1
|
Uhrbom M, Muhl L, Genové G, Liu J, Palmgren H, Alexandersson I, Karlsson F, Zhou AX, Lunnerdal S, Gustafsson S, Buyandelger B, Petkevicius K, Ahlstedt I, Karlsson D, Aasehaug L, He L, Jeansson M, Betsholtz C, Peng XR. Adipose stem cells are sexually dimorphic cells with dual roles as preadipocytes and resident fibroblasts. Nat Commun 2024; 15:7643. [PMID: 39223126 DOI: 10.1038/s41467-024-51867-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Cell identities are defined by intrinsic transcriptional networks and spatio-temporal environmental factors. Here, we explored multiple factors that contribute to the identity of adipose stem cells, including anatomic location, microvascular neighborhood, and sex. Our data suggest that adipose stem cells serve a dual role as adipocyte precursors and fibroblast-like cells that shape the adipose tissue's extracellular matrix in an organotypic manner. We further find that adipose stem cells display sexual dimorphism regarding genes involved in estrogen signaling, homeobox transcription factor expression and the renin-angiotensin-aldosterone system. These differences could be attributed to sex hormone effects, developmental origin, or both. Finally, our data demonstrate that adipose stem cells are distinct from mural cells, and that the state of commitment to adipogenic differentiation is linked to their anatomic position in the microvascular niche. Our work supports the importance of sex and microvascular function in adipose tissue physiology.
Collapse
Affiliation(s)
- Martin Uhrbom
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden.
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Lars Muhl
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden
- Centre for Cancer Biomarkers CCBIO, Department of Clinical Medicine, University of Bergen, 5020, Bergen, Norway
| | - Guillem Genové
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden
| | - Jianping Liu
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden
| | - Henrik Palmgren
- Bioscience Renal, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ida Alexandersson
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Fredrik Karlsson
- Data Sciences & Quantitative Biology, Discovery Sciences, R&D AstraZeneca, Gothenburg, Sweden
| | - Alex-Xianghua Zhou
- Bioscience Renal, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sandra Lunnerdal
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Sonja Gustafsson
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden
| | - Byambajav Buyandelger
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden
| | - Kasparas Petkevicius
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Ingela Ahlstedt
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Daniel Karlsson
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leif Aasehaug
- Bioscience Cardiovascular, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 23, Uppsala, Sweden
| | - Marie Jeansson
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden
| | - Christer Betsholtz
- Department of Medicine, Huddinge, Karolinska Institutet Campus Flemingsberg, Neo building, 141 52, Huddinge, Sweden.
- Department of Immunology, Genetics and Pathology, Uppsala University, 751 23, Uppsala, Sweden.
| | - Xiao-Rong Peng
- Bioscience Metabolism, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| |
Collapse
|
2
|
Valeri E, Breggion S, Barzaghi F, Abou Alezz M, Crivicich G, Pagani I, Forneris F, Sartirana C, Costantini M, Costi S, Marino A, Chiarotto E, Colavito D, Cimaz R, Merelli I, Vicenzi E, Aiuti A, Kajaste-Rudnitski A. A novel STING variant triggers endothelial toxicity and SAVI disease. J Exp Med 2024; 221:e20232167. [PMID: 38953896 PMCID: PMC11217899 DOI: 10.1084/jem.20232167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 04/18/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
Gain-of-function mutations in STING cause STING-associated vasculopathy with onset in infancy (SAVI) characterized by early-onset systemic inflammation, skin vasculopathy, and interstitial lung disease. Here, we report and characterize a novel STING variant (F269S) identified in a SAVI patient. Single-cell transcriptomics of patient bone marrow revealed spontaneous activation of interferon (IFN) and inflammatory pathways across cell types and a striking prevalence of circulating naïve T cells was observed. Inducible STING F269S expression conferred enhanced signaling through ligand-independent translocation of the protein to the Golgi, protecting cells from viral infections but preventing their efficient immune priming. Additionally, endothelial cell activation was promoted and further exacerbated by cytokine secretion by SAVI immune cells, resulting in inflammation and endothelial damage. Our findings identify STING F269S mutation as a novel pathogenic variant causing SAVI, highlight the importance of the crosstalk between endothelial and immune cells in the context of lung disease, and contribute to a better understanding of how aberrant STING activation can cause pathology.
Collapse
Affiliation(s)
- Erika Valeri
- San Raffaele Telethon Institute for Gene Therapy, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sara Breggion
- Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Barzaghi
- Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Monah Abou Alezz
- San Raffaele Telethon Institute for Gene Therapy, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Giovanni Crivicich
- Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federico Forneris
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
- Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Claudia Sartirana
- Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Matteo Costantini
- Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Stefania Costi
- Unit of Pediatric Rheumatology, ASST Gaetano Pini-CTO, Milan, Italy
| | - Achille Marino
- Unit of Pediatric Rheumatology, ASST Gaetano Pini-CTO, Milan, Italy
| | | | | | - Rolando Cimaz
- Unit of Pediatric Rheumatology, ASST Gaetano Pini-CTO, Milan, Italy
| | - Ivan Merelli
- San Raffaele Telethon Institute for Gene Therapy, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandro Aiuti
- Vita-Salute San Raffaele University, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Pediatric Immunohematology and Bone Marrow Transplantation Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Anna Kajaste-Rudnitski
- San Raffaele Telethon Institute for Gene Therapy, Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) San Raffaele Scientific Institute, Milan, Italy
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| |
Collapse
|
3
|
Gong N, Zhong W, Alameh MG, Han X, Xue L, El-Mayta R, Zhao G, Vaughan AE, Qin Z, Xu F, Hamilton AG, Kim D, Xu J, Kim J, Teng X, Li J, Liang XJ, Weissman D, Guo W, Mitchell MJ. Tumour-derived small extracellular vesicles act as a barrier to therapeutic nanoparticle delivery. NATURE MATERIALS 2024:10.1038/s41563-024-01961-6. [PMID: 39223270 DOI: 10.1038/s41563-024-01961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/25/2024] [Indexed: 09/04/2024]
Abstract
Nanoparticles are promising for drug delivery applications, with several clinically approved products. However, attaining high nanoparticle accumulation in solid tumours remains challenging. Here we show that tumour cell-derived small extracellular vesicles (sEVs) block nanoparticle delivery to tumours, unveiling another barrier to nanoparticle-based tumour therapy. Tumour cells secrete large amounts of sEVs in the tumour microenvironment, which then bind to nanoparticles entering tumour tissue and traffic them to liver Kupffer cells for degradation. Knockdown of Rab27a, a gene that controls sEV secretion, decreases sEV levels and improves nanoparticle accumulation in tumour tissue. The therapeutic efficacy of messenger RNAs encoding tumour suppressing and proinflammatory proteins is greatly improved when co-encapsulated with Rab27a small interfering RNA in lipid nanoparticles. Together, our results demonstrate that tumour cell-derived sEVs act as a defence system against nanoparticle tumour delivery and that this system may be a potential target for improving nanoparticle-based tumour therapies.
Collapse
Affiliation(s)
- Ningqiang Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
- Division of Life Sciences and Medicine, Center for BioAnalytical Chemistry, Hefei National Research Center for Physical Science at the Microscale, University of Science and Technology of China, Hefei, China
| | - Wenqun Zhong
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Xuexiang Han
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Lulu Xue
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Rakan El-Mayta
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Gan Zhao
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew E Vaughan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Zhiyuan Qin
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Fengyuan Xu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Alex G Hamilton
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Dongyoon Kim
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Junchao Xu
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - Xucong Teng
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Jinghong Li
- Department of Chemistry, Tsinghua University, Beijing, China
| | - Xing-Jie Liang
- Chinese Academy of Sciences Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, China
| | - Drew Weissman
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA.
| | - Wei Guo
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
| | - Michael J Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Penn institute for RNA innovation, University of Pennsylvania, Philadelphia, PA, USA.
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
4
|
Luo E, Hao M, Wei L, Zhang X. scDiffusion: conditional generation of high-quality single-cell data using diffusion model. Bioinformatics 2024; 40:btae518. [PMID: 39171840 PMCID: PMC11368386 DOI: 10.1093/bioinformatics/btae518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 08/10/2024] [Accepted: 08/20/2024] [Indexed: 08/23/2024] Open
Abstract
MOTIVATION Single-cell RNA sequencing (scRNA-seq) data are important for studying the laws of life at single-cell level. However, it is still challenging to obtain enough high-quality scRNA-seq data. To mitigate the limited availability of data, generative models have been proposed to computationally generate synthetic scRNA-seq data. Nevertheless, the data generated with current models are not very realistic yet, especially when we need to generate data with controlled conditions. In the meantime, diffusion models have shown their power in generating data with high fidelity, providing a new opportunity for scRNA-seq generation. RESULTS In this study, we developed scDiffusion, a generative model combining the diffusion model and foundation model to generate high-quality scRNA-seq data with controlled conditions. We designed multiple classifiers to guide the diffusion process simultaneously, enabling scDiffusion to generate data under multiple condition combinations. We also proposed a new control strategy called Gradient Interpolation. This strategy allows the model to generate continuous trajectories of cell development from a given cell state. Experiments showed that scDiffusion could generate single-cell gene expression data closely resembling real scRNA-seq data. Also, scDiffusion can conditionally produce data on specific cell types including rare cell types. Furthermore, we could use the multiple-condition generation of scDiffusion to generate cell type that was out of the training data. Leveraging the Gradient Interpolation strategy, we generated a continuous developmental trajectory of mouse embryonic cells. These experiments demonstrate that scDiffusion is a powerful tool for augmenting the real scRNA-seq data and can provide insights into cell fate research. AVAILABILITY AND IMPLEMENTATION scDiffusion is openly available at the GitHub repository https://github.com/EperLuo/scDiffusion or Zenodo https://zenodo.org/doi/10.5281/zenodo.13268742.
Collapse
Affiliation(s)
- Erpai Luo
- MOE Key Lab of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Minsheng Hao
- MOE Key Lab of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Lei Wei
- MOE Key Lab of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xuegong Zhang
- MOE Key Lab of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University, Beijing 100084, China
- School of Life Sciences and School of Medicine, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| |
Collapse
|
5
|
Ball NJ, Ghimire S, Follain G, Pajari AO, Wurzinger D, Vaitkevičiūtė M, Cowell AR, Berki B, Ivaska J, Paatero I, Goult BT, Jacquemet G. TLNRD1 is a CCM complex component and regulates endothelial barrier integrity. J Cell Biol 2024; 223:e202310030. [PMID: 39013281 PMCID: PMC11252447 DOI: 10.1083/jcb.202310030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 04/08/2024] [Accepted: 05/23/2024] [Indexed: 07/18/2024] Open
Abstract
We previously identified talin rod domain-containing protein 1 (TLNRD1) as a potent actin-bundling protein in vitro. Here, we report that TLNRD1 is expressed in the vasculature in vivo. Its depletion leads to vascular abnormalities in vivo and modulation of endothelial cell monolayer integrity in vitro. We demonstrate that TLNRD1 is a component of the cerebral cavernous malformations (CCM) complex through its direct interaction with CCM2, which is mediated by a hydrophobic C-terminal helix in CCM2 that attaches to a hydrophobic groove on the four-helix domain of TLNRD1. Disruption of this binding interface leads to CCM2 and TLNRD1 accumulation in the nucleus and actin fibers. Our findings indicate that CCM2 controls TLNRD1 localization to the cytoplasm and inhibits its actin-bundling activity and that the CCM2-TLNRD1 interaction impacts endothelial actin stress fiber and focal adhesion formation. Based on these results, we propose a new pathway by which the CCM complex modulates the actin cytoskeleton and vascular integrity.
