The endoplasmic reticulum (ER) plays crucial roles in maintaining protein quality control and regulating dynamic Ca2+ storage in eukaryotic cells. However, the proteostasis system involved in ER-mediated protein quality control has not been fully characterized. Here we show that Ca2+ triggers the condensation of PDIA6, an ER-resident disulfide isomerase and molecular chaperone, into quality control granules. In contrast to the condensation mechanism observed for proteins containing low-complexity domains, our results indicate that transient but specific electrostatic interactions occur between the first and the third folded thioredoxin-like domains of PDIA6. We further show that the PDIA6 condensates recruit proinsulin, thereby accelerating the oxidative proinsulin folding and suppressing the proinsulin aggregation inside quality control granules, essential for secretion of insulin. Lee et al. show that Ca²⁺ triggers condensates enriched with PDIA6, an ER-resident disulfide isomerase and chaperone, along with other protein disulfide isomerase family proteins and some chaperones that in turn enhance folding of proinsulin.
{"title":"Ca2+-driven PDIA6 biomolecular condensation ensures proinsulin folding","authors":"Young-Ho Lee, Tomohide Saio, Mai Watabe, Motonori Matsusaki, Shingo Kanemura, Yuxi Lin, Taro Mannen, Tsubura Kuramochi, Yuka Kamada, Katsuya Iuchi, Michiko Tajiri, Kotono Suzuki, Yan Li, Yunseok Heo, Kotone Ishii, Kenta Arai, Kazunori Ban, Mayuko Hashimoto, Shuichiro Oshita, Satoshi Ninagawa, Yoshikazu Hattori, Hiroyuki Kumeta, Airu Takeuchi, Shinji Kajimoto, Hiroya Abe, Eiichiro Mori, Takahiro Muraoka, Takakazu Nakabayashi, Satoko Akashi, Tsukasa Okiyoneda, Michele Vendruscolo, Kenji Inaba, Masaki Okumura","doi":"10.1038/s41556-025-01794-8","DOIUrl":"10.1038/s41556-025-01794-8","url":null,"abstract":"The endoplasmic reticulum (ER) plays crucial roles in maintaining protein quality control and regulating dynamic Ca2+ storage in eukaryotic cells. However, the proteostasis system involved in ER-mediated protein quality control has not been fully characterized. Here we show that Ca2+ triggers the condensation of PDIA6, an ER-resident disulfide isomerase and molecular chaperone, into quality control granules. In contrast to the condensation mechanism observed for proteins containing low-complexity domains, our results indicate that transient but specific electrostatic interactions occur between the first and the third folded thioredoxin-like domains of PDIA6. We further show that the PDIA6 condensates recruit proinsulin, thereby accelerating the oxidative proinsulin folding and suppressing the proinsulin aggregation inside quality control granules, essential for secretion of insulin. Lee et al. show that Ca²⁺ triggers condensates enriched with PDIA6, an ER-resident disulfide isomerase and chaperone, along with other protein disulfide isomerase family proteins and some chaperones that in turn enhance folding of proinsulin.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"1952-1964"},"PeriodicalIF":19.1,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41556-025-01794-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145484919","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 : 2025-11-10DOI: 10.1038/s41556-025-01825-4
Sangbum Park, David G. Gonzalez, Boris Guirao, Jonathan D. Boucher, Katie Cockburn, Edward D. Marsh, Kailin R. Mesa, Samara Brown, Panteleimon Rompolas, Ann M. Haberman, Yohanns Bellaïche, Valentina Greco
{"title":"Author Correction: Tissue-scale coordination of cellular behaviour promotes epidermal wound repair in live mice","authors":"Sangbum Park, David G. Gonzalez, Boris Guirao, Jonathan D. Boucher, Katie Cockburn, Edward D. Marsh, Kailin R. Mesa, Samara Brown, Panteleimon Rompolas, Ann M. Haberman, Yohanns Bellaïche, Valentina Greco","doi":"10.1038/s41556-025-01825-4","DOIUrl":"10.1038/s41556-025-01825-4","url":null,"abstract":"","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"28 1","pages":"208-208"},"PeriodicalIF":19.1,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41556-025-01825-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145484920","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 : 2025-11-06DOI: 10.1038/s41556-025-01796-6
Daniel Besser, Sina Bartfeld, Stefanie Mahler
The German Stem Cell Network (GSCN) connects science, society and policy to advance stem cell research. Since 2013, it has promoted innovation, ethics and public engagement. Recognizing Europe’s need for stronger collaboration, the GSCN aims to build a pan-European network to enhance research and translation, and to support young scientists.
