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Dimeric R25CPTH(1-34) activates the parathyroid hormone-1 receptor in vitro and stimulates bone formation in osteoporotic female mice.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.97579
Minsoo Noh, Xiangguo Che, Xian Jin, Dong-Kyo Lee, Hyun-Ju Kim, Doo Ri Park, Soo Young Lee, Hunsang Lee, Thomas J Gardella, Je-Yong Choi, Sihoon Lee
{"title":"Dimeric <sup>R25C</sup>PTH(1-34) activates the parathyroid hormone-1 receptor in vitro and stimulates bone formation in osteoporotic female mice.","authors":"Minsoo Noh, Xiangguo Che, Xian Jin, Dong-Kyo Lee, Hyun-Ju Kim, Doo Ri Park, Soo Young Lee, Hunsang Lee, Thomas J Gardella, Je-Yong Choi, Sihoon Lee","doi":"10.7554/eLife.97579","DOIUrl":"https://doi.org/10.7554/eLife.97579","url":null,"abstract":"<p><p>Osteoporosis, characterized by reduced bone density and strength, increases fracture risk, pain, and limits mobility. Established therapies of parathyroid hormone (PTH) analogs effectively promote bone formation and reduce fractures in severe osteoporosis, but their use is limited by potential adverse effects. In the pursuit of safer osteoporosis treatments, we investigated <sup>R25C</sup>PTH, a PTH variant wherein the native arginine at position 25 is substituted by cysteine. These studies were prompted by our finding of high bone mineral density in a hypoparathyroidism patient with the R25C homozygous mutation, and we explored its effects on PTH type-1 receptor (PTH1R) signaling in cells and bone metabolism in mice. Our findings indicate that <sup>R25C</sup>PTH(1-84) forms dimers both intracellularly and extracellularly, and the synthetic dimeric peptide, <sup>R25C</sup>PTH(1-34), exhibits altered activity in PTH1R-mediated cyclic AMP (cAMP) response. Upon a single injection in mice, dimeric <sup>R25C</sup>PTH(1-34) induced acute calcemic and phosphaturic responses comparable to PTH(1-34). Furthermore, repeated daily injections increased calvarial bone thickness in intact mice and improved trabecular and cortical bone parameters in ovariectomized (OVX) mice, akin to PTH(1-34). The overall results reveal a capacity of a dimeric PTH peptide ligand to activate the PTH1R in vitro and in vivo as PTH, suggesting a potential path of therapeutic PTH analog development.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735827","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
Layer 6 corticocortical neurons are a major route for intra- and interhemispheric feedback.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.100478
Simon Weiler, Manuel Teichert, Troy W Margrie
{"title":"Layer 6 corticocortical neurons are a major route for intra- and interhemispheric feedback.","authors":"Simon Weiler, Manuel Teichert, Troy W Margrie","doi":"10.7554/eLife.100478","DOIUrl":"https://doi.org/10.7554/eLife.100478","url":null,"abstract":"<p><p>The neocortex comprises anatomically discrete yet interconnected areas that are symmetrically located across the two hemispheres. Determining the logic of these macrocircuits is necessary for understanding high level brain function. Here in mice, we have mapped the areal and laminar organization of the ipsi- and contralateral cortical projection onto the primary visual, somatosensory, and motor cortices. We find that although the ipsilateral hemisphere is the primary source of cortical input, there is substantial contralateral symmetry regarding the relative contribution and areal identity of input. Laminar analysis of these input areas show that excitatory Layer 6 corticocortical cells (L6 CCs) are a major projection pathway within and between the two hemispheres. Analysis of the relative contribution of inputs from supra- (feedforward) and infragranular (feedback) layers reveals that contra-hemispheric projections reflect a dominant feedback organization compared to their ipsi-cortical counterpart. The magnitude of the interhemispheric difference in hierarchy was largest for sensory and motor projection areas compared to frontal, medial, or lateral brain areas due to a proportional increase in input from L6 neurons. L6 CCs therefore not only mediate long-range cortical communication but also reflect its inherent feedback organization.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735830","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
3D reconstruction of neuronal allometry and neuromuscular projections in asexual planarians using expansion tiling light sheet microscopy.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.101103
