCDi alone or combined with a PARP inhibitor prolongs the survival of BCBM-bearing mice. Furthermore, pharmacological inhibition of SCD enhances antigen presentation by dendritic cells, increases interferon signaling, promotes the infiltration of cytotoxic T cells, and decreases the proportion of exhausted T cells and regulatory T cells (Tregs) in the tumor microenvironment (TME) in a syngeneic mouse model of BCBM. Additionally, SCDi reduces the engagement of immunosuppressive pathways, including the PD-1:PD-L1/PD-L2 and PVR/TIGIT axes in the TME. These findings suggest that SCD inhibition could be an effective strategy to both intrinsically reduce tumor growth and reprogram anti-tumor immunity in the brain microenvironment to treat BCBM.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"562"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971295/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788146","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":"From medical illustration to evolutionary anatomy: Christopher Smith's artistic approach to science.","authors":"","doi":"10.1038/s42003-025-08000-3","DOIUrl":"10.1038/s42003-025-08000-3","url":null,"abstract":"","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"558"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971396/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788111","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":"The crosstalk of monocyte-neutrophil in hair follicles regulates neutrophil transepidermal migration in contact dermatitis.","authors":"Zhan Fan, Yilun Xu, Yafang Lu, Xinlin Li, Mengli Xu, Jinxin Liu, Zhenzhen Cai, Jiayang Liu, Jingping Su, Jialu Wang, Qingming Luo, Zhihong Zhang, Zheng Liu","doi":"10.1038/s42003-025-07960-w","DOIUrl":"10.1038/s42003-025-07960-w","url":null,"abstract":"<p><p>The excessive accumulation of neutrophils within the epidermis is a significant hallmark of cutaneous diseases; however, the mechanisms governing neutrophil transepidermal migration (NTEM) remain inadequately understood. In this study, we develop trichromatic-fluorescence-labeled chimeric mice by utilizing Cx3cr1<sup>GFP/+</sup>Lyz2<sup>RFP/+</sup> mice as bone marrow donors and Krt14<sup>YFP/+</sup> mice as recipients. This approach enables us to visualize the process of NTEM and the crosstalk between neutrophils and monocytes in a murine model of irritant contact dermatitis (ICD). Intravital imaging reveals a preferential transmigration of neutrophils through hair follicle (HF), where dermal neutrophils exhibit limited mobility and interact with dermal monocytes. Notably, 18 h following hapten exposure, dermal neutrophils continuously migrate toward HF regions and form clusters within 3 h. Importantly, MMP-9 is identified as essential for the NTEM process; the depletion of dermal monocytes results in a significant reduction of MMP-9 expression in the skin and inhibits the NTEM process in ICD. Mechanistically, dermal monocytes are found to be a crucial source of the cytokines TNF-α and CXCL2, which promote the upregulation of MMP-9 in neutrophils. Therefore, our results highlight HF regions as crucial gateways for dermal monocyte-modulated NTEM and provide visual insights into the crosstalk between neutrophils and monocytes in inflammatory skin disorders.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"564"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788148","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":"TCP1 promotes the progression of malignant tumours by stabilizing c-Myc through the AKT/GSK-3β and ERK signalling pathways.","authors":"Hekun Liu, Linying Chen, Yuwen Chen, Yiyi Jin, Xiance Chen, Nengjun Ma, Fan Yang, Huixia Bi, Xinxin Wen, Shenmin Xu, Juan Chen, Yanping Lin, Yinghong Yang, Yong Wu, Yuanzhong Chen","doi":"10.1038/s42003-025-07867-6","DOIUrl":"10.1038/s42003-025-07867-6","url":null,"abstract":"<p><p>The chaperonin tailless complex polypeptide 1 (TCP1) is a key subunit of chaperonin containing TCP1 (CCT) that regulates the folding and stability of proteins during cancer progression. Here, the prognostic significance of TCP1 was explored mainly in patients with hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC). We showed that TCP1 expression was significantly greater in clinically malignant tumour tissues than in normal tissues and that high TCP1 expression was associated with poor prognosis. TCP1 suppression not only decreased the proliferation and invasion of cancer cells in vitro but also inhibited tumour growth and metastasis in vivo. The underlying mechanisms were determined by ubiquitination assays and Co-IP (Co-Immunoprecipitation) experiments, and it was found that TCP1 regulated the stability of c-Myc through the RAC-alpha serine/threonine-protein kinase (AKT) /Glycogen synthase kinase 3β (GSK-3β) and extracellular regulated protein kinases (ERK) signalling pathways. Moreover, TCP1 knock-in (TCP1-KI) dramatically promoted the occurrence of diethylnitrosamine (DEN) -induced primary HCC in mice. Our results highlight the critical role of TCP1 in HCC and PDAC and reveal a novel mechanism to suppress HCC and PDAC by targeting c-Myc via the TCP1-induced promotion of the AKT/GSK-3β and ERK signalling pathways. TCP1 is able to modulate the stability of target proteins by multiple pathways, thus promoting the progression of HCC and PDAC. Our study identifies TCP1 as a prognostic novel marker and therapeutic target of HCC and PDAC.