Communications Biology最新文献_第8页

Cigarette smoke induces angiogenic activation in the cancer field through dysregulation of an endothelial microRNA. 香烟烟雾通过内皮细胞microRNA的失调诱导癌症领域的血管生成激活。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-28 DOI: 10.1038/s42003-025-07710-y

Asawari Korde, Anuradha Ramaswamy, Seth Anderson, Lei Jin, Jian-Ge Zhang, Buqu Hu, Walter V Velasco, Lixia Diao, Jing Wang, Margaret A Pisani, Maor Sauler, Daniel J Boffa, Jonathan T Puchalski, Xiting Yan, Seyed Javad Moghaddam, Shervin S Takyar

{"title":"Cigarette smoke induces angiogenic activation in the cancer field through dysregulation of an endothelial microRNA.","authors":"Asawari Korde, Anuradha Ramaswamy, Seth Anderson, Lei Jin, Jian-Ge Zhang, Buqu Hu, Walter V Velasco, Lixia Diao, Jing Wang, Margaret A Pisani, Maor Sauler, Daniel J Boffa, Jonathan T Puchalski, Xiting Yan, Seyed Javad Moghaddam, Shervin S Takyar","doi":"10.1038/s42003-025-07710-y","DOIUrl":"10.1038/s42003-025-07710-y","url":null,"abstract":"Cigarette smoke (CS) creates a \"cancer field\" in the lung that promotes malignant transformation. The molecular changes within this field are not fully characterized. We examined the significance of microRNA-1 (miR-1) downregulation as one of these changes. We found that tumor miR-1 levels in three non-small cell lung cancer cohorts show inverse correlations with the smoking burden. Lung MiR-1 levels follow a spatial gradient, have prognostic significance, and correlate inversely with the molecular markers of injury. In CS-exposed lungs, miR-1 is specifically downregulated in the endothelium. Exposure to CS induces angiogenesis by selectively degrading mature miR-1 via a vascular endothelial growth factor-driven pathway. Applying a multi-step molecular screen, we identified angiogenic genes regulated by miR-1 in the lungs of smokers. Knockdown of one of these genes, Notch homolog protein 3, simulates the anti-angiogenic effects of miR-1. These findings suggest that miR-1 can be used as an indicator of malignant transformation.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"511"},"PeriodicalIF":5.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953391/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742438","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

Neural dynamics of semantic control underlying generative storytelling. 语义控制下的神经动力学生成故事。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-28 DOI: 10.1038/s42003-025-07913-3

Clara Rastelli, Antonino Greco, Chiara Finocchiaro, Gabriele Penazzi, Christoph Braun, Nicola De Pisapia

{"title":"Neural dynamics of semantic control underlying generative storytelling.","authors":"Clara Rastelli, Antonino Greco, Chiara Finocchiaro, Gabriele Penazzi, Christoph Braun, Nicola De Pisapia","doi":"10.1038/s42003-025-07913-3","DOIUrl":"10.1038/s42003-025-07913-3","url":null,"abstract":"Storytelling has been pivotal for the transmission of knowledge across human history, yet the role of semantic control and its associated neural dynamics has been poorly investigated. Here, human participants generated stories that were either appropriate (ordinary), novel (random), or balanced (creative), while recording functional magnetic resonance imaging (fMRI). Deep language models confirmed participants adherence to task instructions. At the neural level, linguistic and visual areas exhibited neural synchrony across participants regardless of the semantic control level, with parietal and frontal regions being more synchronized during random ideation. Importantly, creative stories were differentiated by a multivariate pattern of neural activity in frontal and fronto-temporo-parietal cortices compared to ordinary and random stories. Crucially, similar brain regions were also encoding the features that distinguished the stories. Moreover, we found specific spatial frequency patterns underlying the modulation of semantic control during story generation, while functional coupling in default, salience, and control networks differentiated creative stories with their controls. Remarkably, the temporal irreversibility between visual and high-level areas was higher during creative ideation, suggesting the enhanced hierarchical structure of causal interactions as a neural signature of creative storytelling. Together, our findings highlight the neural mechanisms underlying the regulation of semantic exploration during narrative ideation.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"513"},"PeriodicalIF":5.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742445","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

