Laila M. Rad, Kevin R. Hughes, Sydney N. Wheeler, Joseph T. Decker, Sophia M. Orbach, Angelica Galvan, Jasmine Thornhill, Kate V. Griffin, Hamza Turkistani, Russell R. Urie, David N. Irani, Lonnie D. Shea, Aaron H. Morris
Primary progressive multiple sclerosis (MS) is a demyelinating autoimmune disease with only a single class of FDA-approved treatment, B cell depletion. Novel treatments could emerge from a deeper understanding of the interplay between multiple cell types within diseased tissue throughout progression. We initially describe an engineered biomaterial–based immunological niche (IN) as a surrogate for diseased tissue to investigate immune cell function and phenotype dynamics throughout a chronic progressive mouse model of MS. Using these niches, we identify an array of dysregulated CC chemokine signaling as potential targets. We then develop antigen-loaded nanoparticles that reduce CC chemokine signaling, while delivering antigen. These nanoparticles serve as an antigen-specific treatment, and a single injection reduces disease burden, even if administered after symptomatic disease onset. This report demonstrates proof of principle of a biomaterial scaffold as a diseased tissue surrogate that can monitor immune function, identify potential drug targets, and guide the development of a therapeutic.
{"title":"Engineered immunological niche directs therapeutic development in models of progressive multiple sclerosis","authors":"Laila M. Rad, Kevin R. Hughes, Sydney N. Wheeler, Joseph T. Decker, Sophia M. Orbach, Angelica Galvan, Jasmine Thornhill, Kate V. Griffin, Hamza Turkistani, Russell R. Urie, David N. Irani, Lonnie D. Shea, Aaron H. Morris","doi":"10.1073/pnas.2409852122","DOIUrl":"https://doi.org/10.1073/pnas.2409852122","url":null,"abstract":"Primary progressive multiple sclerosis (MS) is a demyelinating autoimmune disease with only a single class of FDA-approved treatment, B cell depletion. Novel treatments could emerge from a deeper understanding of the interplay between multiple cell types within diseased tissue throughout progression. We initially describe an engineered biomaterial–based immunological niche (IN) as a surrogate for diseased tissue to investigate immune cell function and phenotype dynamics throughout a chronic progressive mouse model of MS. Using these niches, we identify an array of dysregulated CC chemokine signaling as potential targets. We then develop antigen-loaded nanoparticles that reduce CC chemokine signaling, while delivering antigen. These nanoparticles serve as an antigen-specific treatment, and a single injection reduces disease burden, even if administered after symptomatic disease onset. This report demonstrates proof of principle of a biomaterial scaffold as a diseased tissue surrogate that can monitor immune function, identify potential drug targets, and guide the development of a therapeutic.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"10 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401514","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}
Bacteria frequently inhabit surface-attached communities where rich “social” interactions can significantly alter their population-level behavior, including their response to antibiotics. Understanding these collective effects in spatially heterogeneous communities is an ongoing challenge. Here, we investigated the spatial organization that emerges from antibiotic exposure in initially randomly distributed communities containing antibiotic-resistant and -sensitive strains of Enterococcus faecalis , an opportunistic pathogen. We identified that a range of complex spatial structures emerged in the population homeland—the inoculated region that microbes inhabit prior to range expansion—which depended on initial colony composition and antibiotic concentration. We found that these arrangements were explained by cooperative interactions between resistant and sensitive subpopulations with a variable spatial scale, the result of dynamic zones of protection afforded to sensitive cells by growing populations of enzyme-producing resistant neighbors. Using a combination of experiments and mathematical models, we explored the complex spatiotemporal interaction dynamics that create these patterns, and predicted spatial arrangements of sensitive and resistant subpopulations under new conditions. We illustrated how spatial population dynamics in the homeland affect subsequent range expansion, both because they modulate the composition of the initial expanding front, and through long-range cooperation between the homeland and the expanding region. Finally, we showed that these spatial constraints resulted in populations whose size and composition differed markedly from matched populations in well-stirred (planktonic) cultures. These findings underscore the importance of spatial structure and cooperation, long-studied features in theoretical ecology, for determining the fate of bacterial communities under antibiotic exposure.