Collapse
Affiliation(s)
- Neil J. Ball
- School of Biosciences, University of Kent, Canterbury, UK
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Sujan Ghimire
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Gautier Follain
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ada O. Pajari
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Diana Wurzinger
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | - Monika Vaitkevičiūtė
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
| | | | - Bence Berki
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Johanna Ivaska
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Department of Life Technologies, University of Turku, Turku, Finland
- Western Finnish Cancer Center (FICAN West), University of Turku, Turku, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
| | - Ilkka Paatero
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Benjamin T. Goult
- School of Biosciences, University of Kent, Canterbury, UK
- Department of Biochemistry, Cell and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Guillaume Jacquemet
- Faculty of Science and Engineering, Cell Biology, Åbo Akademi University, Turku, Finland
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku and Åbo Akademi University, Turku, Finland
- Turku Bioimaging, University of Turku and Åbo Akademi University, Turku, Finland
| |
Collapse
|
6
|
Ortiz JA, Ghazalli N, Lopez K, Rawson J, McCown EM, Oh E, Irimia JM, Jou K, Mares J, Chen MH, Wu X, Zook HN, Quijano JC, Erdem N, Lizarraga A, Kandeel F, Fueger PT, Thurmond DC, Ku HT. Trefoil Factor 2 Expressed by the Murine Pancreatic Acinar Cells Is Required for the Development of Islets and for β-Cell Function During Aging. Diabetes 2024; 73:1447-1461. [PMID: 38905124 PMCID: PMC11333379 DOI: 10.2337/db23-0490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 06/10/2024] [Indexed: 06/23/2024]
Abstract
Exocrine-to-endocrine cross talk in the pancreas is crucial to maintain β-cell function. However, the molecular mechanisms underlying this cross talk are largely undefined. Trefoil factor 2 (Tff2) is a secreted factor known to promote the proliferation of β-cells in vitro, but its physiological role in vivo in the pancreas is unknown. Also, it remains unclear which pancreatic cell type expresses Tff2 protein. We therefore created a mouse model with a conditional knockout of Tff2 in the murine pancreas. We find that the Tff2 protein is preferentially expressed in acinar but not ductal or endocrine cells. Tff2 deficiency in the pancreas reduces β-cell mass on embryonic day 16.5. However, homozygous mutant mice are born without a reduction of β-cells and with acinar Tff3 compensation by day 7. When mice are aged to 1 year, both male and female homozygous and male heterozygous mutants develop impaired glucose tolerance without affected insulin sensitivity. Perifusion analysis reveals that the second phase of glucose-stimulated insulin secretion from islets is reduced in aged homozygous mutant compared with controls. Collectively, these results demonstrate a previously unknown role of Tff2 as an exocrine acinar cell-derived protein required for maintaining functional endocrine β-cells in mice. ARTICLE HIGHLIGHTS
Collapse
Affiliation(s)
- Jose A. Ortiz
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| | - Nadiah Ghazalli
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| | - Kassandra Lopez
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| | - Jeffrey Rawson
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | - Erika M. McCown
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | - Eunjin Oh
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | - Jose M. Irimia
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
- Comprehensive Metabolic Phenotyping Core, City of Hope, Duarte, CA
| | - Kevin Jou
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | - Jacob Mares
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | | | - Xiwei Wu
- Comprehensive Metabolic Phenotyping Core, City of Hope, Duarte, CA
| | - Heather N. Zook
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| | - Janine C. Quijano
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | - Neslihan Erdem
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| | - Anahy Lizarraga
- Eugene and Ruth Roberts Summer Student Academy, City of Hope, Duarte, CA
| | - Fouad Kandeel
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | - Patrick T. Fueger
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
- Comprehensive Metabolic Phenotyping Core, City of Hope, Duarte, CA
| | - Debbie C. Thurmond
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
- Department of Molecular & Cellular Endocrinology, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
| | - Hsun Teresa Ku
- Department of Translational Research and Cellular Therapeutics, Arthur Riggs Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA
- Irell and Manella School of Biological Sciences, Beckman Research Institute, City of Hope, Duarte, CA
| |
Collapse
|
7
|
Kabir AU, Zeng C, Subramanian M, Wu J, Kim M, Krchma K, Wang X, Halabi CM, Pan H, Wickline SA, Fremont DH, Artyomov MN, Choi K. ZBTB46 coordinates angiogenesis and immunity to control tumor outcome. Nat Immunol 2024; 25:1546-1554. [PMID: 39134750 DOI: 10.1038/s41590-024-01936-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/16/2024] [Indexed: 09/01/2024]
Abstract
Tumor angiogenesis and immunity show an inverse correlation in cancer progression and outcome1. Here, we report that ZBTB46, a repressive transcription factor and a widely accepted marker for classical dendritic cells (DCs)2,3, controls both tumor angiogenesis and immunity. Zbtb46 was downregulated in both DCs and endothelial cells by tumor-derived factors to facilitate robust tumor growth. Zbtb46 downregulation led to a hallmark pro-tumor microenvironment (TME), including dysfunctional vasculature and immunosuppressive conditions. Analysis of human cancer data revealed a similar association of low ZBTB46 expression with an immunosuppressive TME and a worse prognosis. In contrast, enforced Zbtb46 expression led to TME changes to restrict tumor growth. Mechanistically, Zbtb46-deficient endothelial cells were highly angiogenic, and Zbtb46-deficient bone marrow progenitors upregulated Cebpb and diverted the DC program to immunosuppressive myeloid lineage output, potentially explaining the myeloid lineage skewing phenomenon in cancer4. Conversely, enforced Zbtb46 expression normalized tumor vessels and, by suppressing Cebpb, skewed bone marrow precursors toward immunostimulatory myeloid lineage output, leading to an immune-hot TME. Remarkably, Zbtb46 mRNA treatment synergized with anti-PD1 immunotherapy to improve tumor management in preclinical models. These findings identify ZBTB46 as a critical factor for angiogenesis and for myeloid lineage skewing in cancer and suggest that maintaining its expression could have therapeutic benefits.
Collapse
Affiliation(s)
- Ashraf Ul Kabir
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Carisa Zeng
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Madhav Subramanian
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Jun Wu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Minseo Kim
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Karen Krchma
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Xiaoli Wang
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Carmen M Halabi
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Hua Pan
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Samuel A Wickline
- Health Heart Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Daved H Fremont
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Maxim N Artyomov
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Kyunghee Choi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
8
|
Yao D, Wang X, Liu J, Xu XQ. Rbm24 modulates neuronal RNA splicing to restrict cognitive dysfunction. Int J Biol Macromol 2024; 276:133853. [PMID: 39004256 DOI: 10.1016/j.ijbiomac.2024.133853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/24/2024] [Accepted: 07/11/2024] [Indexed: 07/16/2024]
Abstract
Synaptic dysfunction is associated with early neurodegenerative changes and cognitive deficits. Neuronal cell-specific alternative splicing (AS) programs exclusively encode unique neuron- and synapse-specific proteins. However, it remains unclear whether splicing disturbances in neurons influence the pathogenesis of cognitive impairment. Here, we observed that RNA-binding motif protein 24 (RBM24) expression was decreased in Alzheimer's disease (AD) patients. Using conditional RBM24 knockout mice, we demonstrated that deletion of RBM24 in the brain resulted in learning and memory impairment. Electrophysiological recordings from hippocampal slices from mice lacking RBM24 revealed multiple defects in excitatory synaptic function and plasticity. Furthermore, RNA sequencing and splicing analysis showed that RBM24 regulates a network of genes related to cognitive function. Deletion of RBM24 disrupted the AS of synapse-associated genes, including GluR2 and Prrt1, the major disease genes involved in cognitive impairment and memory loss, leading to cognitive dysfunction. Together, our results suggest that the regulation of mRNA splicing by RBM24 is a key process involved in maintaining normal synaptic function and provide novel mechanistic insights into the pathogenesis of AD.
Collapse
Affiliation(s)
- Dongbo Yao
- Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361000, China
| | - Xiaoxia Wang
- Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361000, China
| | - Jing Liu
- Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361000, China
| | - Xiu Qin Xu
- Institute of Stem Cell and Regenerative Medicine, Women and Children's Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361000, China.
| |
Collapse
|
9
|
Read DF, Booth GT, Daza RM, Jackson DL, Gladden RG, Srivatsan SR, Ewing B, Franks JM, Spurrell CH, Gomes AR, O'Day D, Gogate AA, Martin BK, Larson H, Pfleger C, Starita L, Lin Y, Shendure J, Lin S, Trapnell C. Single-cell analysis of chromatin and expression reveals age- and sex-associated alterations in the human heart. Commun Biol 2024; 7:1052. [PMID: 39187646 PMCID: PMC11347658 DOI: 10.1038/s42003-024-06582-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 07/11/2024] [Indexed: 08/28/2024] Open
Abstract
Sex differences and age-related changes in the human heart at the tissue, cell, and molecular level have been well-documented and many may be relevant for cardiovascular disease. However, how molecular programs within individual cell types vary across individuals by age and sex remains poorly characterized. To better understand this variation, we performed single-nucleus combinatorial indexing (sci) ATAC- and RNA-Seq in human heart samples from nine donors. We identify hundreds of differentially expressed genes by age and sex and find epigenetic signatures of variation in ATAC-Seq data in this discovery cohort. We then scale up our single-cell RNA-Seq analysis by combining our data with five recently published single nucleus RNA-Seq datasets of healthy adult hearts. We find variation such as metabolic alterations by sex and immune changes by age in differential expression tests, as well as alterations in abundance of cardiomyocytes by sex and neurons with age. In addition, we compare our adult-derived ATAC-Seq profiles to analogous fetal cell types to identify putative developmental-stage-specific regulatory factors. Finally, we train predictive models of cell-type-specific RNA expression levels utilizing ATAC-Seq profiles to link distal regulatory sequences to promoters, quantifying the predictive value of a simple TF-to-expression regulatory grammar and identifying cell-type-specific TFs. Our analysis represents the largest single-cell analysis of cardiac variation by age and sex to date and provides a resource for further study of healthy cardiac variation and transcriptional regulation at single-cell resolution.
Collapse
Affiliation(s)
- David F Read
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Gregory T Booth
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Riza M Daza
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dana L Jackson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Rula Green Gladden
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Sanjay R Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brent Ewing
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jennifer M Franks
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | | | - Diana O'Day
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Aishwarya A Gogate
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Beth K Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Haleigh Larson
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Christian Pfleger
- University of Washington School of Medicine, Division of Cardiology, Seattle, WA, USA
| | - Lea Starita
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
| | - Yiing Lin
- Department of Surgery, Washington University, St Louis, MO, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Seattle Children's Research Institute, Seattle, WA, USA.
- Howard Hughes Medical Institute, Seattle, WA, USA.
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.
| | - Shin Lin
- University of Washington School of Medicine, Division of Cardiology, Seattle, WA, USA.
| | - Cole Trapnell
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
| |
Collapse
|
10
|
Wang CH, Tsuji T, Wu LH, Yang CY, Huang TL, Sato M, Shamsi F, Tseng YH. Endothelin 3/EDNRB signaling induces thermogenic differentiation of white adipose tissue. Nat Commun 2024; 15:7215. [PMID: 39174539 PMCID: PMC11341701 DOI: 10.1038/s41467-024-51579-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
Thermogenic adipose tissue, consisting of brown and beige fat, regulates nutrient utilization and energy metabolism. Human brown fat is relatively scarce and decreases with obesity and aging. Hence, inducing thermogenic differentiation of white fat offers an attractive way to enhance whole-body metabolic capacity. Here, we show the role of endothelin 3 (EDN3) and endothelin receptor type B (EDNRB) in promoting the browning of white adipose tissue (WAT). EDNRB overexpression stimulates thermogenic differentiation of human white preadipocytes through cAMP-EPAC1-ERK activation. In mice, cold induces the expression of EDN3 and EDNRB in WAT. Deletion of EDNRB in adipose progenitor cells impairs cold-induced beige adipocyte formation in WAT, leading to excessive weight gain, glucose intolerance, and insulin resistance upon high-fat feeding. Injection of EDN3 into WAT promotes browning and improved whole-body glucose metabolism. The findings shed light on the mechanism of WAT browning and offer potential therapeutics for obesity and metabolic disorders.
Collapse
Affiliation(s)
- Chih-Hao Wang
- Graduate Institute of Cell Biology, China Medical University, Taichung City, Taiwan.
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan.
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
| | - Tadataka Tsuji
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Li-Hong Wu
- Graduate Institute of Cell Biology, China Medical University, Taichung City, Taiwan
| | - Cheng-Ying Yang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung City, Taiwan
| | - Tian Lian Huang
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Mari Sato
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
| | - Farnaz Shamsi
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA
- Department of Molecular Pathobiology, College of Dentistry, New York University, New York, NY, USA
| | - Yu-Hua Tseng
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
11
|
Gulati GS, D'Silva JP, Liu Y, Wang L, Newman AM. Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00768-2. [PMID: 39169166 DOI: 10.1038/s41580-024-00768-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2024] [Indexed: 08/23/2024]
Abstract
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has emerged as a tool to contextualize single cells in multicellular neighbourhoods and to identify spatially recurrent phenotypes, or ecotypes. These technologies have generated vast datasets with targeted-transcriptome and whole-transcriptome profiles of hundreds to millions of cells. Such data have provided new insights into developmental hierarchies, cellular plasticity and diverse tissue microenvironments, and spurred a burst of innovation in computational methods for single-cell analysis. In this Review, we discuss recent advancements, ongoing challenges and prospects in identifying and characterizing cell states and multicellular neighbourhoods. We discuss recent progress in sample processing, data integration, identification of subtle cell states, trajectory modelling, deconvolution and spatial analysis. Furthermore, we discuss the increasing application of deep learning, including foundation models, in analysing single-cell and spatial transcriptomics data. Finally, we discuss recent applications of these tools in the fields of stem cell biology, immunology, and tumour biology, and the future of single-cell and spatial transcriptomics in biological research and its translation to the clinic.
Collapse
Affiliation(s)
- Gunsagar S Gulati
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Yunhe Liu
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Aaron M Newman
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
| |
Collapse
|
12
|
Mulenge F, Gern OL, Busker LM, Aringo A, Ghita L, Waltl I, Pavlou A, Kalinke U. Transcriptomic analysis unveils bona fide molecular signatures of microglia under conditions of homeostasis and viral encephalitis. J Neuroinflammation 2024; 21:203. [PMID: 39153993 PMCID: PMC11330067 DOI: 10.1186/s12974-024-03197-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024] Open
Abstract
Microglia serve as a front-line defense against neuroinvasive viral infection, however, determination of their actual transcriptional profiles under conditions of health and disease is challenging. Here, we used various experimental approaches to delineate the transcriptional landscape of microglia during viral infection. Intriguingly, multiple activation genes were found to be artificially induced in sorted microglia and we demonstrated that shear stress encountered during cell sorting was one of the key inducers. Post-hoc analysis revealed that publicly available large-scale single-cell RNA sequencing datasets were significantly tainted by aberrant signatures that are associated with cell sorting. By exploiting the ribosomal tagging approach, we developed a strategy to enrich microglia-specific transcripts by comparing immunoprecipitated RNA with total RNA. Such enriched transcripts were instrumental in defining bona fide signatures of microglia under conditions of health and virus infection. These unified microglial signatures may serve as a benchmark to retrospectively assess ex vivo artefacts from available atlases. Leveraging the microglial translatome, we found enrichment of genes implicated in T-cell activation and cytokine production during the course of VSV infection. These data linked microglia with T-cell re-stimulation and further underscored that microglia are involved in shaping antiviral T-cell responses in the brain. Collectively, our study defines the transcriptional landscape of microglia under steady state and during viral encephalitis and highlights cellular interactions between microglia and T cells that contribute to the control of virus dissemination.
Collapse
Affiliation(s)
- Felix Mulenge
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Olivia Luise Gern
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Lena Mareike Busker
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
- Department of Pathology, University of Veterinary Medicine Hannover, 30559, Foundation, Hannover, Germany
| | - Angela Aringo
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Luca Ghita
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
- , Genentech, South San Francisco, CA, 94080, USA
| | - Inken Waltl
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Andreas Pavlou
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, Centre for Experimental and Clinical Infection Research, a joint venture between The Helmholtz-Centre for Infection Research, Hannover Medical School, TWINCORE, Feodor-Lynen-Str. 7, 30625, Hannover, Germany.