{"title":"Bridging science, society and policy with the German Stem Cell Network","authors":"Daniel Besser, Sina Bartfeld, Stefanie Mahler","doi":"10.1038/s41556-025-01796-6","DOIUrl":"10.1038/s41556-025-01796-6","url":null,"abstract":"The German Stem Cell Network (GSCN) connects science, society and policy to advance stem cell research. Since 2013, it has promoted innovation, ethics and public engagement. Recognizing Europe’s need for stronger collaboration, the GSCN aims to build a pan-European network to enhance research and translation, and to support young scientists.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"1877-1880"},"PeriodicalIF":19.1,"publicationDate":"2025-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145447340","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 : 2025-11-04DOI: 10.1038/s41556-025-01792-w
Yuanzhuo Zhou, Kohei Asai, Hirohisa Kyogoku, Tomoya S. Kitajima
Chromosome mis-segregation during meiosis in oocytes causes miscarriages and congenital diseases. Ageing-associated premature chromosome separation is a major cause of mis-segregation. Effective prevention of premature chromosome separation has not yet been achieved. Here we design protein-based artificial kinetochores that act as decoys to prevent premature chromosome separation. Designed artificial kinetochore-like decoys are submicroscale clusters of NDC80-NUF2-tethered protein particles that can establish a biorientation-like state by competing with chromosomal kinetochores for HURP-decorated microtubules. This competition reduces excessive bipolar microtubule pulling forces exerted on chromosomes, thereby effectively preventing premature chromosome separation during meiosis I and II in aged mouse oocytes. These effects suppress egg aneuploidy. This study provides a decoy strategy with biocompatible artificial kinetochores to prevent ageing-associated meiotic errors in oocytes. Zhou et al. design protein-based artificial kinetochore constructs as decoys to prevent premature chromosomal separation in aged oocytes. These constructs compete with chromosomal kinetochores, reducing excessive bipolar microtubule pulling forces.
{"title":"Designing protein-based artificial kinetochores as decoys to prevent meiotic errors in oocytes","authors":"Yuanzhuo Zhou, Kohei Asai, Hirohisa Kyogoku, Tomoya S. Kitajima","doi":"10.1038/s41556-025-01792-w","DOIUrl":"10.1038/s41556-025-01792-w","url":null,"abstract":"Chromosome mis-segregation during meiosis in oocytes causes miscarriages and congenital diseases. Ageing-associated premature chromosome separation is a major cause of mis-segregation. Effective prevention of premature chromosome separation has not yet been achieved. Here we design protein-based artificial kinetochores that act as decoys to prevent premature chromosome separation. Designed artificial kinetochore-like decoys are submicroscale clusters of NDC80-NUF2-tethered protein particles that can establish a biorientation-like state by competing with chromosomal kinetochores for HURP-decorated microtubules. This competition reduces excessive bipolar microtubule pulling forces exerted on chromosomes, thereby effectively preventing premature chromosome separation during meiosis I and II in aged mouse oocytes. These effects suppress egg aneuploidy. This study provides a decoy strategy with biocompatible artificial kinetochores to prevent ageing-associated meiotic errors in oocytes. Zhou et al. design protein-based artificial kinetochore constructs as decoys to prevent premature chromosomal separation in aged oocytes. These constructs compete with chromosomal kinetochores, reducing excessive bipolar microtubule pulling forces.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"2007-2018"},"PeriodicalIF":19.1,"publicationDate":"2025-11-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41556-025-01792-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145434234","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 : 2025-10-31DOI: 10.1038/s41556-025-01801-y
Eliana Ibrahimi, Brooke N. Wolford
Statistical thinking is a core part of solid, trustworthy biology. However, many studies still include insufficient sample sizes, have poor experimental design or select an incorrect statistical method for the hypothesis being tested. Here we present ten statistical tips for cell biology.
