Proceedings of the National Academy of Sciences of the United States of America最新文献

{"title":"The kinesin KIF3AC recycles endocytosed integrin to polarize new adhesion formation toward the leading edge.","authors":"Johnny A Z Rockenbach, Guilherme P F Nader, Susumu Antoku, Gregg G Gundersen","doi":"10.1073/pnas.2513776122","DOIUrl":"10.1073/pnas.2513776122","url":null,"abstract":"<p><p>The recycling of integrin endocytosed during focal adhesion (FA) disassembly is critical for cell migration and contributes to the polarized formation of new FAs toward the leading edge. How this occurs is unclear. Here, we sought to identify the kinesin motor protein(s) that is involved in recycling endocytosed integrin back to the plasma membrane. We show that the kinesin-2 heterodimer, KIF3AC, and the Rab11 adaptor protein Rab coupling protein (RCP) are required for FA reformation after the disassembly of FAs in mouse and human fibroblasts. In the absence of KIF3AC, integrin does not return to the cell surface after FA disassembly and is found in the Rab11 endocytic recycling compartment. Biochemical pulldowns revealed that KIF3C associated with β1 integrin in an RCP-dependent fashion, but only after FA disassembly. KIF3AC knockdown inhibited cell migration, trafficking of RCP toward the leading edge, and polarized formation of FAs at the leading edge. These results show that KIF3AC promotes cell migration by recycling integrin so that it generates new FAs in a polarized fashion.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2513776122"},"PeriodicalIF":9.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699278","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}

{"title":"Integrating spatial omics and single-cell mass spectrometry imaging reveals tumor–host metabolic interplay in hepatocellular carcinoma","authors":"Panpan Chen, Haoyuan Geng, Bangzhen Ma, Yaqi Zhang, Zihan Zhu, Min Li, Shiping Chen, Xiao Wang, Chenglong Sun","doi":"10.1073/pnas.2505789122","DOIUrl":"https://doi.org/10.1073/pnas.2505789122","url":null,"abstract":"Metabolic crosstalk among diverse cellular populations contributes to shaping a competitive and symbiotic tumor microenvironment (TME) to influence cancer progression and immune responses, highlighting vulnerabilities that can be exploited for cancer therapy. Using a spatial multiomics platform to study the cell-specific metabolic spectrum in hepatocellular carcinoma (HCC), we map the metabolic interactions between different cells in the HCC TME and identify a unique tumor-immune-cancer-associated fibroblast (CAF) “interface” zone, where cell–cell interactions are enhanced and accompanied by significant upregulation of lactic acid and long-chain polyunsaturated fatty acids. Further combining single-cell mass spectrometry imaging of patient-derived tumor organoids, cocultured CAFs, and macrophages, we demonstrate that CAFs increase glycolysis and secrete lactic acid to the surrounding microenvironment to drive immunosuppressive macrophage M2 polarization. These findings facilitate the understanding of cancer-associated metabolic interactions in complex TME and provide clues for targeted clinical therapies.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"11 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737155","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}

{"title":"Leveraging chromatin packing domains to target chemoevasion in vivo.","authors":"Jane Frederick, Ranya K A Virk, I Chae Ye, Luay M Almassalha, Greta M Wodarcyk, David VanDerway, Ruyi Gong, Cody L Dunton, Tiffany Kuo, Karla I Medina, Margarita Loxas, Jared T Ahrendsen, Demirkan B Gursel, Paola Carrillo Gonzalez, Rikkert J Nap, Saira John, Vasundhara Agrawal, Nicholas M Anthony, John Carinato, Wing Shun Li, Rivaan Kakkaramadam, Surbhi Jain, Shohreh Shahabi, Guillermo A Ameer, Igal G Szleifer, Vadim Backman","doi":"10.1073/pnas.2425319122","DOIUrl":"10.1073/pnas.2425319122","url":null,"abstract":"<p><p>Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains. However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based model that connects chromatin organization to cell fate decisions, such as survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional activity through macromolecular crowding. The model accurately predicts chemoevasion in vitro, suggesting that changes in packing domains affect the likelihood of survival. Consistent results across diverse cancer types indicate that the model captures fundamental principles of chromatin-mediated adaptation, independent of the specific cancer or chemotherapy mechanisms involved. Based on these insights, we hypothesized that compounds capable of modulating packing domains, termed Transcriptional Plasticity Regulators (TPRs), could prevent cellular adaptation to chemotherapy. We conducted a proof-of-concept compound screen using live-cell chromatin imaging to identify several TPRs that synergistically enhanced chemotherapy-induced cell death. The most effective TPR significantly improved therapeutic outcomes in a patient-derived xenograft model of ovarian cancer. These findings underscore the central role of chromatin in cellular adaptation to cytotoxic stress and present a framework for enhancing cancer therapies, with broad potential across multiple cancer types.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2425319122"},"PeriodicalIF":9.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144691338","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}