{"title":"Spatial population dynamics of bacterial colonies with social antibiotic resistance","authors":"Marlis K. Denk-Lobnig, Kevin B. Wood","doi":"10.1073/pnas.2417065122","DOIUrl":"https://doi.org/10.1073/pnas.2417065122","url":null,"abstract":"Bacteria frequently inhabit surface-attached communities where rich “social” interactions can significantly alter their population-level behavior, including their response to antibiotics. Understanding these collective effects in spatially heterogeneous communities is an ongoing challenge. Here, we investigated the spatial organization that emerges from antibiotic exposure in initially randomly distributed communities containing antibiotic-resistant and -sensitive strains of <jats:italic>Enterococcus faecalis</jats:italic> , an opportunistic pathogen. We identified that a range of complex spatial structures emerged in the population homeland—the inoculated region that microbes inhabit prior to range expansion—which depended on initial colony composition and antibiotic concentration. We found that these arrangements were explained by cooperative interactions between resistant and sensitive subpopulations with a variable spatial scale, the result of dynamic zones of protection afforded to sensitive cells by growing populations of enzyme-producing resistant neighbors. Using a combination of experiments and mathematical models, we explored the complex spatiotemporal interaction dynamics that create these patterns, and predicted spatial arrangements of sensitive and resistant subpopulations under new conditions. We illustrated how spatial population dynamics in the homeland affect subsequent range expansion, both because they modulate the composition of the initial expanding front, and through long-range cooperation between the homeland and the expanding region. Finally, we showed that these spatial constraints resulted in populations whose size and composition differed markedly from matched populations in well-stirred (planktonic) cultures. These findings underscore the importance of spatial structure and cooperation, long-studied features in theoretical ecology, for determining the fate of bacterial communities under antibiotic exposure.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"61 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401552","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}
Lauren N. Rust, Jochen M. Wettengel, Sreya Biswas, Junghyun Ryu, Nadine Piekarski, Sofiya Yusova, Savannah S. Lutz, Spandana Naldiga, Brayden J. Hinrichs, Michelle N. Sullivan, Jamie O. Lo, Ulrike Protzer, Jeremy V. Smedley, Jonah B. Sacha, Carol B. Hanna, Benjamin N. Bimber, Jon D. Hennebold, Benjamin J. Burwitz
Hepatitis B virus (HBV) poses a significant global health challenge, necessitating the urgent development of curative therapeutics. However, this progress is impeded by the lack of robust, immunocompetent preclinical animal models due to HBV’s strict species specificity. We previously showed that vector-mediated expression of the HBV entry receptor, human sodium-taurocholate cotransporting polypeptide (hNTCP), renders macaques fully susceptible to HBV infection. In this study, we have generated transgenic macaques expressing hNTCP, marking the creation of the first transgenic nonhuman primate model for infectious disease research. We used PiggyBac (PB) transposon technology to insert a liver-specific hNTCP expression cassette into rhesus macaque zygotes and transferred the resulting embryos into surrogate females, resulting in two healthy transgenic offspring. In both animals, hNTCP is highly and selectively expressed in the liver. Most importantly, we show that isolated hepatocytes from these monkeys are susceptible to HBV infection. These findings lay the foundation for the development of a nonhuman primate HBV model, facilitating the advancement and validation of curative HBV therapies.
{"title":"Liver-specific transgenic expression of human NTCP in rhesus macaques confers HBV susceptibility on primary hepatocytes","authors":"Lauren N. Rust, Jochen M. Wettengel, Sreya Biswas, Junghyun Ryu, Nadine Piekarski, Sofiya Yusova, Savannah S. Lutz, Spandana Naldiga, Brayden J. Hinrichs, Michelle N. Sullivan, Jamie O. Lo, Ulrike Protzer, Jeremy V. Smedley, Jonah B. Sacha, Carol B. Hanna, Benjamin N. Bimber, Jon D. Hennebold, Benjamin J. Burwitz","doi":"10.1073/pnas.2413771122","DOIUrl":"https://doi.org/10.1073/pnas.2413771122","url":null,"abstract":"Hepatitis B virus (HBV) poses a significant global health challenge, necessitating the urgent development of curative therapeutics. However, this progress is impeded by the lack of robust, immunocompetent preclinical animal models due to HBV’s strict species specificity. We previously showed that vector-mediated expression of the HBV entry receptor, human sodium-taurocholate cotransporting polypeptide (hNTCP), renders macaques fully susceptible to HBV infection. In this study, we have generated transgenic macaques expressing hNTCP, marking the creation of the first transgenic nonhuman primate model for infectious disease research. We used PiggyBac (PB) transposon technology to insert a liver-specific hNTCP expression cassette into rhesus macaque zygotes and transferred the resulting embryos into surrogate females, resulting in two healthy transgenic offspring. In both animals, hNTCP is highly and selectively expressed in the liver. Most importantly, we show that isolated hepatocytes from these monkeys are susceptible to HBV infection. These findings lay the foundation for the development of a nonhuman primate HBV model, facilitating the advancement and validation of curative HBV therapies.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"21 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401473","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}
Entao Zhang, Yang Wang, Thomas W. Crowther, Weicheng Sun, Shiping Chen, Daowei Zhou, Zhouping Shangguan, Jianhui Huang, Jin-Sheng He, Yanfen Wang, Jiandong Sheng, Lisong Tang, Xinrong Li, Ming Dong, Yan Wu, Shuijin Hu, Yongfei Bai, Guirui Yu
Experimental studies have shown that symbiotic relationships between arbuscular mycorrhizal (AM) fungi and host plants can regulate soil organic carbon (SOC) storage. Although the impacts of mycorrhiza are highly context-dependent, it remains unclear how these effects vary across broad spatial scales. Based on data from 2296 field sites across grassland ecosystems of China, here we show that mycorrhizal fungi symbiosis enhances SOC storage in the topsoil and subsoil through increasing plant diversity and elevating biomass allocation to belowground. SOC storage is significantly higher in both the topsoil and subsoil in systems dominated by obligate mycorrhizal (OM) and facultative mycorrhizal (FM) plants than those dominated by nonmycorrhizal (NM) plants. Also, the relative abundance of OM plants increases at the expense of FM plants as temperature and precipitation increase. These findings provide valuable insights into the potential mechanisms by which mycorrhizal fungi may influence grassland plant diversity and SOC storage in the context of global change.
