Communications Biology最新文献

Author Correction: Gasdermin-D pores induce an inactivating caspase-4 cleavage that limits IL-18 production in the intestinal epithelium. 作者更正：Gasdermin-D气孔诱导灭活caspase-4裂解，限制肠上皮中IL-18的产生。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-31 DOI: 10.1038/s42003-025-08266-7

J K Bruce, L Y Li, Y Tang, E Forster, N J Winsor, P Y Bi, C Krustev, S Keely, J E Lee, J R Rohde, H Y Gaisano, D J Philpott, S E Girardin

引用次数: 0

Sustained strain applied at high rates drives dynamic tensioning in epithelial cells. 高速率的持续应变驱动上皮细胞的动态张力。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-31 DOI: 10.1038/s42003-025-08210-9

Bahareh Tajvidi Safa, Jordan Rosenbohm, Amir Monemian Esfahani, Grayson Minnick, Amir Ostadi Moghaddam, Nickolay V Lavrik, Changjin Huang, Guillaume Charras, Alexandre Kabla, Ruiguo Yang

{"title":"Sustained strain applied at high rates drives dynamic tensioning in epithelial cells.","authors":"Bahareh Tajvidi Safa, Jordan Rosenbohm, Amir Monemian Esfahani, Grayson Minnick, Amir Ostadi Moghaddam, Nickolay V Lavrik, Changjin Huang, Guillaume Charras, Alexandre Kabla, Ruiguo Yang","doi":"10.1038/s42003-025-08210-9","DOIUrl":"https://doi.org/10.1038/s42003-025-08210-9","url":null,"abstract":"Epithelial cells experience long lasting loads of different magnitudes and rates. How they adapt to these loads strongly impacts tissue health. Yet, much remains unknown about the evolution of cellular stress in response to sustained strain. Here, by subjecting cell pairs to sustained strain, we report a bimodal stress response, where in addition to the typically observed stress relaxation, a subset of cells exhibits a dynamic tensioning process with significant elevation in stress within 100 s, resembling active pulling-back in muscle fibers. Strikingly, the fraction of cells exhibiting tensioning increases with increasing strain rate. The tensioning response is accompanied by actin remodeling, and perturbation to actin abrogates it, supporting cell contractility's role in the response. Collectively, our data show that epithelial cells adjust their tensional states over short timescales in a strain-rate dependent manner to adapt to sustained strains, demonstrating that the active pulling-back behavior could be a common protective mechanism against environmental stress.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"843"},"PeriodicalIF":5.2,"publicationDate":"2025-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144191594","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}

引用次数: 0

Leveraging multivariate information for community detection in functional brain networks. 利用多变量信息在功能性脑网络中进行社区检测。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08198-2

Maria Grazia Puxeddu, Maria Pope, Thomas F Varley, Joshua Faskowitz, Olaf Sporns

{"title":"Leveraging multivariate information for community detection in functional brain networks.","authors":"Maria Grazia Puxeddu, Maria Pope, Thomas F Varley, Joshua Faskowitz, Olaf Sporns","doi":"10.1038/s42003-025-08198-2","DOIUrl":"https://doi.org/10.1038/s42003-025-08198-2","url":null,"abstract":"Brain functioning relies on specialized systems whose integration enables cognition and behavior. Network science provides tools to model the brain as a set of interconnected brain regions wherein those segregated systems (modules) can be identified by optimizing the weights of pairwise connections within them. However, knowledge alone of these pairwise connections might not suffice: brain dynamics are also engendered by higher-order interactions that simultaneously involve multiple brain areas. Here, we propose a community detection algorithm that accounts for multivariate interactions and finds modules of brain regions whose activity is maximally redundant. We compared redundancy-dominated modules to those identified with conventional methods, uncovering a new organization of the transmodal cortex. Moreover, by identifying a spatial resolution where within-module redundancy and between-module synergy are maximally balanced, we captured a higher-order manifestation of the interplay between segregation and integration of information. Finally, we distinguish brain regions with high and low topological specialization based on their contribution to within- or between-module redundancy, and we observed how redundant modules reconfigure across the lifespan. Altogether, the results show a modular organization of the brain that accounts for higher-order interactions and pave the way for future investigations that might link it to cognition, behavior, or disease.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"840"},"PeriodicalIF":5.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186736","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}

