bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022‒05‒29
38 papers selected by
Fawaz Alzaïd
Sorbonne Université
  1. The CD8α-PILRα interaction maintains CD8+ T cell quiescence.
  2. Challenges in digital medicine applications in under-resourced settings.
  3. A vaccine targeting resistant tumours by dual T cell plus NK cell attack.
  4. The potential of polygenic scores to improve cost and efficiency of clinical trials.
  5. Mitochondrial uncouplers induce proton leak by activating AAC and UCP1.
  6. Signal requirement for cortical potential of transplantable human neuroepithelial stem cells.
  7. The case for increasing diversity in tissue-based functional genomics datasets to understand human disease susceptibility.
  8. Mitochondrial damage-associated molecular patterns trigger arginase-dependent lymphocyte immunoregulation.
  9. Epigenetic regulation of T cell exhaustion.
  10. Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation.
  11. Robust temporal map of human in vitro myelopoiesis using single-cell genomics.
  12. The UPRmt preserves mitochondrial import to extend lifespan.
  13. An injury-responsive Rac-to-Rho GTPase switch drives activation of muscle stem cells through rapid cytoskeletal remodeling.
  14. STING agonist delivery by tumour-penetrating PEG-lipid nanodiscs primes robust anticancer immunity.
  15. Deubiquitinases in cell death and inflammation.
  16. Developmental dynamics of two bipotent thymic epithelial progenitor types.
  17. Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation.
  18. 3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin.
  19. NLRP3 licenses NLRP11 for inflammasome activation in human macrophages.
  20. CCR5 closes the temporal window for memory linking.
  21. Adolescent sleep shapes social novelty preference in mice.
  22. Mouse splenocyte enrichment strategies via negative selection for broadened single-cell transcriptomics.
  23. Translation initiation site of mRNA is selected through dynamic interaction with the ribosome.
  24. Functional IKK/NF-κB signaling in pancreatic stellate cells is essential to prevent autoimmune pancreatitis.
  25. Integrative analysis of mitochondrial metabolic dynamics in reprogramming human fibroblast cells.
  26. Plin2-mediated lipid droplet mobilization accelerates exit from pluripotency by lipidomic remodeling and histone acetylation.
  27. Extracellular mitochondria drive CD8 T cell dysfunction in trauma by upregulating CD39.
  28. Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and weight regain in mice.
  29. HIV UTR, LTR, and Epigenetic Immunity.
  30. Defining an exhaustion-like program that restrains autoreactive CD8+ T cells.
  31. Generation of specialized blood vessels via lymphatic transdifferentiation.
  32. Lipid metabolism dysfunction induced by age-dependent DNA methylation accelerates aging.
  33. New perspectives on the origins and heterogeneity of mast cells.
  34. Depletion of skeletal muscle satellite cells attenuates pathology in muscular dystrophy.
  35. CIS and TGF-β regulatory pathways influence immunity to bacterial infection.
  36. Influence of NAFLD and bariatric surgery on hepatic and adipose tissue mitochondrial biogenesis and respiration.
  37. A breakdown in microglial metabolic reprogramming causes internalization dysfunction of α-synuclein in a mouse model of Parkinson's disease.
  38. Remuscularization with triiodothyronine and β1-blocker therapy reverses post-ischemic left ventricular dysfunction and adverse remodeling.
  1. Science. 2022 May 27. 376(6596): 996-1001
    The CD8α-PILRα interaction maintains CD8+ T cell quiescence.
    Linghua Zheng, Xue Han, Sheng Yao, Yuwen Zhu, John Klement, Shirley Wu, Lan Ji, Gefeng Zhu, Xiaoxiao Cheng, Zuzana Tobiasova, Weiwei Yu, Baozhu Huang, Matthew D Vesely, Jun Wang, Jianping Zhang, Edward Quinlan, Lieping Chen.
      T cell quiescence is essential for maintaining a broad repertoire against a large pool of diverse antigens from microbes and tumors, but the underlying molecular mechanisms remain largely unknown. We show here that CD8α is critical for the maintenance of CD8+ T cells in a physiologically quiescent state in peripheral lymphoid organs. Upon inducible deletion of CD8α, both naïve and memory CD8+ T cells spontaneously acquired activation phenotypes and subsequently died without exposure to specific antigens. PILRα was identified as a ligand for CD8α in both mice and humans, and disruption of this interaction was able to break CD8+ T cell quiescence. Thus, peripheral T cell pool size is actively maintained by the CD8α-PILRα interaction in the absence of antigen exposure.
    DOI:  https://doi.org/10.1126/science.aaz8658
  2. Nat Commun. 2022 May 26. 13(1): 3020
    Challenges in digital medicine applications in under-resourced settings.
      
    DOI:  https://doi.org/10.1038/s41467-022-30728-3
  3. Nature. 2022 May 25.
    A vaccine targeting resistant tumours by dual T cell plus NK cell attack.
    Soumya Badrinath, Maxence O Dellacherie, Aileen Li, Shiwei Zheng, Xixi Zhang, Miguel Sobral, Jason W Pyrdol, Kathryn L Smith, Yuheng Lu, Sabrina Haag, Hamza Ijaz, Fawn Connor-Stroud, Tsuneyasu Kaisho, Glenn Dranoff, Guo-Cheng Yuan, David J Mooney, Kai W Wucherpfennig.