{"title":"Mycorrhiza increases plant diversity and soil carbon storage in grasslands","authors":"Entao Zhang, Yang Wang, Thomas W. Crowther, Weicheng Sun, Shiping Chen, Daowei Zhou, Zhouping Shangguan, Jianhui Huang, Jin-Sheng He, Yanfen Wang, Jiandong Sheng, Lisong Tang, Xinrong Li, Ming Dong, Yan Wu, Shuijin Hu, Yongfei Bai, Guirui Yu","doi":"10.1073/pnas.2412556122","DOIUrl":"https://doi.org/10.1073/pnas.2412556122","url":null,"abstract":"Experimental studies have shown that symbiotic relationships between arbuscular mycorrhizal (AM) fungi and host plants can regulate soil organic carbon (SOC) storage. Although the impacts of mycorrhiza are highly context-dependent, it remains unclear how these effects vary across broad spatial scales. Based on data from 2296 field sites across grassland ecosystems of China, here we show that mycorrhizal fungi symbiosis enhances SOC storage in the topsoil and subsoil through increasing plant diversity and elevating biomass allocation to belowground. SOC storage is significantly higher in both the topsoil and subsoil in systems dominated by obligate mycorrhizal (OM) and facultative mycorrhizal (FM) plants than those dominated by nonmycorrhizal (NM) plants. Also, the relative abundance of OM plants increases at the expense of FM plants as temperature and precipitation increase. These findings provide valuable insights into the potential mechanisms by which mycorrhizal fungi may influence grassland plant diversity and SOC storage in the context of global change.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"16 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401477","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}
Nitesh Kumar Khandelwal, Meghna Gupta, Paras Kumar, Sree Ganesh Balasubramani, Ignacia Echeverria, Robert M. Stroud
Urate provides ~50% of the reducing potential in human and primate plasma which is key to detoxifying reactive oxygen by-products of cellular metabolism. Urate is the endpoint of purine metabolism in primates, and its concentration in plasma is a balance between excretion from kidney and intestine, and subsequent reabsorption in and through cells of kidney proximal tubules to maintain a regulated concentration in plasma. SLC2A9 is the primary transporter that returns urate from the basolateral side of kidney tubule cells back to plasma. A shorter splice variant of SLC2A9 is directed to the apical surface where several transporters recapture urate from the tubule back into cells. Too high a concentration in plasma causes hyperuricemia, is linked to gout, and favors kidney stone formation. To understand the molecular basis of uric acid transport and the role of disease-causing mutations in SLC2A9, we determined structures of human SLC2A9 in its apo form, and its urate-bound form by cryo-EM, at resolution of 3.3 Å and 4.1 Å respectively. Both structures are captured in an inward open conformation. Using the inward-facing structure as a template we modeled the outward-facing conformation to understand the alternating access mechanism. Alternative salt bridge pairs on the cytoplasmic side suggest a mechanism that can balance the energetics of the inward open and outward open states. The location of disease-causing mutants suggests their role in impacting function. Our structures elucidate the molecular basis for urate selectivity and transport and provide a platform for future structure-based drug discovery aimed at reducing plasma urate levels in diseases of hyperuricemia and gout.
