Pub Date : 2025-08-18DOI: 10.1038/s41422-025-01164-x
Kui Xu, Guoying Hua, Mingdi Wu, Haihang Zhang, Jingda Liu, Hu Feng, Erwei Zuo
The vast scope but limited-supporting evidence in sequence databases hinders identification of proteins with specific functionality. Here, we experimentally characterized catalytic efficiency, target site window, motif preference, and off-target activity of 1100 apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC)-like family cytidine deaminases (CDs) fused with nCas9 in HEK293T cells, thereby generating the largest dataset of experimentally validated functions for a single protein family to date. These data, together with amino acid sequence, three-dimensional structure, and eight additional features, were used to construct a machine learning (ML) model, AlphaCD, which showed high accuracy in predicting catalytic efficiency (0.92) and off-target activity (0.84), as well as target windows (0.73) and catalytic motifs (0.78). We applied the trained model to predict the above catalytic features of 21,335 CDs in Uniprot, and subsampling of 28 CDs further validated its prediction accuracy (0.84, 0.87, 0.75, 0.73, respectively). Alanine scanning-based mutagenesis was then employed to reduce off-targets in one example CD, which produced a remarkably high fidelity, high efficiency cytosine base editor, thus demonstrating AlphaCD application in high-accuracy, high-throughput protein functional characterization, and providing a strategy for accelerated characterization of other proteins.
{"title":"AlphaCD: a machine learning model capable of highly accurate characterization for 21,335 cytidine deaminases","authors":"Kui Xu, Guoying Hua, Mingdi Wu, Haihang Zhang, Jingda Liu, Hu Feng, Erwei Zuo","doi":"10.1038/s41422-025-01164-x","DOIUrl":"10.1038/s41422-025-01164-x","url":null,"abstract":"The vast scope but limited-supporting evidence in sequence databases hinders identification of proteins with specific functionality. Here, we experimentally characterized catalytic efficiency, target site window, motif preference, and off-target activity of 1100 apolipoprotein B mRNA-editing enzyme, catalytic polypeptide (APOBEC)-like family cytidine deaminases (CDs) fused with nCas9 in HEK293T cells, thereby generating the largest dataset of experimentally validated functions for a single protein family to date. These data, together with amino acid sequence, three-dimensional structure, and eight additional features, were used to construct a machine learning (ML) model, AlphaCD, which showed high accuracy in predicting catalytic efficiency (0.92) and off-target activity (0.84), as well as target windows (0.73) and catalytic motifs (0.78). We applied the trained model to predict the above catalytic features of 21,335 CDs in Uniprot, and subsampling of 28 CDs further validated its prediction accuracy (0.84, 0.87, 0.75, 0.73, respectively). Alanine scanning-based mutagenesis was then employed to reduce off-targets in one example CD, which produced a remarkably high fidelity, high efficiency cytosine base editor, thus demonstrating AlphaCD application in high-accuracy, high-throughput protein functional characterization, and providing a strategy for accelerated characterization of other proteins.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"35 10","pages":"750-761"},"PeriodicalIF":25.9,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871708","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}
Pub Date : 2025-08-18DOI: 10.1038/s41422-025-01163-y
Brianna Jarboe, Maria Shubina, Ryan A. Langlois, David F. Boyd, Siddharth Balachandran
Roughly 1 billion people are infected by Influenza A viruses (IAVs) worldwide each year, resulting in approximately half a million deaths. Particularly concerning is the threat of IAV spillover from avian and other animal reservoirs. The recent outbreak of highly pathogenic avian influenza H5N1 in US dairy cows highlights this concern. While viruses that enter human populations from such zoonotic transmission typically lack the ability to transmit effectively between humans, they may be only a few mutations from acquiring this capacity. These newly adapted viruses have the potential to be significantly more virulent than seasonal strains. A major contributor to influenza pathology is the over-exuberant immune response to the virus, particularly when the infection is present in distal pulmonary tissues. Maladaptive immune pathway over-activation can drive tissue damage and pathology, often independently of effective viral control. Anti-inflammatories targeting host-initiated pathological processes hold promise, but these avenues require a thorough understanding of virus-triggered lung inflammation before they can be fully exploited. In this review, we will discuss recent advances in our understanding of the cell types that are targeted by IAV, the consequences of IAV infection on the biology of these cells, and their contribution to lung pathology in influenza. We will also discuss how virus-induced hyper-inflammatory responses present new entry-points for therapeutic intervention, showcasing Z-form nucleic acid-binding protein 1 (ZBP1)-initiated necroptosis as an example of one such pathway.