      Most cancer vaccines target peptide antigens, necessitating personalization owing to the vast inter-individual diversity in major histocompatibility complex (MHC) molecules that present peptides to T cells. Furthermore, tumours frequently escape T cell-mediated immunity through mechanisms that interfere with peptide presentation1. Here we report a cancer vaccine that induces a coordinated attack by diverse T cell and natural killer (NK) cell populations. The vaccine targets the MICA and MICB (MICA/B) stress proteins expressed by many human cancers as a result of DNA damage2. MICA/B serve as ligands for the activating NKG2D receptor on T cells and NK cells, but tumours evade immune recognition by proteolytic MICA/B cleavage3,4. Vaccine-induced antibodies increase the density of MICA/B proteins on the surface of tumour cells by inhibiting proteolytic shedding, enhance presentation of tumour antigens by dendritic cells to T cells and augment the cytotoxic function of NK cells. Notably, this vaccine maintains efficacy against MHC class I-deficient tumours resistant to cytotoxic T cells through the coordinated action of NK cells and CD4+ T cells. The vaccine is also efficacious in a clinically important setting: immunization following surgical removal of primary, highly metastatic tumours inhibits the later outgrowth of metastases. This vaccine design enables protective immunity even against tumours with common escape mutations.
    DOI:  https://doi.org/10.1038/s41586-022-04772-4
  4. Nat Commun. 2022 May 25. 13(1): 2922
    The potential of polygenic scores to improve cost and efficiency of clinical trials.
    Akl C Fahed, Anthony A Philippakis, Amit V Khera.
      
    DOI:  https://doi.org/10.1038/s41467-022-30675-z
  5. Nature. 2022 May 25.
    Mitochondrial uncouplers induce proton leak by activating AAC and UCP1.
    Ambre M Bertholet, Andrew M Natale, Paola Bisignano, Junji Suzuki, Andriy Fedorenko, James Hamilton, Tatiana Brustovetsky, Lawrence Kazak, Ryan Garrity, Edward T Chouchani, Nickolay Brustovetsky, Michael Grabe, Yuriy Kirichok.
      Mitochondria generate heat due to H+ leak (IH) across their inner membrane1. IH results from the action of long-chain fatty acids on uncoupling protein 1 (UCP1) in brown fat2-6 and ADP/ATP carrier (AAC) in other tissues1,7-9, but the underlying mechanism is poorly understood. As evidence of pharmacological activators of IH through UCP1 and AAC is lacking, IH is induced by protonophores such as 2,4-dinitrophenol (DNP) and cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP)10,11. Although protonophores show potential in combating obesity, diabetes and fatty liver in animal models12-14, their clinical potential for treating human disease is limited due to indiscriminately increasing H+ conductance across all biological membranes10,11 and adverse side effects15. Here we report the direct measurement of IH induced by DNP, FCCP and other common protonophores and find that it is dependent on AAC and UCP1. Using molecular structures of AAC, we perform a computational analysis to determine the binding sites for protonophores and long-chain fatty acids, and find that they overlap with the putative ADP/ATP-binding site. We also develop a mathematical model that proposes a mechanism of uncoupler-dependent IH through AAC. Thus, common protonophoric uncouplers are synthetic activators of IH through AAC and UCP1, paving the way for the development of new and more specific activators of these two central mediators of mitochondrial bioenergetics.
    DOI:  https://doi.org/10.1038/s41586-022-04747-5
  6. Nat Commun. 2022 May 23. 13(1): 2844
    Signal requirement for cortical potential of transplantable human neuroepithelial stem cells.
    Balazs V Varga, Maryam Faiz, Helena Pivonkova, Gabriel Khelifi, Huijuan Yang, Shangbang Gao, Emma Linderoth, Mei Zhen, Ragnhildur Thora Karadottir, Samer M Hussein, Andras Nagy.
      The cerebral cortex develops from dorsal forebrain neuroepithelial progenitor cells. Following the initial expansion of the progenitor cell pool, these cells generate neurons of all the cortical layers and then astrocytes and oligodendrocytes. Yet, the regulatory pathways that control the expansion and maintenance of the progenitor cell pool are currently unknown. Here we define six basic pathway components that regulate proliferation of cortically specified human neuroepithelial stem cells (cNESCs) in vitro without the loss of cerebral cortex developmental potential. We show that activation of FGF and inhibition of BMP and ACTIVIN A signalling are required for long-term cNESC proliferation. We also demonstrate that cNESCs preserve dorsal telencephalon-specific potential when GSK3, AKT and nuclear CATENIN-β1 activity are low. Remarkably, regulation of these six pathway components supports the clonal expansion of cNESCs. Moreover, cNESCs differentiate into lower- and upper-layer cortical neurons in vitro and in vivo. The identification of mechanisms that drive the neuroepithelial stem cell self-renewal and differentiation and preserve this potential in vitro is key to developing regenerative and cell-based therapeutic approaches to treat neurological conditions.
    DOI:  https://doi.org/10.1038/s41467-022-29839-8
  7. Nat Commun. 2022 May 25. 13(1): 2907
    The case for increasing diversity in tissue-based functional genomics datasets to understand human disease susceptibility.
    Erping Long, Montserrat García-Closas, Stephen J Chanock, M Constanza Camargo, Nicholas E Banovich, Jiyeon Choi.
      
    DOI:  https://doi.org/10.1038/s41467-022-30650-8
  8. Cell Rep. 2022 May 24. pii: S2211-1247(22)00620-9. [Epub ahead of print]39(8): 110847
    Mitochondrial damage-associated molecular patterns trigger arginase-dependent lymphocyte immunoregulation.
    Lauren P Westhaver, Sarah Nersesian, Adam Nelson, Leah K MacLean, Emily B Carter, Derek Rowter, Jun Wang, Boris L Gala-Lopez, Andrew W Stadnyk, Brent Johnston, Jeanette E Boudreau.