Jing Lu, Hao Xu, Dongyue Wang, Yanlu Chen, Takeshi Inoue, Liang Gao, Kai Lei
{"title":"3D reconstruction of neuronal allometry and neuromuscular projections in asexual planarians using expansion tiling light sheet microscopy.","authors":"Jing Lu, Hao Xu, Dongyue Wang, Yanlu Chen, Takeshi Inoue, Liang Gao, Kai Lei","doi":"10.7554/eLife.101103","DOIUrl":"10.7554/eLife.101103","url":null,"abstract":"<p><p>The intricate coordination of the neural network in planarian growth and regeneration has remained largely unrevealed, partly due to the challenges of imaging the CNS in three dimensions (3D) with high resolution and within a reasonable timeframe. To address this gap in systematic imaging of the CNS in planarians, we adopted high-resolution, nanoscale imaging by combining tissue expansion and tiling light-sheet microscopy, achieving up to fourfold linear expansion. Using an automatic 3D cell segmentation pipeline, we quantitatively profiled neurons and muscle fibers at the single-cell level in over 400 wild-type planarians during homeostasis and regeneration. We validated previous observations of neuronal cell number changes and muscle fiber distribution. We found that the increase in neuron cell number tends to lag behind the rapid expansion of somatic cells during the later phase of homeostasis. By imaging the planarian with up to 120 nm resolution, we also observed distinct muscle distribution patterns at the anterior and posterior poles. Furthermore, we investigated the effects of <i>β-catenin-1</i> RNAi on muscle fiber distribution at the posterior pole, consistent with changes in anterior-posterior polarity. The glial cells were observed to be close in contact with dorsal-ventral muscle fibers. Finally, we observed disruptions in neural-muscular networks in <i>inr-1</i> RNAi planarians. These findings provide insights into the detailed structure and potential functions of the neural-muscular system in planarians and highlight the accessibility of our imaging tool in unraveling the biological functions underlying their diverse phenotypes and behaviors.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729437","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
A peptide-neurotensin conjugate that crosses the blood-brain barrier induces pharmacological hypothermia associated with anticonvulsant, neuroprotective, and anti-inflammatory properties following status epilepticus in mice.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.100527
Lotfi Ferhat, Rabia Soussi, Maxime Masse, Grigorios Kyriatzis, Stéphane Girard, Fanny Gassiot, Nicolas Gaudin, Mathieu Laurencin, Anne Bernard, Angélique Bôle, Géraldine Ferracci, Maria Smirnova, François Roman, Vincent Dive, Salvatore Cisternino, Jamal Temsamani, Marion David, Pascaline Lécorché, Guillaume Jacquot, Michel Khrestchatisky
{"title":"A peptide-neurotensin conjugate that crosses the blood-brain barrier induces pharmacological hypothermia associated with anticonvulsant, neuroprotective, and anti-inflammatory properties following status epilepticus in mice.","authors":"Lotfi Ferhat, Rabia Soussi, Maxime Masse, Grigorios Kyriatzis, Stéphane Girard, Fanny Gassiot, Nicolas Gaudin, Mathieu Laurencin, Anne Bernard, Angélique Bôle, Géraldine Ferracci, Maria Smirnova, François Roman, Vincent Dive, Salvatore Cisternino, Jamal Temsamani, Marion David, Pascaline Lécorché, Guillaume Jacquot, Michel Khrestchatisky","doi":"10.7554/eLife.100527","DOIUrl":"10.7554/eLife.100527","url":null,"abstract":"<p><p>Preclinical and clinical studies show that mild to moderate hypothermia is neuroprotective in sudden cardiac arrest, ischemic stroke, perinatal hypoxia/ischemia, traumatic brain injury, and seizures. Induction of hypothermia largely involves physical cooling therapies, which induce several clinical complications, while some molecules have shown to be efficient in pharmacologically induced hypothermia (PIH). Neurotensin (NT), a 13 amino acid neuropeptide that regulates body temperature, interacts with various receptors to mediate its peripheral and central effects. NT induces PIH when administered intracerebrally. However, these effects are not observed if NT is administered peripherally, due to its rapid degradation and poor passage of the blood-brain barrier (BBB). We conjugated NT to peptides that bind the low-density lipoprotein receptor (LDLR) to generate 'vectorized' forms of NT with enhanced BBB permeability. We evaluated their effects in epileptic conditions following peripheral administration. One of these