Social tolerance and role model diversity increase tool use learning opportunities across chimpanzee ontogeny. 社会宽容度和榜样多样性增加了黑猩猩在整个个体发育过程中学习使用工具的机会。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-28 DOI: 10.1038/s42003-025-07885-4

Oscar Nodé-Langlois, Eléonore Rolland, Cédric Girard-Buttoz, Liran Samuni, Pier Francesco Ferrari, Roman M Wittig, Catherine Crockford

{"title":"Social tolerance and role model diversity increase tool use learning opportunities across chimpanzee ontogeny.","authors":"Oscar Nodé-Langlois, Eléonore Rolland, Cédric Girard-Buttoz, Liran Samuni, Pier Francesco Ferrari, Roman M Wittig, Catherine Crockford","doi":"10.1038/s42003-025-07885-4","DOIUrl":"10.1038/s42003-025-07885-4","url":null,"abstract":"Social learning opportunities shape cognitive skills across species, especially in humans. Although the social environment impacts learning opportunities, the benefits of role model diversity and tolerance on task learning in tool-using species remain poorly understood. To explore these links, we study 2343 peering events (close-range observation of a conspecific) from 35 wild immature (<10 y) chimpanzees (Pan troglodytes verus). We find that chimpanzee peering functions to acquire information more than food, persists during development while peaking around weaning age, and increases with food processing complexity. Role models change throughout development, with increased peering at mothers during early stages and for more complex tasks. Finally, immatures observe many role models, favouring older and more tolerant individuals. We conclude that chimpanzees learn from multiple tolerant individuals, particularly when acquiring complex skills like tool use. Tolerant societies may be necessary for the acquisition and retention of the diverse tool kits rarely found in nature.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"509"},"PeriodicalIF":5.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953367/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742533","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

Defining gastric cancer ecology: the crucial roles of TREM2⁺ macrophages and fibroblasts in tumor microenvironments. 定义胃癌生态：TREM2+巨噬细胞和成纤维细胞在肿瘤微环境中的关键作用。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-28 DOI: 10.1038/s42003-025-07512-2

Qianqian Cao, Dianshui Sun, Can Tu, Jihua Wang, Runjia Fu, Rumei Gong, Yueying Xiao, Qin Liu, Xiaomei Li

{"title":"Defining gastric cancer ecology: the crucial roles of TREM2+ macrophages and fibroblasts in tumor microenvironments.","authors":"Qianqian Cao, Dianshui Sun, Can Tu, Jihua Wang, Runjia Fu, Rumei Gong, Yueying Xiao, Qin Liu, Xiaomei Li","doi":"10.1038/s42003-025-07512-2","DOIUrl":"10.1038/s42003-025-07512-2","url":null,"abstract":"Gastric cancer (GC) remains a major global health challenge, characterized by a complex tumor microenvironment (TME) that significantly influences disease progression and therapeutic outcomes. This study focuses on TREM2+ lipid-associated macrophages (LAM) and cancer-associated fibroblasts (CAFs) in modulating the GC microenvironment. Utilizing advanced single-cell RNA sequencing and bulk RNA analyses, we elucidated the interactive mechanisms through which CAFs enhance the immunosuppressive capabilities of TREM2+ LAMs via the CXCL12-CXCR4 signaling axis. Our findings reveal that this interaction facilitates tumor proliferation and inhibits apoptotic processes in GC cells. In vitro experiments confirmed the modulation of this pathway significantly affects tumor cell viability and invasiveness, underscoring the critical roles of these cellular interactions in promoting GC progression. These insights present TREM2+ LAMs and CAFs as potential therapeutic targets, offering new avenues for improving outcomes in GC treatment.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"514"},"PeriodicalIF":5.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742439","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