{"title":"Structural basis of disease mutation and substrate recognition by the human SLC2A9 transporter","authors":"Nitesh Kumar Khandelwal, Meghna Gupta, Paras Kumar, Sree Ganesh Balasubramani, Ignacia Echeverria, Robert M. Stroud","doi":"10.1073/pnas.2418282122","DOIUrl":"https://doi.org/10.1073/pnas.2418282122","url":null,"abstract":"Urate provides ~50% of the reducing potential in human and primate plasma which is key to detoxifying reactive oxygen by-products of cellular metabolism. Urate is the endpoint of purine metabolism in primates, and its concentration in plasma is a balance between excretion from kidney and intestine, and subsequent reabsorption in and through cells of kidney proximal tubules to maintain a regulated concentration in plasma. SLC2A9 is the primary transporter that returns urate from the basolateral side of kidney tubule cells back to plasma. A shorter splice variant of SLC2A9 is directed to the apical surface where several transporters recapture urate from the tubule back into cells. Too high a concentration in plasma causes hyperuricemia, is linked to gout, and favors kidney stone formation. To understand the molecular basis of uric acid transport and the role of disease-causing mutations in SLC2A9, we determined structures of human SLC2A9 in its apo form, and its urate-bound form by cryo-EM, at resolution of 3.3 Å and 4.1 Å respectively. Both structures are captured in an inward open conformation. Using the inward-facing structure as a template we modeled the outward-facing conformation to understand the alternating access mechanism. Alternative salt bridge pairs on the cytoplasmic side suggest a mechanism that can balance the energetics of the inward open and outward open states. The location of disease-causing mutants suggests their role in impacting function. Our structures elucidate the molecular basis for urate selectivity and transport and provide a platform for future structure-based drug discovery aimed at reducing plasma urate levels in diseases of hyperuricemia and gout.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"8 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401827","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}
Ons Kharrat, Yoshiki Yamaryo-Botté, Rouba Nasreddine, Sébastien Voisin, Thomas Aumer, Bruno P. A. Cammue, Jean-Baptiste Madinier, Thomas Knobloch, Karin Thevissen, Reine Nehmé, Vincent Aucagne, Cyrille Botté, Philippe Bulet, Céline Landon
Fungal infections represent a significant global health concern, with a growing prevalence of antifungal drug resistance. Targeting glucosylceramides (GlcCer), which are functionally important glycosphingolipids (GSL) present in fungal membranes, represents a promising strategy for the development of antifungal drugs. GlcCer are associated with the antifungal activity of certain plant and insect defensins. The 44-residue ETD151 peptide, optimized from butterfly defensins, is active against several fungal pathogens. ETD151 has been shown to induce a multifaceted mechanism of action (MOA) in Botrytis cinerea , a multiresistant phytopathogenic fungus. However, the target has yet to be identified. Our findings demonstrate that the presence of GlcCer in membranes determines the susceptibility of Pichia pastoris and Candida albicans toward ETD151. To ascertain whether this is due to direct molecular recognition, we demonstrate that ETD151 selectively recognizes liposomes containing GlcCer from B. cinerea , which reveals a methylated-sphingoid base structure. The dissociation constant was estimated by microscale thermophoresis to be in the µM range. Finally, fluorescence microscopy revealed that ETD151 localizes preferentially at the surface of B. cinerea . Furthermore, the majority of prokaryotic cells do not contain GSL, which explains their resistance to ETD151. We investigated the susceptibility of Novosphingobium capsulatum , one of the rare GSL-containing bacteria, to ETD151. ETD151 demonstrated transient morphological changes and inhibitory growth activity (IC 50 ~75 µM) with an affinity for the cell surface, emphasizing the critical importance of GSL as target. Understanding the MOA of ETD151 could pave the way for new perspectives in human health and crop protection.