conjugates, VH-N412, displayed improved stability, binding potential to both the LDLR and NTSR-1, rodent/human cross-reactivity and improved brain distribution. In a mouse model of kainate (KA)-induced status epilepticus (SE), VH-N412 elicited rapid hypothermia associated with anticonvulsant effects, potent neuroprotection, and reduced hippocampal inflammation. VH-N412 also reduced sprouting of the dentate gyrus mossy fibers and preserved learning and memory skills in the treated mice. In cultured hippocampal neurons, VH-N412 displayed temperature-independent neuroprotective properties. To the best of our knowledge, this is the first report describing the successful treatment of SE with PIH. In all, our results show that vectorized NT may elicit different neuroprotection mechanisms mediated by hypothermia and/or by intrinsic neuroprotective properties.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729448","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 value of initiating a pursuit in temporal decision-making.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.99957
Elissa Sutlief, Charlie Walters, Tanya Marton, Marshall G Hussain Shuler
{"title":"The value of initiating a pursuit in temporal decision-making.","authors":"Elissa Sutlief, Charlie Walters, Tanya Marton, Marshall G Hussain Shuler","doi":"10.7554/eLife.99957","DOIUrl":"https://doi.org/10.7554/eLife.99957","url":null,"abstract":"<p><p>Reward-rate maximization is a prominent normative principle in behavioral ecology, neuroscience, economics, and AI. Here, we identify, compare, and analyze equations to maximize reward rate when assessing whether to initiate a pursuit. In deriving expressions for the value of a pursuit, we show that time's cost consists of both apportionment and opportunity cost. Reformulating value as a discounting function, we show precisely how a reward-rate-optimal agent's discounting function (1) combines hyperbolic and linear components reflecting apportionment and opportunity costs, and (2) is dependent not only on the considered pursuit's properties but also on time spent and rewards obtained outside the pursuit. This analysis reveals how purported signs of suboptimal behavior (hyperbolic discounting, and the Delay, Magnitude, and Sign effects) are in fact consistent with reward-rate maximization. To better account for observed decision-making errors in humans and animals, we then analyze the impact of misestimating reward-rate-maximizing parameters and find that suboptimal decisions likely stem from errors in assessing time's apportionment-specifically, underweighting time spent outside versus inside a pursuit-which we term the 'Malapportionment Hypothesis'. This understanding of the true pattern of temporal decision-making errors is essential to deducing the learning algorithms and representational architectures actually used by humans and animals.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735849","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
Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in Arabidopsis.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.98896
Maryam Rahmati Ishka, Hayley Sussman, Yunfei Hu, Mashael Daghash Alqahtani, Eric Craft, Ronell Sicat, Minmin Wang, Li'ang Yu, Rachid Ait-Haddou, Bo Li, Georgia Drakakaki, Andrew D L Nelson, Miguel Pineros, Arthur Korte, Łukasz Jaremko, Christa Testerink, Mark Tester, Magdalena M Julkowska
{"title":"Natural variation in salt-induced changes in root:shoot ratio reveals SR3G as a negative regulator of root suberization and salt resilience in <i>Arabidopsis</i>.","authors":"Maryam Rahmati Ishka, Hayley Sussman, Yunfei Hu, Mashael Daghash Alqahtani, Eric Craft, Ronell Sicat, Minmin Wang, Li'ang Yu, Rachid Ait-Haddou, Bo Li, Georgia Drakakaki, Andrew D L Nelson, Miguel Pineros, Arthur Korte, Łukasz Jaremko, Christa Testerink, Mark Tester, Magdalena M Julkowska","doi":"10.7554/eLife.98896","DOIUrl":"https://doi.org/10.7554/eLife.98896","url":null,"abstract":"<p><p>Soil salinity is one of the major threats to agricultural productivity worldwide. Salt stress exposure alters root and shoots growth rates, thereby affecting overall plant performance. While past studies have extensively documented the effect of salt stress on root elongation and shoot development separately, here we take an innovative approach by examining the coordination of root and shoot growth under salt stress conditions. Utilizing a newly developed tool for quantifying the root:shoot ratio in agar-grown <i>Arabidopsis</i> seedlings, we