{"title":"Ten essential tips for robust statistics in cell biology","authors":"Eliana Ibrahimi, Brooke N. Wolford","doi":"10.1038/s41556-025-01801-y","DOIUrl":"10.1038/s41556-025-01801-y","url":null,"abstract":"Statistical thinking is a core part of solid, trustworthy biology. However, many studies still include insufficient sample sizes, have poor experimental design or select an incorrect statistical method for the hypothesis being tested. Here we present ten statistical tips for cell biology.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"1884-1886"},"PeriodicalIF":19.1,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145404896","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 : 2025-10-31DOI: 10.1038/s41556-025-01789-5
Shan Lu, Sitao Zhang, Spencer Oung, Jolene K. Diedrich, Peng Han, Olatz Arnold-Garcia, Takuya Ohkubo, Olubankole Aladesuyi Arogundade, Sonia Vazquez-Sanchez, Ke Zhang, John Ravits, John R. Yates III, Don W. Cleveland
In multiple neurodegenerative diseases, the RNA-binding protein TDP-43 forms cytoplasmic aggregates of distinct morphologies, including skein-like, small rounded granular and large spherical inclusions. Here, whereas the N-terminal self-oligomerization domain regulates TDP-43 demixing into cytoplasmic droplets, inhibition of N-terminal self-oligomerization domain-mediated oligomerization is shown to promote the formation of skein-like inclusions. Utilizing proximity labelling–mass spectrometry, cellular stresses are shown to induce TDP-43 association with actin-binding proteins that include filamins and α-actinin. Small interfering RNA-mediated reduction of filamin in Drosophila ameliorates cell loss from cytoplasmic TDP-43, consistent with the filamin–TDP-43 interaction enhancing cytotoxicity. TDP-43’s association with actin-binding proteins is mediated by BAG3, a HSP70 family nucleotide exchange factor that regulates the proteostasis of actin-binding proteins. BAG2, another HSP70 nucleotide exchange factor, facilitates the formation of small, rounded TDP-43 inclusions. We demonstrate that both TDP-43 self-oligomerization and its binding partners, including HSP70 and cochaperones BAG2 and BAG3, drive the formation of the different types of TDP-43 inclusion. Lu et al. show that, under proteotoxic stress, TDP-43 inclusions of skein-like morphology are guided by the chaperone HSP70 and its nucleotide exchange factor BAG3 to induce TDP-43 co-aggregation with F-actin-bound actin-binding proteins.
{"title":"TDP-43 skein-like inclusions are formed by BAG3- and HSP70-guided co-aggregation with actin-binding proteins","authors":"Shan Lu, Sitao Zhang, Spencer Oung, Jolene K. Diedrich, Peng Han, Olatz Arnold-Garcia, Takuya Ohkubo, Olubankole Aladesuyi Arogundade, Sonia Vazquez-Sanchez, Ke Zhang, John Ravits, John R. Yates III, Don W. Cleveland","doi":"10.1038/s41556-025-01789-5","DOIUrl":"10.1038/s41556-025-01789-5","url":null,"abstract":"In multiple neurodegenerative diseases, the RNA-binding protein TDP-43 forms cytoplasmic aggregates of distinct morphologies, including skein-like, small rounded granular and large spherical inclusions. Here, whereas the N-terminal self-oligomerization domain regulates TDP-43 demixing into cytoplasmic droplets, inhibition of N-terminal self-oligomerization domain-mediated oligomerization is shown to promote the formation of skein-like inclusions. Utilizing proximity labelling–mass spectrometry, cellular stresses are shown to induce TDP-43 association with actin-binding proteins that include filamins and α-actinin. Small interfering RNA-mediated reduction of filamin in Drosophila ameliorates cell loss from cytoplasmic TDP-43, consistent with the filamin–TDP-43 interaction enhancing cytotoxicity. TDP-43’s association with actin-binding proteins is mediated by BAG3, a HSP70 family nucleotide exchange factor that regulates the proteostasis of actin-binding proteins. BAG2, another HSP70 nucleotide exchange factor, facilitates the formation of small, rounded TDP-43 inclusions. We demonstrate that both TDP-43 self-oligomerization and its binding partners, including HSP70 and cochaperones BAG2 and BAG3, drive the formation of the different types of TDP-43 inclusion. Lu et al. show that, under proteotoxic stress, TDP-43 inclusions of skein-like morphology are guided by the chaperone HSP70 and its nucleotide exchange factor BAG3 to induce TDP-43 co-aggregation with F-actin-bound actin-binding proteins.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"1925-1937"},"PeriodicalIF":19.1,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145404894","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 : 2025-10-31DOI: 10.1038/s41556-025-01799-3