      Tissue damage leads to loss of cellular and mitochondrial membrane integrity and release of damage-associated molecular patterns, including those of mitochondrial origin (mitoDAMPs). Here, we describe the lymphocyte response to mitoDAMPs. Using primary cells from mice and human donors, we demonstrate that natural killer (NK) cells and T cells adopt regulatory phenotypes and functions in response to mitoDAMPs. NK cell-mediated cytotoxicity, interferon gamma (IFN-γ) production, T cell proliferation, and in vivo anti-viral T cell activation are all interrupted in the presence of mitoDAMPs or mitoDAMP-rich irradiated cells in in vitro and in vivo assays. Mass spectrometry analysis of mitoDAMPs demonstrates that arginase and products of its enzymatic activity are prevalent in mitoDAMP preparations. Functional validation by arginase inhibition and/or arginine add-back shows that arginine depletion is responsible for the alteration in immunologic polarity. We conclude that lymphocyte responses to mitoDAMPs reflect a highly conserved mechanism that regulates inflammation in response to tissue injury.
    Keywords:  CP: Immunology; NK cell; arginase; arginine metabolism; damage-associated molecular patterns (DAMPs); immunoregulation; lymphocytes; mass spectrometry; mitochondria; natural killer cell; tissue damage
    DOI:  https://doi.org/10.1016/j.celrep.2022.110847
  9. Nat Immunol. 2022 May 27.
    Epigenetic regulation of T cell exhaustion.
    Julia A Belk, Bence Daniel, Ansuman T Satpathy.
      Chronic antigen stimulation during viral infections and cancer can lead to T cell exhaustion, which is characterized by reduced effector function and proliferation, and the expression of inhibitory immune checkpoint receptors. Recent studies have demonstrated that T cell exhaustion results in wholescale epigenetic remodeling that confers phenotypic stability to these cells and prevents T cell reinvigoration by checkpoint blockade. Here, we review foundational technologies to profile the epigenome at multiple scales, including mapping the locations of transcription factors and histone modifications, DNA methylation and three-dimensional genome conformation. We discuss how these technologies have elucidated the development and epigenetic regulation of exhausted T cells and functional implications across viral infection, cancer, autoimmunity and engineered T cell therapies. Finally, we cover emerging multi-omic and genome engineering technologies, current and upcoming opportunities to apply these to T cell exhaustion, and therapeutic opportunities for T cell engineering in the clinic.
    DOI:  https://doi.org/10.1038/s41590-022-01224-z
  10. Nat Genet. 2022 May 26.
    Immune disease risk variants regulate gene expression dynamics during CD4+ T cell activation.
    Blagoje Soskic, Eddie Cano-Gamez, Deborah J Smyth, Kirsty Ambridge, Ziying Ke, Julie C Matte, Lara Bossini-Castillo, Joanna Kaplanis, Lucia Ramirez-Navarro, Anna Lorenc, Nikolina Nakic, Jorge Esparza-Gordillo, Wendy Rowan, David Wille, David F Tough, Paola G Bronson, Gosia Trynka.
      During activation, T cells undergo extensive gene expression changes that shape the properties of cells to exert their effector function. Understanding the regulation of this process could help explain how genetic variants predispose to immune diseases. Here, we mapped genetic effects on gene expression (expression quantitative trait loci (eQTLs)) using single-cell transcriptomics. We profiled 655,349 CD4+ T cells, capturing transcriptional states of unstimulated cells and three time points of cell activation in 119 healthy individuals. This identified 38 cell clusters, including transient clusters that were only present at individual time points of activation. We found 6,407 genes whose expression was correlated with genetic variation, of which 2,265 (35%) were dynamically regulated during activation. Furthermore, 127 genes were regulated by variants associated with immune-mediated diseases, with significant enrichment for dynamic effects. Our results emphasize the importance of studying context-specific gene expression regulation and provide insights into the mechanisms underlying genetic susceptibility to immune-mediated diseases.
    DOI:  https://doi.org/10.1038/s41588-022-01066-3
  11. Nat Commun. 2022 May 24. 13(1): 2885
    Robust temporal map of human in vitro myelopoiesis using single-cell genomics.
    Clara Alsinet, Maria Nascimento Primo, Valentina Lorenzi, Erica Bello, Iva Kelava, Carla P Jones, Roser Vilarrasa-Blasi, Carmen Sancho-Serra, Andrew J Knights, Jong-Eun Park, Beata S Wyspianska, Gosia Trynka, David F Tough, Andrew Bassett, Daniel J Gaffney, Damiana Alvarez-Errico, Roser Vento-Tormo.
      Myeloid cells are central to homeostasis and immunity. Characterising in vitro myelopoiesis protocols is imperative for their use in research, immunotherapies, and understanding human myelopoiesis. Here, we generate a >470K cells molecular map of human induced pluripotent stem cells (iPSC) differentiation into macrophages. Integration with in vivo single-cell atlases shows in vitro differentiation recapitulates features of yolk sac hematopoiesis, before definitive hematopoietic stem cells (HSC) emerge. The diversity of myeloid cells generated, including mast cells and monocytes, suggests that HSC-independent hematopoiesis can produce multiple myeloid lineages. We uncover poorly described myeloid progenitors and conservation between in vivo and in vitro regulatory programs. Additionally, we develop a protocol to produce iPSC-derived dendritic cells (DC) resembling cDC2. Using CRISPR/Cas9 knock-outs, we validate the effects of key transcription factors in macrophage and DC ontogeny. This roadmap of myeloid differentiation is an important resource for investigating human fetal hematopoiesis and new therapeutic opportunities.
