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Correction: Genomic basis for drought resistance in European beech forests threatened by climate change. 更正:受气候变化威胁的欧洲山毛榉林抗旱性的基因组基础。
IF 6.4 1区 生物学
eLife Pub Date : 2024-09-06 DOI: 10.7554/eLife.102872
Markus Pfenninger, Friederike Reuss, Angelika KIebler, Philipp Schönnenbeck, Cosima Caliendo, Susanne Gerber, Berardino Cocchiararo, Sabrina Reuter, Nico Blüthgen, Karsten Mody, Bagdevi Mishra, Miklós Bálint, Marco Thines, Barbara Feldmeyer
{"title":"Correction: Genomic basis for drought resistance in European beech forests threatened by climate change.","authors":"Markus Pfenninger, Friederike Reuss, Angelika KIebler, Philipp Schönnenbeck, Cosima Caliendo, Susanne Gerber, Berardino Cocchiararo, Sabrina Reuter, Nico Blüthgen, Karsten Mody, Bagdevi Mishra, Miklós Bálint, Marco Thines, Barbara Feldmeyer","doi":"10.7554/eLife.102872","DOIUrl":"10.7554/eLife.102872","url":null,"abstract":"<p><p></p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11379452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139640","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
Novel cyclic homogeneous oscillation detection method for high accuracy and specific characterization of neural dynamics 新颖的循环同质振荡检测方法,用于高精度和特定的神经动力学特征描述
IF 7.7 1区 生物学
eLife Pub Date : 2024-09-06 DOI: https://doi.org/10.7554/elife.91605.3
Hohyun Cho, Markus Adamek, Jon T Willie, Peter Brunner
{"title":"Novel cyclic homogeneous oscillation detection method for high accuracy and specific characterization of neural dynamics","authors":"Hohyun Cho, Markus Adamek, Jon T Willie, Peter Brunner","doi":"https://doi.org/10.7554/elife.91605.3","DOIUrl":"https://doi.org/https://doi.org/10.7554/elife.91605.3","url":null,"abstract":"Determining the presence and frequency of neural oscillations is essential to understanding dynamic brain function. Traditional methods that detect peaks over 1/<i>f</i> noise within the power spectrum fail to distinguish between the fundamental frequency and harmonics of often highly non-sinusoidal neural oscillations. To overcome this limitation, we define fundamental criteria that characterize neural oscillations and introduce the cyclic homogeneous oscillation (CHO) detection method. We implemented these criteria based on an autocorrelation approach to determine an oscillation’s fundamental frequency. We evaluated CHO by verifying its performance on simulated non-sinusoidal oscillatory bursts and validated its ability to determine the fundamental frequency of neural oscillations in electrocorticographic (ECoG), electroencephalographic (EEG), and stereoelectroencephalographic (SEEG) signals recorded from 27 human subjects. Our results demonstrate that CHO outperforms conventional techniques in accurately detecting oscillations. In summary, CHO demonstrates high precision and specificity in detecting neural oscillations in time and frequency domains. The method’s specificity enables the detailed study of non-sinusoidal characteristics of oscillations, such as the degree of asymmetry and waveform of an oscillation. Furthermore, CHO can be applied to identify how neural oscillations govern interactions throughout the brain and to determine oscillatory biomarkers that index abnormal brain function.","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185772","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
Reversions mask the contribution of adaptive evolution in microbiomes 逆转掩盖了微生物组适应性进化的贡献
IF 7.7 1区 生物学
eLife Pub Date : 2024-09-06 DOI: https://doi.org/10.7554/elife.93146
Paul A Torrillo, Tami D Lieberman
{"title":"Reversions mask the contribution of adaptive evolution in microbiomes","authors":"Paul A Torrillo, Tami D Lieberman","doi":"https://doi.org/10.7554/elife.93146","DOIUrl":"https://doi.org/https://doi.org/10.7554/elife.93146","url":null,"abstract":"When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by d<sub>N</sub>/d<sub>S</sub>, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of d<sub>N</sub>/d<sub>S</sub>. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the d<sub>N</sub>/d<sub>S</sub> decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of <i>Bacteroides</i> genomes. The success of the adaptive reversion model argues for interpreting low values of d<sub>N</sub>/d<sub>S</sub> obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185768","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
Reversions mask the contribution of adaptive evolution in microbiomes. 逆转掩盖了微生物组适应性进化的贡献。
IF 6.4 1区 生物学
eLife Pub Date : 2024-09-06 DOI: 10.7554/eLife.93146
Paul A Torrillo, Tami D Lieberman