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"563"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971430/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788147","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":"Flexible integration of spatial and expression information for precise spot embedding via ZINB-based graph-enhanced autoencoder.","authors":"Jiacheng Leng, Jiating Yu, Ling-Yun Wu, Hongyang Chen","doi":"10.1038/s42003-025-07965-5","DOIUrl":"10.1038/s42003-025-07965-5","url":null,"abstract":"<p><p>Domain identification is a critical problem in spatially resolved transcriptomics data analysis, which aims to identify distinct spatial domains within a tissue that maintain both spatial continuity and expression consistency. The degree of coupling between expression data and spatial information in different datasets often varies significantly. Some regions have intact and clear boundaries, while others exhibit blurred boundaries with high intra-domain expression similarity. However, most domain identification methods do not adequately integrate expression and spatial information to flexibly identify different types of domains. To address these issues, we introduce Spot2vector, a computational framework that leverages a graph-enhanced autoencoder integrating zero-inflated negative binomial distribution modeling, combining both graph convolutional networks and graph attention networks to extract the latent embeddings of spots. Spot2vector encodes and integrates spatial and expression information, enabling effective identification of domains with diverse spatial patterns across spatially resolved transcriptomics data generated by different platforms. The decoders enable us to decipher the distribution and generation mechanisms of data while improving expression quality through denoising. Extensive validation and analyses demonstrate that Spot2vector excels in enhancing domain identification accuracy, effectively reducing data dimensionality, improving expression recovery and denoising, and precisely capturing spatial gene expression patterns.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"556"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788110","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}
Chuan He, Paraskevas Filippidis, Steven H Kleinstein, Leying Guan
{"title":"Partially characterized topology guides reliable anchor-free scRNA-integration.","authors":"Chuan He, Paraskevas Filippidis, Steven H Kleinstein, Leying Guan","doi":"10.1038/s42003-025-07988-y","DOIUrl":"10.1038/s42003-025-07988-y","url":null,"abstract":"<p><p>Single-cell RNA sequencing (scRNA-seq) is an important technique for obtaining biological insights at cellular resolution, with scRNA-seq batch integration a key step before downstream statistical analysis. Despite the plethora of methods proposed, achieving reliable batch correction while preserving the heterogeneity of biological signals that define cell type continues to pose a challenge. To address this, we propose scCRAFT, an autoencoder model that separates cell-type-related signals from batch effects for reliable multi-batch integration. scCRAFT integrates three key loss components: a reconstruction loss for observation reconstruction, a multi-domain adaptation loss to eliminate batch effects, and an innovative dual-resolution triplet loss to preserve intra-batch, introduced as an effective mechanism to counteract the over-correction effect of domain adaptation loss amid heterogeneous cell distributions across batches. We show that scCRAFT effectively manages unbalanced batches, rare cell types, and batch-specific cell phenotypes in simulations, and surpasses state-of-the-art methods in a diverse set of real datasets.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"561"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788141","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}
Ruixiang Wu, Jinhuai Xu, Chunpeng Li, Zhaoji Zhang, Shu Lin, Ling-Yun Li, Ya-Tang Li
{"title":"Preference-independent saliency map in the mouse superior colliculus.","authors":"Ruixiang Wu, Jinhuai Xu, Chunpeng Li, Zhaoji Zhang, Shu Lin, Ling-Yun Li, Ya-Tang Li","doi":"10.1038/s42003-025-08006-x","DOIUrl":"10.1038/s42003-025-08006-x","url":null,"abstract":"<p><p>Detecting salient stimuli in a visual scene is crucial for animal survival, yet how the brain encodes visual saliency remains unclear. Here, using two-photon calcium imaging, we reveal a preference-independent saliency map in the superficial superior colliculus of awake mice. Salient stimuli evoke stronger responses than uniform stimuli in both excitatory and inhibitory neurons, with similar encoding patterns across both cell types. The strongest response occurs when a salient stimulus is centered within the receptive field, with contextual effects extending approximately 40°. Response amplitude scales with saliency strength but remains independent of neurons' orientation or motion direction preferences. Notably, saliency-encoding neurons exhibit weak orientation and direction selectivity, indicating a complementary relationship between saliency and feature maps. Importantly, this preference-independent saliency encoding does not require cortical inputs. These findings provide insights into the neural mechanisms underlying visual saliency detection.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"565"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788142","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":"Glucocorticoids regulate the expression of Srsf1 through Hdac4/Foxc1 axis to induce apoptosis of osteoblasts.","authors":"Hong Luo, Tao Wang, Zhihong Xie, Fanchao Li, Chengyou Yang, Wentao Dong, Jianhua Wu, Qiang Wang, Fengyang Xu, Jiong Liu, Fei Zhang, Wuxun Peng","doi":"10.1038/s42003-025-07989-x","DOIUrl":"10.1038/s42003-025-07989-x","url":null,"abstract":"<p><p>Further study of the mechanism of glucocorticoid (GC)-induced osteoblast (OB) apoptosis is highly important for the prevention and treatment of GC-induced osteoporosis and osteonecrosis. Serine/arginine-rich splicing factor 1 (Srsf1) expression was downregulated in a dose-dependent manner during GC-induced OB apoptosis. Knockdown of Srsf1 significantly promotes GC-induced OB apoptosis, while overexpression of Srsf1 significantly inhibits GC-induced OB apoptosis. Mechanistically, GC induces the up-regulation of histone deacetylase 4 (Hdac4) in OB, and inhibits the expression of transcription activator forkhead box C1 (Foxc1) by reducing the levels of histone H3 lysine 9 acetylation (H3K9ac) and H3K27ac in the promoter region of Foxc1, thereby down-regulating Srsf1. Next, SRSF1 regulates GC-induced OB apoptosis by regulating Bcl-2 modifying factor (Bmf) alternative splicing. From the perspective of alternative splicing, this study demonstrates that Srsf1 and its regulatory mechanism may serve as a new target for the prevention and treatment of GC-induced osteoporosis and osteonecrosis.</p>","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"566"},"PeriodicalIF":5.2,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971326/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788138","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}