    DOI:  https://doi.org/10.1038/s41467-022-30557-4
  12. J Cell Biol. 2022 Jul 04. pii: e202201071. [Epub ahead of print]221(7):
    The UPRmt preserves mitochondrial import to extend lifespan.
    Nan Xin, Jenni Durieux, Chunxia Yang, Suzanne Wolff, Hyun-Eui Kim, Andrew Dillin.
      The mitochondrial unfolded protein response (UPRmt) is dedicated to promoting mitochondrial proteostasis and is linked to extreme longevity. The key regulator of this process is the transcription factor ATFS-1, which, upon UPRmt activation, is excluded from the mitochondria and enters the nucleus to regulate UPRmt genes. However, the repair proteins synthesized as a direct result of UPRmt activation must be transported into damaged mitochondria that had previously excluded ATFS-1 owing to reduced import efficiency. To address this conundrum, we analyzed the role of the import machinery when the UPRmt was induced. Using in vitro and in vivo analysis of mitochondrial proteins, we surprisingly find that mitochondrial import increases when the UPRmt is activated in an ATFS-1-dependent manner, despite reduced mitochondrial membrane potential. The import machinery is upregulated, and an intact import machinery is essential for UPRmt-mediated lifespan extension. ATFS-1 has a weak mitochondrial targeting sequence (MTS), allowing for dynamic subcellular localization during the initial stages of UPRmt activation.
    DOI:  https://doi.org/10.1083/jcb.202201071
  13. Cell Stem Cell. 2022 May 15. pii: S1934-5909(22)00169-2. [Epub ahead of print]
    An injury-responsive Rac-to-Rho GTPase switch drives activation of muscle stem cells through rapid cytoskeletal remodeling.
    Allison P Kann, Margaret Hung, Wei Wang, Jo Nguyen, Penney M Gilbert, Zhuhao Wu, Robert S Krauss.
      Many tissues harbor quiescent stem cells that are activated upon injury, subsequently proliferating and differentiating to repair tissue damage. Mechanisms by which stem cells sense injury and transition from quiescence to activation, however, remain largely unknown. Resident skeletal muscle stem cells (MuSCs) are essential orchestrators of muscle regeneration and repair. Here, with a combination of in vivo and ex vivo approaches, we show that quiescent MuSCs have elaborate, Rac GTPase-promoted cytoplasmic projections that respond to injury via the upregulation of Rho/ROCK signaling, facilitating projection retraction and driving downstream activation events. These early events involve rapid cytoskeletal rearrangements and occur independently of exogenous growth factors. This mechanism is conserved across a broad range of MuSC activation models, including injury, disease, and genetic loss of quiescence. Our results redefine MuSC activation and present a central mechanism by which quiescent stem cells initiate responses to injury.
    Keywords:  GTPase; Rac1; Rho; cytoskeleton; mechanosignaling; muscle stem cell; quiescence; satellite cell; stem cell activation; stem cell niche
    DOI:  https://doi.org/10.1016/j.stem.2022.04.016
  14. Nat Mater. 2022 May 23.
    STING agonist delivery by tumour-penetrating PEG-lipid nanodiscs primes robust anticancer immunity.
    Eric L Dane, Alexis Belessiotis-Richards, Coralie Backlund, Jianing Wang, Kousuke Hidaka, Lauren E Milling, Sachin Bhagchandani, Mariane B Melo, Shengwei Wu, Na Li, Nathan Donahue, Kaiyuan Ni, Leyuan Ma, Masanori Okaniwa, Molly M Stevens, Alfredo Alexander-Katz, Darrell J Irvine.
      Activation of the innate immune STimulator of INterferon Genes (STING) pathway potentiates antitumour immunity, but systemic delivery of STING agonists to tumours is challenging. We conjugated STING-activating cyclic dinucleotides (CDNs) to PEGylated lipids (CDN-PEG-lipids; PEG, polyethylene glycol) via a cleavable linker and incorporated them into lipid nanodiscs (LNDs), which are discoid nanoparticles formed by self-assembly. Compared to state-of-the-art liposomes, intravenously administered LNDs carrying CDN-PEG-lipid (LND-CDNs) exhibited more efficient penetration of tumours, exposing the majority of tumour cells to STING agonist. A single dose of LND-CDNs induced rejection of established tumours, coincident with immune memory against tumour rechallenge. Although CDNs were not directly tumoricidal, LND-CDN uptake by cancer cells correlated with robust T-cell activation by promoting CDN and tumour antigen co-localization in dendritic cells. LNDs thus appear promising as a vehicle for robust delivery of compounds throughout solid tumours, which can be exploited for enhanced immunotherapy.
    DOI:  https://doi.org/10.1038/s41563-022-01251-z
  15. Biochem J. 2022 May 27. 479(10): 1103-1119
    Deubiquitinases in cell death and inflammation.
    Kim Newton, Alexander D Gitlin.
      Apoptosis, pyroptosis, and necroptosis are distinct forms of programmed cell death that eliminate infected, damaged, or obsolete cells. Many proteins that regulate or are a part of the cell death machinery undergo ubiquitination, a post-translational modification made by ubiquitin ligases that modulates protein abundance, localization, and/or activity. For example, some ubiquitin chains target proteins for degradation, while others function as scaffolds for the assembly of signaling complexes. Deubiquitinases (DUBs) are the proteases that counteract ubiquitin ligases by cleaving ubiquitin from their protein substrates. Here, we review the DUBs that have been found to suppress or promote apoptosis, pyroptosis, or necroptosis.