{"title":"The antimicrobial activity of ETD151 defensin is dictated by the presence of glycosphingolipids in the targeted organisms","authors":"Ons Kharrat, Yoshiki Yamaryo-Botté, Rouba Nasreddine, Sébastien Voisin, Thomas Aumer, Bruno P. A. Cammue, Jean-Baptiste Madinier, Thomas Knobloch, Karin Thevissen, Reine Nehmé, Vincent Aucagne, Cyrille Botté, Philippe Bulet, Céline Landon","doi":"10.1073/pnas.2415524122","DOIUrl":"https://doi.org/10.1073/pnas.2415524122","url":null,"abstract":"Fungal infections represent a significant global health concern, with a growing prevalence of antifungal drug resistance. Targeting glucosylceramides (GlcCer), which are functionally important glycosphingolipids (GSL) present in fungal membranes, represents a promising strategy for the development of antifungal drugs. GlcCer are associated with the antifungal activity of certain plant and insect defensins. The 44-residue ETD151 peptide, optimized from butterfly defensins, is active against several fungal pathogens. ETD151 has been shown to induce a multifaceted mechanism of action (MOA) in <jats:italic>Botrytis cinerea</jats:italic> , a multiresistant phytopathogenic fungus. However, the target has yet to be identified. Our findings demonstrate that the presence of GlcCer in membranes determines the susceptibility of <jats:italic>Pichia pastoris</jats:italic> and <jats:italic>Candida albicans</jats:italic> toward ETD151. To ascertain whether this is due to direct molecular recognition, we demonstrate that ETD151 selectively recognizes liposomes containing GlcCer from <jats:italic>B. cinerea</jats:italic> , which reveals a methylated-sphingoid base structure. The dissociation constant was estimated by microscale thermophoresis to be in the µM range. Finally, fluorescence microscopy revealed that ETD151 localizes preferentially at the surface of <jats:italic>B. cinerea</jats:italic> . Furthermore, the majority of prokaryotic cells do not contain GSL, which explains their resistance to ETD151. We investigated the susceptibility of <jats:italic>Novosphingobium capsulatum</jats:italic> , one of the rare GSL-containing bacteria, to ETD151. ETD151 demonstrated transient morphological changes and inhibitory growth activity (IC <jats:sub>50</jats:sub> ~75 µM) with an affinity for the cell surface, emphasizing the critical importance of GSL as target. Understanding the MOA of ETD151 could pave the way for new perspectives in human health and crop protection.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"9 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401474","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}
Lien Nguyen, Ramadan Ajredini, Shu Guo, Lisa E. L. Romano, Rodrigo F. Tomas, Logan R. Bell, Paul T. Ranum, Tao Zu, Monica Bañez Coronel, Chase P. Kelley, Javier Redding-Ochoa, Evangelos Nizamis, Alexandra Melloni, Theresa R. Connors, Angelica Gaona, Kiruphagaran Thangaraju, Olga Pletnikova, H. Brent Clark, Beverly L. Davidson, Anthony T. Yachnis, Todd E. Golde, XiangYang Lou, Eric T. Wang, Alan E. Renton, Alison Goate, Paul N. Valdmanis, Stefan Prokop, Juan C. Troncoso, Bradley T. Hyman, Laura P. W. Ranum
Alzheimer’s disease (AD) affects more than 10% of the population ≥65 y of age, but the underlying biological risks of most AD cases are unclear. We show anti-poly-glycine-arginine (a-polyGR) positive aggregates frequently accumulate in sporadic AD autopsy brains (45/80 cases). We hypothesize that these aggregates are caused by one or more polyGR-encoding repeat expansion mutations. We developed a CRISPR/deactivated-Cas9 enrichment strategy to identify candidate GR-encoding repeat expansion mutations directly from genomic DNA isolated from a-polyGR(+) AD cases. Using this approach, we isolated an interrupted (GGGAGA) n intronic expansion within a SINE-VNTR-Alu element in CASP8 ( CASP8 -GGGAGA EXP ). Immunostaining using a-polyGR and locus-specific C-terminal antibodies demonstrate that the CASP8 -GGGAGA EXP expresses hybrid poly(GR)n(GE)n(RE)n proteins that accumulate in CASP8 -GGGAGA EXP (+) AD brains. In cells, expression of CASP8 -GGGAGA EXP minigenes leads to increased p-Tau (Ser202/Thr205) levels. Consistent with other types of repeat-associated non-AUG (RAN) proteins, poly(GR)n(GE)n(RE)n protein levels are increased by stress. Additionally, levels of these stress-induced proteins are reduced by metformin. Association studies show specific aggregate promoting interrupted CASP8 -GGGAGA EXP sequence variants found in ~3.6% of controls and 7.5% AD cases increase AD risk [ CASP8 -GGGAGA-AD-R1; OR 2.2, 95% CI (1.5185 to 3.1896), P = 3.1 × 10 −5 ]. Cells transfected with a high-risk CASP8 -GGGAGA-AD-R1 variant show increased toxicity and increased levels of poly(GR)n(GE)n(RE)n aggregates. Taken together, these data identify polyGR(+) aggregates as a frequent and unexpected type of brain pathology in AD and CASP8 -GGGAGA-AD-R1 alleles as a relatively common AD risk factor. Taken together, these data support a model in which CASP8 -GGGAGA EXP alleles combined with stress increase AD risk.