{"title":"Reversions mask the contribution of adaptive evolution in microbiomes.","authors":"Paul A Torrillo, Tami D Lieberman","doi":"10.7554/eLife.93146","DOIUrl":"10.7554/eLife.93146","url":null,"abstract":"<p><p>When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by d<sub>N</sub>/d<sub>S</sub>, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of d<sub>N</sub>/d<sub>S</sub>. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the d<sub>N</sub>/d<sub>S</sub> decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of <i>Bacteroides</i> genomes. The success of the adaptive reversion model argues for interpreting low values of d<sub>N</sub>/d<sub>S</sub> obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11379459/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142143042","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
The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder. 在选择更为有效的脊椎动物物种中,蛋白质结构域的内在结构紊乱程度更高。
IF 6.4 1区 生物学
eLife Pub Date : 2024-09-06 DOI: 10.7554/eLife.87335
Catherine A Weibel, Andrew L Wheeler, Jennifer E James, Sara M Willis, Hanon McShea, Joanna Masel
{"title":"The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder.","authors":"Catherine A Weibel, Andrew L Wheeler, Jennifer E James, Sara M Willis, Hanon McShea, Joanna Masel","doi":"10.7554/eLife.87335","DOIUrl":"10.7554/eLife.87335","url":null,"abstract":"<p><p>The nearly neutral theory of molecular evolution posits variation among species in the effectiveness of selection. In an idealized model, the census population size determines both this minimum magnitude of the selection coefficient required for deleterious variants to be reliably purged, and the amount of neutral diversity. Empirically, an 'effective population size' is often estimated from the amount of putatively neutral genetic diversity and is assumed to also capture a species' effectiveness of selection. A potentially more direct measure of the effectiveness of selection is the degree to which selection maintains preferred codons. However, past metrics that compare codon bias across species are confounded by among-species variation in %GC content and/or amino acid composition. Here, we propose a new Codon Adaptation Index of Species (CAIS), based on Kullback-Leibler divergence, that corrects for both confounders. We demonstrate the use of CAIS correlations, as well as the Effective Number of Codons, to show that the protein domains of more highly adapted vertebrate species evolve higher intrinsic structural disorder.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11379457/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142139657","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
Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE 利用 AlphaFold2-RAVE 增强 AlphaFold2 在蛋白质构象选择性药物发现方面的能力
IF 7.7 1区 生物学
eLife Pub Date : 2024-09-06 DOI: https://doi.org/10.7554/elife.99702.3
Xinyu Gu, Akashnathan Aranganathan, Pratyush Tiwary
{"title":"Empowering AlphaFold2 for protein conformation selective drug discovery with AlphaFold2-RAVE","authors":"Xinyu Gu, Akashnathan Aranganathan, Pratyush Tiwary","doi":"https://doi.org/10.7554/elife.99702.3","DOIUrl":"https://doi.org/https://doi.org/10.7554/elife.99702.3","url":null,"abstract":"Small-molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2’s strides in protein native structure prediction, its focus on apo structures overlooks ligands and associated holo structures. Moreover, designing selective drugs often benefits from the targeting of diverse metastable conformations. Therefore, direct application of AlphaFold2 models in virtual screening and drug discovery remains tentative. Here, we demonstrate an AlphaFold2-based framework combined with all-atom enhanced sampling molecular dynamics and Induced Fit docking, named AF2RAVE-Glide, to conduct computational model-based small-molecule binding of metastable protein kinase conformations, initiated from protein sequences. We demonstrate the AF2RAVE-Glide workflow on three different mammalian protein kinases and their type I and II inhibitors, with special emphasis on binding of known type II kinase inhibitors which target the metastable classical DFG-out state. These states are not easy to sample from AlphaFold2. Here, we demonstrate how with AF2RAVE these metastable conformations can be sampled for different kinases with high enough accuracy to enable subsequent docking of known type II kinase inhibitors with more than 50% success rates across docking calculations. We believe the protocol should be deployable for other kinases and more proteins generally.","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185774","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
Using recurrent neural network to estimate irreducible stochasticity in human choice behavior 利用递归神经网络估算人类选择行为中的不可还原随机性
IF 7.7 1区 生物学
eLife Pub Date : 2024-09-06 DOI: https://doi.org/10.7554/elife.90082.3
Yoav Ger, Moni Shahar, Nitzan Shahar