    Keywords:  apoptosis; deubiquitinase; necroptosis; pyroptosis
    DOI:  https://doi.org/10.1042/BCJ20210735
  16. Nature. 2022 May 25.
    Developmental dynamics of two bipotent thymic epithelial progenitor types.
    Anja Nusser, Sagar, Jeremy B Swann, Brigitte Krauth, Dagmar Diekhoff, Lesly Calderon, Christiane Happe, Dominic Grün, Thomas Boehm.
      T cell development in the thymus is essential for cellular immunity and depends on the organotypic thymic epithelial microenvironment. In comparison with other organs, the size and cellular composition of the thymus are unusually dynamic, as exemplified by rapid growth and high T cell output during early stages of development, followed by a gradual loss of functional thymic epithelial cells and diminished naive T cell production with age1-10. Single-cell RNA sequencing (scRNA-seq) has uncovered an unexpected heterogeneity of cell types in the thymic epithelium of young and aged adult mice11-18; however, the identities and developmental dynamics of putative pre- and postnatal epithelial progenitors have remained unresolved1,12,16,17,19-27. Here we combine scRNA-seq and a new CRISPR-Cas9-based cellular barcoding system in mice to determine qualitative and quantitative changes in the thymic epithelium over time. This dual approach enabled us to identify two principal progenitor populations: an early bipotent progenitor type biased towards cortical epithelium and a postnatal bipotent progenitor population biased towards medullary epithelium. We further demonstrate that continuous autocrine provision of Fgf7 leads to sustained expansion of thymic microenvironments without exhausting the epithelial progenitor pools, suggesting a strategy to modulate the extent of thymopoietic activity.
    DOI:  https://doi.org/10.1038/s41586-022-04752-8
  17. Proc Natl Acad Sci U S A. 2022 May 31. 119(22): e2201883119
    Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation.
    Katerina Kraft, Kathryn E Yost, Sedona E Murphy, Andreas Magg, Yicheng Long, M Ryan Corces, Jeffrey M Granja, Lars Wittler, Stefan Mundlos, Thomas R Cech, Alistair N Boettiger, Howard Y Chang.
      SignificanceThe relationship between long-range Polycomb-associated chromatin contacts and the linear propagation of histone H3 lysine 27 trimethylation (H3K27me3) by Polycomb repressive complex 2 (PRC2) is not well-characterized. Here, we nominate a role for developmental loci as genomic architectural elements that enable long-range spreading of H3K27me3. Polycomb-associated loops are disrupted upon loss of PRC2 binding and deletion of loop anchors results in alterations of H3K27me3 deposition and ectopic gene expression. These results suggest that Polycomb-mediated genome architecture is important for gene repression during embryonic development.
    Keywords:  3D genome; Polycomb-group proteins; RNA-mediated Polycomb loops; epigenetic silencing; heterochromatin
    DOI:  https://doi.org/10.1073/pnas.2201883119
  18. STAR Protoc. 2022 Jun 17. 3(2): 101382
    3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin.
    Xianfu Yi, Menghan Luo, Xiangling Feng, Yao Zhou, Jianhua Wang, Mulin Jun Li.
      Precise identification of context-specific transcriptional regulators (TRs) cooperation facilitates the understanding of complex gene regulation. However, previous methods are highly reliant on the availability of ChIPped TRs. Here, we provide a protocol for running 3DCoop, a pipeline for computational inference of cell type-specific TR cooperation in 3D chromatin by integrating TR motifs, open chromatin profiles, gene expression, and chromatin loops. 3DCoop provides a feasible solution to study the potential interplay among TRs across multiple human or mouse tissue/cell types. For complete details on the use and execution of this protocol, please refer to Yi et al. (2021).
    Keywords:  Bioinformatics; Gene Expression; Genetics; Genomics; Systems biology
    DOI:  https://doi.org/10.1016/j.xpro.2022.101382
  19. Nat Immunol. 2022 May 27.
    NLRP3 licenses NLRP11 for inflammasome activation in human macrophages.
    Anu Gangopadhyay, Savita Devi, Shivendra Tenguria, Jessica Carriere, Huyen Nguyen, Elisabeth Jäger, Hemisha Khatri, Lan H Chu, Rojo A Ratsimandresy, Andrea Dorfleutner, Christian Stehlik.
      Intracellular sensing of stress and danger signals initiates inflammatory innate immune responses by triggering inflammasome assembly, caspase-1 activation and pyroptotic cell death as well as the release of interleukin 1β (IL-1β), IL-18 and danger signals. NLRP3 broadly senses infectious patterns and sterile danger signals, resulting in the tightly coordinated and regulated assembly of the NLRP3 inflammasome, but the precise mechanisms are incompletely understood. Here, we identified NLRP11 as an essential component of the NLRP3 inflammasome in human macrophages. NLRP11 interacted with NLRP3 and ASC, and deletion of NLRP11 specifically prevented NLRP3 inflammasome activation by preventing inflammasome assembly, NLRP3 and ASC polymerization, caspase-1 activation, pyroptosis and cytokine release but did not affect other inflammasomes. Restored expression of NLRP11, but not NLRP11 lacking the PYRIN domain (PYD), restored inflammasome activation. NLRP11 was also necessary for inflammasome responses driven by NLRP3 mutations that cause cryopyrin-associated periodic syndrome (CAPS). Because NLRP11 is not expressed in mice, our observations emphasize the specific complexity of inflammasome regulation in humans.
    DOI:  https://doi.org/10.1038/s41590-022-01220-3
  20. Nature. 2022 May 25.
    CCR5 closes the temporal window for memory linking.
