Pub Date : 2026-02-03DOI: 10.1038/s41556-025-01859-8
Daniel Neville, Daniel T. Ferguson, Emily B. Heikamp, Zhihao Lai, Graham W. Magor, Charlene Lam, Olivia G. Dobbs, Vita Levina, Kathy Knezevic, James J. The, Shania Alex, Stephen C. Suits, Bradon Rumler, Michael Uckelmann, Laure Talarmain, Enid Y. N. Lam, Andrew C. Perkins, Scott A. Armstrong, Charles C. Bell, Chen Davidovich, Omer Gilan
DOT1L and Menin are essential cofactors for the oncogenic activity of MLL fusion proteins (MLL-FPs) in leukaemia. However, the mechanisms underpinning the therapeutic effects of their inhibitors remain unclear. Here we identify a critical role for the non-canonical Polycomb repressive complex 1.1 (PRC1.1) in mediating the cellular responses to DOT1L and Menin inhibitors. Menin inhibition induces PRC1.1-dependent deposition of H2AK119ub to silence a subset of MLL-FP targets, whereas DOT1L inhibition results in a genome-wide increase in H2AK119ub. We show that enhanced PRC1.1 activity arises specifically from the progressive loss of DOT1L-mediated H3K79 methylation, independent of MLL-FP displacement or transcriptional repression. This regulatory crosstalk is conserved across cell types and is driven by direct biochemical antagonism between H3K79 methylation and PRC1 activity. Together, our findings establish DOT1L as a component of transcriptional memory co-opted in leukaemia and suggest it serves as the missing link balancing the opposing forces of the MLL–Polycomb axis. Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibitors in mixed-lineage leukaemia.
{"title":"DOT1L provides transcriptional memory through PRC1.1 antagonism","authors":"Daniel Neville, Daniel T. Ferguson, Emily B. Heikamp, Zhihao Lai, Graham W. Magor, Charlene Lam, Olivia G. Dobbs, Vita Levina, Kathy Knezevic, James J. The, Shania Alex, Stephen C. Suits, Bradon Rumler, Michael Uckelmann, Laure Talarmain, Enid Y. N. Lam, Andrew C. Perkins, Scott A. Armstrong, Charles C. Bell, Chen Davidovich, Omer Gilan","doi":"10.1038/s41556-025-01859-8","DOIUrl":"10.1038/s41556-025-01859-8","url":null,"abstract":"DOT1L and Menin are essential cofactors for the oncogenic activity of MLL fusion proteins (MLL-FPs) in leukaemia. However, the mechanisms underpinning the therapeutic effects of their inhibitors remain unclear. Here we identify a critical role for the non-canonical Polycomb repressive complex 1.1 (PRC1.1) in mediating the cellular responses to DOT1L and Menin inhibitors. Menin inhibition induces PRC1.1-dependent deposition of H2AK119ub to silence a subset of MLL-FP targets, whereas DOT1L inhibition results in a genome-wide increase in H2AK119ub. We show that enhanced PRC1.1 activity arises specifically from the progressive loss of DOT1L-mediated H3K79 methylation, independent of MLL-FP displacement or transcriptional repression. This regulatory crosstalk is conserved across cell types and is driven by direct biochemical antagonism between H3K79 methylation and PRC1 activity. Together, our findings establish DOT1L as a component of transcriptional memory co-opted in leukaemia and suggest it serves as the missing link balancing the opposing forces of the MLL–Polycomb axis. Neville, Ferguson et al. show that non-canonical Polycomb repressive complex 1.1-mediated gene silencing is antagonized by DOT1L and is required for the therapeutic efficacy of Menin and DOT1L inhibitors in mixed-lineage leukaemia.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"28 2","pages":"307-322"},"PeriodicalIF":19.1,"publicationDate":"2026-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.comhttps://www.nature.com/articles/s41556-025-01859-8.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146102115","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 : 2026-02-02DOI: 10.1038/s41556-025-01860-1
Eric K. F. Donahue, Nathaniel L. Hepowit, Elizabeth M. Ruark, Alexandra G. Mulligan, Brennen Keuchel, Nicholas D. Urban, Li Peng, Stedman Stephens, Derek J. Johnson, Natalie S. Wallace, Lauren P. Jackson, Mark H. Ellisman, Rafael Arrojo e Drigo, Andrew W. Folkmann, Matthias C. Truttmann, Jason A. MacGurn, Kristopher Burkewitz
The endoplasmic reticulum (ER) comprises an array of subdomains, each defined by a characteristic structure and function. Although altered ER processes are linked to age-onset pathogenesis, it is unclear whether shifts in ER structure or dynamics underlie these functional changes. Here we establish ER structural and functional remodelling as a conserved feature of ageing across yeast, Caenorhabditis elegans and mammals. Focusing on C. elegans as the exemplar of metazoan ageing, we reveal striking age-related reductions in ER volume across diverse tissues and a morphological shift from rough sheets to tubular ER. This morphological transition corresponds with large-scale shifts in ER proteome composition from protein synthesis to lipid metabolism, a phenomenon conserved in mammalian tissues. We show that Atg8 and ULK1-dependent ER-phagy drives age-associated ER remodelling through tissue-specific factors, including the previously uncharacterized ER-phagy regulator TMEM-131 and the IRE-1–XBP-1 branch of the unfolded protein response. Providing support for a model where ER remodelling is adaptive, diverse lifespan-extending paradigms downscale and remodel ER morphology throughout life. Furthermore, mTOR-dependent lifespan extension in yeast and worms requires ER-phagy, indicating that ER remodelling is a proactive and protective response during ageing. These results reveal ER-phagy and ER dynamics as pronounced, underappreciated mechanisms of both normal ageing and age-delaying interventions.