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625, Hannover, Germany.
| |
Collapse
|
13
|
Simon M, Stüve P, Schmidleithner L, Bittner S, Beumer N, Strieder N, Schmidl C, Pant A, Gebhard C, Eigenberger A, Rehli M, Prantl L, Hehlgans T, Brors B, Imbusch CD, Delacher M, Feuerer M. Single-cell chromatin accessibility and transposable element landscapes reveal shared features of tissue-residing immune cells. Immunity 2024; 57:1975-1993.e10. [PMID: 39047731 DOI: 10.1016/j.immuni.2024.06.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 03/12/2024] [Accepted: 06/28/2024] [Indexed: 07/27/2024]
Abstract
Tissue adaptation is required for regulatory T (Treg) cell function within organs. Whether this program shares aspects with other tissue-localized immune populations is unclear. Here, we analyzed single-cell chromatin accessibility data, including the transposable element (TE) landscape of CD45+ immune cells from colon, skin, adipose tissue, and spleen. We identified features of organ-specific tissue adaptation across different immune cells. Focusing on tissue Treg cells, we found conservation of the Treg tissue adaptation program in other tissue-localized immune cells, such as amphiregulin-producing T helper (Th)17 cells. Accessible TEs can act as regulatory elements, but their contribution to tissue adaptation is not understood. TE landscape analysis revealed an enrichment of specific transcription factor binding motifs in TE regions within accessible chromatin peaks. TEs, specifically from the LTR family, were located in enhancer regions and associated with tissue adaptation. These findings broaden our understanding of immune tissue residency and provide an important step toward organ-specific immune interventions.
Collapse
Affiliation(s)
- Malte Simon
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany; Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Chair for Immunology, University Regensburg, 93053 Regensburg, Germany
| | - Philipp Stüve
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Chair for Immunology, University Regensburg, 93053 Regensburg, Germany
| | - Lisa Schmidleithner
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Chair for Immunology, University Regensburg, 93053 Regensburg, Germany
| | - Sebastian Bittner
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Chair for Immunology, University Regensburg, 93053 Regensburg, Germany
| | - Niklas Beumer
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany; DKFZ-Hector Cancer Institute at the University Medical Center Mannheim, 68167 Mannheim, Germany; Division of Personalized Medical Oncology, DKFZ, 69120 Heidelberg, Germany; Department of Personalized Oncology, University Hospital Mannheim, Medical Faculty Mannheim, University of Heidelberg, 68167 Mannheim, Germany
| | | | | | - Asmita Pant
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Chair for Immunology, University Regensburg, 93053 Regensburg, Germany
| | - Claudia Gebhard
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany
| | - Andreas Eigenberger
- Department of Plastic, Hand, and Reconstructive Surgery, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Michael Rehli
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Department of Internal Medicine III, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Lukas Prantl
- Department of Plastic, Hand, and Reconstructive Surgery, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Thomas Hehlgans
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Chair for Immunology, University Regensburg, 93053 Regensburg, Germany
| | - Benedikt Brors
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany; German Cancer Consortium (DKTK), DKFZ, 69120 Heidelberg, Germany; Medical Faculty Heidelberg and Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Charles D Imbusch
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Michael Delacher
- Institute of Immunology, University Medical Center Mainz, 55131 Mainz, Germany; Research Center for Immunotherapy, University Medical Center Mainz, 55131 Mainz, Germany
| | - Markus Feuerer
- Leibniz Institute for Immunotherapy, 93053 Regensburg, Germany; Chair for Immunology, University Regensburg, 93053 Regensburg, Germany.
| |
Collapse
|
14
|
Tao L, Yang X, Ge C, Zhang P, He W, Xu X, Li X, Chen W, Yu Y, Zhang H, Chen SD, Pan XY, Su Y, Xu C, Yu Y, Zheng MH, Min J, Wang F. Integrative clinical and preclinical studies identify FerroTerminator1 as a potent therapeutic drug for MASH. Cell Metab 2024:S1550-4131(24)00284-5. [PMID: 39142286 DOI: 10.1016/j.cmet.2024.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/27/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
The complex etiological factors associated with metabolic dysfunction-associated fatty liver disease (MAFLD), including perturbed iron homeostasis, and the unclear nature by which they contribute to disease progression have resulted in a limited number of effective therapeutic interventions. Here, we report that patients with metabolic dysfunction-associated steatohepatitis (MASH), a pathological subtype of MAFLD, exhibit excess hepatic iron and that it has a strong positive correlation with disease progression. FerroTerminator1 (FOT1) effectively reverses liver injury across multiple MASH models without notable toxic side effects compared with clinically approved iron chelators. Mechanistically, our multi-omics analyses reveal that FOT1 concurrently inhibits hepatic iron accumulation and c-Myc-Acsl4-triggered ferroptosis in various MASH models. Furthermore, MAFLD cohort studies suggest that serum ferritin levels might serve as a predictive biomarker for FOT1-based therapy in MASH. These findings provide compelling evidence to support FOT1 as a promising novel therapeutic option for all stages of MAFLD and for future clinical trials.
Collapse
Affiliation(s)
- Liang Tao
- School of Basic Medical Sciences, School of Public Health, School of Pharmaceutical Science, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xinquan Yang
- The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China; School of Public Health, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Chaodong Ge
- The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China; School of Public Health, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Peng Zhang
- School of Basic Medical Sciences, School of Public Health, School of Pharmaceutical Science, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Wenjian He
- School of Basic Medical Sciences, School of Public Health, School of Pharmaceutical Science, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Xingbo Xu
- The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Xin Li
- School of Basic Medical Sciences, School of Public Health, School of Pharmaceutical Science, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Wenteng Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Yingying Yu
- The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Huai Zhang
- Department of Biostatistics and Medical Record, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; MAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Sui-Dan Chen
- Department of Pathology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiao-Yan Pan
- Department of Endocrinology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yunxing Su
- The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Chengfu Xu
- Department of Gastroenterology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Yongping Yu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang Province, China
| | - Ming-Hua Zheng
- MAFLD Research Center, Department of Hepatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China; Key Laboratory of Diagnosis and Treatment for The Development of Chronic Liver Disease in Zhejiang Province, Wenzhou, Zhejiang, China.
| | - Junxia Min
- The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China.
| | - Fudi Wang
- School of Basic Medical Sciences, School of Public Health, School of Pharmaceutical Science, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang 421001, China; The Second Affiliated Hospital, The First Affiliated Hospital, Institute of Translational Medicine, School of Public Health, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou 310058, China; School of Public Health, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China.
| |
Collapse
|
15
|
Gongye X, Xia P, Ma T, Chai Y, Chen Z, Zhu Y, Qu C, Liu J, Guo WW, Zhang M, Liu Y, Tian M, Yuan Y. Liver Extracellular Vesicles and Particles Enriched β-Sitosterol Effectively Promote Liver Regeneration in Mice. Int J Nanomedicine 2024; 19:8117-8137. [PMID: 39139504 PMCID: PMC11319097 DOI: 10.2147/ijn.s465346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 07/31/2024] [Indexed: 08/15/2024] Open
Abstract
Background The liver's regenerative capacity allows it to repair itself after injury. Extracellular vesicles and particles (EVPs) in the liver's interstitial space are crucial for signal transduction, metabolism, and immune regulation. Understanding the role and mechanism of liver-derived EVPs in regeneration is significant, particularly after partial hepatectomy, where the mechanisms remain unclear. Methods A 70% hepatectomy model was established in mice, and EVPs were isolated and characterized using electron microscopy, nanocharacterization, and Western blot analysis. Combined metabolomic and transcriptomic analyses revealed β-sitosterol enrichment in EVPs and activation of the Hedgehog signaling pathway during regeneration. The role of β-sitosterol in EVPs on the Hedgehog pathway and its targets were identified using qRT-PCR, Western blot analysis. The regulation of carnitine synthesis by this pathway was determined using a dual luciferase assay. The effect of a β-sitosterol diet on liver regeneration was verified in mice. Results After 70% hepatectomy, the liver successfully regenerated without liver failure or death. At 24 hours post-surgery, tissue staining showed transient regeneration-associated steatosis (TRAS), with increased Ki67 positivity at 48 hours. EVPs displayed a spherical lipid bilayer structure with particle sizes of 70-130 nm. CD9, CD63, and CD81 in liver-derived EVPs were confirmed. Transcriptomic and metabolomic analyses showed EVPs supplementation significantly promoted carnitine synthesis and fatty acid oxidation. Tissue staining confirmed accelerated TRAS resolution and enhanced liver regeneration with EVP supplementation. Mass spectrometry identified β-sitosterol in EVPs, which binds to Smo protein, activating the Hedgehog pathway. This led to the nuclear transport of Gli3, stimulating Setd5 transcription and inducing carnitine synthesis, thereby accelerating fatty acid oxidation. Mice with increased β-sitosterol intake showed faster TRAS resolution and liver regeneration compared to controls. Conclusion Liver-derived EVPs promote regeneration after partial hepatectomy. β-sitosterol from EVPs accelerates fatty acid oxidation and promotes liver regeneration by activating Hedgehog signaling pathway.
Collapse
Affiliation(s)
- Xiangdong Gongye
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Peng Xia
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Tianyin Ma
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Yibo Chai
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Zhang Chen
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Yimin Zhu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Chengming Qu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Jie Liu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Wing Wa Guo
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Minghe Zhang
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Yingyi Liu
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Ming Tian
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
| | - Yufeng Yuan
- Department of Hepatobiliary & Pancreatic Surgery, Zhongnan Hospital of Wuhan University, Wuhan, People’s Republic of China
- Clinical Medicine Research Center for Minimally Invasive Procedure of Hepatobiliary & Pancreatic Diseases of Hubei Province, Hubei, People’s Republic of China
- Taikang Center for Life and Medical Sciences of Wuhan University, Wuhan, People’s Republic of China
| |
Collapse
|
16
|
Guinn MT, Fernandez R, Lau S, Loor G. Transcriptomic Signatures in Lung Allografts and Their Therapeutic Implications. Biomedicines 2024; 12:1793. [PMID: 39200257 PMCID: PMC11351513 DOI: 10.3390/biomedicines12081793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 07/20/2024] [Accepted: 08/01/2024] [Indexed: 09/02/2024] Open
Abstract
Ex vivo lung perfusion (EVLP) is a well-established method of lung preservation in clinical transplantation. Transcriptomic analyses of cells and tissues uncover gene expression patterns which reveal granular molecular pathways and cellular programs under various conditions. Coupling EVLP and transcriptomics may provide insights into lung allograft physiology at a molecular level with the potential to develop targeted therapies to enhance or repair the donor lung. This review examines the current landscape of transcriptional analysis of lung allografts in the context of state-of-the-art therapeutics that have been developed to optimize lung allograft function.
Collapse
Affiliation(s)
- Michael Tyler Guinn
- Division of Cardiothoracic Transplantation and Circulatory Support, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; (M.T.G.)
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Ramiro Fernandez
- Division of Cardiothoracic Transplantation and Circulatory Support, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; (M.T.G.)
| | - Sean Lau
- Department of Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Gabriel Loor
- Division of Cardiothoracic Transplantation and Circulatory Support, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX 77030, USA; (M.T.G.)
| |
Collapse
|
17
|
Skinner DJ, Lemaire P, Mani M. Physical modeling of embryonic transcriptomes identifies collective modes of gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.26.605398. [PMID: 39131269 PMCID: PMC11312445 DOI: 10.1101/2024.07.26.605398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Starting from one totipotent cell, complex multicellular organisms form through a series of differentiation and morphogenetic events, culminating in a multitude of cell types arranged in a functional and intricate spatial pattern. To do so, cells coordinate with each other, resulting in dynamics which follow a precise developmental trajectory, constraining the space of possible embryo-to-embryo variation. Using recent single-cell sequencing data of early ascidian embryos, we leverage natural variation together with modeling and inference techniques from statistical physics to investigate development at the level of a complete interconnected embryo - an embryonic transcriptome. After developing a robust and biophysically motivated approach to identifying distinct transcriptomic states or cell types, a statistical analysis reveals correlations within embryos and across cell types demonstrating the presence of collective variation. From these intra-embryo correlations, we infer minimal networks of cell-cell interactions, which reveal the collective modes of gene expression. Our work demonstrates how the existence and nature of spatial interactions along with the collective modes of expression that they give rise to can be inferred from single-cell gene expression measurements, opening up a wider range of biological questions that can be addressed using sequencing-based modalities.
Collapse
Affiliation(s)
- Dominic J Skinner
- Center for Computational Biology, Flatiron Institute, 162 5th Ave, New York, NY 10010, USA
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Patrick Lemaire
- CRBM, Université de Montpellier, CNRS, 34293 Montpellier, France
| | - Madhav Mani
- NSF-Simons Center for Quantitative Biology, Northwestern University, 2205 Tech Drive, Evanston, IL 60208, USA
- Department of Engineering Sciences and Applied Mathematics, Northwestern University, Evanston, IL 60208, USA
| |
Collapse
|
18
|
Madrigal A, Lu T, Soto LM, Najafabadi HS. A unified model for interpretable latent embedding of multi-sample, multi-condition single-cell data. Nat Commun 2024; 15:6573. [PMID: 39097589 PMCID: PMC11298001 DOI: 10.1038/s41467-024-50963-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 07/23/2024] [Indexed: 08/05/2024] Open
Abstract
Single-cell analysis across multiple samples and conditions requires quantitative modeling of the interplay between the continuum of cell states and the technical and biological sources of sample-to-sample variability. We introduce GEDI, a generative model that identifies latent space variations in multi-sample, multi-condition single-cell datasets and attributes them to sample-level covariates. GEDI enables cross-sample cell state mapping on par with state-of-the-art integration methods, cluster-free differential gene expression analysis along the continuum of cell states, and machine learning-based prediction of sample characteristics from single-cell data. GEDI can also incorporate gene-level prior knowledge to infer pathway and regulatory network activities in single cells. Finally, GEDI extends all these concepts to previously unexplored modalities that require joint consideration of dual measurements, such as the joint analysis of exon inclusion/exclusion reads to model alternative cassette exon splicing, or spliced/unspliced reads to model the mRNA stability landscapes of single cells.
Collapse
Affiliation(s)
- Ariel Madrigal
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, H3A 0G1, Canada
| | - Tianyuan Lu
- Lady Davis Institute for Medical Research, Montreal, QC, H3T 1E2, Canada
- Department of Statistical Sciences, University of Toronto, Toronto, ON, M5S 1A1, Canada
- Department of Population Health Sciences, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Larisa M Soto
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, H3A 0G1, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, H3A 0C7, Canada.
- Victor P. Dahdaleh Institute of Genomic Medicine, Montreal, QC, H3A 0G1, Canada.