{"title":"Using recurrent neural network to estimate irreducible stochasticity in human choice behavior","authors":"Yoav Ger, Moni Shahar, Nitzan Shahar","doi":"https://doi.org/10.7554/elife.90082.3","DOIUrl":"https://doi.org/https://doi.org/10.7554/elife.90082.3","url":null,"abstract":"Theoretical computational models are widely used to describe latent cognitive processes. However, these models do not equally explain data across participants, with some individuals showing a bigger predictive gap than others. In the current study, we examined the use of theory-independent models, specifically recurrent neural networks (RNNs), to classify the source of a predictive gap in the observed data of a single individual. This approach aims to identify whether the low predictability of behavioral data is mainly due to noisy decision-making or misspecification of the theoretical model. First, we used computer simulation in the context of reinforcement learning to demonstrate that RNNs can be used to identify model misspecification in simulated agents with varying degrees of behavioral noise. Specifically, both prediction performance and the number of RNN training epochs (i.e., the point of early stopping) can be used to estimate the amount of stochasticity in the data. Second, we applied our approach to an empirical dataset where the actions of low IQ participants, compared with high IQ participants, showed lower predictability by a well-known theoretical model (i.e., Daw’s hybrid model for the two-step task). Both the predictive gap and the point of early stopping of the RNN suggested that model misspecification is similar across individuals. This led us to a provisional conclusion that low IQ subjects are mostly noisier compared to their high IQ peers, rather than being more misspecified by the theoretical model. We discuss the implications and limitations of this approach, considering the growing literature in both theoretical and data-driven computational modeling in decision-making science.","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185766","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
Early moderate prenatal alcohol exposure and maternal diet impact offspring DNA methylation across species 产前早期中度酒精暴露和母体饮食对不同物种后代 DNA 甲基化的影响
IF 7.7 1区 生物学
eLife Pub Date : 2024-09-06 DOI: https://doi.org/10.7554/elife.92135.3
Mitchell Bestry, Alexander N Larcombe, Nina Kresoje, Emily K Chivers, Chloe Bakker, James P Fitzpatrick, Elizabeth J Elliott, Jeffrey M Craig, Evelyne Muggli, Jane Halliday, Delyse Hutchinson, Sam Buckberry, Ryan Lister, Martyn Symons, David Martino
{"title":"Early moderate prenatal alcohol exposure and maternal diet impact offspring DNA methylation across species","authors":"Mitchell Bestry, Alexander N Larcombe, Nina Kresoje, Emily K Chivers, Chloe Bakker, James P Fitzpatrick, Elizabeth J Elliott, Jeffrey M Craig, Evelyne Muggli, Jane Halliday, Delyse Hutchinson, Sam Buckberry, Ryan Lister, Martyn Symons, David Martino","doi":"https://doi.org/10.7554/elife.92135.3","DOIUrl":"https://doi.org/https://doi.org/10.7554/elife.92135.3","url":null,"abstract":"Alcohol consumption in pregnancy can affect genome regulation in the developing offspring but results have been contradictory. We employed a physiologically relevant murine model of short-term moderate prenatal alcohol exposure (PAE) resembling common patterns of alcohol consumption in pregnancy in humans. Early moderate PAE was sufficient to affect site-specific DNA methylation in newborn pups without altering behavioural outcomes in adult littermates. Whole-genome bisulfite sequencing of neonatal brain and liver revealed stochastic influence on DNA methylation that was mostly tissue-specific, with some perturbations likely originating as early as gastrulation. DNA methylation differences were enriched in non-coding genomic regions with regulatory potential indicative of broad effects of alcohol on genome regulation. Replication studies in human cohorts with fetal alcohol spectrum disorder suggested some effects were metastable at genes linked to disease-relevant traits including facial morphology, intelligence, educational attainment, autism, and schizophrenia. In our murine model, a maternal diet high in folate and choline protected against some of the damaging effects of early moderate PAE on DNA methylation. Our studies demonstrate that early moderate exposure is sufficient to affect fetal genome regulation even in the absence of overt phenotypic changes and highlight a role for preventative maternal dietary interventions.","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-09-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185773","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
Mir221/222 drive synovial hyperplasia and arthritis by targeting cell cycle inhibitors and chromatin remodeling components. Mir221/222 通过靶向细胞周期抑制剂和染色质重塑成分驱动滑膜增生和关节炎。
IF 6.4 1区 生物学
eLife Pub Date : 2024-09-05 DOI: 10.7554/eLife.84698
Fani Roumelioti, Christos Tzaferis, Dimitris Konstantopoulos, Dimitra Papadopoulou, Alejandro Prados, Maria Sakkou, Anastasios Liakos, Panagiotis Chouvardas, Theodore Meletakos, Yiannis Pandis, Niki Karagianni, Maria C Denis, Maria Fousteri, Maria Armaka, George Kollias