Qiaochu Li, Konstantin Weiss, Fuateima Niwa, Jan Riemer, Thorsten Hoppe
The mitochondrial proteome is remodelled to meet metabolic demands, but how metabolic cues regulate mitochondrial protein turnover remains unclear. Here we identify a conserved, nutrient-responsive mechanism in which the amino acid leucine suppresses ubiquitin-dependent degradation of outer mitochondrial membrane (OMM) proteins, stabilizing key components of the protein import machinery and expanding the mitochondrial proteome to enhance metabolic respiration. Leucine inhibits the amino acid sensor GCN2, which selectively reduces the E3 ubiquitin ligase cofactor SEL1L at mitochondria. Depletion of SEL1L phenocopies the effect of leucine, elevating OMM protein abundance and mitochondrial respiration. Disease-associated defects in leucine catabolism and OMM protein turnover impair fertility in Caenorhabditis elegans and render human lung cancer cells resistant to inhibition of mitochondrial protein import. These findings define a leucine–GCN2–SEL1L axis that links nutrient sensing to mitochondrial proteostasis, with implications for metabolic disorders and cancer. Li et al. uncover a connection between metabolic cues and mitochondrial protein degradation, showing that specifically leucine stabilizes outer mitochondrial membrane proteins by inhibiting ubiquitylation and promoting mitochondrial respiration.
{"title":"Leucine inhibits degradation of outer mitochondrial membrane proteins to adapt mitochondrial respiration","authors":"Qiaochu Li, Konstantin Weiss, Fuateima Niwa, Jan Riemer, Thorsten Hoppe","doi":"10.1038/s41556-025-01799-3","DOIUrl":"10.1038/s41556-025-01799-3","url":null,"abstract":"The mitochondrial proteome is remodelled to meet metabolic demands, but how metabolic cues regulate mitochondrial protein turnover remains unclear. Here we identify a conserved, nutrient-responsive mechanism in which the amino acid leucine suppresses ubiquitin-dependent degradation of outer mitochondrial membrane (OMM) proteins, stabilizing key components of the protein import machinery and expanding the mitochondrial proteome to enhance metabolic respiration. Leucine inhibits the amino acid sensor GCN2, which selectively reduces the E3 ubiquitin ligase cofactor SEL1L at mitochondria. Depletion of SEL1L phenocopies the effect of leucine, elevating OMM protein abundance and mitochondrial respiration. Disease-associated defects in leucine catabolism and OMM protein turnover impair fertility in Caenorhabditis elegans and render human lung cancer cells resistant to inhibition of mitochondrial protein import. These findings define a leucine–GCN2–SEL1L axis that links nutrient sensing to mitochondrial proteostasis, with implications for metabolic disorders and cancer. Li et al. uncover a connection between metabolic cues and mitochondrial protein degradation, showing that specifically leucine stabilizes outer mitochondrial membrane proteins by inhibiting ubiquitylation and promoting mitochondrial respiration.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"1889-1901"},"PeriodicalIF":19.1,"publicationDate":"2025-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41556-025-01799-3.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145404895","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 : 2025-10-29DOI: 10.1038/s41556-025-01790-y
Mike Lange, Michele Wölk, Vivian Wen Li, Cody E. Doubravsky, Joseph M. Hendricks, Shunji Kato, Yurika Otoki, Benjamin Styler, Sean L. Johnson, Cynthia A. Harris, Kiyotaka Nakagawa, Isabel F. Snodgrass, Dohee Kim, John W. Newman, Maria Fedorova, James A. Olzmann
Lipid droplets (LDs) are organelles that store and supply lipids, based on cellular needs. Although mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here we identify LD-localized ferroptosis suppressor protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, inducing polyunsaturated fatty acid-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality-control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the build-up of oxidized lipids and induction of ferroptosis. Lange et al. identify a lipid droplet quality control pathway in which FSP1 safeguards stored neutral lipids from lipid peroxidation, thereby preventing the induction of ferroptosis.