{"title":"<i>Cdc42</i> defect reveals insights into microvilli organization and function in T cell immunity.","authors":"Won-Chang Soh, Sang-Moo Park, Jeong-Su Park, Hatice Karabulut, Hee-Tae Kang, Sun-Kyoung Kang, Min-Sang Kim, Jihwan Park, Sunjae Lee, Hye-Ran Kim, Chang-Duk Jun","doi":"10.1073/pnas.2505291122","DOIUrl":"https://doi.org/10.1073/pnas.2505291122","url":null,"abstract":"<p><p>Microvilli on T cells differ from those on epithelial cells, exhibiting filopodia-like characteristics that facilitate the clustering of molecules essential for sensing and cell migration. Recently, they have also been recognized as the structures from which T cell immunological synaptosomes (TIS) are released. In this study, we examined a key determinant of microvilli organization during T cell development and explored the functional roles of these structures, particularly in relation to T cell behaviors. During thymocyte maturation, single-positive thymocytes were found to develop more and longer microvilli than double-positive thymocytes. However, the deletion or inhibition of Cdc42, a small Rho family protein, significantly reduced both the number and length of microvilli in single-positive thymocytes, leading to decreased cell mass. This reduction in microvilli correlates with a decrease in antigen recognition, leading to diminished T cell activation and adhesion, as well as reduced TIS production, while intrinsic migratory properties remain unaffected. These findings highlight the filopodia-like characteristics of T cell microvilli. In this context, Cdc42 contributes significantly to microvilli formation, thereby shaping T cell function.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2505291122"},"PeriodicalIF":9.4,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144715174","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}

{"title":"Nonsubstrate PI(4,5)P 2 interacts with the interdomain linker to control electrochemical coupling in voltage-sensing phosphatase (VSP)","authors":"Natsuki Mizutani, Yasushige Yonezawa, Atsushi Nakagawa, Yasushi Okamura","doi":"10.1073/pnas.2500651122","DOIUrl":"https://doi.org/10.1073/pnas.2500651122","url":null,"abstract":"Voltage-sensing phosphatase (VSP) comprises a voltage sensor domain (VSD) and a cytoplasmic catalytic region (CCR), achieving a unique electrochemical signal conversion. Previous studies suggest that phosphatidylinositol 4,5-bisphosphate (PI(4,5)P <jats:sub>2</jats:sub> ), a membrane phospholipid known to be critical for activities of diverse voltage-gated ion channels, associates with a linker connecting the VSD with the CCR of VSP and regulates VSD-CCR coupling. However, the details of PI(4,5)P <jats:sub>2</jats:sub> interaction with the linker of VSP remain elusive. Here, we exploit advantage of sensitivity of a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), to changes in local environment to study interaction between PI(4,5)P <jats:sub>2</jats:sub> and the linker of <jats:italic toggle=\"yes\">Ciona intestinalis</jats:italic> VSP (Ci-VSP). We found that a conserved tyrosine residue (Y255) as well as neighboring basic residues interacts with PI(4,5)P <jats:sub>2</jats:sub> and this interaction was maintained in G365A Ci-VSP mutant which lacks the substrate PI(4,5)P <jats:sub>2</jats:sub> at the active site and Ci-VSP/human phosphatase and tensin homolog (PTEN) chimera which does not dephosphorylate PI(4,5)P <jats:sub>2</jats:sub> , indicating that the linker interacts with nonsubstrate, regulatory PI(4,5)P <jats:sub>2</jats:sub> outside the active site. Molecular dynamics simulations demonstrated that the linker formed stable interaction with PI(4,5)P <jats:sub>2</jats:sub> in the activated state. These findings indicate that regulation of coupling to an effector region downstream of the VSD through PI(4,5)P <jats:sub>2</jats:sub> binding to the linker is shared among voltage-dependent membrane proteins.","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":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144736746","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}