{"title":"<i>Mir221/222</i> drive synovial hyperplasia and arthritis by targeting cell cycle inhibitors and chromatin remodeling components.","authors":"Fani Roumelioti, Christos Tzaferis, Dimitris Konstantopoulos, Dimitra Papadopoulou, Alejandro Prados, Maria Sakkou, Anastasios Liakos, Panagiotis Chouvardas, Theodore Meletakos, Yiannis Pandis, Niki Karagianni, Maria C Denis, Maria Fousteri, Maria Armaka, George Kollias","doi":"10.7554/eLife.84698","DOIUrl":"10.7554/eLife.84698","url":null,"abstract":"<p><p>miRNAs constitute fine-tuners of gene expression and are implicated in a variety of diseases spanning from inflammation to cancer. miRNA expression is deregulated in rheumatoid arthritis (RA); however, their specific role in key arthritogenic cells such as the synovial fibroblast (SF) remains elusive. Previous studies have shown that <i>Mir221/222</i> expression is upregulated in RA SFs. Here, we demonstrate that TNF and IL-1β but not IFN-γ activated <i>Mir221</i>/222 gene expression in murine SFs. SF-specific overexpression of <i>Mir221/222</i> in huTNFtg mice led to further expansion of SFs and disease exacerbation, while its total ablation led to reduced SF expansion and attenuated disease. <i>Mir221/222</i> overexpression altered the SF transcriptional profile igniting pathways involved in cell cycle and ECM (extracellular matrix) regulation. Validation of targets of <i>Mir221/222</i> revealed cell cycle inhibitors <i>Cdkn1b</i> and <i>Cdkn1c</i>, as well as the epigenetic regulator <i>Smarca1</i>. Single-cell ATAC-seq data analysis revealed increased <i>Mir221</i>/222 gene activity in pathogenic SF subclusters and transcriptional regulation by <i>Rela</i>, <i>Relb</i>, <i>Junb</i>, <i>Bach1</i>, and <i>Nfe2l2</i>. Our results establish an SF-specific pathogenic role of <i>Mir221/222</i> in arthritis and suggest that its therapeutic targeting in specific subpopulations could lead to novel fibroblast-targeted therapies.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":6.4,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11377061/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142132108","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
Mir221/222 drive synovial hyperplasia and arthritis by targeting cell cycle inhibitors and chromatin remodeling components Mir221/222 通过靶向细胞周期抑制剂和染色质重塑成分驱动滑膜增生和关节炎
IF 7.7 1区 生物学
eLife Pub Date : 2024-09-05 DOI: https://doi.org/10.7554/elife.84698
Fani Roumelioti, Christos Tzaferis, Dimitris Konstantopoulos, Dimitra Papadopoulou, Alejandro Prados, Maria Sakkou, Anastasios Liakos, Panagiotis Chouvardas, Theodore Meletakos, Yiannis Pandis, Niki Karagianni, Maria C Denis, Maria Fousteri, Maria Armaka, George Kollias
{"title":"Mir221/222 drive synovial hyperplasia and arthritis by targeting cell cycle inhibitors and chromatin remodeling components","authors":"Fani Roumelioti, Christos Tzaferis, Dimitris Konstantopoulos, Dimitra Papadopoulou, Alejandro Prados, Maria Sakkou, Anastasios Liakos, Panagiotis Chouvardas, Theodore Meletakos, Yiannis Pandis, Niki Karagianni, Maria C Denis, Maria Fousteri, Maria Armaka, George Kollias","doi":"https://doi.org/10.7554/elife.84698","DOIUrl":"https://doi.org/https://doi.org/10.7554/elife.84698","url":null,"abstract":"miRNAs constitute fine-tuners of gene expression and are implicated in a variety of diseases spanning from inflammation to cancer. miRNA expression is deregulated in rheumatoid arthritis (RA); however, their specific role in key arthritogenic cells such as the synovial fibroblast (SF) remains elusive. Previous studies have shown that <i>Mir221/222</i> expression is upregulated in RA SFs. Here, we demonstrate that TNF and IL-1β but not IFN-γ activated <i>Mir221</i>/222 gene expression in murine SFs. SF-specific overexpression of <i>Mir221/222</i> in huTNFtg mice led to further expansion of SFs and disease exacerbation, while its total ablation led to reduced SF expansion and attenuated disease. <i>Mir221/222</i> overexpression altered the SF transcriptional profile igniting pathways involved in cell cycle and ECM (extracellular matrix) regulation. Validation of targets of <i>Mir221/222</i> revealed cell cycle inhibitors <i>Cdkn1b</i> and <i>Cdkn1c</i>, as well as the epigenetic regulator <i>Smarca1</i>. Single-cell ATAC-seq data analysis revealed increased <i>Mir221</i>/222 gene activity in pathogenic SF subclusters and transcriptional regulation by <i>Rela</i>, <i>Relb</i>, <i>Junb</i>, <i>Bach1</i>, and <i>Nfe2l2</i>. Our results establish an SF-specific pathogenic role of <i>Mir221/222</i> in arthritis and suggest that its therapeutic targeting in specific subpopulations could lead to novel fibroblast-targeted therapies.","PeriodicalId":11640,"journal":{"name":"eLife","volume":null,"pages":null},"PeriodicalIF":7.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142185788","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
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