{"title":"ER remodelling is a feature of ageing and depends on ER-phagy","authors":"Eric K. F. Donahue, Nathaniel L. Hepowit, Elizabeth M. Ruark, Alexandra G. Mulligan, Brennen Keuchel, Nicholas D. Urban, Li Peng, Stedman Stephens, Derek J. Johnson, Natalie S. Wallace, Lauren P. Jackson, Mark H. Ellisman, Rafael Arrojo e Drigo, Andrew W. Folkmann, Matthias C. Truttmann, Jason A. MacGurn, Kristopher Burkewitz","doi":"10.1038/s41556-025-01860-1","DOIUrl":"https://doi.org/10.1038/s41556-025-01860-1","url":null,"abstract":"The endoplasmic reticulum (ER) comprises an array of subdomains, each defined by a characteristic structure and function. Although altered ER processes are linked to age-onset pathogenesis, it is unclear whether shifts in ER structure or dynamics underlie these functional changes. Here we establish ER structural and functional remodelling as a conserved feature of ageing across yeast, Caenorhabditis elegans and mammals. Focusing on C. elegans as the exemplar of metazoan ageing, we reveal striking age-related reductions in ER volume across diverse tissues and a morphological shift from rough sheets to tubular ER. This morphological transition corresponds with large-scale shifts in ER proteome composition from protein synthesis to lipid metabolism, a phenomenon conserved in mammalian tissues. We show that Atg8 and ULK1-dependent ER-phagy drives age-associated ER remodelling through tissue-specific factors, including the previously uncharacterized ER-phagy regulator TMEM-131 and the IRE-1–XBP-1 branch of the unfolded protein response. Providing support for a model where ER remodelling is adaptive, diverse lifespan-extending paradigms downscale and remodel ER morphology throughout life. Furthermore, mTOR-dependent lifespan extension in yeast and worms requires ER-phagy, indicating that ER remodelling is a proactive and protective response during ageing. These results reveal ER-phagy and ER dynamics as pronounced, underappreciated mechanisms of both normal ageing and age-delaying interventions.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"217 1","pages":""},"PeriodicalIF":21.3,"publicationDate":"2026-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146102116","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 : 2026-01-30DOI: 10.1038/s41556-025-01868-7
The transcription factor p53 enables phosphoethanolamine scavenging to support increased membrane phospholipid synthesis during senescence. Perturbing lipid synthesis or recycling compromises the fitness of senescent cells, with implications for targeting these cells in disease states.
{"title":"A p53-controlled lysosomal recycling circuit fuels phospholipid synthesis","authors":"","doi":"10.1038/s41556-025-01868-7","DOIUrl":"10.1038/s41556-025-01868-7","url":null,"abstract":"The transcription factor p53 enables phosphoethanolamine scavenging to support increased membrane phospholipid synthesis during senescence. Perturbing lipid synthesis or recycling compromises the fitness of senescent cells, with implications for targeting these cells in disease states.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"28 2","pages":"222-223"},"PeriodicalIF":19.1,"publicationDate":"2026-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146088993","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 : 2026-01-26DOI: 10.1038/s41556-025-01869-6
Massimiliano Stagi
A newly discovered acidic nanolayer that envelopes lysosomes reveals that proton gradients extend beyond the organelle lumen, identifying a nanoscale regulatory interface that links luminal pH, TMEM175-mediated proton efflux, organelle positioning and neurodegeneration.
Pub Date : 2026-01-23DOI: 10.1038/s41556-025-01858-9
Ali Can Savas, Sergei I. Grivennikov
Spatial organization of the tumour microenvironment is instrumental for tumour progression or sensitivity to therapies. A new study reveals that tumour-associated highly glycolytic SLC2A1+ macrophages create metabolic borders that limit cytotoxic T cells and immunotherapeutic responses in lung cancer, providing a ‘metabolic–spatial’ framework for overcoming resistance to checkpoint blockade.