{"title":"FSP1-mediated lipid droplet quality control prevents neutral lipid peroxidation and ferroptosis","authors":"Mike Lange, Michele Wölk, Vivian Wen Li, Cody E. Doubravsky, Joseph M. Hendricks, Shunji Kato, Yurika Otoki, Benjamin Styler, Sean L. Johnson, Cynthia A. Harris, Kiyotaka Nakagawa, Isabel F. Snodgrass, Dohee Kim, John W. Newman, Maria Fedorova, James A. Olzmann","doi":"10.1038/s41556-025-01790-y","DOIUrl":"10.1038/s41556-025-01790-y","url":null,"abstract":"Lipid droplets (LDs) are organelles that store and supply lipids, based on cellular needs. Although mechanisms preventing oxidative damage to membrane phospholipids are established, the vulnerability of LD neutral lipids to peroxidation and protective mechanisms are unknown. Here we identify LD-localized ferroptosis suppressor protein 1 (FSP1) as a critical regulator that prevents neutral lipid peroxidation by recycling coenzyme Q10 (CoQ10) to its lipophilic antioxidant form. Lipidomics reveal that FSP1 loss leads to the accumulation of oxidized triacylglycerols and cholesteryl esters, and biochemical reconstitution of FSP1 with CoQ10 and NADH suppresses triacylglycerol peroxidation in vitro. Notably, inducing polyunsaturated fatty acid-rich LDs triggers triacylglycerol peroxidation and LD-initiated ferroptosis when FSP1 activity is impaired. These findings uncover the first LD lipid quality-control pathway, wherein LD-localized FSP1 maintains neutral lipid integrity to prevent the build-up of oxidized lipids and induction of ferroptosis. Lange et al. identify a lipid droplet quality control pathway in which FSP1 safeguards stored neutral lipids from lipid peroxidation, thereby preventing the induction of ferroptosis.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"1902-1913"},"PeriodicalIF":19.1,"publicationDate":"2025-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41556-025-01790-y.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145381937","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}
International efforts have yielded extensive single-cell time-series atlas datasets, such as those on mouse embryogenesis, providing a reference for mapping disease models across biomedical research. However, effectively using such data for temporal analysis of individual datasets is challenging due to the intricate nature of cell states and the tight coupling between time stamps and experimental batches. Here we introduce TemporalVAE, a deep generative model in a dual-objective setting that infers the biological time of each cell from a compressed latent space, even in a zero-shot setting. With a mouse development atlas, we demonstrated its scalability with millions of cells, accuracy in atlas-based cell staging across platforms and interpretability by identifying temporally sensitive genes with in silico perturbation. TemporalVAE effectively stages cells during human peri-implantation under both in vivo and in vitro conditions, and supports cross-primate comparisons among human, cynomolgus and marmoset embryos, highlighting its potential for broad biomedical applications. Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, enabling single-cell developmental stage inference.