- McGill Centre for RNA Sciences, McGill University, Montreal, Canada.
| |
Collapse
|
19
|
Korb A, Tajbakhsh S, Comai GE. Functional specialisation and coordination of myonuclei. Biol Rev Camb Philos Soc 2024; 99:1164-1195. [PMID: 38477382 DOI: 10.1111/brv.13063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 01/30/2024] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
Myofibres serve as the functional unit for locomotion, with the sarcomere as fundamental subunit. Running the entire length of this structure are hundreds of myonuclei, located at the periphery of the myofibre, juxtaposed to the plasma membrane. Myonuclear specialisation and clustering at the centre and ends of the fibre are known to be essential for muscle contraction, yet the molecular basis of this regionalisation has remained unclear. While the 'myonuclear domain hypothesis' helped explain how myonuclei can independently govern large cytoplasmic territories, novel technologies have provided granularity on the diverse transcriptional programs running simultaneously within the syncytia and added a new perspective on how myonuclei communicate. Building upon this, we explore the critical cellular and molecular sources of transcriptional and functional heterogeneity within myofibres, discussing the impact of intrinsic and extrinsic factors on myonuclear programs. This knowledge provides new insights for understanding muscle development, repair, and disease, but also opens avenues for the development of novel and precise therapeutic approaches.
Collapse
Affiliation(s)
- Amaury Korb
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| | - Shahragim Tajbakhsh
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| | - Glenda E Comai
- Institut Pasteur, Université Paris Cité, CNRS UMR 3738, Stem Cells & Development Unit, 25 rue du Dr. Roux, Institut Pasteur, Paris, F-75015, France
| |
Collapse
|
20
|
Zhang J, Wang E, Li Q, Peng Y, Jin H, Naseem S, Sun B, Park S, Choi S, Li X. GSK3 regulation Wnt/β-catenin signaling affects adipogenesis in bovine skeletal muscle fibro/adipogenic progenitors. Int J Biol Macromol 2024; 275:133639. [PMID: 38969042 DOI: 10.1016/j.ijbiomac.2024.133639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/31/2024] [Accepted: 06/22/2024] [Indexed: 07/07/2024]
Abstract
Clarifying the cellular origin and regulatory mechanisms of intramuscular fat (IMF) deposition is crucial for improving beef quality. Here, we used single-nucleus RNA sequencing to analyze the structure and heterogeneity of skeletal muscle cell populations in different developmental stages of Yanbian cattle and identified eight cell types in two developmental stages of calves and adults. Among them, fibro/adipogenic progenitors (FAPs) expressing CD29 (ITGA7)pos and CD56 (NCAM1)neg surface markers were committed to IMF deposition in beef cattle and expressed major Wnt ligands and receptors. LY2090314/XAV-939 was used to activate/inhibit Wnt/β-catenin signal. The results showed that the blockade of Glycogen Synthase Kinase 3 (GSK3) by LY2090314 promoted the stabilization of β-catenin and reduced the expression of genes related adipogenic differentiation (e.g., PPARγ and C/EBPα) in bovine FAPs, confirming the anti-adipogenic effect of GSK3. XAV-939 inhibition of the Wnt/β-catenin pathway promoted the lipid accumulation capacity of FAPs. Furthermore, we found that blocking GSK3 enhanced the paracrine effects of FAPs-MuSCs and increased myotube formation in muscle satellite cells (MuSCs). Overall, our results outline a single-cell atlas of skeletal muscle development in Yanbian cattle, revealed the role of Wnt/GSK3/β-catenin signaling in FAPs adipogenesis, and provide a theoretical basis for further regulation of bovine IMF deposition.
Collapse
Affiliation(s)
- Junfang Zhang
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China; Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Department of Animal Science, Yanbian University, Yanji 133002, China
| | - Enze Wang
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Department of Animal Science, Yanbian University, Yanji 133002, China
| | - Qiang Li
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Department of Animal Science, Yanbian University, Yanji 133002, China
| | - Yinghua Peng
- Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun 130112, China
| | - Huaina Jin
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Department of Animal Science, Yanbian University, Yanji 133002, China
| | - Sajida Naseem
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Department of Animal Science, Yanbian University, Yanji 133002, China
| | - Bin Sun
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Department of Animal Science, Yanbian University, Yanji 133002, China
| | - Sungkwon Park
- Department of Food Science and Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Seongho Choi
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Xiangzi Li
- Engineering Research Center of North-East Cold Region Beef Cattle Science & Technology Innovation, Ministry of Education, Department of Animal Science, Yanbian University, Yanji 133002, China.
| |
Collapse
|
21
|
Rosen Y, Brbić M, Roohani Y, Swanson K, Li Z, Leskovec J. Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN. Nat Methods 2024; 21:1492-1500. [PMID: 38366243 PMCID: PMC11310084 DOI: 10.1038/s41592-024-02191-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint analysis of cross-species datasets to homologous genes. Here we present SATURN, a deep learning method for learning universal cell embeddings that encodes genes' biological properties using protein language models. By coupling protein embeddings from language models with RNA expression, SATURN integrates datasets profiled from different species regardless of their genomic similarity. SATURN can detect functionally related genes coexpressed across species, redefining differential expression for cross-species analysis. Applying SATURN to three species whole-organism atlases and frog and zebrafish embryogenesis datasets, we show that SATURN can effectively transfer annotations across species, even when they are evolutionarily remote. We also demonstrate that SATURN can be used to find potentially divergent gene functions between glaucoma-associated genes in humans and four other species.
Collapse
Affiliation(s)
- Yanay Rosen
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Maria Brbić
- School of Computer and Communication Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Yusuf Roohani
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kyle Swanson
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Ziang Li
- Department of Computer Science and Technology, Tsinghua University, Beijing, China
| | - Jure Leskovec
- Department of Computer Science, Stanford University, Stanford, CA, USA.
| |
Collapse
|
22
|
Perez-Gutierrez L, Li P, Ferrara N. Endothelial cell diversity: the many facets of the crystal. FEBS J 2024; 291:3287-3302. [PMID: 36266750 DOI: 10.1111/febs.16660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 10/03/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022]
Abstract
Endothelial cells (ECs) form the inner lining of blood vessels and play crucial roles in angiogenesis. While it has been known for a long time that there are considerable differences among ECs from lymphatic and blood vessels, as well as among arteries, veins and capillaries, the full repertoire of endothelial diversity is only beginning to be elucidated. It has become apparent that the role of ECs is not just limited to their exchange functions. Indeed, a multitude of organ-specific functions, including release of growth factors, regulation of immune functions, have been linked to ECs. Recent years have seen a surge into the identification of spatiotemporal molecular and functional heterogeneity of ECs, supported by technologies such as single-cell RNA sequencing (scRNA-seq), lineage tracing and intersectional genetics. Together, these techniques have spurred the generation of epigenomic, transcriptomic and proteomic signatures of ECs. It is now clear that ECs across organs and in different vascular beds, but even within the same vessel, have unique molecular identities and employ specialized molecular mechanisms to fulfil highly specialized needs. Here, we focus on the molecular heterogeneity of the endothelium in different organs and pathological conditions.
Collapse
Affiliation(s)
- Lorena Perez-Gutierrez
- Department of Pathology, Moores Cancer Center, University of California, San Diego, CA, USA
| | - Pin Li
- Department of Pathology, Moores Cancer Center, University of California, San Diego, CA, USA
| | - Napoleone Ferrara
- Department of Pathology, Moores Cancer Center, University of California, San Diego, CA, USA
| |
Collapse
|
23
|
Ljungholm PL, Ermund A, Söderlund Garsveden MM, Pettersson VL, Gustafsson JK. The anion exchanger slc26a3 regulates colonic mucus expansion during steady state and in response to prostaglandin E 2, while Cftr regulates de novo mucus release in response to carbamylcholine. Pflugers Arch 2024; 476:1209-1219. [PMID: 38829391 PMCID: PMC11271379 DOI: 10.1007/s00424-024-02975-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/02/2024] [Accepted: 05/19/2024] [Indexed: 06/05/2024]
Abstract
The intestinal epithelium is covered by mucus that protects the tissue from the luminal content. Studies have shown that anion secretion via the cystic fibrosis conductance regulator (Cftr) regulates mucus formation in the small intestine. However, mechanisms regulating mucus formation in the colon are less understood. The aim of this study was to explore the role of anion transport in the regulation of mucus formation during steady state and in response to carbamylcholine (CCh) and prostaglandin E2 (PGE2). The broad-spectrum anion transport inhibitor 4,4'-diisothiocyanatostilbene-2,2'-disulfonate (DIDS), CftrdF508 (CF) mice, and the slc26a3 inhibitor SLC26A3-IN-2 were used to inhibit anion transport. In the distal colon, steady-state mucus expansion was reduced by SLC26A3-IN-2 and normal in CF mice. PGE2 stimulated mucus expansion without de novo mucus release in wild type (WT) and CF colon via slc26a3 sensitive mechanisms, while CCh induced de novo mucus secretion in WT but not in CF colon. However, when added simultaneously, CCh and PGE2 stimulated de novo mucus secretion in the CF colon via DIDS-sensitive pathways. A similar response was observed in CF ileum that responded to CCh and PGE2 with DIDS-sensitive de novo mucus secretion. In conclusion, this study suggests that slc26a3 regulates colonic mucus expansion, while Cftr regulates CCh-induced de novo mucus secretion from ileal and distal colon crypts. Furthermore, these findings demonstrate that in the absence of a functional Cftr channel, parallel stimulation with CCh and PGE2 activates additional anion transport processes that help release mucus from intestinal goblet cells.
Collapse
Affiliation(s)
- Penny L Ljungholm
- Department of Physiology, University of Gothenburg, Medicinaregatan 11, Box 432, 405 30, Gothenburg, Sweden
| | - Anna Ermund
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | | | - Victor L Pettersson
- Department of Physiology, University of Gothenburg, Medicinaregatan 11, Box 432, 405 30, Gothenburg, Sweden
| | - Jenny K Gustafsson
- Department of Physiology, University of Gothenburg, Medicinaregatan 11, Box 432, 405 30, Gothenburg, Sweden.
- Department of Medical Chemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
24
|
Borrelli C, Roberts M, Eletto D, Hussherr MD, Fazilaty H, Valenta T, Lafzi A, Kretz JA, Guido Vinzoni E, Karakatsani A, Adivarahan S, Mannhart A, Kimura S, Meijs A, Baccouche Mhamedi F, Acar IE, Handler K, Ficht X, Platt RJ, Piscuoglio S, Moor AE. In vivo interaction screening reveals liver-derived constraints to metastasis. Nature 2024; 632:411-418. [PMID: 39048831 PMCID: PMC11306111 DOI: 10.1038/s41586-024-07715-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
It is estimated that only 0.02% of disseminated tumour cells are able to seed overt metastases1. While this suggests the presence of environmental constraints to metastatic seeding, the landscape of host factors controlling this process remains largely unclear. Here, combining transposon technology2 and fluorescence niche labelling3, we developed an in vivo CRISPR activation screen to systematically investigate the interactions between hepatocytes and metastatic cells. We identify plexin B2 as a critical host-derived regulator of liver colonization in colorectal and pancreatic cancer and melanoma syngeneic mouse models. We dissect a mechanism through which plexin B2 interacts with class IV semaphorins on tumour cells, leading to KLF4 upregulation and thereby promoting the acquisition of epithelial traits. Our results highlight the essential role of signals from the liver parenchyma for the seeding of disseminated tumour cells before the establishment of a growth-promoting niche. Our findings further suggest that epithelialization is required for the adaptation of CRC metastases to their new tissue environment. Blocking the plexin-B2-semaphorin axis abolishes metastatic colonization of the liver and therefore represents a therapeutic strategy for the prevention of hepatic metastases. Finally, our screening approach, which evaluates host-derived extrinsic signals rather than tumour-intrinsic factors for their ability to promote metastatic seeding, is broadly applicable and lays a framework for the screening of environmental constraints to metastasis in other organs and cancer types.
Collapse
Affiliation(s)
- Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Morgan Roberts
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Davide Eletto
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Hassan Fazilaty
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Tomas Valenta
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Laboratory of Cell and Developmental Biology, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Atefeh Lafzi
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Jonas A Kretz
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Elena Guido Vinzoni
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | | | - Ardian Mannhart
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Shoichiro Kimura
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Ab Meijs
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | | | - Ilhan E Acar
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Kristina Handler
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Xenia Ficht
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Randall J Platt
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
| | - Salvatore Piscuoglio
- IRCCS Humanitas Research Hospital, Milan, Italy
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland.
| |
Collapse
|
25
|
Ghosh G, Shannon AE, Searle BC. Data acquisition approaches for single cell proteomics. Proteomics 2024:e2400022. [PMID: 39088833 DOI: 10.1002/pmic.202400022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 08/03/2024]
Abstract
Single-cell proteomics (SCP) aims to characterize the proteome of individual cells, providing insights into complex biological systems. It reveals subtle differences in distinct cellular populations that bulk proteome analysis may overlook, which is essential for understanding disease mechanisms and developing targeted therapies. Mass spectrometry (MS) methods in SCP allow the identification and quantification of thousands of proteins from individual cells. Two major challenges in SCP are the limited material in single-cell samples necessitating highly sensitive analytical techniques and the efficient processing of samples, as each biological sample requires thousands of single cell measurements. This review discusses MS advancements to mitigate these challenges using data-dependent acquisition (DDA) and data-independent acquisition (DIA). Additionally, we examine the use of short liquid chromatography gradients and sample multiplexing methods that increase the sample throughput and scalability of SCP experiments. We believe these methods will pave the way for improving our understanding of cellular heterogeneity and its implications for systems biology.