{"title":"Metabolic borders shape immune resistance","authors":"Ali Can Savas, Sergei I. Grivennikov","doi":"10.1038/s41556-025-01858-9","DOIUrl":"10.1038/s41556-025-01858-9","url":null,"abstract":"Spatial organization of the tumour microenvironment is instrumental for tumour progression or sensitivity to therapies. A new study reveals that tumour-associated highly glycolytic SLC2A1+ macrophages create metabolic borders that limit cytotoxic T cells and immunotherapeutic responses in lung cancer, providing a ‘metabolic–spatial’ framework for overcoming resistance to checkpoint blockade.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"28 2","pages":"217-219"},"PeriodicalIF":19.1,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146041423","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 : 2026-01-23DOI: 10.1038/s41556-025-01866-9
Flavia Fontanesi
Damaged mitochondria must be removed to preserve organelle function, and a quality control pathway segregates damaged peripheral subdomains into small MTFP1-enriched mitochondria targeted for degradation. A study now identifies MISO as the key factor that promotes subdomain formation and links mitochondrial dynamics, quality control and mtDNA homeostasis.
{"title":"Mitochondrial quality control relies on MISO","authors":"Flavia Fontanesi","doi":"10.1038/s41556-025-01866-9","DOIUrl":"10.1038/s41556-025-01866-9","url":null,"abstract":"Damaged mitochondria must be removed to preserve organelle function, and a quality control pathway segregates damaged peripheral subdomains into small MTFP1-enriched mitochondria targeted for degradation. A study now identifies MISO as the key factor that promotes subdomain formation and links mitochondrial dynamics, quality control and mtDNA homeostasis.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"28 2","pages":"210-211"},"PeriodicalIF":19.1,"publicationDate":"2026-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146033863","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}
Lysosomes maintain a highly acidic lumen to regulate H+-dependent hydrolase-mediated degradation, but how protons are ‘leaked’ out to regulate organellar functions through cytosolic effectors remains unknown. Here we developed DNA nanodevices on the cytosolic leaflet of lysosomal membranes to monitor juxta-organellar pH in cells. Unexpectedly, we revealed a radiating acidic layer (up to 21 nm in thickness) on the outer surface of all lysosomes, typically 0.2–0.7 pH units more acidic than the neutral cytosol. This acidic nanolayer is established and maintained primarily by TMEM175, a lysosomal H+ efflux channel associated with Parkinson’s disease. Activation of TMEM175 causes opposite pH changes on both sides of lysosomes; however, it is the juxta-lysosomal, not the luminal, acidity that determines lysosome positioning in cells with dynein adaptor RILP acting as a juxta-lysosomal pH sensor. Hence, through inside-out proton conduits, lysosomes create a steady acidic surrounding that acts as a nano-interface for cytosolic machineries to regulate organellar activities. Tan and colleagues develop DNA nanodevices to detect the pH of the lysosomal outer surface, observing an acidic layer generated by TMEM175 that regulates lysosome positioning in response to changes in juxta-lysosomal pH.
{"title":"DNA nanodevices detect an acidic nanolayer on the lysosomal surface","authors":"Yutong Zhang, Meiqin Hu, Yaping Meng, Xin Wang, Fangqian Huang, Ping Li, Yuting Zhuo, Danzhen Chen, Zhimin Wang, Qiang Zhang, Hui Wu, Yao He, Yulin Du, Haoxing Xu, Liping Qiu, Weihong Tan","doi":"10.1038/s41556-025-01855-y","DOIUrl":"10.1038/s41556-025-01855-y","url":null,"abstract":"Lysosomes maintain a highly acidic lumen to regulate H+-dependent hydrolase-mediated degradation, but how protons are ‘leaked’ out to regulate organellar functions through cytosolic effectors remains unknown. Here we developed DNA nanodevices on the cytosolic leaflet of lysosomal membranes to monitor juxta-organellar pH in cells. Unexpectedly, we revealed a radiating acidic layer (up to 21 nm in thickness) on the outer surface of all lysosomes, typically 0.2–0.7 pH units more acidic than the neutral cytosol. This acidic nanolayer is established and maintained primarily by TMEM175, a lysosomal H+ efflux channel associated with Parkinson’s disease. Activation of TMEM175 causes opposite pH changes on both sides of lysosomes; however, it is the juxta-lysosomal, not the luminal, acidity that determines lysosome positioning in cells with dynein adaptor RILP acting as a juxta-lysosomal pH sensor. Hence, through inside-out proton conduits, lysosomes create a steady acidic surrounding that acts as a nano-interface for cytosolic machineries to regulate organellar activities. Tan and colleagues develop DNA nanodevices to detect the pH of the lysosomal outer surface, observing an acidic layer generated by TMEM175 that regulates lysosome positioning in response to changes in juxta-lysosomal pH.","PeriodicalId":18977,"journal":{"name":"Nature Cell Biology","volume":"28 2","pages":"285-295"},"PeriodicalIF":19.1,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146005981","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}
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