Lysine (Lys/K) residues serve as major hubs for post-translational modifications (PTMs) owing to the chemical versatility of their ε-amino groups, giving rise to diverse regulatory functions. Accurate and efficient identification of modified lysine residues therefore requires computational models that can effectively capture both sequence and structural information while minimizing domain-specific feature engineering. In this study, we propose a unified deep learning framework for lysine PTM site identification that integrates sequence representations derived from a protein language model with atom-level three-dimensional structural features. This framework can be consistently applied to multiple lysine PTM types using a shared modeling strategy. As an application, we used the model to predict potential PTM site on human C-type lectin domain family 12 member A (hCLEC12A) and evaluated their functional relevance through all-atom molecular dynamics simulations. The simulations indicate that the predicted lysine residues influence the stability and binding behavior of the hCLEC12A-antibody 50C1 complex. Overall, this work presents an integrative computational framework for lysine PTM site mining and functional analysis.
{"title":"Mining lysine post-translational modification sites by integrating protein language model representations with structural context","authors":"Mengqi Luo, Xiaohong Zhu, Chen Bai, Arieh Warshel, Luonan Chen","doi":"10.1073/pnas.2529141123","DOIUrl":"https://doi.org/10.1073/pnas.2529141123","url":null,"abstract":"Lysine (Lys/K) residues serve as major hubs for post-translational modifications (PTMs) owing to the chemical versatility of their ε-amino groups, giving rise to diverse regulatory functions. Accurate and efficient identification of modified lysine residues therefore requires computational models that can effectively capture both sequence and structural information while minimizing domain-specific feature engineering. In this study, we propose a unified deep learning framework for lysine PTM site identification that integrates sequence representations derived from a protein language model with atom-level three-dimensional structural features. This framework can be consistently applied to multiple lysine PTM types using a shared modeling strategy. As an application, we used the model to predict potential PTM site on human C-type lectin domain family 12 member A (hCLEC12A) and evaluated their functional relevance through all-atom molecular dynamics simulations. The simulations indicate that the predicted lysine residues influence the stability and binding behavior of the hCLEC12A-antibody 50C1 complex. Overall, this work presents an integrative computational framework for lysine PTM site mining and functional analysis.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"13 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146146107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pavle Boskovic, Rotem Shalita, Wenqing Gao, Hailey Vernon, Yu Lin Deng, Marco Colonna, Robbie G. Majzner, Ido Amit, Jonathan Kipnis
Alzheimer’s disease (AD) is the prevailing cause of age-associated dementia worldwide. Current standard of care relies on antibody-based immunotherapy. However, antibody-based approaches carry risks for patients, and their effects on cognition are marginal. Increasing evidence suggests that T cells contribute to AD onset and progression. Unlike the cytotoxic effects of CD8 + cells, CD4 + T cells capable of regulating inflammation show promise in reducing pathology and improving cognitive outcomes in mouse models of AD and in aging. Here, we sought to exploit the beneficial properties of CD4 + T cells while circumventing the need for TCR and peptide–MHC antigen discovery, thereby providing a potential universal therapeutic approach. To achieve this, we engineered CD4 + T cells with chimeric antigen receptors (CARs) targeting fibrillar forms of aggregated amyloid-β. Our findings demonstrate that optimized CAR-T cells can alter amyloid deposition in the dura and reduce parenchymal pathology in the brain. Furthermore, we observed that CAR-T treatment promotes the expansion and recruitment of endogenous CD4 + T cells into the brain parenchyma and leptomeninges. In summary, we established the feasibility of amyloid plaque–specific CAR-T cells as a potential therapeutic avenue for AD. These findings highlight the potential of CD4 + CAR-T therapy not only to modify amyloid pathology but also to reshape the immune landscape of the CNS, paving the way for future development of cellular immunotherapies for neurodegenerative disease.