引用次数: 0

Unveiling an Arpp-19 phosphorylation switch that grants chromosome stability. 揭示赋予染色体稳定性的Arpp-19磷酸化开关。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08281-8

Angela Flavia Serpico, Caterina Pisauro, Asia Trano, Domenico Grieco

{"title":"Unveiling an Arpp-19 phosphorylation switch that grants chromosome stability.","authors":"Angela Flavia Serpico, Caterina Pisauro, Asia Trano, Domenico Grieco","doi":"10.1038/s42003-025-08281-8","DOIUrl":"https://doi.org/10.1038/s42003-025-08281-8","url":null,"abstract":"During cell division, the onset of mitosis is granted by activation of cyclin B-dependent kinase 1 (Cdk1), master mitotic kinase, coordinated with inactivation of Cdk1-counteracting phosphatases. PP2A-B55, a major of these phosphatases, is inhibited in mitosis by Arpp-19 and Ensa, two very similar proteins, once phosphorylated by the Cdk1-stimulated kinase Greatwall (Gwl). We show here that Arpp-19 is also phosphorylated in a Cdk1-dependent manner at serine 23, a site missing in mammalian Ensa, in mitotic human cells and dephosphorylated at this site during mitosis exit. Moreover, we found that this phosphorylation control grants chromosome stability since substituting endogenous Arpp-19 with a S23-Arpp-19 phosphorylation-resistant mutant increased the frequency of chromosome segregation errors and accelerated the timing of mitosis exit. Conversely, substitution with a S23-Arpp-19 phosphorylation-mimicking mutant delayed mitosis exit. S23-Arpp-19 dephosphorylation resisted to the potent PP2A inhibitor Okadaic Acid but required the phosphatase Fcp1. Our data unveil a phosphorylation switch that grants timely mitosis exit and chromosome stability.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"841"},"PeriodicalIF":5.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186742","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}

引用次数: 0

RBAP48 facilitates the oral squamous cell carcinoma process in an androgen receptor-dependent and independent manners. RBAP48以雄激素受体依赖和独立的方式促进口腔鳞状细胞癌的进程。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08215-4

Xue Wang, Guangqi Yan, Hao Li, Chunyu Wang, Ye Kang, Shengli Wang, Wei Liu, Lin Lin, Renlong Zou, Kai Zeng, Manlin Wang, Ruina Luan, Baosheng Zhou, Yu Bai, Dongjun Yang, Bolin Ning, Ge Sun, Yue Zhao

{"title":"RBAP48 facilitates the oral squamous cell carcinoma process in an androgen receptor-dependent and independent manners.","authors":"Xue Wang, Guangqi Yan, Hao Li, Chunyu Wang, Ye Kang, Shengli Wang, Wei Liu, Lin Lin, Renlong Zou, Kai Zeng, Manlin Wang, Ruina Luan, Baosheng Zhou, Yu Bai, Dongjun Yang, Bolin Ning, Ge Sun, Yue Zhao","doi":"10.1038/s42003-025-08215-4","DOIUrl":"10.1038/s42003-025-08215-4","url":null,"abstract":"Oral squamous cell carcinoma (OSCC) progresses from epithelial cell proliferation to malignancy. Given the higher proportion of male patients compared to female patients, the androgen signaling pathway is believed to play a significant role in promoting epithelial cell proliferation. However, the underlying molecular mechanisms remain unclear. Here, we identified RBAP48 as a novel androgen receptor (AR) co-activator in OSCC cells. Our results show that RBAP48 was highly expressed in OSCC tumor tissues from patients with a poor prognosis. Further, RBAP48 knockdown decreased genome-wide oncogene transcription. RBAP48 and AR interacted to activate CCND1 and RAB31 transcription, and upregulated RELA and CCNE1 mRNA expression through an AR-independent pathway. Additionally, RBAP48 promoted OSCC cell proliferation and was involved in the cellular response to drugs and external compounds in vitro, ultimately driving cancer progression. Our results indicate that RBAP48 is a novel oncogene and a promising target for predicting and treating OSCC progression.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"829"},"PeriodicalIF":5.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12122889/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144179756","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}

引用次数: 0

Quantitative benchmarking of nuclear segmentation algorithms in multiplexed immunofluorescence imaging for translational studies. 用于翻译研究的多路免疫荧光成像中核分割算法的定量基准。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08184-8