(p)ppGpp-mediated GTP homeostasis ensures survival and antibiotic tolerance of Staphylococcus aureus. (p) ppgpp介导的GTP稳态确保金黄色葡萄球菌的存活和抗生素耐受性。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-28 DOI: 10.1038/s42003-025-07910-6

Andrea Salzer, Sophia Ingrassia, Parvati Iyer, Lisa Sauer, Johanna Rapp, Ronja Dobritz, Jennifer Müller, Hannes Link, Christiane Wolz

{"title":"(p)ppGpp-mediated GTP homeostasis ensures survival and antibiotic tolerance of Staphylococcus aureus.","authors":"Andrea Salzer, Sophia Ingrassia, Parvati Iyer, Lisa Sauer, Johanna Rapp, Ronja Dobritz, Jennifer Müller, Hannes Link, Christiane Wolz","doi":"10.1038/s42003-025-07910-6","DOIUrl":"10.1038/s42003-025-07910-6","url":null,"abstract":"Antibiotic tolerance in non-growing bacterial populations is of major concern regarding antibiotic treatment failures. Whether and how the messenger molecule (p)ppGpp contributes to this phenomenon is controversial. We show for Staphylococcus aureus that (p)ppGpp-dependent restriction of the GTP pool is essential for the culturability of starved cells. Survival was independent of the GTP-responsive regulator CodY. Elevated GTP levels in a starved (p)ppGpp-deficient mutant led to quiescent state characterised by alterations in membrane architecture and a decrease of the proton motive force (PMF). This was accompanied by dysregulation of components involved in electron transport, including qoxABCD, encoding the main terminal oxidase. Increasing qoxABCD transcription by mutation of the transcription start site (iATP to iGTP) partially restored the culturability of the (p)ppGpp-deficient mutant. Thus, regulation of nucleotide-dependent promoters by altered nucleotide levels contribute to starvation adaptability. Loss of PMF under high GTP conditions also renders bacteria susceptible to antibiotics. Thus, targeting the PMF or nucleotide availability may be a valuable strategy to combat antibiotic tolerance.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"508"},"PeriodicalIF":5.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953324/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742436","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

Diffusion MRI GAN synthesizing fibre orientation distribution data using generative adversarial networks. 利用生成对抗网络合成纤维取向分布数据的扩散MRI GAN。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-28 DOI: 10.1038/s42003-025-07936-w

Sebastian Vellmer, Dogu Baran Aydogan, Timo Roine, Alberto Cacciola, Thomas Picht, Lucius S Fekonja

{"title":"Diffusion MRI GAN synthesizing fibre orientation distribution data using generative adversarial networks.","authors":"Sebastian Vellmer, Dogu Baran Aydogan, Timo Roine, Alberto Cacciola, Thomas Picht, Lucius S Fekonja","doi":"10.1038/s42003-025-07936-w","DOIUrl":"https://doi.org/10.1038/s42003-025-07936-w","url":null,"abstract":"Machine learning may enhance clinical data analysis but requires large amounts of training data, which are scarce for rare pathologies. While generative neural network models can create realistic synthetic data such as 3D MRI volumes and, thus, augment training datasets, the generation of complex data remains challenging. Fibre orientation distributions (FODs) represent one such complex data type, modelling diffusion as spherical harmonics with stored weights as multiple three-dimensional volumes. We successfully trained an α-WGAN combining a generative adversarial network and a variational autoencoder to generate synthetic FODs, using the Human Connectome Project (HCP) data. Our resulting synthetic FODs produce anatomically accurate fibre bundles and connectomes, with properties matching those from our validation dataset. Our approach extends beyond FODs and could be adapted for generating various types of complex medical imaging data, particularly valuable for augmenting limited clinical datasets.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"512"},"PeriodicalIF":5.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953217/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742440","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

Prey size mediates interference competition and predation dynamics in a large carnivore community. 在大型食肉动物群落中，猎物的大小调节着干扰竞争和捕食动态。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-28 DOI: 10.1038/s42003-025-07779-5