{"title":"Engineering chimeric antigen receptor CD4 T cells for Alzheimer’s disease","authors":"Pavle Boskovic, Rotem Shalita, Wenqing Gao, Hailey Vernon, Yu Lin Deng, Marco Colonna, Robbie G. Majzner, Ido Amit, Jonathan Kipnis","doi":"10.1073/pnas.2530977123","DOIUrl":"https://doi.org/10.1073/pnas.2530977123","url":null,"abstract":"Alzheimer’s disease (AD) is the prevailing cause of age-associated dementia worldwide. Current standard of care relies on antibody-based immunotherapy. However, antibody-based approaches carry risks for patients, and their effects on cognition are marginal. Increasing evidence suggests that T cells contribute to AD onset and progression. Unlike the cytotoxic effects of CD8 <jats:sup>+</jats:sup> cells, CD4 <jats:sup>+</jats:sup> T cells capable of regulating inflammation show promise in reducing pathology and improving cognitive outcomes in mouse models of AD and in aging. Here, we sought to exploit the beneficial properties of CD4 <jats:sup>+</jats:sup> T cells while circumventing the need for TCR and peptide–MHC antigen discovery, thereby providing a potential universal therapeutic approach. To achieve this, we engineered CD4 <jats:sup>+</jats:sup> T cells with chimeric antigen receptors (CARs) targeting fibrillar forms of aggregated amyloid-β. Our findings demonstrate that optimized CAR-T cells can alter amyloid deposition in the dura and reduce parenchymal pathology in the brain. Furthermore, we observed that CAR-T treatment promotes the expansion and recruitment of endogenous CD4 <jats:sup>+</jats:sup> T cells into the brain parenchyma and leptomeninges. In summary, we established the feasibility of amyloid plaque–specific CAR-T cells as a potential therapeutic avenue for AD. These findings highlight the potential of CD4 <jats:sup>+</jats:sup> CAR-T therapy not only to modify amyloid pathology but also to reshape the immune landscape of the CNS, paving the way for future development of cellular immunotherapies for neurodegenerative disease.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"13 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146146141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
David Salom, Diana S. Suder, Wei Huang, Arum Wu, Els Pardon, Jan Steyaert, Philip D. Kiser, Derek J. Taylor, Shane Gonen, Krzysztof Palczewski
Rhodopsin, the most intensively studied G protein–coupled receptor (GPCR), is activated by light-induced isomerization of its chromophore 11- cis -retinal. This study employed cryogenic electron microscopy (cryo-EM) to investigate rhodopsin structure using a megabody (Mb7) as a negative allosteric modulator. Three distinct cryo-EM structures were solved: ground-state rhodopsin, photoactivated rhodopsin, and apo-rhodopsin, all in complex with Mb7. Photoactivated rhodopsin and apo-rhodopsin, both in complex with Mb7, maintain a conformation remarkably similar to ground-state rhodopsin rather than adopting a Meta-II-like conformation. Structural elements, including the conserved residues of the NPxxY motif and the ionic lock, remain in positions corresponding to inactive rhodopsin. The megabody forms extensive interactions with rhodopsin’s extracellular loop 2, N terminus, and glycans. The findings demonstrate that Mb7 stabilizes photoactivated rhodopsin in a Meta-I-like conformation, preventing progression to the active Meta-II state through specific immobilization of the extracellular domain. This work establishes a foundation for cryo-EM-guided discovery of ligands modulating rhodopsin.