Abishek Sankaranarayanan, Georgii Khachaturov, Kimberly S Smythe, Shachi Mittal

{"title":"Quantitative benchmarking of nuclear segmentation algorithms in multiplexed immunofluorescence imaging for translational studies.","authors":"Abishek Sankaranarayanan, Georgii Khachaturov, Kimberly S Smythe, Shachi Mittal","doi":"10.1038/s42003-025-08184-8","DOIUrl":"https://doi.org/10.1038/s42003-025-08184-8","url":null,"abstract":"Multiplexed imaging techniques require identifying different cell types in the tissue. To utilize their potential for cellular and molecular analysis, high throughput and accurate analytical approaches are needed in parsing vast amounts of data, particularly in clinical settings. Nuclear segmentation errors propagate in all downstream steps of cell phenotyping and single-cell spatial analyses. Here, we benchmark and compare the nuclear segmentation tools commonly used in multiplexed immunofluorescence data by evaluating their performance across 7 tissue types encompassing ~20,000 labeled nuclei from human tissue samples. Pre-trained deep learning models outperform classical nuclear segmentation algorithms. Overall, Mesmer is recommended as it exhibits the highest nuclear segmentation accuracy with 0.67 F1-score at an IoU threshold of 0.5 on our composite dataset. Pre-trained StarDist model is recommended in case of limited computational resources, providing ~12x run time improvement with CPU compute and ~4x improvement with the GPU compute over Mesmer, but it struggles in dense nuclear regions.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"836"},"PeriodicalIF":5.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186739","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}

引用次数: 0

Author Correction: Differential response of tissue engineered skeletal muscle from rheumatoid arthritis patients and healthy controls. 作者更正：类风湿关节炎患者和健康对照者组织工程骨骼肌的差异反应。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08286-3

Catherine E Oliver, Jonathan L Carter, James S Hong, Mingzhi Xu, William E Kraus, Kim M Huffman, George A Truskey

引用次数: 0

Substantial loss of trawlable biomass and lack of recovery in a marine ecosystem. 海洋生态系统中可拖网生物量的大量损失和缺乏恢复。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08240-3

Jacob Burbank, Nicolas Rolland, Jenni L McDermid, François Turcotte, Tyler D Tunney, Daniel Ricard, François-Étienne Sylvain

{"title":"Substantial loss of trawlable biomass and lack of recovery in a marine ecosystem.","authors":"Jacob Burbank, Nicolas Rolland, Jenni L McDermid, François Turcotte, Tyler D Tunney, Daniel Ricard, François-Étienne Sylvain","doi":"10.1038/s42003-025-08240-3","DOIUrl":"https://doi.org/10.1038/s42003-025-08240-3","url":null,"abstract":"Profound changes in species assemblages are occurring in marine ecosystems worldwide and are essential to document. Here we use 51 years (1971-2021) of fishery-independent data from a standardized bottom-trawl research vessel survey (6440 independent fishing locations) in the southern Gulf of St. Lawrence covering 70,091 km² to evaluate trends in marine community structure and trawlable biomass across 122 fish and crustacean taxa. Survey data indicate a substantial decline in biomass and increase in turnover for taxa susceptible to bottom-trawl fishing gear in the southern Gulf of St. Lawrence marine ecosystem that corresponds with the reduction of several predatory fish and a major regime shift around the early 1990's. Unlike other marine regime shift examples, we observe a substantial net loss of trawlable biomass in the community, with limited compensatory response in small fish and crustacean biomass over nearly 30 years following the depletion of predatory groundfish. Overall, this unique case of reduced biomass and shift in community structure highlights the importance of maintaining and analyzing fishery-independent surveys over extended time series. Such information is vital to assessing the state of marine ecosystems and developing plans for recovery, as we face a future of untold challenges in managing marine ecosystems worldwide.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"831"},"PeriodicalIF":5.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186740","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}

引用次数: 0

The distinct transcriptomic signature of the resolution phase fibroblast-like synoviocytes supports endothelial cell dysfunction. 分化期成纤维细胞样滑膜细胞的独特转录组特征支持内皮细胞功能障碍。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08250-1

Surabhi Gautam, Jayla Elan Whittaker, Rushi Vekariya, Sergio Ramirez-Perez, Umesh Gangishetti, Hicham Drissi, Pallavi Bhattaram