Jack W Rabe, Wesley J Binder, Colby B Anton, Connor J Meyer, Matthew C Metz, Brian J Smith, Toni K Ruth, Kerry M Murphy, Joseph K Bump, Douglas W Smith, Daniel R Stahler

{"title":"Prey size mediates interference competition and predation dynamics in a large carnivore community.","authors":"Jack W Rabe, Wesley J Binder, Colby B Anton, Connor J Meyer, Matthew C Metz, Brian J Smith, Toni K Ruth, Kerry M Murphy, Joseph K Bump, Douglas W Smith, Daniel R Stahler","doi":"10.1038/s42003-025-07779-5","DOIUrl":"https://doi.org/10.1038/s42003-025-07779-5","url":null,"abstract":"Direct competition for resources is especially fierce among predators, leading to disproportionately strong effects on fitness and functional roles. These competitive effects are exacerbated in complex predator guilds with dominance hierarchies that have clear winners and losers. The direct costs of losing these competitions are well understood, but the drivers of such interactions, and their indirect effects on prey, are not. We evaluate the drivers of interference competition for cougars, and how such competition affects cougar-prey dynamics, by leveraging 23 years of cougar predation data from Yellowstone National Park, USA. We show that the effect of prey size is context-dependent, negatively affecting how often cougars kill ungulate prey but positively affecting how often wolves/bears find and steal cougar kills. Further, cougars increasingly kill smaller prey as larger, primary prey density decreases. Handling time is shorter for smaller prey, leading to less kleptoparasitism by wolves and bears when primary prey density is lower. Our study counters the theory suggesting that interference competition should increase at kills when prey density declines, interspecific competitor density increases, or kill rates increase. We demonstrate that predator, competitor, and prey traits drive the strength of and even dampen interference competition, possibly increasing coexistence in complex communities.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"424"},"PeriodicalIF":5.2,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11953360/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143742446","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

How individual variation shapes ecological niches in two Pipistrellus bat species. 个体变异如何影响两种蝙蝠的生态位。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-27 DOI: 10.1038/s42003-025-07948-6

Markus Milchram, Alexander Bruckner, Edwin Kniha, Lukas Landler, Ina Hoxha, Guido Reiter, Samira Linhart, Monica Sageder, Thomas Zechmeister, Marcela Suarez-Rubio

{"title":"How individual variation shapes ecological niches in two Pipistrellus bat species.","authors":"Markus Milchram, Alexander Bruckner, Edwin Kniha, Lukas Landler, Ina Hoxha, Guido Reiter, Samira Linhart, Monica Sageder, Thomas Zechmeister, Marcela Suarez-Rubio","doi":"10.1038/s42003-025-07948-6","DOIUrl":"10.1038/s42003-025-07948-6","url":null,"abstract":"Niche partitioning is a crucial mechanism explaining species coexistence and biodiversity; however, the role of individual variation is less understood. As global changes reshuffle species communities, understanding coexistence mechanisms is vital. In this study, we use two co-occurring, morphologically similar bat species, Nathusius' pipistrelle (Pipistrellus nathusii) and the range-expanding Kuhl's pipistrelle (P. kuhlii), as models. We examine their niche partitioning across habitats and time, considering individual variations by analysing the spatio-temporal habitat selection of 58 radio-tracked individuals. For resource assessment, we use metabarcoding of guano samples. Our results show that individual variation in both species exceeded species-level differences. Nathusius' pipistrelle exhibits greater between-individual variation, while the range-expanding Kuhl's pipistrelle shows stronger within-individual variation, probably facilitating its expansion. This study emphasises the significance of individual variation in investigating animal niche partitioning. It suggests a contribution of within-individual variation in the range expansion of bat species, reshaping animal communities under global change.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"503"},"PeriodicalIF":5.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950338/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729134","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

Isolation and cultivation of a novel freshwater magnetotactic coccus FCR-1 containing unchained magnetosomes. 含非链磁小体的新型淡水趋磁球菌FCR-1的分离与培养。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-27 DOI: 10.1038/s42003-025-07981-5