{"title":"Structural analysis of rhodopsin states in megabody complexes","authors":"David Salom, Diana S. Suder, Wei Huang, Arum Wu, Els Pardon, Jan Steyaert, Philip D. Kiser, Derek J. Taylor, Shane Gonen, Krzysztof Palczewski","doi":"10.1073/pnas.2532336123","DOIUrl":"https://doi.org/10.1073/pnas.2532336123","url":null,"abstract":"Rhodopsin, the most intensively studied G protein–coupled receptor (GPCR), is activated by light-induced isomerization of its chromophore 11- <jats:italic toggle=\"yes\">cis</jats:italic> -retinal. This study employed cryogenic electron microscopy (cryo-EM) to investigate rhodopsin structure using a megabody (Mb7) as a negative allosteric modulator. Three distinct cryo-EM structures were solved: ground-state rhodopsin, photoactivated rhodopsin, and apo-rhodopsin, all in complex with Mb7. Photoactivated rhodopsin and apo-rhodopsin, both in complex with Mb7, maintain a conformation remarkably similar to ground-state rhodopsin rather than adopting a Meta-II-like conformation. Structural elements, including the conserved residues of the NPxxY motif and the ionic lock, remain in positions corresponding to inactive rhodopsin. The megabody forms extensive interactions with rhodopsin’s extracellular loop 2, N terminus, and glycans. The findings demonstrate that Mb7 stabilizes photoactivated rhodopsin in a Meta-I-like conformation, preventing progression to the active Meta-II state through specific immobilization of the extracellular domain. This work establishes a foundation for cryo-EM-guided discovery of ligands modulating rhodopsin.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"17 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129329","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap
The transcription factor complex White Collar Complex (WCC) functions both as a photoreceptor and as the circadian positive element. In response to light, WCC acutely activates ~5% of all genes, whereas in the dark it influences expression of about 40% of the transcriptome. Among WCC targets is frq , which is acutely light-activated through the pLRE ( proximal Light-Response Element ) and circadian-regulated through the C-box ( Clock-box ) promoter element that is not responsible for light-driven expression. The FRQ–FRH complex (FFC), which includes CK-1a, represses WCC activity at the C-box by phosphorylating WCC at >95 sites, but FFC has no described role in the light. We validated the expectation that FFC also silences C-box promoters in constant light, thereby confirming two classes of WCC targets: C-box -like genes that are normally repressed in light and pLRE -like genes that remain light-active despite FFC-driven WCC phosphorylation. Derepression of C-box -like promoters in frq -null fungi may explain reported noncircadian phenotypes such as reduced virulence and conidiation. Reanalysis of WCC circadian regulation revealed that, while most WCC is phosphorylated and repressed at dusk, subsequent circadian activation results from transient dephosphorylation of only a small subset of the WCC pool. This small active pool drives frq expression, nucleating the FFC, which rephosphorylates WCC to repress it again, generating a phosphorylation/dephosphorylation cycle that can persist for days without new WCC synthesis. The realization that both FFC and WCC are regulated primarily through phosphorylation rather than protein turnover leaves the circadian oscillator looking much like a “phoscillator,” emphasizing the primacy of posttranslational regulation in timekeeping.
{"title":"A daily cycle of White Collar Complex dephosphorylation sustains circadian rhythmicity in Neurospora","authors":"Bin Wang, Xiaoying Zhou, Jennifer J. Loros, Jay C. Dunlap","doi":"10.1073/pnas.2525126123","DOIUrl":"https://doi.org/10.1073/pnas.2525126123","url":null,"abstract":"The transcription factor complex White Collar Complex (WCC) functions both as a photoreceptor and as the circadian positive element. In response to light, WCC acutely activates ~5% of all genes, whereas in the dark it influences expression of about 40% of the transcriptome. Among WCC targets is <jats:italic toggle=\"yes\">frq</jats:italic> , which is acutely light-activated through the <jats:italic toggle=\"yes\">pLRE</jats:italic> ( <jats:italic toggle=\"yes\">proximal Light-Response Element</jats:italic> ) and circadian-regulated through the <jats:italic toggle=\"yes\">C-box</jats:italic> ( <jats:italic toggle=\"yes\">Clock-box</jats:italic> ) promoter element that is not responsible for light-driven expression. The FRQ–FRH complex (FFC), which includes CK-1a, represses WCC activity at the <jats:italic toggle=\"yes\">C-box</jats:italic> by phosphorylating WCC at >95 sites, but FFC has no described role in the light. We validated the expectation that FFC also silences <jats:italic toggle=\"yes\">C-box</jats:italic> promoters in constant light, thereby confirming two classes of WCC targets: <jats:italic toggle=\"yes\">C-box</jats:italic> -like genes that are normally repressed in light and <jats:italic toggle=\"yes\">pLRE</jats:italic> -like genes that remain light-active despite FFC-driven WCC phosphorylation. Derepression of <jats:italic toggle=\"yes\">C-box</jats:italic> -like promoters in <jats:italic toggle=\"yes\">frq</jats:italic> -null