Collapse
Affiliation(s)
- Gautam Ghosh
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Ariana E Shannon
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
| | - Brian C Searle
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
- Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA
| |
Collapse
|
26
|
Kiefer MF, Meng Y, Yang N, Vahrenbrink M, Wulff S, Li C, Wowro SJ, Petricek KM, Sommerfeld M, Flores RE, Obermayer B, Piepelow K, Klaus S, Hartl K, Guillot A, Tacke F, Sigal M, Schupp M. Intestinal retinol saturase is implicated in the development of obesity and epithelial homeostasis upon injury. Am J Physiol Endocrinol Metab 2024; 327:E203-E216. [PMID: 38895981 DOI: 10.1152/ajpendo.00035.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
Retinol saturase (RetSat) is an oxidoreductase involved in lipid metabolism and the cellular sensitivity to peroxides. RetSat is highly expressed in metabolic organs like the liver and adipose tissue and its global loss in mice increases body weight and adiposity. The regulation of RetSat expression and its function in the intestine are unexplored. Here, we show that RetSat is present in different segments of the digestive system, localizes to intestinal epithelial cells, and is upregulated by feeding mice high-fat diet (HFD). Intestine-specific RetSat deletion in adult mice did not affect nutrient absorption and energy homeostasis basally, but lowered body weight gain and fat mass of HFD-fed mice, potentially via increasing locomotor activity. Moreover, jejunal expression of genes related to β-oxidation and cholesterol efflux was decreased, and colonic cholesterol content was reduced upon RetSat deletion. In colitis, which we show to downregulate intestinal RetSat expression in humans and mice, RetSat ablation improved epithelial architecture of the murine colon. Thus, intestinal RetSat expression is regulated by dietary interventions and inflammation, and its loss reduces weight gain upon HFD feeding and alleviates epithelial damage upon injury.NEW & NOTEWORTHY Retinol saturase (RetSat) is an oxidoreductase with unknown function in the intestine. We found that RetSat localizes in intestinal epithelial cells and that its deletion reduced weight gain and fat mass in obese mice. In colitis, which decreased intestinal RetSat expression in humans and mice, RetSat ablation improved the epithelial architecture of the murine colon, presumably by decreasing ROS production, thus rendering RetSat a novel target for metabolic and inflammatory bowel disease.
Collapse
Affiliation(s)
- Marie F Kiefer
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Bioanalytics Unit, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Yueming Meng
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Na Yang
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Madita Vahrenbrink
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sascha Wulff
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Chen Li
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sylvia J Wowro
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Konstantin M Petricek
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Manuela Sommerfeld
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Roberto E Flores
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Benedikt Obermayer
- Core Unit Bioinformatics, Berlin Institute of Health, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Karolin Piepelow
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, Nuthetal, Germany
| | - Susanne Klaus
- Department of Physiology of Energy Metabolism, German Institute of Human Nutrition (DIfE) Potsdam-Rehbrücke, Nuthetal, Germany
- Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Kimberly Hartl
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Adrien Guillot
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Michael Sigal
- Department of Hepatology and Gastroenterology, Campus Virchow-Klinikum (CVK) and Campus Charité Mitte (CCM), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Michael Schupp
- Max Rubner Center (MRC) for Cardiovascular Metabolic Renal Research, Institute of Pharmacology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| |
Collapse
|
27
|
Wälchli T, Ghobrial M, Schwab M, Takada S, Zhong H, Suntharalingham S, Vetiska S, Gonzalez DR, Wu R, Rehrauer H, Dinesh A, Yu K, Chen ELY, Bisschop J, Farnhammer F, Mansur A, Kalucka J, Tirosh I, Regli L, Schaller K, Frei K, Ketela T, Bernstein M, Kongkham P, Carmeliet P, Valiante T, Dirks PB, Suva ML, Zadeh G, Tabar V, Schlapbach R, Jackson HW, De Bock K, Fish JE, Monnier PP, Bader GD, Radovanovic I. Single-cell atlas of the human brain vasculature across development, adulthood and disease. Nature 2024; 632:603-613. [PMID: 38987604 PMCID: PMC11324530 DOI: 10.1038/s41586-024-07493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 04/30/2024] [Indexed: 07/12/2024]
Abstract
A broad range of brain pathologies critically relies on the vasculature, and cerebrovascular disease is a leading cause of death worldwide. However, the cellular and molecular architecture of the human brain vasculature remains incompletely understood1. Here we performed single-cell RNA sequencing analysis of 606,380 freshly isolated endothelial cells, perivascular cells and other tissue-derived cells from 117 samples, from 68 human fetuses and adult patients to construct a molecular atlas of the developing fetal, adult control and diseased human brain vasculature. We identify extensive molecular heterogeneity of the vasculature of healthy fetal and adult human brains and across five vascular-dependent central nervous system (CNS) pathologies, including brain tumours and brain vascular malformations. We identify alteration of arteriovenous differentiation and reactivated fetal as well as conserved dysregulated genes and pathways in the diseased vasculature. Pathological endothelial cells display a loss of CNS-specific properties and reveal an upregulation of MHC class II molecules, indicating atypical features of CNS endothelial cells. Cell-cell interaction analyses predict substantial endothelial-to-perivascular cell ligand-receptor cross-talk, including immune-related and angiogenic pathways, thereby revealing a central role for the endothelium within brain neurovascular unit signalling networks. Our single-cell brain atlas provides insights into the molecular architecture and heterogeneity of the developing, adult/control and diseased human brain vasculature and serves as a powerful reference for future studies.
Collapse
Affiliation(s)
- Thomas Wälchli
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland.
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland.
| | - Moheb Ghobrial
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Marc Schwab
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Institute for Regenerative Medicine, University of Zurich, Zurich, Switzerland
| | - Shigeki Takada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Neurosurgery, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Hang Zhong
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Samuel Suntharalingham
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sandra Vetiska
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | | | - Ruilin Wu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Anuroopa Dinesh
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
| | - Kai Yu
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
| | - Edward L Y Chen
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jeroen Bisschop
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Fiona Farnhammer
- Group Brain Vasculature and Perivascular Niche, Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ann Mansur
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Joanna Kalucka
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Itay Tirosh
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Luca Regli
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Karl Schaller
- Department of Neurosurgery, University of Geneva Medical Center & Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Karl Frei
- Group of CNS Angiogenesis and Neurovascular Link, Neuroscience Center Zurich, University of Zurich and University Hospital Zurich, Zurich, Switzerland
- Division of Neurosurgery, University Hospital Zurich, Zurich, Switzerland
| | - Troy Ketela
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Mark Bernstein
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Paul Kongkham
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- MacFeeters-Hamilton Centre for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB & Department of Oncology, KU Leuven, Leuven, Belgium
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, P. R. China
- Laboratory of Angiogenesis and Vascular Heterogeneity, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Taufik Valiante
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Krembil Brain Institute, Division of Clinical and Computational Neuroscience, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Institute of Biomaterials and Biomedical Engineering and Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Peter B Dirks
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Arthur and Sonia Labatt Brain Tumor Research Center, Departments of Surgery and Molecular Genetics, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mario L Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Viviane Tabar
- Department of Neurosurgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, ETH Zurich/University of Zurich, Zurich, Switzerland
| | - Hartland W Jackson
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute of Cancer Research, Toronto, Ontario, Canada
| | - Katrien De Bock
- Laboratory of Exercise and Health, Institute of Exercise and Health, Department of Health Sciences and Technology; Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jason E Fish
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Toronto General Hospital Research Institute, University Health Network, Toronto, Ontario, Canada
- Peter Munk Cardiac Centre, University Health Network, Toronto, Ontario, Canada
| | - Philippe P Monnier
- Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Krembil Research Institute, Vision Division, Krembil Discovery Tower, Toronto, Ontario, Canada
- Department of Ophthalmology and Vision Sciences, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Gary D Bader
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - Ivan Radovanovic
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
- Division of Experimental and Translational Neuroscience, Krembil Brain Institute, Krembil Research Institute, Toronto Western Hospital, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Sprott Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
28
|
Wang Q, Lan X, Ke H, Xu S, Huang C, Wang J, Wang X, Huang T, Wu X, Chen M, Guo Y, Zeng L, Tian XL, Xiang Y. Histone β-hydroxybutyrylation is critical in reversal of sarcopenia. Aging Cell 2024:e14284. [PMID: 39076122 DOI: 10.1111/acel.14284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/30/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
Sarcopenia, a leading cause for global disability and mortality, is an age-related muscular disorder, characterized by accelerated muscle mass loss and functional decline. It is known that caloric restriction (CR), ketogenic diet or endurance exercise lessen sarcopenia and elevate circulating β-hydroxybutyrate (β-HB) levels. Whether the elevated β-HB is essential to the reversal of sarcopenia, however, remains unclear. Here we show in both Caenorhabditis elegans and mouse models that an increase of β-HB reverse myofiber atrophy and improves motor functions at advanced ages. β-HB-induced histone lysine β-hydroxybutyrylation (Kbhb) is indispensable for the reversal of sarcopenia. Histone Kbhb enhances transcription of genes associated with mitochondrial pathways, including oxidative phosphorylation, ATP metabolic process and aerobic respiration. This ultimately leads to improve mitochondrial integrity and enhance mitochondrial respiration. The histone Kbhb are validated in mouse model with CR. Thus, we demonstrate that β-HB induces histone Kbhb, increases mitochondrial function, and reverses sarcopenia.
Collapse
Affiliation(s)
- Qiquan Wang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Xinqiang Lan
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Hao Ke
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Siman Xu
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Chunping Huang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Jiali Wang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Xiang Wang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Tiane Huang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Xia Wu
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Mengxin Chen
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Yingqi Guo
- Institutional Center for Shared Technologies and Facilities of the Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Lin Zeng
- Institutional Center for Shared Technologies and Facilities of the Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Li Tian
- Aging and Vascular Diseases, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| | - Yang Xiang
- Metabolic Control and Aging, Human Aging Research Institute and School of Life Science, Nanchang University, and Jiangxi Key Laboratory of Aging and Diseases, Nanchang, China
| |
Collapse
|
29
|
Ranard KM, Appel B. Creation of a novel zebrafish model with low DHA status to study the role of maternal nutrition during neurodevelopment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.30.605803. [PMID: 39131270 PMCID: PMC11312534 DOI: 10.1101/2024.07.30.605803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Docosahexaenoic acid (DHA), a dietary omega-3 fatty acid, is a major building block of brain cell membranes. Offspring rely on maternal DHA transfer to meet their neurodevelopmental needs, but DHA sources are lacking in the American diet. Low DHA status is linked to altered immune responses, white matter defects, impaired vision, and an increased risk of psychiatric disorders during development. However, the underlying cellular mechanisms involved are largely unknown, and advancements in the field have been limited by the existing tools and animal models. Zebrafish are an excellent model for studying neurodevelopmental mechanisms. Embryos undergo rapid external development and are optically transparent, enabling direct observation of individual cells and dynamic cell-cell interactions in a way that is not possible in rodents. Here, we create a novel DHA-deficient zebrafish model by 1) disrupting elovl2, a key gene in the DHA biosynthesis pathway, via CRISPR-Cas9 genome editing, and 2) feeding mothers a DHA-deficient diet. We show that low DHA status during development is associated with a small eye morphological phenotype and demonstrate that even the morphologically normal siblings exhibit dysregulated gene pathways related to vision and stress response. Future work using our zebrafish model could reveal the cellular and molecular mechanisms by which low DHA status leads to neurodevelopmental abnormalities and provide insight into maternal nutritional strategies that optimize infant brain health.
Collapse
Affiliation(s)
- Katherine M Ranard
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bruce Appel
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| |
Collapse
|
30
|
Antounians L, Figueira RL, Kukreja B, Litvack ML, Zani-Ruttenstock E, Khalaj K, Montalva L, Doktor F, Obed M, Blundell M, Wu T, Chan C, Wagner R, Lacher M, Wilson MD, Post M, Kalish BT, Zani A. Fetal hypoplastic lungs have multilineage inflammation that is reversed by amniotic fluid stem cell extracellular vesicle treatment. SCIENCE ADVANCES 2024; 10:eadn5405. [PMID: 39058789 PMCID: PMC11277482 DOI: 10.1126/sciadv.adn5405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 06/21/2024] [Indexed: 07/28/2024]
Abstract
Antenatal administration of extracellular vesicles from amniotic fluid stem cells (AFSC-EVs) reverses features of pulmonary hypoplasia in models of congenital diaphragmatic hernia (CDH). However, it remains unknown which lung cellular compartments and biological pathways are affected by AFSC-EV therapy. Herein, we conducted single-nucleus RNA sequencing (snRNA-seq) on rat fetal CDH lungs treated with vehicle or AFSC-EVs. We identified that intra-amniotically injected AFSC-EVs reach the fetal lung in rats with CDH, where they promote lung branching morphogenesis and epithelial cell differentiation. Moreover, snRNA-seq revealed that rat fetal CDH lungs have a multilineage inflammatory signature with macrophage enrichment, which is reversed by AFSC-EV treatment. Macrophage enrichment in CDH fetal rat lungs was confirmed by immunofluorescence, flow cytometry, and inhibition studies with GW2580. Moreover, we validated macrophage enrichment in human fetal CDH lung autopsy samples. Together, this study advances knowledge on the pathogenesis of pulmonary hypoplasia and further evidence on the value of an EV-based therapy for CDH fetuses.
Collapse
Affiliation(s)
- Lina Antounians
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Rebeca Lopes Figueira
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Bharti Kukreja
- Neurosciences and Mental Health Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Michael L. Litvack
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Elke Zani-Ruttenstock
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Kasra Khalaj
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Louise Montalva
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Fabian Doktor
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Mikal Obed
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Matisse Blundell
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Taiyi Wu
- Neurosciences and Mental Health Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
| | - Cadia Chan
- Genetics and Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Richard Wagner
- Department of Pediatric Surgery, Leipzig University, Leipzig 04109, Germany
| | - Martin Lacher
- Department of Pediatric Surgery, Leipzig University, Leipzig 04109, Germany
| | - Michael D. Wilson
- Genetics and Genome Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
| | - Martin Post
- Translational Medicine Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5T 1P5, Canada
| | - Brian T. Kalish
- Neurosciences and Mental Health Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Department of Molecular Genetics, University of Toronto, Toronto M5S 1A8, Canada
- Division of Neonatology, The Hospital for Sick Children, Toronto M5G 1X8, Canada
| | - Augusto Zani
- Developmental and Stem Cell Biology Program, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto M5G 0A4, Canada
- Division of General and Thoracic Surgery, The Hospital for Sick Children, Toronto M5G 1X8, Canada
- Department of Surgery, University of Toronto, Toronto M5T 1P5, Canada
| |
Collapse
|
31
|
Lin Y, Pan Z, Zeng Y, Yang Y, Dai Z. Detecting novel cell type in single-cell chromatin accessibility data via open-set domain adaptation. Brief Bioinform 2024; 25:bbae370. [PMID: 39073828 DOI: 10.1093/bib/bbae370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/27/2024] [Accepted: 07/15/2024] [Indexed: 07/30/2024] Open
Abstract
Recent advances in single-cell technologies enable the rapid growth of multi-omics data. Cell type annotation is one common task in analyzing single-cell data. It is a challenge that some cell types in the testing set are not present in the training set (i.e. unknown cell types). Most scATAC-seq cell type annotation methods generally assign each cell in the testing set to one known type in the training set but neglect unknown cell types. Here, we present OVAAnno, an automatic cell types annotation method which utilizes open-set domain adaptation to detect unknown cell types in scATAC-seq data. Comprehensive experiments show that OVAAnno successfully identifies known and unknown cell types. Further experiments demonstrate that OVAAnno also performs well on scRNA-seq data. Our codes are available online at https://github.com/lisaber/OVAAnno/tree/master.