found that salt stress results in a loss of coordination between root and shoot growth rates. We identify a specific gene cluster encoding domain-of-unknown-function 247 (DUF247), and characterize one of these genes as <u>S</u>alt <u>R</u>oot:shoot <u>R</u>atio <u>R</u>egulator <u>G</u>ene (SR3G). Further analysis elucidates the role of SR3G as a negative regulator of salt stress tolerance, revealing its function in regulating shoot growth, root suberization, and sodium accumulation. We further characterize that <i>SR3G</i> expression is modulated by <i>WRKY75</i> transcription factor, known as a positive regulator of salt stress tolerance. Finally, we show that the salt stress sensitivity of <i>wrky75</i> mutant is completely diminished when it is combined with <i>sr3g</i> mutation. Together, our results demonstrate that utilizing root:shoot ratio as an architectural feature leads to the discovery of a new stress resilience gene. The study's innovative approach and findings not only contribute to our understanding of plant stress tolerance mechanisms but also open new avenues for genetic and agronomic strategies to enhance crop environmental resilience.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735837","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
Deciphering the preeclampsia-specific immune microenvironment and the role of pro-inflammatory macrophages at the maternal-fetal interface.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.100002
Haiyi Fei, Xiaowen Lu, Zhan Shi, Xiu Liu, Cuiyu Yang, Xiaohong Zhu, Yuhan Lin, Ziqun Jiang, Jianmin Wang, Dong Huang, Liu Liu, Songying Zhang, Lingling Jiang
{"title":"Deciphering the preeclampsia-specific immune microenvironment and the role of pro-inflammatory macrophages at the maternal-fetal interface.","authors":"Haiyi Fei, Xiaowen Lu, Zhan Shi, Xiu Liu, Cuiyu Yang, Xiaohong Zhu, Yuhan Lin, Ziqun Jiang, Jianmin Wang, Dong Huang, Liu Liu, Songying Zhang, Lingling Jiang","doi":"10.7554/eLife.100002","DOIUrl":"10.7554/eLife.100002","url":null,"abstract":"<p><p>Preeclampsia (PE), a major cause of maternal and perinatal mortality with highly heterogeneous causes and symptoms, is usually complicated by gestational diabetes mellitus (GDM). However, a comprehensive understanding of the immune microenvironment in the placenta of PE and the differences between PE and GDM is still lacking. In this study, cytometry by time of flight indicated that the frequencies of memory-like Th17 cells (CD45RA<sup>-</sup>CCR7<sup>+</sup>IL-17A<sup>+</sup>CD4<sup>+</sup>), memory-like CD8<sup>+</sup> T cells (CD38<sup>+</sup>CXCR3<sup>-</sup>CCR7<sup>+</sup>Helios<sup>-</sup>CD127<sup>-</sup>CD8<sup>+</sup>) and pro-inflam Macs (CD206<sup>-</sup>CD163<sup>-</sup>CD38<sup>mid</sup>CD107a<sup>low</sup>CD86<sup>mid</sup>HLA-DR<sup>mid</sup>CD14<sup>+</sup>) were increased, while the frequencies of anti-inflam Macs (CD206<sup>+</sup>CD163<sup>-</sup>CD86<sup>mid</sup>CD33<sup>+</sup>HLA-DR<sup>+</sup>CD14<sup>+</sup>) and granulocyte myeloid-derived suppressor cells (gMDSCs, CD11b<sup>+</sup>CD15<sup>hi</sup>HLA-DR<sup>low</sup>) were decreased in the placenta of PE compared with that of normal pregnancy (NP), but not in that of GDM or GDM&PE. The pro-inflam Macs were positively correlated with memory-like Th17 cells and memory-like CD8<sup>+</sup> T cells but negatively correlated with gMDSCs. Single-cell RNA sequencing revealed that transferring the F4/80<sup>+</sup>CD206<sup>-</sup> pro-inflam Macs with a Folr2<sup>+</sup>Ccl7<sup>+</sup>Ccl8<sup>+</sup>C1qa<sup>+</sup>C1qb<sup>+</sup>C1qc<sup>+</sup> phenotype from the uterus of PE mice to normal pregnant mice induced the production of memory-like IL-17a<sup>+</sup>Rora<sup>+</sup>Il1r1<sup>+</sup>TNF<sup>+</sup>Cxcr6<sup>+</sup>S100a4<sup>+</sup>CD44<sup>+</sup> Th17 cells via IGF1-IGF1R, which contributed to the development and recurrence of PE. Pro-inflam Macs also induced the production of memory-like CD8<sup>+</sup> T cells but inhibited the production of Ly6g<sup>+</sup>S100a8<sup>+</sup>S100a9<sup>+</sup>Retnlg<sup>+</sup>Wfdc21<sup>+</sup> gMDSCs at the maternal-fetal interface, leading to PE-like symptoms in mice. In conclusion, this study revealed the PE-specific immune cell network, which was regulated by pro-inflam Macs, providing new ideas about the pathogenesis of PE.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729451","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