fungi may explain reported noncircadian phenotypes such as reduced virulence and conidiation. Reanalysis of WCC circadian regulation revealed that, while most WCC is phosphorylated and repressed at dusk, subsequent circadian activation results from transient dephosphorylation of only a small subset of the WCC pool. This small active pool drives <jats:italic toggle=\"yes\">frq</jats:italic> expression, nucleating the FFC, which rephosphorylates WCC to repress it again, generating a phosphorylation/dephosphorylation cycle that can persist for days without new WCC synthesis. The realization that both FFC and WCC are regulated primarily through phosphorylation rather than protein turnover leaves the circadian oscillator looking much like a “phoscillator,” emphasizing the primacy of posttranslational regulation in timekeeping.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"26 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129341","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chao Deng, Xinyi Ma, Hui Lu, Hongyu Zhao, Jingsi Ming, Tao Wang
Current single-cell profiling technologies enable the capture of multiple cellular modalities, providing valuable insights into complex biological systems. While a substantial amount of single-cell multimodal data has been generated and accumulated, most of these datasets are unpaired, characterized by distinct feature spaces and a lack of cell-wise correspondence. The absence of explicit linkages between modalities poses a fundamental challenge for data integration and interpretation. To address this, we introduce SuperMap, a statistical learning method designed for the integrative analyses of unpaired multimodal data. SuperMap directly learns cross-modal mappings from unpaired data to effectively bridge and link different modalities, facilitating a variety of downstream analysis tasks. Comprehensive benchmarking and real-world applications demonstrate the superior performance of SuperMap in enhancing cell-type identification, improving diagonal integration, enabling regulatory analysis, and revealing epigenomic priming events to specify cell differentiation directions for trajectory inference.
{"title":"Bridging unpaired single-cell multimodal data for integrative analyses with SuperMap","authors":"Chao Deng, Xinyi Ma, Hui Lu, Hongyu Zhao, Jingsi Ming, Tao Wang","doi":"10.1073/pnas.2505182123","DOIUrl":"https://doi.org/10.1073/pnas.2505182123","url":null,"abstract":"Current single-cell profiling technologies enable the capture of multiple cellular modalities, providing valuable insights into complex biological systems. While a substantial amount of single-cell multimodal data has been generated and accumulated, most of these datasets are unpaired, characterized by distinct feature spaces and a lack of cell-wise correspondence. The absence of explicit linkages between modalities poses a fundamental challenge for data integration and interpretation. To address this, we introduce SuperMap, a statistical learning method designed for the integrative analyses of unpaired multimodal data. SuperMap directly learns cross-modal mappings from unpaired data to effectively bridge and link different modalities, facilitating a variety of downstream analysis tasks. Comprehensive benchmarking and real-world applications demonstrate the superior performance of SuperMap in enhancing cell-type identification, improving diagonal integration, enabling regulatory analysis, and revealing epigenomic priming events to specify cell differentiation directions for trajectory inference.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"91 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chang Sun, Jennifer N. Jahncke, Kevin M. Wright, Eric Gouaux
GABA A receptors (GABA A Rs) mediate fast inhibitory neurotransmission in the brain and are assembled from 19 subunit isoforms into multiple pentameric assemblies. Although α1-containing GABA A Rs are broadly expressed and are pharmacologically important, the molecular diversity of native α1-based assemblies in specific brain regions remains incompletely understood. Here, we use immunofluorescence, mass spectrometry, and cryogenic electron microscopy (cryo-EM) to characterize the spatial distribution, subunit composition, and structural architecture of native α1-containing GABA A Rs in the rat cerebellum. Confocal microscopy reveals robust colocalization of α1 and γ2 subunits across cerebellar layers, including prominent labeling at glomerular synapses. Biochemical purification and proteomic analysis identify a range of α, β, and γ subunits, along with abundant α6 and δ subunits. Using cryo-EM and automated subunit identification, we resolve eight α1-containing receptor assemblies, including the first structure of α6-containing receptors. We further determine the binding mode of the α6-selective pyrazoloquinolinone modulator PZ-II-029 at the α + /γ – interface, showing ligand-induced expansion of the entire extracellular domain (ECD). Together, our study defines the structure and subunit composition of the α1-containing cerebellar GABA A Rs and elaborates the molecular interactions between native receptors and pyrazoloquinolinone, thereby laying the groundwork for brain region and subunit-specific pharmacology.