{"title":"TemporalVAE: atlas-assisted temporal mapping of time-series single-cell transcriptomes during embryogenesis","authors":"Yijun Liu, Fangxin Cai, Melania Barile, Yi Chang, Dandan Cao, Yuanhua Huang","doi":"10.1038/s41556-025-01787-7","DOIUrl":"10.1038/s41556-025-01787-7","url":null,"abstract":"International efforts have yielded extensive single-cell time-series atlas datasets, such as those on mouse embryogenesis, providing a reference for mapping disease models across biomedical research. However, effectively using such data for temporal analysis of individual datasets is challenging due to the intricate nature of cell states and the tight coupling between time stamps and experimental batches. Here we introduce TemporalVAE, a deep generative model in a dual-objective setting that infers the biological time of each cell from a compressed latent space, even in a zero-shot setting. With a mouse development atlas, we demonstrated its scalability with millions of cells, accuracy in atlas-based cell staging across platforms and interpretability by identifying temporally sensitive genes with in silico perturbation. TemporalVAE effectively stages cells during human peri-implantation under both in vivo and in vitro conditions, and supports cross-primate comparisons among human, cynomolgus and marmoset embryos, highlighting its potential for broad biomedical applications. Liu et al. present TemporalVAE, a method for integrating single-cell time course data. The model proposes a workflow to determine the biological timing of samples and its temporally sensitive genes, enabling single-cell developmental stage inference.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 11","pages":"1982-1992"},"PeriodicalIF":19.1,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145381135","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}
Pseudouridine (Ψ) is one of the most abundant RNA modifications in human cells, introduced post-transcriptionally by pseudouridine synthases (PUS). Despite its prevalence, the biological functions of Ψ remain poorly understood, largely due to the limited knowledge linking specific PUS enzymes to their targets. Here, to address this gap, we systematically knocked out or knocked down nine stand-alone PUS in HCT116 cells and mapped their Ψ profiles using 2-bromoacrylamide-assisted cyclization sequencing. Through this approach, we uncovered previously unknown targets of several PUS enzymes, including RPUSD1, RPUSD2, PUS3, PUSL1 and PUS7L. In addition, we revealed that TRUB1 and PUS10 function redundantly to catalyse the highly conserved Ψ55 modification in cytosolic tRNAs. Intriguingly, we found that RPUSD3 and TRUB2 do not exhibit noticeable enzymatic activities in human cells. By integrating these findings with earlier results for TRUB1, PUS7 and PUS1, we constructed a comprehensive map of stand-alone PUS-dependent Ψ modifications across human tRNAs. Using this map, we further demonstrated that different PUS enzymes introduce Ψ modifications at distinct stages of pre-tRNA processing. Xu, Kong, Li, Pisignano and colleagues provide a map of pseudouridine sites in human noncoding RNA. Using a systematic knockout approach, they associate each pseudouridine site with the activity of a specific pseudouridine synthase.
{"title":"A comprehensive tRNA pseudouridine map uncovers targets dependent on human stand-alone pseudouridine synthases","authors":"Haiqi Xu, Linzhen Kong, Mengjie Li, Giuseppina Pisignano, Jingfei Cheng, Feng Feng, Parinaz Mehdipour, Chun-Xiao Song","doi":"10.1038/s41556-025-01803-w","DOIUrl":"10.1038/s41556-025-01803-w","url":null,"abstract":"Pseudouridine (Ψ) is one of the most abundant RNA modifications in human cells, introduced post-transcriptionally by pseudouridine synthases (PUS). Despite its prevalence, the biological functions of Ψ remain poorly understood, largely due to the limited knowledge linking specific PUS enzymes to their targets. Here, to address this gap, we systematically knocked out or knocked down nine stand-alone PUS in HCT116 cells and mapped their Ψ profiles using 2-bromoacrylamide-assisted cyclization sequencing. Through this approach, we uncovered previously unknown targets of several PUS enzymes, including RPUSD1, RPUSD2, PUS3, PUSL1 and PUS7L. In addition, we revealed that TRUB1 and PUS10 function redundantly to catalyse the highly conserved Ψ55 modification in cytosolic tRNAs. Intriguingly, we found that RPUSD3 and TRUB2 do not exhibit noticeable enzymatic activities in human cells. By integrating these findings with earlier results for TRUB1, PUS7 and PUS1, we constructed a comprehensive map of stand-alone PUS-dependent Ψ modifications across human tRNAs. Using this map, we further demonstrated that different PUS enzymes introduce Ψ modifications at distinct stages of pre-tRNA processing. Xu, Kong, Li, Pisignano and colleagues provide a map of pseudouridine sites in human noncoding RNA. Using a systematic knockout approach, they associate each pseudouridine site with the activity of a specific pseudouridine synthase.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"27 12","pages":"2186-2197"},"PeriodicalIF":19.1,"publicationDate":"2025-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41556-025-01803-w.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145357637","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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