Collapse
Affiliation(s)
- Yuefan Lin
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zixiang Pan
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuansong Zeng
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| | - Zhiming Dai
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China
| |
Collapse
|
32
|
Fu Q, Dong C, Liu Y, Xia X, Liu G, Zhong F, Liu L. A comparison of scRNA-seq annotation methods based on experimentally labeled immune cell subtype dataset. Brief Bioinform 2024; 25:bbae392. [PMID: 39120646 PMCID: PMC11312369 DOI: 10.1093/bib/bbae392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/04/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Cell-type annotation is a critical step in single-cell data analysis. With the development of numerous cell annotation methods, it is necessary to evaluate these methods to help researchers use them effectively. Reference datasets are essential for evaluation, but currently, the cell labels of reference datasets mainly come from computational methods, which may have computational biases and may not reflect the actual cell-type outcomes. This study first constructed an experimentally labeled immune cell-subtype single-cell dataset of the same batch and systematically evaluated 18 cell annotation methods. We assessed those methods under five scenarios, including intra-dataset validation, immune cell-subtype validation, unsupervised clustering, inter-dataset annotation, and unknown cell-type prediction. Accuracy and ARI were evaluation metrics. The results showed that SVM, scBERT, and scDeepSort were the best-performing supervised methods. Seurat was the best-performing unsupervised clustering method, but it couldn't fully fit the actual cell-type distribution. Our results indicated that experimentally labeled immune cell-subtype datasets revealed the deficiencies of unsupervised clustering methods and provided new dataset support for supervised methods.
Collapse
Affiliation(s)
- Qiqing Fu
- Institutes of Biomedical Sciences, Fudan University, 200032 Shanghai, P.R. China
| | - Chenyu Dong
- Institutes of Biomedical Sciences, Fudan University, 200032 Shanghai, P.R. China
| | - Yunhe Liu
- Institutes of Biomedical Sciences, Fudan University, 200032 Shanghai, P.R. China
| | - Xiaoqiong Xia
- Institutes of Biomedical Sciences, Fudan University, 200032 Shanghai, P.R. China
| | - Gang Liu
- Institutes of Biomedical Sciences, Fudan University, 200032 Shanghai, P.R. China
| | - Fan Zhong
- Intelligent Medicine Institute, Fudan University, 200032 Shanghai, P.R. China
| | - Lei Liu
- Intelligent Medicine Institute, Fudan University, 200032 Shanghai, P.R. China
| |
Collapse
|
33
|
Furrer R, Handschin C. Molecular aspects of the exercise response and training adaptation in skeletal muscle. Free Radic Biol Med 2024:S0891-5849(24)00572-0. [PMID: 39059515 DOI: 10.1016/j.freeradbiomed.2024.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/13/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024]
Abstract
Skeletal muscle plasticity enables an enormous potential to adapt to various internal and external stimuli and perturbations. Most notably, changes in contractile activity evoke a massive remodeling of biochemical, metabolic and force-generating properties. In recent years, a large number of signals, sensors, regulators and effectors have been implicated in these adaptive processes. Nevertheless, our understanding of the molecular underpinnings of training adaptation remains rudimentary. Specifically, the mechanisms that underlie signal integration, output coordination, functional redundancy and other complex traits of muscle adaptation are unknown. In fact, it is even unclear how stimulus-dependent specification is brought about in endurance or resistance exercise. In this review, we will provide an overview on the events that describe the acute perturbations in single endurance and resistance exercise bouts. Furthermore, we will provide insights into the molecular principles of long-term training adaptation. Finally, current gaps in knowledge will be identified, and strategies for a multi-omic and -cellular analyses of the molecular mechanisms of skeletal muscle plasticity that are engaged in individual, acute exercise bouts and chronic training adaptation discussed.
Collapse
Affiliation(s)
- Regula Furrer
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
| | | |
Collapse
|
34
|
Sanz-Flores M, Ruiz-Torres M, Aguirre-Portolés C, El Bakkali A, Salvador-Barberó B, Villarroya-Beltri C, Ortega S, Megías D, Gerlich DW, Álvarez-Fernández M, Malumbres M. PP2A-B55 phosphatase counteracts Ki-67-dependent chromosome individualization during mitosis. Cell Rep 2024; 43:114494. [PMID: 39003739 PMCID: PMC11290319 DOI: 10.1016/j.celrep.2024.114494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/10/2024] [Accepted: 06/26/2024] [Indexed: 07/16/2024] Open
Abstract
Cell cycle progression is regulated by the orderly balance between kinase and phosphatase activities. PP2A phosphatase holoenzymes containing the B55 family of regulatory B subunits function as major CDK1-counteracting phosphatases during mitotic exit in mammals. However, the identification of the specific mitotic roles of these PP2A-B55 complexes has been hindered by the existence of multiple B55 isoforms. Here, through the generation of loss-of-function genetic mouse models for the two ubiquitous B55 isoforms (B55α and B55δ), we report that PP2A-B55α and PP2A-B55δ complexes display overlapping roles in controlling the dynamics of proper chromosome individualization and clustering during mitosis. In the absence of PP2A-B55 activity, mitotic cells display increased chromosome individualization in the presence of enhanced phosphorylation and perichromosomal loading of Ki-67. These data provide experimental evidence for a regulatory mechanism by which the balance between kinase and PP2A-B55 phosphatase activity controls the Ki-67-mediated spatial organization of the mass of chromosomes during mitosis.
Collapse
Affiliation(s)
- María Sanz-Flores
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Miguel Ruiz-Torres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Aicha El Bakkali
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | | | | | | | - Daniel W Gerlich
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria
| | - Mónica Álvarez-Fernández
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Health Research Institute of Asturias (ISPA), University Institute of Oncology of Asturias (IUOPA), University of Oviedo, Oviedo, Spain.
| | - Marcos Malumbres
- Cell Division and Cancer Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain; Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Barcelona, Spain; ICREA, Barcelona, Spain.
| |
Collapse
|
35
|
Mattar P, Reginato A, Lavados C, Das D, Kalyani M, Martinez-Lopez N, Sharma M, Skovbjerg G, Skytte JL, Roostalu U, Subbarayan R, Picarda E, Zang X, Zhang J, Guha C, Schwartz G, Rajbhandari P, Singh R. Insulin and leptin oscillations license food-entrained browning and metabolic flexibility. Cell Rep 2024; 43:114390. [PMID: 38900636 DOI: 10.1016/j.celrep.2024.114390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/23/2024] [Accepted: 06/06/2024] [Indexed: 06/22/2024] Open
Abstract
Timed feeding drives adipose browning, although the integrative mechanisms for the same remain unclear. Here, we show that twice-a-night (TAN) feeding generates biphasic oscillations of circulating insulin and leptin, representing their entrainment by timed feeding. Insulin and leptin surges lead to marked cellular, functional, and metabolic remodeling of subcutaneous white adipose tissue (sWAT), resulting in increased energy expenditure. Single-cell RNA-sequencing (scRNA-seq) analyses and flow cytometry demonstrate a role for insulin and leptin surges in innate lymphoid type 2 (ILC2) cell recruitment and sWAT browning, since sWAT depot denervation or loss of leptin or insulin receptor signaling or ILC2 recruitment each dampens TAN feeding-induced sWAT remodeling and energy expenditure. Consistently, recreating insulin and leptin oscillations via once-a-day timed co-injections is sufficient to favorably remodel innervated sWAT. Innervation is necessary for sWAT remodeling, since denervation of sWAT, but not brown adipose tissue (BAT), blocks TAN-induced sWAT remodeling and resolution of inflammation. In sum, reorganization of nutrient-sensitive pathways remodels sWAT and drives the metabolic benefits of timed feeding.
Collapse
Affiliation(s)
- Pamela Mattar
- Department of Medicine, Division of Digestive Diseases, University of Los Angeles, Los Angeles, CA, USA
| | - Andressa Reginato
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Christian Lavados
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Debajyoti Das
- Department of Medicine, Division of Digestive Diseases, University of Los Angeles, Los Angeles, CA, USA
| | - Manu Kalyani
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nuria Martinez-Lopez
- Department of Medicine, Division of Digestive Diseases, University of Los Angeles, Los Angeles, CA, USA; Comprehensive Liver Research Center at UCLA, University of Los Angeles, Los Angeles, CA, USA
| | - Mridul Sharma
- Department of Medicine, Division of Digestive Diseases, University of Los Angeles, Los Angeles, CA, USA
| | | | | | | | | | - Elodie Picarda
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xingxing Zang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jinghang Zhang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Chandan Guha
- Radiation Oncology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gary Schwartz
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Prashant Rajbhandari
- Department of Medicine, Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rajat Singh
- Department of Medicine, Division of Digestive Diseases, University of Los Angeles, Los Angeles, CA, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA; Comprehensive Liver Research Center at UCLA, University of Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
36
|
Noller K, Cahan P. Cell cycle expression heterogeneity predicts degree of differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.19.604184. [PMID: 39091773 PMCID: PMC11291076 DOI: 10.1101/2024.07.19.604184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Methods that predict fate potential or degree of differentiation from transcriptomic data have identified rare progenitor populations and uncovered developmental regulatory mechanisms. However, some state-of-the-art methods are too computationally burdensome for emerging large-scale data and all methods make inaccurate predictions in certain biological systems. We developed a method in R (stemFinder) that predicts single cell differentiation time based on heterogeneity in cell cycle gene expression. Our method is computationally tractable and is as good as or superior to competitors. As part of our benchmarking, we implemented four different performance metrics to assist potential users in selecting the tool that is most apt for their application. Finally, we explore the relationship between differentiation time and cell fate potential by analyzing a lineage tracing dataset with clonally labelled hematopoietic cells, revealing that metrics of differentiation time are correlated with the number of downstream lineages.
Collapse
Affiliation(s)
- Kathleen Noller
- Institute for Cell Engineering, Johns Hopkins University, Baltimore MD USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD USA
| | - Patrick Cahan
- Institute for Cell Engineering, Johns Hopkins University, Baltimore MD USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore MD USA
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore MD USA
| |
Collapse
|
37
|
Zhao Y, Kohl C, Rosebrock D, Hu Q, Hu Y, Vingron M. CAbiNet: joint clustering and visualization of cells and genes for single-cell transcriptomics. Nucleic Acids Res 2024; 52:e57. [PMID: 38850160 PMCID: PMC11260446 DOI: 10.1093/nar/gkae480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 04/10/2024] [Accepted: 05/27/2024] [Indexed: 06/10/2024] Open
Abstract
A fundamental analysis task for single-cell transcriptomics data is clustering with subsequent visualization of cell clusters. The genes responsible for the clustering are only inferred in a subsequent step. Clustering cells and genes together would be the remit of biclustering algorithms, which are often bogged down by the size of single-cell data. Here we present 'Correspondence Analysis based Biclustering on Networks' (CAbiNet) for joint clustering and visualization of single-cell RNA-sequencing data. CAbiNet performs efficient co-clustering of cells and their respective marker genes and jointly visualizes the biclusters in a non-linear embedding for easy and interactive visual exploration of the data.
Collapse
Affiliation(s)
- Yan Zhao
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Clemens Kohl
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Daniel Rosebrock
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Qinan Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Yuhui Hu
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055, Guangdong, P.R. China
- Joint Laboratory of Guangdong-Hong Kong Universities for Vascular Homeostasis and Diseases, School of Medicine, Southern University of Science and Technology,1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 1088 Xueyuan Avenue, Shenzhen 518055 Guangdong, P.R. China
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| |
Collapse
|
38
|
Madigan LA, Jaime D, Chen I, Fallon JR. MuSK-BMP signaling in adult muscle stem cells maintains quiescence and regulates myofiber size. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.17.541238. [PMID: 37292636 PMCID: PMC10245747 DOI: 10.1101/2023.05.17.541238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A central question in adult stem cell biology is elucidating the signaling pathways regulating their dynamics and function in diverse physiological and age-related contexts. Muscle stem cells in adults (Satellite Cells; SCs) are generally quiescent but can activate and contribute to muscle repair and growth. Here we tested the role of the MuSK-BMP pathway in regulating adult SC quiescence by deletion of the BMP-binding MuSK Ig3 domain ('ΔIg3-MuSK'). At 3 months of age SC and myonuclei numbers and myofiber size were comparable to WT. However, at 5 months of age SC density was decreased while myofiber size, myonuclear number and grip strength were increased - indicating that SCs had activated and productively fused into the myofibers over this interval. Transcriptomic analysis showed that SCs from uninjured ΔIg3-MuSK mice exhibit signatures of activation. Regeneration experiments showed that ΔIg3-MuSK SCs maintain full stem cell function. Expression of ΔIg3-MuSK in adult SCs was sufficient to break quiescence and increase myofiber size. We conclude that the MuSK-BMP pathway regulates SC quiescence and myofiber size in a cell autonomous, age-dependent manner. Targeting MuSK-BMP signaling in muscle stem cells thus emerges a therapeutic strategy for promoting muscle growth and function in the settings of injury, disease, and aging. Highlights MuSK, in its role as a BMP co-receptor, regulates adult muscle stem cell quiescenceThe MuSK-BMP pathway acts cell autonomouslyIncreased muscle size and function with preservation of myonuclear density and stemness in mice with attenuated MuSK-BMP signaling.