    Yang Shen, Miou Zhou, Denise Cai, Daniel Almeida Filho, Giselle Fernandes, Ying Cai, André F de Sousa, Min Tian, Nury Kim, Jinsu Lee, Deanna Necula, Chengbin Zhou, Shuoyi Li, Shelbi Salinas, Andy Liu, Xiaoman Kang, Masakazu Kamata, Ayal Lavi, Shan Huang, Tawnie Silva, Won Do Heo, Alcino J Silva.
      Real-world memories are formed in a particular context and are often not acquired or recalled in isolation1-5. Time is a key variable in the organization of memories, as events that are experienced close in time are more likely to be meaningfully associated, whereas those that are experienced with a longer interval are not1-4. How the brain segregates events that are temporally distinct is unclear. Here we show that a delayed (12-24 h) increase in the expression of C-C chemokine receptor type 5 (CCR5)-an immune receptor that is well known as a co-receptor for HIV infection6,7-after the formation of a contextual memory determines the duration of the temporal window for associating or linking that memory with subsequent memories. This delayed expression of CCR5 in mouse dorsal CA1 neurons results in a decrease in neuronal excitability, which in turn negatively regulates neuronal memory allocation, thus reducing the overlap between dorsal CA1 memory ensembles. Lowering this overlap affects the ability of one memory to trigger the recall of the other, and therefore closes the temporal window for memory linking. Our findings also show that an age-related increase in the neuronal expression of CCR5 and its ligand CCL5 leads to impairments in memory linking in aged mice, which could be reversed with a Ccr5 knockout and a drug approved by the US Food and Drug Administration (FDA) that inhibits this receptor, a result with clinical implications. Altogether, the findings reported here provide insights into the molecular and cellular mechanisms that shape the temporal window for memory linking.
    DOI:  https://doi.org/10.1038/s41586-022-04783-1
  21. Nat Neurosci. 2022 May 26.
    Adolescent sleep shapes social novelty preference in mice.
    Wen-Jie Bian, Chelsie L Brewer, Julie A Kauer, Luis de Lecea.
      Sleep disturbances frequently occur in neurodevelopmental disorders such as autism, but the developmental role of sleep is largely unexplored, and a causal relationship between developmental sleep defects and behavioral consequences in adulthood remains elusive. Here, we show that in mice, sleep disruption (SD) in adolescence, but not in adulthood, causes long-lasting impairment in social novelty preference. Furthermore, adolescent SD alters the activation and release patterns of dopaminergic neurons in the ventral tegmental area (VTA) in response to social novelty. This developmental sleep function is mediated by balanced VTA activity during adolescence; chemogenetic excitation mimics, whereas silencing rescues, the social deficits of adolescent SD. Finally, we show that in Shank3-mutant mice, improving sleep or rectifying VTA activity during adolescence ameliorates adult social deficits. Together, our results identify a critical role of sleep and dopaminergic activity in the development of social interaction behavior.
    DOI:  https://doi.org/10.1038/s41593-022-01076-8
  22. STAR Protoc. 2022 Jun 17. 3(2): 101402
    Mouse splenocyte enrichment strategies via negative selection for broadened single-cell transcriptomics.
    Thomas T Schulze, Andrew J Neville, Ryan C Chapman, Paul H Davis.
      Mammalian splenic tissue is rich in functional immune cells, primarily lymphocytes which can mask low-abundance populations in downstream analyses. This protocol enriches minority immune cell populations from mouse spleen via immunomagnetic negative depletion to generate an untouched enriched cell fraction. Enriched cells are then spiked with untouched splenocytes in a controlled repopulation, validated by flow cytometry and results in a single-cell transcriptomic clustering analysis with a broadened cellular landscape.
    Keywords:  Antibody; Bioinformatics; Cell Biology; Cell isolation; Cell separation/fractionation; Flow Cytometry/Mass Cytometry; Gene Expression; Immunology; Model Organisms; Molecular Biology; RNAseq; Sequence analysis; Sequencing; Single Cell
    DOI:  https://doi.org/10.1016/j.xpro.2022.101402
  23. Proc Natl Acad Sci U S A. 2022 May 31. 119(22): e2118099119
    Translation initiation site of mRNA is selected through dynamic interaction with the ribosome.
    Yi-Lan Chen, Jin-Der Wen.
      SignificanceRibosomes translate the genetic codes of messenger RNA (mRNA) to make proteins. Translation must begin at the correct initiation site; otherwise, abnormal proteins will be produced. Here, we show that a short ribosome-specific sequence in the upstream followed by an unstructured downstream sequence is a favorable initiation site. Those mRNAs lacking either of these two characteristics do not associate tightly with the ribosome. Initiator transfer RNA (tRNA) and initiation factors facilitate the binding. However, when the downstream site forms structures, initiation factor 3 triggers the dissociation of the accommodated initiator tRNA and the subsequent disassembly of the ribosome-mRNA complex. Thus, initiation factors help the ribosome distinguish unfavorable structured sequences that may not act as the mRNA translation initiation site.
    Keywords:  initiation factors; optical tweezers; single-molecule; smFRET; translation initiation
    DOI:  https://doi.org/10.1073/pnas.2118099119
  24. Commun Biol. 2022 May 27. 5(1): 509
    Functional IKK/NF-κB signaling in pancreatic stellate cells is essential to prevent autoimmune pancreatitis.
    Lap Kwan Chan, Miltiadis Tsesmelis, Melanie Gerstenlauer, Frank Leithäuser, Alexander Kleger, Lukas Daniel Frick, Harald Jacob Maier, Thomas Wirth.