{"title":"Lung cell fates during influenza","authors":"Brianna Jarboe, Maria Shubina, Ryan A. Langlois, David F. Boyd, Siddharth Balachandran","doi":"10.1038/s41422-025-01163-y","DOIUrl":"10.1038/s41422-025-01163-y","url":null,"abstract":"Roughly 1 billion people are infected by Influenza A viruses (IAVs) worldwide each year, resulting in approximately half a million deaths. Particularly concerning is the threat of IAV spillover from avian and other animal reservoirs. The recent outbreak of highly pathogenic avian influenza H5N1 in US dairy cows highlights this concern. While viruses that enter human populations from such zoonotic transmission typically lack the ability to transmit effectively between humans, they may be only a few mutations from acquiring this capacity. These newly adapted viruses have the potential to be significantly more virulent than seasonal strains. A major contributor to influenza pathology is the over-exuberant immune response to the virus, particularly when the infection is present in distal pulmonary tissues. Maladaptive immune pathway over-activation can drive tissue damage and pathology, often independently of effective viral control. Anti-inflammatories targeting host-initiated pathological processes hold promise, but these avenues require a thorough understanding of virus-triggered lung inflammation before they can be fully exploited. In this review, we will discuss recent advances in our understanding of the cell types that are targeted by IAV, the consequences of IAV infection on the biology of these cells, and their contribution to lung pathology in influenza. We will also discuss how virus-induced hyper-inflammatory responses present new entry-points for therapeutic intervention, showcasing Z-form nucleic acid-binding protein 1 (ZBP1)-initiated necroptosis as an example of one such pathway.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"35 10","pages":"707-718"},"PeriodicalIF":25.9,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41422-025-01163-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871709","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}
Pub Date : 2025-08-06DOI: 10.1038/s41422-025-01146-z
Mingqian Huang, Mengqi Chen, Gege Yuan, Yiqiang Cui, Bin Shen, Zhaode Liu, Bohang Zhang, Junqing Chen, Dingdong Chen, Shuangshuang Qiu, Yichun Zhang, Li Liu, Lianju Qin, Yunfei Zhu, Jiayin Liu, Hao Zhang, Jun Wu, Yan Yuan, Jiahao Sha
Pluripotent stem cells (PSCs) have been derived from various species, but most culture systems stabilize only a single PSC type. By contrast, epiblast cells in vivo exist along a continuum and interact dynamically with both embryonic and extraembryonic cells, interactions missing in standard PSC cultures. This absence limits the self-organizing potential of PSCs and leads to disorganized tissue formation in teratomas. To address this, we developed a unified culture system that supports the stable differentiation of epiblast-like cells into multiple key human gastrulating cell types, collectively called human gastrulating stem cells (hGaSCs). hGaSCs, composed of endoderm-like, mesoderm-like, ectoderm-like, amnion ectoderm-like, and primordial germ cell-like cells, maintain a stable balance during long-term culture. In 3D culture, hGaSCs self-assemble into gastruloid-like structures (hGaSC-gastruloids) that model aspects of a Carnegie Stage 7 human embryo, including gastrulation and germ layer specification. Using hGaSC-gastruloids, we modeled the effects of valproic acid (VPA) on human gastrulation and uncovered molecular pathways underlying VPA-induced malformations. When transplanted into the seminiferous tubules, hGaSCs formed embryo-like structures, progressing through fetal tissue and organ development, unlike the disorganized growth seen in teratomas. In conclusion, hGaSCs provide a versatile platform to study human gastrulation, early organogenesis, developmental defects, and drug teratogenicity, with promising applications in tissue and organ generation from cultured stem cells.