Hirokazu Shimoshige, Keiichi Yanagisawa, Masayuki Miyazaki, Yoshihiro Takaki, Shigeru Shimamura, Hidetaka Nomaki, Mizuki Fukui, Hiroki Shirakawa, Hideki Kobayashi, Azuma Taoka, Toru Maekawa

{"title":"Isolation and cultivation of a novel freshwater magnetotactic coccus FCR-1 containing unchained magnetosomes.","authors":"Hirokazu Shimoshige, Keiichi Yanagisawa, Masayuki Miyazaki, Yoshihiro Takaki, Shigeru Shimamura, Hidetaka Nomaki, Mizuki Fukui, Hiroki Shirakawa, Hideki Kobayashi, Azuma Taoka, Toru Maekawa","doi":"10.1038/s42003-025-07981-5","DOIUrl":"10.1038/s42003-025-07981-5","url":null,"abstract":"Magnetotactic bacteria are ubiquitous aquatic prokaryotes that have the ability to biomineralize magnetite (Fe3O4) and/or greigite (Fe3S4) nanoparticles called magnetosomes. Magnetotactic cocci belonging to the class \"Ca. Magnetococcia\" are most frequently identified in freshwater habitats, but remain uncultivated. Here, we report for the first time axenic cultivation of freshwater magnetotactic coccus FCR-1 isolated from Chichijima, Japan. Strain FCR-1 grows microaerophilically in a semi-solid gellan gum medium. We find that strain FCR-1 biomineralizes Fe3O4 nanoparticles, which are not chained, into a cell. Based on phylogenomic analysis, compared with strains of the class \"Ca. Magnetococcia\", strain FCR-1 represents a novel genus of candidate family \"Ca. Magnetaquicoccaceae\" within the class \"Ca. Magnetococcia\" and we tentatively name this novel genus \"Ca. Magnetaquiglobus chichijimensis\". Our isolate provides a promising tool for elucidating the functions of unchained magnetosomes, the global distribution of magnetotactic bacteria and the origin of magnetotaxis.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"505"},"PeriodicalIF":5.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950176/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729183","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

A personalized metabolic modelling approach through integrated analysis of RNA-Seq-based genomic variants and gene expression levels in Alzheimer's disease. 通过综合分析阿尔茨海默病中基于rna - seq的基因组变异和基因表达水平的个性化代谢建模方法。

IF 5.2 1区生物学

Communications Biology Pub Date : 2025-03-27 DOI: 10.1038/s42003-025-07941-z

Dilara Uzuner Odongo, Atılay İlgün, Fatma Betül Bozkurt, Tunahan Çakır

{"title":"A personalized metabolic modelling approach through integrated analysis of RNA-Seq-based genomic variants and gene expression levels in Alzheimer's disease.","authors":"Dilara Uzuner Odongo, Atılay İlgün, Fatma Betül Bozkurt, Tunahan Çakır","doi":"10.1038/s42003-025-07941-z","DOIUrl":"10.1038/s42003-025-07941-z","url":null,"abstract":"Generating condition-specific metabolic models by mapping gene expression data to genome-scale metabolic models (GEMs) is a routine approach to elucidate disease mechanisms from a metabolic perspective. On the other hand, integrating variants that perturb enzyme functionality from the same RNA-seq data may enhance GEM accuracy, offering insights into genome-wide metabolic pathology. Our study pioneers the extraction of both transcriptomic and genomic data from the same RNA-seq data to reconstruct personalized metabolic models. We map genes with significantly higher load of pathogenic variants in Alzheimer's disease (AD) onto a human GEM together with the gene expression data. Comparative analysis of the resulting personalized patient metabolic models with the control models shows enhanced accuracy in detecting AD-associated metabolic pathways compared to the case where only expression data is mapped on the GEM. Besides, several otherwise would-be missed pathways are annotated in AD by considering the effect of genomic variants.","PeriodicalId":10552,"journal":{"name":"Communications Biology","volume":"8 1","pages":"502"},"PeriodicalIF":5.2,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11950204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729127","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