{"title":"Cryo-EM structure and polar assembly of the PS2 S-layer of Corynebacterium glutamicum","authors":"Adrià Sogues, Mike Sleutel, Julienne Petit, Daniela Megrian, Nicolas Bayan, Anne Marie Wehenkel, Han Remaut","doi":"10.1073/pnas.2426928122","DOIUrl":"https://doi.org/10.1073/pnas.2426928122","url":null,"abstract":"The polar-growing <jats:italic toggle=\"yes\">Corynebacteriales</jats:italic> have a complex cell envelope architecture characterized by the presence of a specialized outer membrane composed of mycolic acids. In some <jats:italic toggle=\"yes\">Corynebacteriales</jats:italic> , this mycomembrane is further supported by a proteinaceous surface layer or “S-layer,” whose function, structure, and mode of assembly remain largely enigmatic. Here, we isolated ex vivo PS2 S-layers from the industrially important <jats:italic toggle=\"yes\">Corynebacterium glutamicum</jats:italic> and determined its atomic structure by 3D cryo-EM reconstruction. PS2 monomers consist of a six-helix bundle “core,” a three-helix bundle “arm,” and a C-terminal transmembrane (TM) helix. The PS2 core oligomerizes into hexameric units anchored in the mycomembrane by a channel-like coiled-coil of the TM helices. The PS2 arms mediate trimeric lattice contacts, crystallizing the hexameric units into an intricate semipermeable lattice. Using pulse-chase live cell imaging, we show that the PS2 lattice is incorporated at the poles, coincident with the actinobacterial elongasome. Finally, phylogenetic analysis shows a paraphyletic distribution and dispersed chromosomal location of PS2 in <jats:italic toggle=\"yes\">Corynebacteriales</jats:italic> as a result of multiple recombination events and losses. These findings expand our understanding of S-layer biology and enable applications of membrane-supported self-assembling bioengineered materials.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"26 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737042","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}

{"title":"Prg4 + fibroadipogenic progenitors in muscle are crucial for bone fracture repair","authors":"Qi He, Jiawei Lu, Qiushi Liang, Lutian Yao, Tingfang Sun, Huan Wang, Michael Duffy, Xi Jiang, Yuewei Lin, Ji-Hyung Lee, Jaimo Ahn, Nathaniel A. Dyment, Foteini Mourkioti, Joel D. Boerckel, Ling Qin","doi":"10.1073/pnas.2417806122","DOIUrl":"https://doi.org/10.1073/pnas.2417806122","url":null,"abstract":"Clinically, compromised fracture healing often occurs at sites with less muscle coverage and muscle flaps can provide the necessary healing environment for appropriate healing in severe bone loss. However, the underlying mechanisms are largely unknown. Here, we established a mouse reporter model for studying muscle cell contribution to bone fracture repair. Analyzing skeletal muscle scRNA-seq datasets revealed that <jats:italic toggle=\"yes\">Prg4</jats:italic> marks a fibroadipogenic progenitor (FAP) subpopulation. In mice, <jats:italic toggle=\"yes\">Prg4</jats:italic> + cells were specifically located in the skeletal muscle, but not at the periosteum or inside cortical bone. These cells expressed FAP markers, responded to muscle injury, and became periosteal cells under normal and muscle injury conditions. Fracture fragmented muscle fibers, rapidly expanded <jats:italic toggle=\"yes\">Prg4</jats:italic> + FAPs at the injury site and promoted their migration into the fracture gap. Later, they gave rise to many chondrocytes, osteoblasts, and osteocytes in the outer periphery of callus next to muscle. In repaired bones, the descendants of <jats:italic toggle=\"yes\">Prg4</jats:italic> + FAPs were detected as mesenchymal progenitors in the periosteum and osteocytes at the prior fracture site. A second fracture activated those cells and stimulated them to become osteoblasts in the inner part of callus. Importantly, ablation of <jats:italic toggle=\"yes\">Prg4</jats:italic> + FAPs impaired fracture healing and functional repair. In an intramembranous bone injury model (drill-hole), <jats:italic toggle=\"yes\">Prg4</jats:italic> + FAPs became periosteal cells, but their contribution to bone defect repair was significantly less than in fractures. Taken together, we demonstrate the critical role of FAPs in endochondral bone repair and uncover a mechanism by which mesenchymal progenitors transform from muscle to cortical bone.","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"6 1","pages":""},"PeriodicalIF":11.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737163","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}

{"title":"Essential new insights into human cerebellar Purkinje cell biology from studies of essential tremor.","authors":"Kathleen J Millen","doi":"10.1073/pnas.2514663122","DOIUrl":"https://doi.org/10.1073/pnas.2514663122","url":null,"abstract":"","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"7 1","pages":"e2514663122"},"PeriodicalIF":11.1,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144737402","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}