{"title":"Establishment of human gastrulating stem cells with the capacity of stable differentiation into multiple gastrulating cell types","authors":"Mingqian Huang, Mengqi Chen, Gege Yuan, Yiqiang Cui, Bin Shen, Zhaode Liu, Bohang Zhang, Junqing Chen, Dingdong Chen, Shuangshuang Qiu, Yichun Zhang, Li Liu, Lianju Qin, Yunfei Zhu, Jiayin Liu, Hao Zhang, Jun Wu, Yan Yuan, Jiahao Sha","doi":"10.1038/s41422-025-01146-z","DOIUrl":"10.1038/s41422-025-01146-z","url":null,"abstract":"Pluripotent stem cells (PSCs) have been derived from various species, but most culture systems stabilize only a single PSC type. By contrast, epiblast cells in vivo exist along a continuum and interact dynamically with both embryonic and extraembryonic cells, interactions missing in standard PSC cultures. This absence limits the self-organizing potential of PSCs and leads to disorganized tissue formation in teratomas. To address this, we developed a unified culture system that supports the stable differentiation of epiblast-like cells into multiple key human gastrulating cell types, collectively called human gastrulating stem cells (hGaSCs). hGaSCs, composed of endoderm-like, mesoderm-like, ectoderm-like, amnion ectoderm-like, and primordial germ cell-like cells, maintain a stable balance during long-term culture. In 3D culture, hGaSCs self-assemble into gastruloid-like structures (hGaSC-gastruloids) that model aspects of a Carnegie Stage 7 human embryo, including gastrulation and germ layer specification. Using hGaSC-gastruloids, we modeled the effects of valproic acid (VPA) on human gastrulation and uncovered molecular pathways underlying VPA-induced malformations. When transplanted into the seminiferous tubules, hGaSCs formed embryo-like structures, progressing through fetal tissue and organ development, unlike the disorganized growth seen in teratomas. In conclusion, hGaSCs provide a versatile platform to study human gastrulation, early organogenesis, developmental defects, and drug teratogenicity, with promising applications in tissue and organ generation from cultured stem cells.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"35 10","pages":"719-734"},"PeriodicalIF":25.9,"publicationDate":"2025-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144786740","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}
Pub Date : 2025-08-01DOI: 10.1038/s41422-025-01160-1
Bianca Calí, Andrea Alimonti
{"title":"Neutrophil maturation holds the secret to human tumor suppression","authors":"Bianca Calí, Andrea Alimonti","doi":"10.1038/s41422-025-01160-1","DOIUrl":"10.1038/s41422-025-01160-1","url":null,"abstract":"","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"35 9","pages":"619-620"},"PeriodicalIF":25.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41422-025-01160-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755723","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}
Pub Date : 2025-08-01DOI: 10.1038/s41422-025-01157-w
Tao Jin, Yang Yang, Yu Guo, Yi Zhang, Qiumin Le, Nan Huang, Xing Liu, Jintai Yu, Lan Ma, Feifei Wang
Engram cells storing episodic memories are allocated to separate neuronal ensembles. However, how these ensembles maintain their stability to drive precise memory expression, and whether their destabilization contributes to aging-related memory deficits, remain elusive. Here, we show that during contextual fear memory consolidation, neuronal pentraxin 1 (NPTX1) in Fos transcription-dependent ensemble (F-RAM) of the dentate gyrus (DG) promotes memory expression in the fear context. NPTX1 facilitates Kv7.2 channel-mediated inhibition of engram cell hyperexcitability, thereby restricting the response of these cells to excitatory inputs from medial entorhinal cortex. Meanwhile, NPTX2 enhances the perisomatic inhibition of Npas4 transcription-dependent ensemble (N-RAM) by parvalbumin+ (PV+) interneurons, thereby preventing fear memory overgeneralization. Pharmacological activation of Kv7.2 channels or chemogenetic activation of PV+ interneurons repaired memory deficits caused by engram-specific NPTX depletion. Contextual fear memory precision and NPTX expression in DG engram cells were decreased in aged mice. Overexpressing NPTX1 in F-RAM ensemble or the AMPAR-binding domain of NPTX2 in N-RAM ensemble rescued contextual fear memory deficits. These findings elucidate that the coordination of NPTX1 and NPTX2 prevents engram ensembles from becoming hyperactive and provide a causal link between engram network destabilization and aging-related contextual fear memory deficits.
{"title":"Disturbed engram network caused by NPTX downregulation underlies aging-related contextual fear memory deficits","authors":"Tao Jin, Yang Yang, Yu Guo, Yi Zhang, Qiumin Le, Nan Huang, Xing Liu, Jintai Yu, Lan Ma, Feifei Wang","doi":"10.1038/s41422-025-01157-w","DOIUrl":"10.1038/s41422-025-01157-w","url":null,"abstract":"Engram cells storing episodic memories are allocated to separate neuronal ensembles. However, how these ensembles maintain their stability to drive precise memory expression, and whether their destabilization contributes to aging-related memory deficits, remain elusive. Here, we show that during contextual fear memory consolidation, neuronal pentraxin 1 (NPTX1) in Fos transcription-dependent ensemble (F-RAM) of the dentate gyrus (DG) promotes memory expression in the fear context. NPTX1 facilitates Kv7.2 