{"title":"CASP8 intronic expansion identified by poly-glycine-arginine pathology increases Alzheimer’s disease risk","authors":"Lien Nguyen, Ramadan Ajredini, Shu Guo, Lisa E. L. Romano, Rodrigo F. Tomas, Logan R. Bell, Paul T. Ranum, Tao Zu, Monica Bañez Coronel, Chase P. Kelley, Javier Redding-Ochoa, Evangelos Nizamis, Alexandra Melloni, Theresa R. Connors, Angelica Gaona, Kiruphagaran Thangaraju, Olga Pletnikova, H. Brent Clark, Beverly L. Davidson, Anthony T. Yachnis, Todd E. Golde, XiangYang Lou, Eric T. Wang, Alan E. Renton, Alison Goate, Paul N. Valdmanis, Stefan Prokop, Juan C. Troncoso, Bradley T. Hyman, Laura P. W. Ranum","doi":"10.1073/pnas.2416885122","DOIUrl":"https://doi.org/10.1073/pnas.2416885122","url":null,"abstract":"Alzheimer’s disease (AD) affects more than 10% of the population ≥65 y of age, but the underlying biological risks of most AD cases are unclear. We show anti-poly-glycine-arginine (a-polyGR) positive aggregates frequently accumulate in sporadic AD autopsy brains (45/80 cases). We hypothesize that these aggregates are caused by one or more polyGR-encoding repeat expansion mutations. We developed a CRISPR/deactivated-Cas9 enrichment strategy to identify candidate GR-encoding repeat expansion mutations directly from genomic DNA isolated from a-polyGR(+) AD cases. Using this approach, we isolated an interrupted (GGGAGA) <jats:sub>n</jats:sub> intronic expansion within a SINE-VNTR-Alu element in <jats:italic>CASP8</jats:italic> ( <jats:italic>CASP8</jats:italic> -GGGAGA <jats:sup>EXP</jats:sup> ). Immunostaining using a-polyGR and locus-specific C-terminal antibodies demonstrate that the <jats:italic>CASP8</jats:italic> -GGGAGA <jats:sup>EXP</jats:sup> expresses hybrid poly(GR)n(GE)n(RE)n proteins that accumulate in <jats:italic>CASP8</jats:italic> -GGGAGA <jats:sup>EXP</jats:sup> (+) AD brains. In cells, expression of <jats:italic>CASP8</jats:italic> -GGGAGA <jats:sup>EXP</jats:sup> minigenes leads to increased p-Tau (Ser202/Thr205) levels. Consistent with other types of repeat-associated non-AUG (RAN) proteins, poly(GR)n(GE)n(RE)n protein levels are increased by stress. Additionally, levels of these stress-induced proteins are reduced by metformin. Association studies show specific aggregate promoting interrupted <jats:italic>CASP8</jats:italic> -GGGAGA <jats:sup>EXP</jats:sup> sequence variants found in ~3.6% of controls and 7.5% AD cases increase AD risk [ <jats:italic>CASP8</jats:italic> -GGGAGA-AD-R1; OR 2.2, 95% CI (1.5185 to 3.1896), <jats:italic>P</jats:italic> = 3.1 × 10 <jats:sup>−5</jats:sup> ]. Cells transfected with a high-risk <jats:italic>CASP8</jats:italic> -GGGAGA-AD-R1 variant show increased toxicity and increased levels of poly(GR)n(GE)n(RE)n aggregates. Taken together, these data identify polyGR(+) aggregates as a frequent and unexpected type of brain pathology in AD and <jats:italic>CASP8</jats:italic> -GGGAGA-AD-R1 alleles as a relatively common AD risk factor. Taken together, these data support a model in which <jats:italic>CASP8</jats:italic> -GGGAGA <jats:sup>EXP</jats:sup> alleles combined with stress increase AD risk.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"45 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401478","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}
Richard A. Boyle, Edmund R. R. Moody, Gunnar Babcock, Daniel W. McShea, Sandra Álvarez-Carretero, Timothy M. Lenton, Philip C. J. Donoghue
The average long-term impact of Darwinian evolution on Earth’s habitability remains extremely uncertain. Recent attempts to reconcile this uncertainty by “Darwinizing” nonreplicating biogeochemical processes subject to persistence-based selection conform with the historicity of the geochemical record but lack mechanistic clarity. Here, we present a theoretical framework showing how: 1) A biogeochemical “cycle-biota-variant” (CBV) can be defined non-arbitrarily as one biologically facilitated pathway for net recycling of an essential element, plus the genotypes driving the relevant interconversion reactions. 2) Distinct CBVs can be individuated if they have climatic or geochemical side effects that feed-back on relative persistence. 3) The separation of spatial/temporal scales between the dynamics of such effects and those of conventional Darwinian evolution can introduce a degree of randomness into the relationship between CBVs and their Earth system impact properties, loosely analogous to that between the biochemical causes and evolutionary effects of genetic mutation. 4) Threshold behavior in climate feedback can accentuate biotic impacts and lead to CBV-level “competitive exclusion”. 5) CBV-level persistence selection is observationally distinguishable from genotype-level selection by strong covariance between “internal” CBV properties (genotypes and reactions) and “external” climatic effects, which we argue is analogous to the covariance between fitness and traits under conventional Darwinian selection. These factors cannot circumvent the basic fact that local natural selection will often favor phenotypes that ultimately destabilize large-scale geochemical/climatic properties. However, we claim that our results nevertheless demonstrate the theoretical coherence of persistence-selection between non-replicating life–environment interaction patterns and therefore have broad biogeochemical applicability.