Electrophysiology and morphology of human cortical supragranular pyramidal cells in a wide age range.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.100390
Pál Barzó, Ildikó Szöts, Martin Tóth, Éva Adrienn Csajbók, Gábor Molnár, Gábor Tamás
{"title":"Electrophysiology and morphology of human cortical supragranular pyramidal cells in a wide age range.","authors":"Pál Barzó, Ildikó Szöts, Martin Tóth, Éva Adrienn Csajbók, Gábor Molnár, Gábor Tamás","doi":"10.7554/eLife.100390","DOIUrl":"10.7554/eLife.100390","url":null,"abstract":"<p><p>The basic excitatory neurons of the cerebral cortex, the pyramidal cells, are the most important signal integrators for the local circuit. They have quite characteristic morphological and electrophysiological properties that are known to be largely constant with age in the young and adult cortex. However, the brain undergoes several dynamic changes throughout life, such as in the phases of early development and cognitive decline in the aging brain. We set out to search for intrinsic cellular changes in supragranular pyramidal cells across a broad age range: from birth to 85 y of age and we found differences in several biophysical properties between defined age groups. During the first year of life, subthreshold and suprathreshold electrophysiological properties changed in a way that shows that pyramidal cells become less excitable with maturation, but also become temporarily more precise. According to our findings, the morphological features of the three-dimensional reconstructions from different life stages showed consistent morphological properties and systematic dendritic spine analysis of an infantile and an old pyramidal cell showed clear significant differences in the distribution of spine shapes. Overall, the changes that occur during development and aging may have lasting effects on the properties of pyramidal cells in the cerebral cortex. Understanding these changes is important to unravel the complex mechanisms underlying brain development, cognition, and age-related neurodegenerative diseases.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729459","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
Functionally important residues from graph analysis of coevolved dynamic couplings.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.105005
Manming Xu, Sarath Chandra Dantu, James A Garnett, Robert A Bonomo, Alessandro Pandini, Shozeb Haider
{"title":"Functionally important residues from graph analysis of coevolved dynamic couplings.","authors":"Manming Xu, Sarath Chandra Dantu, James A Garnett, Robert A Bonomo, Alessandro Pandini, Shozeb Haider","doi":"10.7554/eLife.105005","DOIUrl":"https://doi.org/10.7554/eLife.105005","url":null,"abstract":"<p><p>The relationship between protein dynamics and function is essential for understanding biological processes and developing effective therapeutics. Functional sites within proteins are critical for activities such as substrate binding, catalysis, and structural changes. Existing computational methods for the predictions of functional residues are trained on sequence, structural, and experimental data, but they do not explicitly model the influence of evolution on protein dynamics. This overlooked contribution is essential as it is known that evolution can fine-tune protein dynamics through compensatory mutations either to improve the proteins' performance or diversify its function while maintaining the same structural scaffold. To model this critical contribution, we introduce DyNoPy, a computational method that combines residue coevolution analysis with molecular dynamics simulations, revealing hidden correlations between functional sites. DyNoPy constructs a graph model of residue-residue interactions, identifies communities of key residue groups, and annotates critical sites based on their roles. By leveraging the concept of coevolved dynamical couplings-residue pairs with critical dynamical interactions that have been preserved during evolution-DyNoPy offers a powerful method for predicting and analysing protein evolution and dynamics. We demonstrate the effectiveness of DyNoPy on SHV-1 and PDC-3, chromosomally encoded β-lactamases linked to antibiotic resistance, highlighting its potential to inform drug design and address pressing healthcare challenges.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"14 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735852","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
Compositional editing of extracellular matrices by CRISPR/Cas9 engineering of human mesenchymal stem cell lines.