Collapse
|
39
|
Huang Y, Liu Z, Li M, Wang D, Ye J, Hu Q, Zhang Q, Lin Y, Chen R, Liang X, Li X, Lin X. Deciphering the impact of aging on splenic endothelial cell heterogeneity and immunosenescence through single-cell RNA sequencing analysis. Immun Ageing 2024; 21:48. [PMID: 39026350 PMCID: PMC11256597 DOI: 10.1186/s12979-024-00452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 07/01/2024] [Indexed: 07/20/2024]
Abstract
BACKGROUND Aging is associated with significant structural and functional changes in the spleen, leading to immunosenescence, yet the detailed effects on splenic vascular endothelial cells (ECs) and their immunomodulatory roles are not fully understood. In this study, a single-cell RNA (scRNA) atlas of EC transcriptomes from young and aged mouse spleens was constructed to reveal age-related molecular changes, including increased inflammation and reduced vascular development and also the potential interaction between splenic endothelial cells and immune cells. RESULTS Ten clusters of splenic endothelial cells were identified. DEGs analysis across different EC clusters revealed the molecular changes with aging, showing the increase in the overall inflammatory microenvironment and the loss in vascular development function of aged ECs. Notably, four EC clusters with immunological functions were identified, suggesting an Endothelial-to-Immune-like Cell Transition (EndICLT) potentially driven by aging. Pseudotime analysis of the Immunology4 cluster further indicated a possible aging-induced transitional state, potentially initiated by Ctss gene activation. Finally, the effects of aging on cell signaling communication between different EC clusters and immune cells were analyzed. CONCLUSIONS This comprehensive atlas elucidates the complex interplay between ECs and immune cells in the aging spleen, offering new insights into endothelial heterogeneity, reprogramming, and the mechanisms of immunosenescence.
Collapse
Affiliation(s)
- Yanjing Huang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Zhong Liu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Mengke Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Dongliang Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jinguo Ye
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qiuling Hu
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Qikai Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Yuheng Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Rongxin Chen
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Xuanwei Liang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China
| | - Xingyi Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Xianchai Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Sun Yat-sen University, Guangzhou, 510060, China.
| |
Collapse
|
40
|
Wu L, Lin H, Li S, Huang Y, Sun Y, Shu S, Luo T, Liang T, Lai W, Rao J, Hu Z, Peng H. Macrophage iron dyshomeostasis promotes aging-related renal fibrosis. Aging Cell 2024:e14275. [PMID: 39016438 DOI: 10.1111/acel.14275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/31/2024] [Accepted: 07/01/2024] [Indexed: 07/18/2024] Open
Abstract
Renal aging, marked by the accumulation of senescent cells and chronic low-grade inflammation, leads to renal interstitial fibrosis and impaired function. In this study, we investigate the role of macrophages, a key regulator of inflammation, in renal aging by analyzing kidney single-cell RNA sequencing data of C57BL/6J mice from 8 weeks to 24 months. Our findings elucidate the dynamic changes in the proportion of kidney cell types during renal aging and reveal that increased macrophage infiltration contributes to chronic low-grade inflammation, with these macrophages exhibiting senescence and activation of ferroptosis signaling. CellChat analysis indicates enhanced communications between macrophages and tubular cells during aging. Suppressing ferroptosis alleviates macrophage-mediated tubular partial epithelial-mesenchymal transition in vitro, thereby mitigating the expression of fibrosis-related genes. Using SCENIC analysis, we infer Stat1 as a key age-related transcription factor promoting iron dyshomeostasis and ferroptosis in macrophages by regulating the expression of Pcbp1, an iron chaperone protein that inhibits ferroptosis. Furthermore, through virtual screening and molecular docking from a library of anti-aging compounds, we construct a docking model targeting Pcbp1, which indicates that the natural small molecule compound Rutin can suppress macrophage senescence and ferroptosis by preserving Pcbp1. In summary, our study underscores the crucial role of macrophage iron dyshomeostasis and ferroptosis in renal aging. Our results also suggest Pcbp1 as an intervention target in aging-related renal fibrosis and highlight Rutin as a potential therapeutic agent in mitigating age-related renal chronic low-grade inflammation and fibrosis.
Collapse
Affiliation(s)
- Lingzhi Wu
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hongchun Lin
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shaomin Li
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuebo Huang
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yuxiang Sun
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shuangshuang Shu
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ting Luo
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tiantian Liang
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weiyan Lai
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jialing Rao
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zhaoyong Hu
- Nephrology Division, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Hui Peng
- Nephrology Division, Department of Medicine, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Clinical Nephrology (Sun Yat-sen University) and Guangdong Provincial Key Laboratory of Nephrology, Guangzhou, China
| |
Collapse
|
41
|
Song YM, Ge JY, Ding M, Zheng YW. Key factor screening in mouse NASH model using single-cell sequencing combined with machine learning. Heliyon 2024; 10:e33597. [PMID: 39040415 PMCID: PMC11260934 DOI: 10.1016/j.heliyon.2024.e33597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Aims To identify and analyze genes closely related to the progression of nonalcoholic steatohepatitis (NASH) by employing a combination of single-cell RNA sequencing and machine-learning algorithms. Main methods Single-cell RNA sequencing (scRNA-seq) analysis was performed to find the cell population with the most significant differences between the Chow and NASH groups. This approach was used to validate the developmental trajectory of this cell population and investigate changes in cellular communication and important signaling pathways among these cells. Subsequently, high dimensional Weighted Gene Co-expression Network Analysis (hdWGCNA) was used to find the key modules in NASH. Machine learning analyses were performed to further identify core genes. Deep learning techniques were applied to elucidate the correlation between core genes and immune cells. The accuracy of this correlation was further confirmed using deep learning techniques, specifically Convolutional Neural Networks. Key findings By comparing scRNA-seq data between the Chow and NASH groups, we have observed a notable distinction existing in the Kupffer cell population. Signaling interactions between hepatic macrophages and other cells were significantly heightened in the NASH group. Through subsequent analysis of macrophage subtypes and key modules, we identified 150 genes tightly associated with NASH. Finally, we highlighted the 16 most significant core genes using multiple iterations of machine learning. Furthermore, we pointed out the close relationship between core genes and immune cells. Significances Using scRNA-seq analysis and machine learning, we can distinguish NASH-related genes from large genetic datasets, providing theoretical support in finding potential targets for the development of novel therapies.
Collapse
Affiliation(s)
- Yu-Mu Song
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
| | - Jian-Yun Ge
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
| | - Min Ding
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
- Institute of Regenerative Medicine, and Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yun-Wen Zheng
- Guangdong Provincial Key Laboratory of Large Animal Models for Biomedicine, and South China Institute of Large Animal Models for Biomedicine, School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong, China
- Institute of Regenerative Medicine, and Department of Dermatology, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Medical and Life Sciences, Faculty of Pharmaceutical Sciences, Tokyo Univ of Science, Noda, Chiba, Japan
- Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
42
|
Renigunta V, Xhaferri N, Shaikh IG, Schlegel J, Bisen R, Sanvido I, Kalpachidou T, Kummer K, Oliver D, Leitner MG, Lindner M. A versatile functional interaction between electrically silent K V subunits and K V7 potassium channels. Cell Mol Life Sci 2024; 81:301. [PMID: 39003683 PMCID: PMC11335225 DOI: 10.1007/s00018-024-05312-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 07/15/2024]
Abstract
Voltage-gated K+ (KV) channels govern K+ ion flux across cell membranes in response to changes in membrane potential. They are formed by the assembly of four subunits, typically from the same family. Electrically silent KV channels (KVS), however, are unable to conduct currents on their own. It has been assumed that these KVS must obligatorily assemble with subunits from the KV2 family into heterotetrameric channels, thereby giving rise to currents distinct from those of homomeric KV2 channels. Herein, we show that KVS subunits indeed also modulate the activity, biophysical properties and surface expression of recombinant KV7 isoforms in a subunit-specific manner. Employing co-immunoprecipitation, and proximity labelling, we unveil the spatial coexistence of KVS and KV7 within a single protein complex. Electrophysiological experiments further indicate functional interaction and probably heterotetramer formation. Finally, single-cell transcriptomic analyses identify native cell types in which this KVS and KV7 interaction may occur. Our findings demonstrate that KV cross-family interaction is much more versatile than previously thought-possibly serving nature to shape potassium conductance to the needs of individual cell types.
Collapse
Affiliation(s)
- Vijay Renigunta
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Nermina Xhaferri
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Imran Gousebasha Shaikh
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Jonathan Schlegel
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Rajeshwari Bisen
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Ilaria Sanvido
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Kai Kummer
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Dominik Oliver
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, 35037, Marburg, Germany
| | - Michael G Leitner
- Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria.
| | - Moritz Lindner
- Department of Neurophysiology, Institute of Physiology and Pathophysiology, Philipps-University Marburg, 35037, Marburg, Germany.
- The Nuffield Laboratory of Ophthalmology, Sleep and Circadian Neuroscience Institute, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.
- Department of Ophthalmology, Philipps University Marburg, 35037, Marburg, Germany.
| |
Collapse
|
43
|
Qin L, Liu Z, Guo S, Han Y, Wang X, Ren W, Chen J, Zhen H, Nie C, Xing KK, Chen T, Südhof TC, Sun Y, Zhang B. Astrocytic Neuroligin-3 influences gene expression and social behavior, but is dispensable for synapse number. Mol Psychiatry 2024:10.1038/s41380-024-02659-6. [PMID: 39003414 DOI: 10.1038/s41380-024-02659-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/26/2024] [Accepted: 07/02/2024] [Indexed: 07/15/2024]
Abstract
Neuroligin-3 (Nlgn3) is an autism-associated cell-adhesion molecule that interacts with neurexins and is robustly expressed in both neurons and astrocytes. Neuronal Nlgn3 is an essential regulator of synaptic transmission but the function of astrocytic Nlgn3 is largely unknown. Given the high penetrance of Nlgn3 mutations in autism and the emerging role of astrocytes in neuropsychiatric disorders, we here asked whether astrocytic Nlgn3 might shape neural circuit properties in the cerebellum similar to neuronal Nlgn3. Imaging of tagged Nlgn3 protein produced by CRISPR/Cas9-mediated genome editing showed that Nlgn3 is enriched in the cell body but not the fine processes of cerebellar astrocytes (Bergmann glia). Astrocyte-specific knockout of Nlgn3 did not detectably alter the number of synapses, synaptic transmission, or astrocyte morphology in mouse cerebellum. However, spatial transcriptomic analyses revealed a significant shift in gene expression among multiple cerebellar cell types after the deletion of astrocytic Nlgn3. Hence, in contrast to neuronal Nlgn3, astrocytic Nlgn3 in the cerebellum is not involved in shaping synapses but may modulate gene expression in specific brain areas.
Collapse
Affiliation(s)
- Liming Qin
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Zhili Liu
- BGI Research, Shenzhen, 518083, China
- Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Hong Kong, China
| | - Sile Guo
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Ying Han
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Xiankun Wang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Wen Ren
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Jiewen Chen
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, 518132, China
| | - Hefu Zhen
- BGI Research, Shenzhen, 518083, China
| | - Chao Nie
- BGI Research, Shenzhen, 518083, China
| | - Ke-Ke Xing
- Department of Anatomy and K.K. Leung Brain Research Centre, Fourth Military Medical University, Xi'an, 710032, China
| | - Tao Chen
- Department of Anatomy and K.K. Leung Brain Research Centre, Fourth Military Medical University, Xi'an, 710032, China
| | - Thomas C Südhof
- Department of molecular and cellular physiology, Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, 94043, USA.
| | - Yuzhe Sun
- BGI Research, Shenzhen, 518083, China.
- BGI Research, 102601, Beijing, China.
- Shenzhen Key Laboratory of Neurogenomics, BGI-Shenzhen, Shenzhen, 518120, China.
| | - Bo Zhang
- School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China.
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen, 518132, China.
| |
Collapse
|
44
|
Basu R, Kulkarni P, Swegan D, Duran-Ortiz S, Ahmad A, Caggiano LJ, Davis E, Walsh C, Brenya E, Koshal A, Brody R, Sandbhor U, Neggers SJCMM, Kopchick JJ. Growth Hormone Receptor Antagonist Markedly Improves Gemcitabine Response in a Mouse Xenograft Model of Human Pancreatic Cancer. Int J Mol Sci 2024; 25:7438. [PMID: 39000545 PMCID: PMC11242728 DOI: 10.3390/ijms25137438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 07/16/2024] Open
Abstract
Chemotherapy treatment against pancreatic ductal adenocarcinoma (PDAC) is thwarted by tumoral activation of multiple therapy resistance pathways. The growth hormone (GH)-GH receptor (GHR) pair is a covert driver of multimodal therapy resistance in cancer and is overexpressed in PDAC tumors, yet the therapeutic potential of targeting the same has not been explored. Here, we report that GHR expression is a negative prognostic factor in patients with PDAC. Combinations of gemcitabine with different GHR antagonists (GHRAs) markedly improve therapeutic outcomes in nude mice xenografts. Employing cultured cells, mouse xenografts, and analyses of the human PDAC transcriptome, we identified that attenuation of the multidrug transporter and epithelial-to-mesenchymal transition programs in the tumors underlie the observed augmentation of chemotherapy efficacy by GHRAs. Moreover, in human PDAC patients, GHR expression strongly correlates with a gene signature of tumor promotion and immune evasion, which corroborate with that in syngeneic tumors in wild-type vs. GH transgenic mice. Overall, we found that GH action in PDAC promoted a therapy-refractory gene signature in vivo, which can be effectively attenuated by GHR antagonism. Our results collectively present a proof of concept toward considering GHR antagonists to improve chemotherapeutic outcomes in the highly chemoresistant PDAC.