GABA A受体（GABA A Rs）介导大脑中的快速抑制性神经传递，并由19个亚基亚型组装成多个五聚体组装体。尽管含有α1的GABA A Rs广泛表达并且具有重要的药理学意义，但在特定脑区域中基于α1的天然组装的分子多样性仍然不完全清楚。本研究采用免疫荧光、质谱和低温电镜（cro - em）对大鼠小脑中天然含α1的GABA A Rs的空间分布、亚基组成和结构结构进行了表征。共聚焦显微镜显示α1和γ2亚基在小脑各层的共定位，包括在肾小球突触的显著标记。生化纯化和蛋白质组学分析鉴定出一系列α、β和γ亚基，以及丰富的α6和δ亚基。利用低温电镜和自动亚基鉴定，我们分析了8个含α1受体组合，包括含α6受体的第一个结构。我们进一步确定了α6选择性吡唑喹啉酮调节剂PZ-II-029在α + /γ -界面的结合模式，显示了配体诱导的整个细胞外结构域（ECD）的扩张。我们的研究明确了含α1的小脑GABA A Rs的结构和亚基组成，阐述了天然受体与吡唑喹啉酮之间的分子相互作用，从而为脑区和亚基特异性药理学奠定了基础。
{"title":"Molecular assemblies and pharmacology of cerebellar GABA A receptors","authors":"Chang Sun, Jennifer N. Jahncke, Kevin M. Wright, Eric Gouaux","doi":"10.1073/pnas.2524504123","DOIUrl":"https://doi.org/10.1073/pnas.2524504123","url":null,"abstract":"GABA <jats:sub>A</jats:sub> receptors (GABA <jats:sub>A</jats:sub> Rs) mediate fast inhibitory neurotransmission in the brain and are assembled from 19 subunit isoforms into multiple pentameric assemblies. Although α1-containing GABA <jats:sub>A</jats:sub> Rs are broadly expressed and are pharmacologically important, the molecular diversity of native α1-based assemblies in specific brain regions remains incompletely understood. Here, we use immunofluorescence, mass spectrometry, and cryogenic electron microscopy (cryo-EM) to characterize the spatial distribution, subunit composition, and structural architecture of native α1-containing GABA <jats:sub>A</jats:sub> Rs in the rat cerebellum. Confocal microscopy reveals robust colocalization of α1 and γ2 subunits across cerebellar layers, including prominent labeling at glomerular synapses. Biochemical purification and proteomic analysis identify a range of α, β, and γ subunits, along with abundant α6 and δ subunits. Using cryo-EM and automated subunit identification, we resolve eight α1-containing receptor assemblies, including the first structure of α6-containing receptors. We further determine the binding mode of the α6-selective pyrazoloquinolinone modulator PZ-II-029 at the α <jats:sup>+</jats:sup> /γ <jats:sup>–</jats:sup> interface, showing ligand-induced expansion of the entire extracellular domain (ECD). Together, our study defines the structure and subunit composition of the α1-containing cerebellar GABA <jats:sub>A</jats:sub> Rs and elaborates the molecular interactions between native receptors and pyrazoloquinolinone, thereby laying the groundwork for brain region and subunit-specific pharmacology.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"15 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Zhibo Li, Clément Bielinski, Anke Lindner, Blaise Delmotte, Olivia du Roure
The control of particle trajectories in structured microfluidic environments has significantly advanced sorting technologies, most notably through deterministic lateral displacement (DLD). While previous works have largely targeted rigid, near-spherical particles, the sorting of flexible, anisotropic objects such as fibers remains largely unexplored. Here, we combine experiments and simulations to demonstrate how tilted pillar arrays enable efficient, length-based separation of flexible fibers. We find that these arrays act as band-pass filters, selectively inducing lateral migration in fibers whose lengths are close to the array period. Fibers significantly shorter or longer exhibit small lateral deviation. This migration arises from the interplay of fluid–structure interactions between fibers and the complex flow and steric interactions with the pillars. Depending on their length, fibers exhibit distinct transport regimes: short fibers zigzag in between pillars following the flow, intermediate length fibers exhibit wrapping and jumping from one pillar to another, leading to lateral displacement, and long fibers deform extensively, following mixed zigzag-jump trajectories with small lateral migration. We identify the mechanical tension that develops in the fiber when wrapped around the pillars as the driving mechanism of cross-streamline transport. Leveraging this band-pass effect, we designed a highly efficient separation device to collect monodisperse fiber suspensions. Our findings not only expand the functional scope of DLD-like systems but also open avenues for understanding transport of anisotropic objects in porous media.