      Pancreatic stellate cells (PSCs) are resident cells in the exocrine pancreas which contribute to pancreatic fibrogenesis and inflammation. Studies on NF-κB in pancreatitis so far focused mainly on the parenchymal and myeloid compartments. Here we show a protective immunomodulatory function of NF-κB in PSCs. Conditional deletion of NEMO (IKKγ) in PSCs leads to spontaneous pancreatitis with elevated circulating IgM, IgG and antinuclear autoantibodies (ANA) within 18 weeks. When further challenged with caerulein, NEMOΔCol1a2 mice show an exacerbated autoimmune phenotype characterized by increased infiltration of eosinophils, B and T lymphocytes with reduced latency period. Transcriptomic profiling shows that NEMOΔCol1a2 mice display molecular signatures resembling autoimmune pancreatitis patients. Mechanistically, we show that PSCΔNEMO cells produce high levels of CCL24 ex vivo which contributes to eosinophil recruitment, as neutralization with a CCL24 antibody abolishes the transwell migration of eosinophils. Our findings uncover an unexpected immunomodulatory role specifically of NF-κB in PSCs during pancreatitis.
    DOI:  https://doi.org/10.1038/s42003-022-03371-3
  25. STAR Protoc. 2022 Jun 17. 3(2): 101401
    Integrative analysis of mitochondrial metabolic dynamics in reprogramming human fibroblast cells.
    Young Cha, Pierre Leblanc, Yean Ju Hong, Kwang-Soo Kim.
      Mitochondrial dynamics play critical roles in both tissue homeostasis and somatic cell reprogramming. Here, we provide integrated guidance for assessing mitochondrial function and dynamics while reprogramming human fibroblasts via an integrated analysis approach. This protocol includes instructions for mitochondrial metabolic analysis in real time and flow cytometry-based assessment of mitochondrial mass and membrane potential. We also describe a protocol for quantification of mitochondrial network and key metabolites. For complete details on the use and execution of this protocol, please refer to Cha et al. (2021).
    Keywords:  Cell Biology; Cell culture; Cell-based Assays; Flow Cytometry/Mass Cytometry; Metabolism; Microscopy; Stem Cells
    DOI:  https://doi.org/10.1016/j.xpro.2022.101401
  26. Cell Death Differ. 2022 May 25.
    Plin2-mediated lipid droplet mobilization accelerates exit from pluripotency by lipidomic remodeling and histone acetylation.
    Yi Wu, Keshi Chen, Linpeng Li, Zhihong Hao, Tianyu Wang, Yang Liu, Guangsuo Xing, Zichao Liu, Heying Li, Hao Yuan, Jianghuan Lu, Cheng Zhang, Jinye Zhang, Danyun Zhao, Junwei Wang, Jinfu Nie, Dan Ye, Guangjin Pan, Wai-Yee Chan, Xingguo Liu.
      Metabolic switch is critical for cell fate determination through metabolic functions, epigenetic modifications, and gene expression. However, the mechanisms underlying these alterations and their functional roles remain unclear. Here, we show that Plin2-mediated moderate lipid hydrolysis is critical for pluripotency of embryonic stem cells (ESCs). Upon exit from pluripotency, lipid droplet (LD)-associated protein Plin2 is recognized by Hsc70 and degraded via chaperone-mediated autophagy to facilitate LD mobilization. Enhancing lipid hydrolysis by Plin2 knockout promotes pluripotency exit, which is recovered by ATGL inhibition. Mechanistically, excessive lipid hydrolysis induces a dramatic lipidomic remodeling characterized by decreased cardiolipin and phosphatidylethanolamine, which triggers defects in mitochondrial cristae and fatty acid oxidation, resulting in reduced acetyl-CoA and histone acetylation. Our results reveal how LD mobilization is regulated and its critical role in ESC pluripotency, and indicate the mechanism linking LD homeostasis to mitochondrial remodeling and epigenetic regulation, which might shed light on development and diseases.
    DOI:  https://doi.org/10.1038/s41418-022-01018-8
  27. Thorax. 2022 May 25. pii: thoraxjnl-2021-218047. [Epub ahead of print]
    Extracellular mitochondria drive CD8 T cell dysfunction in trauma by upregulating CD39.
    Shilpa Tiwari-Heckler, Ghee Rye Lee, James Harbison, Carola Ledderose, Eva Csizmadia, David Melton, Quanzhi Zhang, Wolfgang Junger, Guanqing Chen, Carl J Hauser, Leo E Otterbein, Maria Serena Longhi, Simon Christopher Robson.
      RATIONALE: The increased mortality and morbidity seen in critically injured patients appears associated with systemic inflammatory response syndrome (SIRS) and immune dysfunction, which ultimately predisposes to infection. Mitochondria released by injury could generate danger molecules, for example, ATP, which in turn would be rapidly scavenged by ectonucleotidases, expressed on regulatory immune cells.OBJECTIVE: To determine the association between circulating mitochondria, purinergic signalling and immune dysfunction after trauma.
    METHODS: We tested the impact of hepatocyte-derived free mitochondria on blood-derived and lung-derived CD8 T cells in vitro and in experimental mouse models in vivo. In parallel, immune phenotypic analyses were conducted on blood-derived CD8 T cells obtained from trauma patients.
    RESULTS: Isolated intact mitochondria are functional and generate ATP ex vivo. Extracellular mitochondria perturb CD8+ T cells in co-culture, inducing select features of immune exhaustion in vitro. These effects are modulated by scavenging ATP, modelled by addition of apyrase in vitro. Injection of intact mitochondria into recipient mice markedly upregulates the ectonucleotidase CD39, and other immune checkpoint markers in circulating CD8+ T cells. We note that mice injected with mitochondria, prior to instilling bacteria into the lung, exhibit more severe lung injury, characterised by elevated neutrophil influx and by changes in CD8+ T cell cytotoxic capacity. Importantly, the development of SIRS in injured humans, is likewise associated with disordered purinergic signalling and CD8 T cell dysfunction.