IF 6.4 1区 生物学
eLife Pub Date : 2025-03-28 DOI: 10.7554/eLife.96941
Sujeethkumar Prithiviraj, Alejandro Garcia Garcia, Karin Linderfalk, Bai Yiguang, Sonia Ferveur, Ludvig Nilsén Falck, Agatheeswaran Subramaniam, Sofie Mohlin, David Hidalgo Gil, Steven J Dupard, Dimitra Zacharaki, Deepak Bushan Raina, Paul E Bourgine
{"title":"Compositional editing of extracellular matrices by CRISPR/Cas9 engineering of human mesenchymal stem cell lines.","authors":"Sujeethkumar Prithiviraj, Alejandro Garcia Garcia, Karin Linderfalk, Bai Yiguang, Sonia Ferveur, Ludvig Nilsén Falck, Agatheeswaran Subramaniam, Sofie Mohlin, David Hidalgo Gil, Steven J Dupard, Dimitra Zacharaki, Deepak Bushan Raina, Paul E Bourgine","doi":"10.7554/eLife.96941","DOIUrl":"10.7554/eLife.96941","url":null,"abstract":"<p><p>Tissue engineering strategies predominantly rely on the production of living substitutes, whereby implanted cells actively participate in the regenerative process. Beyond cost and delayed graft availability, the patient-specific performance of engineered tissues poses serious concerns on their clinical translation ability. A more exciting paradigm consists in exploiting cell-laid, engineered extracellular matrices (eECMs), which can be used as off-the-shelf materials. Here, the regenerative capacity solely relies on the preservation of the eECM structure and embedded signals to instruct an endogenous repair. We recently described the possibility to exploit custom human stem cell lines for eECM manufacturing. In addition to the conferred standardization, the availability of such cell lines opened avenues for the design of tailored eECMs by applying dedicated genetic tools. In this study, we demonstrated the exploitation of CRISPR/Cas9 as a high precision system for editing the composition and function of eECMs. Human mesenchymal stromal/stem cell (hMSC) lines were modified to knock out vascular endothelial growth factor (VEGF) and Runt-related transcription factor 2 (RUNX2) and assessed for their capacity to generate osteoinductive cartilage matrices. We report the successful editing of hMSCs, subsequently leading to targeted VEGF and RUNX2-knockout cartilage eECMs. Despite the absence of VEGF, eECMs retained full capacity to instruct ectopic endochondral ossification. Conversely, RUNX2-edited eECMs exhibited impaired hypertrophy, reduced ectopic ossification, and superior cartilage repair in a rat osteochondral defect. In summary, our approach can be harnessed to identify the necessary eECM factors driving endogenous repair. Our work paves the road toward the compositional eECMs editing and their exploitation in broad regenerative contexts.</p>","PeriodicalId":11640,"journal":{"name":"eLife","volume":"13 ","pages":""},"PeriodicalIF":6.4,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143729449","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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