{"title":"A microfluidic band-pass filter for flexible fiber separation","authors":"Zhibo Li, Clément Bielinski, Anke Lindner, Blaise Delmotte, Olivia du Roure","doi":"10.1073/pnas.2520537123","DOIUrl":"https://doi.org/10.1073/pnas.2520537123","url":null,"abstract":"The control of particle trajectories in structured microfluidic environments has significantly advanced sorting technologies, most notably through deterministic lateral displacement (DLD). While previous works have largely targeted rigid, near-spherical particles, the sorting of flexible, anisotropic objects such as fibers remains largely unexplored. Here, we combine experiments and simulations to demonstrate how tilted pillar arrays enable efficient, length-based separation of flexible fibers. We find that these arrays act as band-pass filters, selectively inducing lateral migration in fibers whose lengths are close to the array period. Fibers significantly shorter or longer exhibit small lateral deviation. This migration arises from the interplay of fluid–structure interactions between fibers and the complex flow and steric interactions with the pillars. Depending on their length, fibers exhibit distinct transport regimes: short fibers zigzag in between pillars following the flow, intermediate length fibers exhibit wrapping and jumping from one pillar to another, leading to lateral displacement, and long fibers deform extensively, following mixed zigzag-jump trajectories with small lateral migration. We identify the mechanical tension that develops in the fiber when wrapped around the pillars as the driving mechanism of cross-streamline transport. Leveraging this band-pass effect, we designed a highly efficient separation device to collect monodisperse fiber suspensions. Our findings not only expand the functional scope of DLD-like systems but also open avenues for understanding transport of anisotropic objects in porous media.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"91 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nikol Labecka, Jenny M. Andersson, Emma Sparr, Kevin Roger
Evaporation from a multicomponent aqueous mixture not only establishes a hydration gradient but may also lead to composition gradients in the other components. Here, we show that such a gradient induces a strong segregation between two phospholipids that differ only in the saturation of their acyl chains. Using high-resolution confocal Raman microscopy combined with small- and wide-angle X-ray scattering, we simultaneously resolve local composition and structure along the evaporation direction. We find that the saturated phospholipid, dipalmitoyl phosphatidylcholine (DPPC), accumulates near the air–liquid interface, while the unsaturated phospholipid, dioleoyl phosphocholine (DOPC), is displaced toward a more hydrated intermediate region, resulting in a complete inversion of their initial proportions. This nonmonotonic lipid gradient reflects the different water swelling capacities of the L β′ and L α lamellar phases favored by DPPC and DOPC, respectively. Despite the system being out of equilibrium, the segregation is quantitatively captured by a description based on local equilibrium chemical potentials and multicomponent diffusion with cross-coupling. Our findings identify hydration gradients as a robust driver of lipid segregation and establish a general framework for predicting transport and organization in evaporating soft-matter systems.