Collapse
MESH Headings
- Animals
- Gemcitabine
- Humans
- Deoxycytidine/analogs & derivatives
- Deoxycytidine/pharmacology
- Deoxycytidine/therapeutic use
- Pancreatic Neoplasms/drug therapy
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- Pancreatic Neoplasms/genetics
- Mice
- Xenograft Model Antitumor Assays
- Receptors, Somatotropin/metabolism
- Receptors, Somatotropin/antagonists & inhibitors
- Receptors, Somatotropin/genetics
- Carcinoma, Pancreatic Ductal/drug therapy
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Carcinoma, Pancreatic Ductal/genetics
- Cell Line, Tumor
- Mice, Nude
- Drug Resistance, Neoplasm/drug effects
- Gene Expression Regulation, Neoplastic/drug effects
- Female
Collapse
Affiliation(s)
- Reetobrata Basu
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Diabetes Institute, Ohio University, Athens, OH 45701, USA
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
| | - Prateek Kulkarni
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Deborah Swegan
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Silvana Duran-Ortiz
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
| | - Arshad Ahmad
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
| | - Lydia J. Caggiano
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Honors Tutorial College, Ohio University, Athens, OH 45701, USA
| | - Emily Davis
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Christopher Walsh
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
| | - Edward Brenya
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
| | - Adeel Koshal
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA;
| | - Rich Brody
- InfinixBio LLC, Columbus, OH 43212, USA; (R.B.); (U.S.)
| | - Uday Sandbhor
- InfinixBio LLC, Columbus, OH 43212, USA; (R.B.); (U.S.)
| | | | - John J. Kopchick
- Edison Biotechnology Institute, Ohio University, Athens, OH 45701, USA; (R.B.); (P.K.); (D.S.); (S.D.-O.); (A.A.); (L.J.C.); (E.D.); (C.W.); (E.B.)
- Diabetes Institute, Ohio University, Athens, OH 45701, USA
- Department of Biomedical Sciences, Heritage College of Osteopathic Medicine, Ohio University, Athens, OH 45701, USA
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA
- Department of Biological Sciences, Ohio University, Athens, OH 45701, USA
- Translational Biomedical Sciences Program, Ohio University, Athens, OH 45701, USA
| |
Collapse
|
45
|
Brückner A, Brandtner A, Rieck S, Matthey M, Geisen C, Fels B, Stei M, Kusche-Vihrog K, Fleischmann BK, Wenzel D. Site-specific genetic and functional signatures of aortic endothelial cells at aneurysm predilection sites in healthy and AngII ApoE -/- mice. Angiogenesis 2024:10.1007/s10456-024-09933-9. [PMID: 38965173 DOI: 10.1007/s10456-024-09933-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/16/2024] [Indexed: 07/06/2024]
Abstract
Aortic aneurysm is characterized by a pathological dilation at specific predilection sites of the vessel and potentially results in life-threatening vascular rupture. Herein, we established a modified "Häutchen method" for the local isolation of endothelial cells (ECs) from mouse aorta to analyze their spatial heterogeneity and potential role in site-specific disease development. When we compared ECs from aneurysm predilection sites of healthy mice with adjacent control segments we found regulation of genes related to extracellular matrix remodeling, angiogenesis and inflammation, all pathways playing a critical role in aneurysm development. We also detected enhanced cortical stiffness of the endothelium at these sites. Gene expression of ECs from aneurysms of the AngII ApoE-/- model when compared to sham animals mimicked expression patterns from predilection sites of healthy animals. Thus, this work highlights a striking genetic and functional regional heterogeneity in aortic ECs of healthy mice, which defines the location of aortic aneurysm formation in disease.
Collapse
Affiliation(s)
- Alexander Brückner
- Life&Brain Center, Medical Faculty, Institute of Physiology I, University of Bonn, Bonn, Germany
| | - Adrian Brandtner
- Life&Brain Center, Medical Faculty, Institute of Physiology I, University of Bonn, Bonn, Germany
| | - Sarah Rieck
- Life&Brain Center, Medical Faculty, Institute of Physiology I, University of Bonn, Bonn, Germany
| | - Michaela Matthey
- Department of Systems Physiology, Medical Faculty, Institute of Physiology, Ruhr University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Caroline Geisen
- Life&Brain Center, Medical Faculty, Institute of Physiology I, University of Bonn, Bonn, Germany
| | - Benedikt Fels
- Institute of Physiology, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), Partner SiteHamburg/Luebeck/Kiel, Luebeck, Germany
| | - Marta Stei
- Heart Center Bonn, Clinic for Internal Medicine II, University Hospital Bonn, Bonn, Germany
| | - Kristina Kusche-Vihrog
- Institute of Physiology, University of Lübeck, Lübeck, Germany
- DZHK (German Research Centre for Cardiovascular Research), Partner SiteHamburg/Luebeck/Kiel, Luebeck, Germany
| | - Bernd K Fleischmann
- Life&Brain Center, Medical Faculty, Institute of Physiology I, University of Bonn, Bonn, Germany
| | - Daniela Wenzel
- Life&Brain Center, Medical Faculty, Institute of Physiology I, University of Bonn, Bonn, Germany.
- Department of Systems Physiology, Medical Faculty, Institute of Physiology, Ruhr University of Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| |
Collapse
|
46
|
Leng F, Mei S, Zhou X, Liu X, Yuan Y, Xu W, Hao C, Guo R, Hao C, Li W, Zhang P. DVsc: An Automated Framework for Efficiently Detecting Viral Infection from Single-cell Transcriptomics Data. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad007. [PMID: 39215426 DOI: 10.1093/gpbjnl/qzad007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 11/13/2023] [Accepted: 12/15/2023] [Indexed: 09/04/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has emerged as a valuable tool for studying cellular heterogeneity in various fields, particularly in virological research. By studying the viral and cellular transcriptomes, the dynamics of viral infection can be investigated at a single-cell resolution. However, limited studies have been conducted to investigate whether RNA transcripts from clinical samples contain substantial amounts of viral RNAs, and a specific computational framework for efficiently detecting viral reads based on scRNA-seq data has not been developed. Hence, we introduce DVsc, an open-source framework for precise quantitative analysis of viral infection from single-cell transcriptomics data. When applied to approximately 200 diverse clinical samples that were infected by more than 10 different viruses, DVsc demonstrated high accuracy in systematically detecting viral infection across a wide array of cell types. This innovative bioinformatics pipeline could be crucial for addressing the potential effects of surreptitiously invading viruses on certain illnesses, as well as for designing novel medicines to target viruses in specific host cell subsets and evaluating the efficacy of treatment. DVsc supports the FASTQ format as an input and is compatible with multiple single-cell sequencing platforms. Moreover, it could also be applied to sequences from bulk RNA sequencing data. DVsc is available at http://62.234.32.33:5000/DVsc.
Collapse
Affiliation(s)
- Fei Leng
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Song Mei
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Xiaolin Zhou
- Institute of Biomedical Engineering, University of Toronto, Toronto, M5S 3G9, Canada
| | - Xuanshi Liu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Yefeng Yuan
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wenjian Xu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Chongyi Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Ruolan Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Peng Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute; MOE Key Laboratory of Major Diseases in Children; Rare Disease Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| |
Collapse
|
47
|
Patel NR, Rajan KC, Chiang MY, Meadows SM. Endothelial Zmiz1 modulates physiological and pathophysiological angiogenesis during retinal development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.30.601426. [PMID: 39005408 PMCID: PMC11244917 DOI: 10.1101/2024.06.30.601426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Angiogenesis is a highly coordinated process involving the control of various endothelial cell behaviors. Mechanisms for transcription factor involvement in the regulation of endothelial cell dynamics and angiogenesis have become better understood, however much remains unknown, especially the role of non-DNA binding transcriptional cofactors. Here, we show that Zmiz1, a transcription cofactor, is enriched in the endothelium and critical for embryonic vascular development, postnatal retinal angiogenesis, and pathological angiogenesis in oxygen induced retinopathy (OIR). In mice, endothelial cell-specific deletion of Zmiz1 during embryogenesis led to lethality due to abnormal angiogenesis and vascular defects. Inducible endothelial cell-specific ablation of Zmiz1 postnatally resulted in impaired retinal vascular outgrowth, decreased vascular density, and increased vessel regression. In addition, angiogenic sprouting in the superficial and deep layers of the retina was markedly reduced. Correspondingly, vascular sprouting in fibrin bead assays was significantly reduced in the absence of Zmiz1, while further in vitro and in vivo evidence also suggested deficits in EC migration. In agreement with the defective sprouting angiogenesis phenotype, gene expression analysis of isolated retinal endothelial cells revealed downregulation of tip-cell enriched genes upon inactivation of Zmiz1. Lastly, our study suggested that endothelial Zmiz1 is critical for intraretinal revascularization following hypoxia exposure in the OIR model. Taken together, these findings begin to define the previously unspecified role of endothelial Zmiz1 in physiological and pathological angiogenesis.
Collapse
Affiliation(s)
- Nehal R Patel
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States
| | - K C Rajan
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States
| | - Mark Y Chiang
- Division of Hematology-Oncology, Department of Internal Medicine, Medical School, University of Michigan, Ann Arbor, MI, United States
| | - Stryder M Meadows
- Department of Cell and Molecular Biology, Tulane University, New Orleans, LA, United States
- Tulane Brain Institute, Tulane University, New Orleans, LA, United States
| |
Collapse
|
48
|
Xu H, Ye Y, Duan R, Gao Y, Hu Y, Gao L. Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in Original Molecular Space. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306770. [PMID: 38711214 PMCID: PMC11234410 DOI: 10.1002/advs.202306770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 04/02/2024] [Indexed: 05/08/2024]
Abstract
Integrating multiple single-cell datasets is essential for the comprehensive understanding of cell heterogeneity. Batch effect is the undesired systematic variations among technologies or experimental laboratories that distort biological signals and hinder the integration of single-cell datasets. However, existing methods typically rely on a selected dataset as a reference, leading to inconsistent integration performance using different references, or embed cells into uninterpretable low-dimensional feature space. To overcome these limitations, a reference-free method, Beaconet, for integrating multiple single-cell transcriptomic datasets in original molecular space by aligning the global distribution of each batch using an adversarial correction network is presented. Through extensive comparisons with 13 state-of-the-art methods, it is demonstrated that Beaconet can effectively remove batch effect while preserving biological variations and is superior to existing unsupervised methods using all possible references in overall performance. Furthermore, Beaconet performs integration in the original molecular feature space, enabling the characterization of cell types and downstream differential expression analysis directly using integrated data with gene-expression features. Additionally, when applying to large-scale atlas data integration, Beaconet shows notable advantages in both time- and space-efficiencies. In summary, Beaconet serves as an effective and efficient batch effect removal tool that can facilitate the integration of single-cell datasets in a reference-free and molecular feature-preserved mode.
Collapse
Affiliation(s)
- Han Xu
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Yusen Ye
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Ran Duan
- School of Electrical and Information EngineeringBeijing University of Civil Engineering and ArchitectureBeijing102616China
| | - Yong Gao
- Department of Computer ScienceThe University of British Columbia OkanaganKelownaBritish ColumbiaV1V 1V7Canada
| | - Yuxuan Hu
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| | - Lin Gao
- School of Computer Science and TechnologyXidian UniversityXi'an710126China
| |
Collapse
|
49
|
Sun K, Liu X, Lan X. A single-cell atlas of chromatin accessibility in mouse organogenesis. Nat Cell Biol 2024; 26:1200-1211. [PMID: 38977846 DOI: 10.1038/s41556-024-01435-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/29/2024] [Indexed: 07/10/2024]
Abstract
Organogenesis is a highly complex and precisely regulated process. Here we profiled the chromatin accessibility in >350,000 cells derived from 13 mouse embryos at four developmental stages from embryonic day (E) 10.5 to E13.5 by SPATAC-seq in a single experiment. The resulting atlas revealed the status of 830,873 candidate cis-regulatory elements in 43 major cell types. By integrating the chromatin accessibility atlas with the previous transcriptomic dataset, we characterized cis-regulatory sequences and transcription factors associated with cell fate commitment, such as Nr5a2 in the development of gastrointestinal tract, which was preliminarily supported by the in vivo experiment in zebrafish. Finally, we integrated this atlas with the previous single-cell chromatin accessibility dataset from 13 adult mouse tissues to delineate the developmental stage-specific gene regulatory programmes within and across different cell types and identify potential molecular switches throughout lineage development. This comprehensive dataset provides a foundation for exploring transcriptional regulation in organogenesis.
Collapse
Affiliation(s)
- Keyong Sun
- School of Medicine, Tsinghua University, Beijing, China
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Xin Liu
- Tsinghua-Peking Center for Life Sciences, Beijing, China
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Xun Lan
- School of Medicine, Tsinghua University, Beijing, China.
- Peking-Tsinghua-NIBS Joint Graduate Program, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
- MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing, China.
| |
Collapse
|
50
|
Yang P, Liu Y, Tong ZW, Huang QH, Xie XH, Mao SY, Ding JH, Lu M, Tan RX, Hu G. The marine-derived compound TAG alleviates Parkinson's disease by restoring RUBCN-mediated lipid metabolism homeostasis. Acta Pharmacol Sin 2024; 45:1366-1380. [PMID: 38538717 PMCID: PMC11192910 DOI: 10.1038/s41401-024-01259-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/29/2024] [Indexed: 06/23/2024] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease, and its prevalence is increasing. Currently, no effective therapies for PD exist. Marine-derived natural compounds are considered important resources for the discovery of new drugs due to their distinctive structures and diverse activities. In this study, tetrahydroauroglaucin (TAG), a polyketide isolated from a marine sponge, was found to have notable neuroprotective effects on MPTP/MPP+-induced neurotoxicity. RNA sequencing analysis and metabolomics revealed that TAG significantly improved lipid metabolism disorder in PD models. Further investigation indicated that TAG markedly decreased the accumulation of lipid droplets (LDs), downregulated the expression of RUBCN, and promoted autophagic flux. Moreover, conditional knockdown of Rubcn notably attenuated PD-like symptoms and the accumulation of LDs, accompanied by blockade of the neuroprotective effect of TAG. Collectively, our results first indicated that TAG, a promising PD therapeutic candidate, could suppress the accumulation of LDs through the RUBCN-autophagy pathway, which highlighted a novel and effective strategy for PD treatment.
Collapse
Affiliation(s)
- Pei Yang
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yang Liu
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Zhi-Wu Tong
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Qian-Hui Huang
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xia-Hong Xie
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Shi-Yu Mao
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, 211116, China
| | - Jian-Hua Ding
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, 211116, China
| | - Ming Lu
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, 211116, China.
| | - Ren-Xiang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Institute of Functional Biomolecules, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Gang Hu
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
- Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, Nanjing, 211116, China.
| |
Collapse
|