channel-mediated inhibition of engram cell hyperexcitability, thereby restricting the response of these cells to excitatory inputs from medial entorhinal cortex. Meanwhile, NPTX2 enhances the perisomatic inhibition of Npas4 transcription-dependent ensemble (N-RAM) by parvalbumin+ (PV+) interneurons, thereby preventing fear memory overgeneralization. Pharmacological activation of Kv7.2 channels or chemogenetic activation of PV+ interneurons repaired memory deficits caused by engram-specific NPTX depletion. Contextual fear memory precision and NPTX expression in DG engram cells were decreased in aged mice. Overexpressing NPTX1 in F-RAM ensemble or the AMPAR-binding domain of NPTX2 in N-RAM ensemble rescued contextual fear memory deficits. These findings elucidate that the coordination of NPTX1 and NPTX2 prevents engram ensembles from becoming hyperactive and provide a causal link between engram network destabilization and aging-related contextual fear memory deficits.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"35 9","pages":"656-674"},"PeriodicalIF":25.9,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41422-025-01157-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144755724","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}
Pub Date : 2025-07-31DOI: 10.1038/s41422-025-01152-1
Chenxi Cui, Lu Zhao, Ali A. Kermani, Shuzong Du, Tanadet Pipatpolkai, Meiqin Jiang, Sagar Chittori, Yong Zi Tan, Jingyi Shi, Lucie Delemotte, Jianmin Cui, Ji Sun
KCNQ1 potassium channels are essential for physiological processes such as cardiac rhythm and intestinal chloride secretion. KCNE family subunits (KCNE1–5) associate with KCNQ1, conferring distinct properties across various tissues. KCNQ1 activation requires membrane depolarization and phosphatidylinositol 4,5-bisphosphate (PIP2) whose cellular levels are controlled by Gαq-coupled GPCR activation. While modulation of KCNQ1’s voltage-dependent activation by KCNE1/3 is well-characterized, their effects on PIP2-dependent gating of KCNQ1 via GPCR signaling remain less understood. Here we resolved structures of KCNQ1–KCNE1 and reassessed the reported KCNQ1–KCNE3 structures with and without PIP2. We revealed that KCNQ1–KCNE1/3 complexes feature two PIP2-binding sites, with KCNE1/3 contributing to a previously overlooked, uncharacterized site involving residues critical for coupling voltage sensor and pore domains. Via this site, KCNE1 and KCNE3 distinctly modulate the PIP2-dependent gating, in addition to the voltage sensitivity, of KCNQ1. Consequently, KCNE3 converts KCNQ1 into a voltage-insensitive PIP2-gated channel governed by GPCR signaling to maintain ion homeostasis in non-excitable cells. KCNE1, by significantly enhancing KCNQ1’s PIP2 affinity and resistance to GPCR regulation, forms predominantly voltage-gated channels with KCNQ1 for conducting the slow-delayed rectifier current in excitable cardiac cells. Our study highlights how KCNE1/3 modulates KCNQ1 gating in different cellular contexts, providing insights into tissue-specifically targeting multi-functional channels.
{"title":"Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function","authors":"Chenxi Cui, Lu Zhao, Ali A. Kermani, Shuzong Du, Tanadet Pipatpolkai, Meiqin Jiang, Sagar Chittori, Yong Zi Tan, Jingyi Shi, Lucie Delemotte, Jianmin Cui, Ji Sun","doi":"10.1038/s41422-025-01152-1","DOIUrl":"10.1038/s41422-025-01152-1","url":null,"abstract":"KCNQ1 potassium channels are essential for physiological processes such as cardiac rhythm and intestinal chloride secretion. KCNE family subunits (KCNE1–5) associate with KCNQ1, conferring distinct properties across various tissues. KCNQ1 activation requires membrane depolarization and phosphatidylinositol 4,5-bisphosphate (PIP2) whose cellular levels are controlled by Gαq-coupled GPCR activation. While modulation of KCNQ1’s voltage-dependent activation by KCNE1/3 is well-characterized, their effects on PIP2-dependent gating of KCNQ1 via GPCR signaling remain less understood. Here we resolved structures of KCNQ1–KCNE1 and reassessed the reported KCNQ1–KCNE3 structures with and without PIP2. We revealed that KCNQ1–KCNE1/3 complexes feature two PIP2-binding sites, with KCNE1/3 contributing to a previously overlooked, uncharacterized site involving residues critical for coupling voltage sensor and pore domains. Via this site, KCNE1 and KCNE3 distinctly modulate the PIP2-dependent gating, in addition to the voltage sensitivity, of KCNQ1. Consequently, KCNE3 converts KCNQ1 into a voltage-insensitive PIP2-gated channel governed by GPCR signaling to maintain ion homeostasis in non-excitable cells. KCNE1, by significantly enhancing KCNQ1’s PIP2 affinity and resistance to GPCR regulation, forms predominantly voltage-gated channels with KCNQ1 for conducting the slow-delayed rectifier current in excitable cardiac cells. Our study highlights how KCNE1/3 modulates KCNQ1 gating in different cellular contexts, providing insights into tissue-specifically targeting multi-functional channels.","PeriodicalId":9926,"journal":{"name":"Cell Research","volume":"35 11","pages":"876-886"},"PeriodicalIF":25.9,"publicationDate":"2025-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41422-025-01152-1.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144759296","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}
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