{"title":"Effects of the gut microbiota on placental angiogenesis and intrauterine growth in gnotobiotic mice.","authors":"Reyan Coskun, ZeNan L Chang, Athziri Marcial Rodríguez, Haoxin Liu, Jiye Cheng, Yael Alippe, Michael S Diamond, Jeffrey I Gordon","doi":"10.1073/pnas.2426341122","DOIUrl":"https://doi.org/10.1073/pnas.2426341122","url":null,"abstract":"<p><p>Environmental causes of intrauterine growth restriction (IUGR) remain poorly characterized. Here, we compare germ-free (GF) and conventionally raised (CONV-R) mice to assess the effects of the gut microbiota on placental/fetal development at embryonic day (E)11.5 (end of placentation) and E17.5 (near term). Pregnancy- and microbiota-associated changes in gene expression occur along the gut, including those related to angiogenesis, while bacterial composition and fermentation activity remain stable. Placental weights at E11.5 and fetal weights at E17.5 are significantly reduced in GF animals. Compared to CONV-R dams, the GF maternal decidua exhibits similar vascular histomorphometric features at E11.5 and E17.5, and numbers of uterine NK-cells (effectors of vascular remodeling) at E11.5. In contrast, angiogenesis is disturbed in the GF fetal-derived placental compartment (junctional and/or labyrinth zones) at E11.5, as judged by i) increased levels of proangiogenic proteins (angiopoietin-2, FGF-2, follistatin, SDF-1, VEGF-A, VEGF-C); ii) increased levels of phos-VEGFR2 and phos-p38-MAPK yet reduction in phos-ERK1/2; and iii) reduced expression of junctional zone glycoprotein genes associated with angiogenesis and fetal growth, resulting in reduced endothelial cell density at the labyrinth zone at E17.5. Colonization of GF mice before pregnancy with cecal microbiota from CONV-R animals rescues fetal growth and altered transcriptomic, proteomic, and immunohistochemical features in the fetal GF placental compartment. Single-nucleus RNA-sequencing demonstrated increased expression of mitochondrial and ribosomal-associated oxidative stress genes in endothelial cell clusters in the GF fetal placental compartment (E11.5, E17.5), mimicking oxidative stress signatures in human IUGR. These results provide a rationale for seeking microbial targets for treating/preventing IUGR.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2426341122"},"PeriodicalIF":9.4,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144715176","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}

{"title":"Differential representations of spatial location by aperiodic and alpha oscillatory activity in working memory.","authors":"Andrew Bender, Chong Zhao, Edward Vogel, Edward Awh, Bradley Voytek","doi":"10.1073/pnas.2506418122","DOIUrl":"10.1073/pnas.2506418122","url":null,"abstract":"<p><p>Decades of research have shown working memory (WM) relies on sustained prefrontal cortical activity and visual extrastriate activity, particularly in the alpha (8 to 12 Hz) frequency range. This alpha activity tracks the spatial location of WM items, even when spatial position is task-irrelevant and no stimulus is currently being presented. Traditional analyses of putative oscillations using bandpass filters, however, conflate oscillations with nonoscillatory aperiodic activity. Here, we reanalyzed seven human electroencephalography visual WM datasets to test the hypothesis that aperiodic activity, which is thought to reflect the relative contributions of excitatory and inhibitory drive-plays a distinct role in visual WM from true alpha oscillations. To do this, we developed a time-resolved spectral parameterization approach to disentangle oscillations from aperiodic activity during WM encoding and maintenance. Across all seven tasks, totaling 112 participants, we captured the representation of spatial location from total alpha power using inverted encoding models (IEMs), replicating traditional analyses. We then trained separate IEMs to estimate the strength of spatial location representation from aperiodic-adjusted alpha (reflecting just the oscillatory component) and aperiodic activity and find that IEM performance improves for aperiodic-adjusted alpha compared to total alpha power that blends the two signals. We also identify a distinct role for aperiodic activity, where IEM performance trained on aperiodic activity is highest during stimulus presentation, but not during the WM maintenance period. Our results emphasize the importance of controlling for aperiodic activity when studying neural oscillations while uncovering a functional role for aperiodic activity in encoding visual WM information.</p>","PeriodicalId":20548,"journal":{"name":"Proceedings of the National Academy of Sciences of the United States of America","volume":"122 30","pages":"e2506418122"},"PeriodicalIF":9.4,"publicationDate":"2025-07-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144699265","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}