{"title":"Persistence selection between simulated biogeochemical cycle variants for their distinct effects on the Earth system","authors":"Richard A. Boyle, Edmund R. R. Moody, Gunnar Babcock, Daniel W. McShea, Sandra Álvarez-Carretero, Timothy M. Lenton, Philip C. J. Donoghue","doi":"10.1073/pnas.2406344122","DOIUrl":"https://doi.org/10.1073/pnas.2406344122","url":null,"abstract":"The average long-term impact of Darwinian evolution on Earth’s habitability remains extremely uncertain. Recent attempts to reconcile this uncertainty by “Darwinizing” nonreplicating biogeochemical processes subject to persistence-based selection conform with the historicity of the geochemical record but lack mechanistic clarity. Here, we present a theoretical framework showing how: 1) A biogeochemical “cycle-biota-variant” (CBV) can be defined non-arbitrarily as one biologically facilitated pathway for net recycling of an essential element, plus the genotypes driving the relevant interconversion reactions. 2) Distinct CBVs can be individuated if they have climatic or geochemical side effects that feed-back on relative persistence. 3) The separation of spatial/temporal scales between the dynamics of such effects and those of conventional Darwinian evolution can introduce a degree of randomness into the relationship between CBVs and their Earth system impact properties, loosely analogous to that between the biochemical causes and evolutionary effects of genetic mutation. 4) Threshold behavior in climate feedback can accentuate biotic impacts and lead to CBV-level “competitive exclusion”. 5) CBV-level persistence selection is observationally distinguishable from genotype-level selection by strong covariance between “internal” CBV properties (genotypes and reactions) and “external” climatic effects, which we argue is analogous to the covariance between fitness and traits under conventional Darwinian selection. These factors cannot circumvent the basic fact that local natural selection will often favor phenotypes that ultimately destabilize large-scale geochemical/climatic properties. However, we claim that our results nevertheless demonstrate the theoretical coherence of persistence-selection between non-replicating life–environment interaction patterns and therefore have broad biogeochemical applicability.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"61 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401470","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}
Elena Quintero, Blanca Arroyo-Correa, Jorge Isla, Francisco Rodríguez-Sánchez, Pedro Jordano
Species-level networks emerge as the combination of interactions spanning multiple individuals, and their study has received considerable attention over the past 30 y. However, less is known about the structure of interaction configurations within species, even though individuals are the actual interacting units in nature. We compiled 46 empirical, individual-based, interaction networks on plant-animal seed dispersal mutualisms, comprising 1,037 plant individuals across 29 species from various regions. We compared the structure of individual-based networks to that of species-based networks and, by extending the niche concept to interaction assemblages, we explored individual plant specialization. Using a Bayesian framework to account for uncertainty derived from sampling, we examined how plant individuals “explore” the interaction niche of their populations. Both individual-based and species-based networks exhibited high variability in network properties, lacking remarkable structural and topological differences between them. Within populations, frugivores’ interaction allocation among plant individuals was highly heterogeneous, with one to three frugivore species dominating interactions. Regardless of species or bioregion, plant individuals displayed a variety of interaction profiles across populations, with a consistently-small percentage of individuals playing a central role and exhibiting high diversity in their interaction assemblage. Plant populations showed variable mid to low levels of niche specialization; and individuals’ interaction niche “breadth” accounted for 70% of the population interaction diversity, on average. Our results highlight how downscaling from species to individual-based networks helps understanding the structuring of interactions within ecological communities and provide an empirical basis for the extension of niche theory to complex mutualistic networks.
{"title":"Downscaling mutualistic networks from species to individuals reveals consistent interaction niches and roles within plant populations","authors":"Elena Quintero, Blanca Arroyo-Correa, Jorge Isla, Francisco Rodríguez-Sánchez, Pedro Jordano","doi":"10.1073/pnas.2402342122","DOIUrl":"https://doi.org/10.1073/pnas.2402342122","url":null,"abstract":"Species-level networks emerge as the combination of interactions spanning multiple individuals, and their study has received considerable attention over the past 30 y. However, less is known about the structure of interaction configurations within species, even though individuals are the actual interacting units in nature. We compiled 46 empirical, individual-based, interaction networks on plant-animal seed dispersal mutualisms, comprising 1,037 plant individuals across 29 species from various regions. We compared the structure of individual-based networks to that of species-based networks and, by extending the niche concept to interaction assemblages, we explored individual plant specialization. Using a Bayesian framework to account for uncertainty derived from sampling, we examined how plant individuals “explore” the interaction niche of their populations. Both individual-based and