{"title":"Hydration gradients drive lipid self-segregation","authors":"Nikol Labecka, Jenny M. Andersson, Emma Sparr, Kevin Roger","doi":"10.1073/pnas.2518553123","DOIUrl":"https://doi.org/10.1073/pnas.2518553123","url":null,"abstract":"Evaporation from a multicomponent aqueous mixture not only establishes a hydration gradient but may also lead to composition gradients in the other components. Here, we show that such a gradient induces a strong segregation between two phospholipids that differ only in the saturation of their acyl chains. Using high-resolution confocal Raman microscopy combined with small- and wide-angle X-ray scattering, we simultaneously resolve local composition and structure along the evaporation direction. We find that the saturated phospholipid, dipalmitoyl phosphatidylcholine (DPPC), accumulates near the air–liquid interface, while the unsaturated phospholipid, dioleoyl phosphocholine (DOPC), is displaced toward a more hydrated intermediate region, resulting in a complete inversion of their initial proportions. This nonmonotonic lipid gradient reflects the different water swelling capacities of the L <jats:sub>β′</jats:sub> and L <jats:sub>α</jats:sub> lamellar phases favored by DPPC and DOPC, respectively. Despite the system being out of equilibrium, the segregation is quantitatively captured by a description based on local equilibrium chemical potentials and multicomponent diffusion with cross-coupling. Our findings identify hydration gradients as a robust driver of lipid segregation and establish a general framework for predicting transport and organization in evaporating soft-matter systems.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"89 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The theoretical possibility for leukemia stem cells (LSCs) to produce both leukemia blasts and dysfunctional immune cells remains underexplored. Here, we investigate three major fusion transcription factor (fTF)-driven acute myeloid leukemia (AML) subtypes [ RUNX1(CBFα)::RUNX1T1 , PML::RARA , and CBFB::MYH11 ] using two optimized single-cell RNA-sequencing technologies to trace fTF expression in 24 de novo AML patients. We demonstrate that the fTFs are widely expressed not only in leukemia blasts but also in differentiated myeloid and lymphoid cells, indicating hematopoietic stem cells or multipotent progenitors (HSCs/MPPs) as LSCs that propagate altered cellular differentiation hierarchies, including immune cells. DNA-FISH confirms the presence of fTFs in T lymphoid and erythroid cells, and targeted sequencing of secondary mutations in sublineages of cells corroborates hierarchical and stepwise leukemogenesis. By tracking RUNX1::RUNX1T1 -expressing cells in patients with or without relapse post–frontline chemotherapy, we highlight the necessity of eradicating LSCs to achieve sustained long-term complete remission and restore a functional immune system capable of suppressing residual disease over time. Comparative single-cell transcriptome analyses further reveal that fTFs are associated with AML subtype-specific differentiation defects in both innate and adaptive immune compartments, suggesting an altered landscape of immune cell–cell communication networks that may facilitate the survival and proliferation of leukemic blasts. Through the examination of intercellular communications among various putative fTF + and normal cell populations, we developed a ligand–receptor (L–R)-based risk-scoring model with independent prognostic value. Collectively, these findings provide insights into the cells of origin of LSCs and the implications of fTF expression for the immune landscape of AML.
{"title":"HSCs/MPPs as cells of origin with altered differentiation hierarchy impairing immunomicroenvironment in PML::RARA and CBFα/β fusion AML","authors":"Niu Qiao, Zi-Xuan Wang, Yu-Liang Zhang, Liu-Qing-Qing Zhang, Hong-Ming Zhu, Xiang-Qin Weng, Yong-Mei Zhu, Wen-Yan Cheng, Jian-Feng Li, Lu Jiang, Xiao-Yu Yan, Guang Yang, Yang Shen, Sheng-Yue Wang, Zhu Chen, Xiao-Jian Sun, Feng Liu, Sai-Juan Chen","doi":"10.1073/pnas.2526334123","DOIUrl":"https://doi.org/10.1073/pnas.2526334123","url":null,"abstract":"The theoretical possibility for leukemia stem cells (LSCs) to produce both leukemia blasts and dysfunctional immune cells remains underexplored. Here, we investigate three major fusion transcription factor (fTF)-driven acute myeloid leukemia (AML) subtypes [ <jats:italic toggle=\"yes\">RUNX1(CBFα)::RUNX1T1</jats:italic> , <jats:italic toggle=\"yes\">PML::RARA</jats:italic> , and <jats:italic toggle=\"yes\">CBFB::MYH11</jats:italic> ] using two optimized single-cell RNA-sequencing technologies to trace fTF expression in 24 de novo AML patients. We demonstrate that the fTFs are widely expressed not only in leukemia blasts but also in differentiated myeloid and lymphoid cells, indicating hematopoietic stem cells or multipotent progenitors (HSCs/MPPs) as LSCs that propagate altered cellular differentiation hierarchies, including immune cells. DNA-FISH confirms the presence of fTFs in T lymphoid and erythroid cells, and targeted sequencing of secondary mutations in sublineages of cells corroborates hierarchical and stepwise leukemogenesis. By tracking <jats:italic toggle=\"yes\">RUNX1::RUNX1T1</jats:italic> -expressing cells in patients with or without relapse post–frontline chemotherapy, we highlight the necessity of