{"title":"The distinct transcriptomic signature of the resolution phase fibroblast-like synoviocytes supports endothelial cell dysfunction.","authors":"Surabhi Gautam, Jayla Elan Whittaker, Rushi Vekariya, Sergio Ramirez-Perez, Umesh Gangishetti, Hicham Drissi, Pallavi Bhattaram","doi":"10.1038/s42003-025-08250-1","DOIUrl":"https://doi.org/10.1038/s42003-025-08250-1","url":null,"abstract":"Patients suffering from rheumatoid arthritis (RA) and related autoimmune joint diseases exhibit cyclic episodes of resolution and exacerbation of joint inflammation, referred to as flares. Fibroblast-like synoviocytes (FLSs) that are epigenetically transformed by chronic inflammation are implicated as the orchestrators of these flares. In this study, we compared the cellular and molecular features of the FLSs during the inflammatory and resolution phases of RA progression. We performed histopathological evaluations of the joints from an inducible tumor necrosis factor-alpha (TNF-α) transgenic mouse model to reveal that phenotypic RA hallmarks including synovial hyperplasia, increased angiogenesis, and macrophage infiltration, were all reversed upon the initiation of resolution. However, the FLSs from the resolution phase joints exhibited a transcriptomic signature reminiscent of a highly inflammatory state. They exhibited a G0/G1 cell cycle arrest accompanied by reduced viability. In addition, factors secreted from the resolution FLSs, induced cell death, and decreased the angiogenic potential in human microvascular and umbilical cord endothelial cells. These findings indicate that the secretome of the resolution phase FLSs impairs endothelial cell function and suggest that understanding the interaction between the FLSs and endothelial cells during the resolution phase of RA is essential for achieving complete remission.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"837"},"PeriodicalIF":5.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186741","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}

引用次数: 0

AMPGen: an evolutionary information-reserved and diffusion-driven generative model for de novo design of antimicrobial peptides. AMPGen：用于抗菌肽从头设计的进化信息保留和扩散驱动的生成模型。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-05-30 DOI: 10.1038/s42003-025-08282-7

Shuwen Jin, Zihan Zeng, Xiyan Xiong, Baicheng Huang, Li Tang, Hongsheng Wang, Xiao Ma, Xiaochun Tang, Guoqing Shao, Xingxu Huang, Feng Lin

{"title":"AMPGen: an evolutionary information-reserved and diffusion-driven generative model for de novo design of antimicrobial peptides.","authors":"Shuwen Jin, Zihan Zeng, Xiyan Xiong, Baicheng Huang, Li Tang, Hongsheng Wang, Xiao Ma, Xiaochun Tang, Guoqing Shao, Xingxu Huang, Feng Lin","doi":"10.1038/s42003-025-08282-7","DOIUrl":"https://doi.org/10.1038/s42003-025-08282-7","url":null,"abstract":"The rapid advancement of artificial intelligence (AI) has enabled de novo design of functional proteins, circumventing the reliance on natural templates or sequencing databases. However, current protein design models are ineffective in generating proteins without stable structures, such as antimicrobial peptides (AMPs), which are short and structurally flexible yet play critical biological roles. To address this challenge, we present AMPGen, an evolutionary information-reserved and diffusion-driven generative model for de novo design of target-specific AMPs. AMPGen innovates AI tools, including a generator, a discriminator, and a scorer, along with biochemical knowledge-based screening programs. The generator employs a pre-trained, order-agnostic autoregressive diffusion model, which performs axial attention to capture protein evolutionary information from multiple sequence alignments (MSAs). The AMP-MSA conditional input raises the success rate of generated AMPs, which are subsequently filtered based on physicochemical properties and assessed by an XGBoost-based discriminator. The final target-specific scoring is performed with an LSTM-based scorer, resulting in high-quality AMP candidates. In this study, of the 40 de novo designed AMP candidates for verification, 38 were successfully synthesized, and among them, 81.58% demonstrated antibacterial activity. These AMPs designed by AMPGen are absent from existing AMP databases, and exhibit high antibacterial capacity, sequence diversity, and broad-spectrum activity.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"839"},"PeriodicalIF":5.2,"publicationDate":"2025-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144186731","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}

引用次数: 0