species-based networks exhibited high variability in network properties, lacking remarkable structural and topological differences between them. Within populations, frugivores’ interaction allocation among plant individuals was highly heterogeneous, with one to three frugivore species dominating interactions. Regardless of species or bioregion, plant individuals displayed a variety of interaction profiles across populations, with a consistently-small percentage of individuals playing a central role and exhibiting high diversity in their interaction assemblage. Plant populations showed variable mid to low levels of niche specialization; and individuals’ interaction niche “breadth” accounted for 70% of the population interaction diversity, on average. Our results highlight how downscaling from species to individual-based networks helps understanding the structuring of interactions within ecological communities and provide an empirical basis for the extension of niche theory to complex mutualistic networks.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"78 3 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401476","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}
Jingruo Zhang, Francisca M. Acosta, Xuewei Wang, Dezhi Zhao, Lidan Zhang, Rui Hua, Qianjin Guo, Leilei Zhong, Ling Qin, Manuel A. Riquelme, Jean X. Jiang
Bone is a dynamic organ constantly undergoing remodeling with both bone formation and resorption. Bone formation is mediated by osteoblasts originating from the differentiation of bone marrow (BM) mesenchymal stem and progenitor cells (BM-MSPCs). However, how bone cells communicate with BM-MSPCs to coordinate bone formation remains largely elusive. Here, we unveil a key role of osteocyte connexin 43 (Cx43) hemichannels in regulating the lineage commitment of BM-MSPCs. Two transgenic mouse models expressing dominant negative Cx43 mutants in osteocytes were used: R76W (inhibiting gap junctions) and Δ130 to 136 (inhibiting both hemichannels and gap junctions). BM-MSPCs from Δ130 to 136 mice showed enhanced adipogenic differentiation and reduced osteogenic potential, leading to increased BM adipocytes. Flow cytometry and single-cell RNA sequencing revealed shifts in BM-MSPC subsets, less osteogenic-biased MSPCs, and more adipogenic-biased MSPCs in Δ130 to 136 mice. Conversely, R76W, with more functional hemichannels, exhibited effects similar to WT mice or even greater opposite effects than Δ130 to 136 mice. Prostaglandin E 2 (PGE 2 ), released from active Cx43 hemichannels, inhibited adipogenesis and promoted osteogenesis via the PGE 2 receptor EP4 and ERK1/2 signaling. Inhibition of Cx43 hemichannels or EP4 led to increased adipogenic-biased MSPCs. Moreover, administration of a Cx43(M1) antibody, which inhibits hemichannels, substantially increased BM adipocytes, accompanied by increased adipogenic-biased MSPCs, and decreased osteogenic-biased MSPCs. Our study highlights the pivotal role of osteocyte Cx43 hemichannels in BM-MSPC fate decision through PGE 2 release, providing insights into the precise and highly regulated communication between matrix-bound bone cells and BM-MSPCs, which dictates bone formation and remodeling.
{"title":"Osteocyte connexin hemichannels and prostaglandin E 2 release dictate bone marrow mesenchymal stromal cell commitment","authors":"Jingruo Zhang, Francisca M. Acosta, Xuewei Wang, Dezhi Zhao, Lidan Zhang, Rui Hua, Qianjin Guo, Leilei Zhong, Ling Qin, Manuel A. Riquelme, Jean X. Jiang","doi":"10.1073/pnas.2412144122","DOIUrl":"https://doi.org/10.1073/pnas.2412144122","url":null,"abstract":"Bone is a dynamic organ constantly undergoing remodeling with both bone formation and resorption. Bone formation is mediated by osteoblasts originating from the differentiation of bone marrow (BM) mesenchymal stem and progenitor cells (BM-MSPCs). However, how bone cells communicate with BM-MSPCs to coordinate bone formation remains largely elusive. Here, we unveil a key role of osteocyte connexin 43 (Cx43) hemichannels in regulating the lineage commitment of BM-MSPCs. Two transgenic mouse models expressing dominant negative Cx43 mutants in osteocytes were used: R76W (inhibiting gap junctions) and Δ130 to 136 (inhibiting both hemichannels and gap junctions). BM-MSPCs from Δ130 to 136 mice showed enhanced adipogenic differentiation and reduced osteogenic potential, leading to increased BM adipocytes. Flow cytometry and single-cell RNA sequencing revealed shifts in BM-MSPC subsets, less osteogenic-biased MSPCs, and more adipogenic-biased MSPCs in Δ130 to 136 mice. Conversely, R76W, with more functional hemichannels, exhibited effects similar to WT mice or even greater opposite effects than Δ130 to 136 mice. Prostaglandin E <jats:sub>2</jats:sub> (PGE <jats:sub>2</jats:sub> ), released from active Cx43 hemichannels, inhibited adipogenesis and promoted osteogenesis via the PGE <jats:sub>2</jats:sub> receptor EP4 and ERK1/2 signaling. Inhibition of Cx43 hemichannels or EP4 led to increased adipogenic-biased MSPCs. Moreover, administration of a Cx43(M1) antibody, which inhibits hemichannels, substantially increased BM adipocytes, accompanied by increased adipogenic-biased MSPCs, and decreased osteogenic-biased MSPCs. Our study highlights the pivotal role of osteocyte Cx43 hemichannels in BM-MSPC fate decision through PGE <jats:sub>2</jats:sub> release, providing insights into the precise and highly regulated communication between matrix-bound bone cells and BM-MSPCs, which dictates bone formation and remodeling.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"1 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143401828","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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