eradicating LSCs to achieve sustained long-term complete remission and restore a functional immune system capable of suppressing residual disease over time. Comparative single-cell transcriptome analyses further reveal that fTFs are associated with AML subtype-specific differentiation defects in both innate and adaptive immune compartments, suggesting an altered landscape of immune cell–cell communication networks that may facilitate the survival and proliferation of leukemic blasts. Through the examination of intercellular communications among various putative fTF <jats:sup>+</jats:sup> and normal cell populations, we developed a ligand–receptor (L–R)-based risk-scoring model with independent prognostic value. Collectively, these findings provide insights into the cells of origin of LSCs and the implications of fTF expression for the immune landscape of AML.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"91 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Steven L. Zhang, Toshihiko Fukushima, Sophie Kirkman, Soo Jin Adrian Koh, Philipp Rothemund, Christoph Keplinger
Actuators drive robotic motion, and their energy conversion efficiency is a key performance metric that informs power consumption. Soft electrostatic actuators promise new opportunities for bioinspired and wearable robotics, being driven by electrical signals and producing high-speed, muscle-like motion. Unlike electromagnetic motors, for which efficiency has been systematically studied, efficiency of soft actuators lacks a standardized definition and measurement method, highlighting the need for a unified framework for the evaluation of their efficiency. Here, we propose a comprehensive method to study electrical-to-mechanical energy conversion in soft electrostatic actuators by analyzing closed cycles on planes spanned by work-conjugate variables: voltage–charge and force–position; our experimental setup allows us to prescribe and measure in real-time all work-conjugate variables and thus, to evaluate efficiency as function of load, electric potential, frequency, and actuator materials. We introduce a practical work cycle to evaluate actuators, and, using Peano-HASEL (Hydraulically Amplified Self-healing ELectrostatic) actuators as a model system, we reveal that efficiency is highly dependent on applied voltage, force, and actuation frequency; within the tested range of parameters, we measure a maximum efficiency of 63.6%, which is more than three times the previously reported value for HASEL actuators. We further study energy losses inherent in mechanical and electrical cycles. We show the general applicability of our method across different electrostatic actuators by applying it to a pure-shear dielectric elastomer actuator (DEA), demonstrating efficiencies up to 62.9%. This comprehensive method will facilitate the study and development of electrostatic actuators for the next generation of highly efficient soft robots.
{"title":"A method to study and enhance the energy efficiency of soft electrostatic actuators","authors":"Steven L. Zhang, Toshihiko Fukushima, Sophie Kirkman, Soo Jin Adrian Koh, Philipp Rothemund, Christoph Keplinger","doi":"10.1073/pnas.2527676123","DOIUrl":"https://doi.org/10.1073/pnas.2527676123","url":null,"abstract":"Actuators drive robotic motion, and their energy conversion efficiency is a key performance metric that informs power consumption. Soft electrostatic actuators promise new opportunities for bioinspired and wearable robotics, being driven by electrical signals and producing high-speed, muscle-like motion. Unlike electromagnetic motors, for which efficiency has been systematically studied, efficiency of soft actuators lacks a standardized definition and measurement method, highlighting the need for a unified framework for the evaluation of their efficiency. Here, we propose a comprehensive method to study electrical-to-mechanical energy conversion in soft electrostatic actuators by analyzing closed cycles on planes spanned by work-conjugate variables: voltage–charge and force–position; our experimental setup allows us to prescribe and measure in real-time all work-conjugate variables and thus, to evaluate efficiency as function of load, electric potential, frequency, and actuator materials. We introduce a practical work cycle to evaluate actuators, and, using Peano-HASEL (Hydraulically Amplified Self-healing ELectrostatic) actuators as a model system, we reveal that efficiency is highly dependent on applied voltage, force, and actuation frequency; within the tested range of parameters, we measure a maximum efficiency of 63.6%, which is more than three times the previously reported value for HASEL actuators. We further study energy losses inherent in mechanical and electrical cycles. We show the general applicability of our method across different electrostatic actuators by applying it to a pure-shear dielectric elastomer actuator (DEA), demonstrating efficiencies up to 62.9%. This comprehensive method will facilitate the study and development of electrostatic actuators for the next generation of highly efficient soft robots.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"4 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2026-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146129322","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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