    CONCLUSION: These studies in experimental models and in a cohort of trauma patients reveal important associations between extracellular mitochondria, aberrant purinergic signalling and immune dysfunction. These pathogenic factors with immune exhaustion are linked to SIRS and could be targeted therapeutically.
    Keywords:  Bacterial Infection; Critical Care; Emergency Medicine; Pneumonia
    DOI:  https://doi.org/10.1136/thoraxjnl-2021-218047
  28. Nat Commun. 2022 May 26. 13(1): 2950
    Multiomics reveals persistence of obesity-associated immune cell phenotypes in adipose tissue during weight loss and weight regain in mice.
    Matthew A Cottam, Heather L Caslin, Nathan C Winn, Alyssa H Hasty.
      Within adipose tissue (AT), immune cells and parenchymal cells closely interact creating a complex microenvironment. In obesity, immune cell derived inflammation contributes to insulin resistance and glucose intolerance. Diet-induced weight loss improves glucose tolerance; however, weight regain further exacerbates the impairment in glucose homeostasis observed with obesity. To interrogate the immunometabolic adaptations that occur in AT during murine weight loss and weight regain, we utilized cellular indexing of transcriptomes and epitopes by sequencing (CITEseq) in male mice. Obesity-induced imprinting of AT immune cells persisted through weight-loss and progressively worsened with weight regain, ultimately leading to impaired recovery of type 2 regulatory cells, activation of antigen presenting cells, T cell exhaustion, and enhanced lipid handling in macrophages in weight cycled mice. This work provides critical groundwork for understanding the immunological causes of weight cycling-accelerated metabolic disease. For further discovery, we provide an open-access web portal of diet-induced AT immune cell imprinting: https://hastylab.shinyapps.io/MAIseq .
    DOI:  https://doi.org/10.1038/s41467-022-30646-4
  29. Viruses. 2022 May 18. pii: 1084. [Epub ahead of print]14(5):
    HIV UTR, LTR, and Epigenetic Immunity.
    Jielin Zhang, Clyde Crumpacker.
      The duel between humans and viruses is unending. In this review, we examine the HIV RNA in the form of un-translated terminal region (UTR), the viral DNA in the form of long terminal repeat (LTR), and the immunity of human DNA in a format of epigenetic regulation. We explore the ways in which the human immune responses to invading pathogenic viral nucleic acids can inhibit HIV infection, exemplified by a chromatin vaccine (cVaccine) to elicit the immunity of our genome-epigenetic immunity towards a cure.
    Keywords:  HIV; chromatin vaccine (cVaccine); cure; epigenetics; super enhancer
    DOI:  https://doi.org/10.3390/v14051084
  30. Nat Immunol. 2022 May 27.
    Defining an exhaustion-like program that restrains autoreactive CD8+ T cells.
      
    DOI:  https://doi.org/10.1038/s41590-022-01211-4
  31. Nature. 2022 May 25.
    Generation of specialized blood vessels via lymphatic transdifferentiation.
    Rudra N Das, Yaara Tevet, Stav Safriel, Yanchao Han, Noga Moshe, Giuseppina Lambiase, Ivan Bassi, Julian Nicenboim, Matthias Brückner, Dana Hirsch, Raya Eilam-Altstadter, Wiebke Herzog, Roi Avraham, Kenneth D Poss, Karina Yaniv.
      The lineage and developmental trajectory of a cell are key determinants of cellular identity. In the vascular system, endothelial cells (ECs) of blood and lymphatic vessels differentiate and specialize to cater to the unique physiological demands of each organ1,2. Although lymphatic vessels were shown to derive from multiple cellular origins, lymphatic ECs (LECs) are not known to generate other cell types3,4. Here we use recurrent imaging and lineage-tracing of ECs in zebrafish anal fins, from early development to adulthood, to uncover a mechanism of specialized blood vessel formation through the transdifferentiation of LECs. Moreover, we demonstrate that deriving anal-fin vessels from lymphatic versus blood ECs results in functional differences in the adult organism, uncovering a link between cell ontogeny and functionality. We further use single-cell RNA-sequencing analysis to characterize the different cellular populations and transition states involved in the transdifferentiation process. Finally, we show that, similar to normal development, the vasculature is rederived from lymphatics during anal-fin regeneration, demonstrating that LECs in adult fish retain both potency and plasticity for generating blood ECs. Overall, our research highlights an innate mechanism of blood vessel formation through LEC transdifferentiation, and provides in vivo evidence for a link between cell ontogeny and functionality in ECs.
    DOI:  https://doi.org/10.1038/s41586-022-04766-2
  32. Signal Transduct Target Ther. 2022 May 25. 7(1): 162
    Lipid metabolism dysfunction induced by age-dependent DNA methylation accelerates aging.
    Xin Li, Jiaqiang Wang, LeYun Wang, Yuanxu Gao, Guihai Feng, Gen Li, Jun Zou, Meixin Yu, Yu Fei Li, Chao Liu, Xue Wei Yuan, Ling Zhao, Hong Ouyang, Jian-Kang Zhu, Wei Li, Qi Zhou, Kang Zhang.
      Epigenetic alterations and metabolic dysfunction are two hallmarks of aging. However, the mechanism of how their interaction regulates aging, particularly in mammals, remains largely unknown. Here we show ELOVL fatty acid elongase 2 (Elovl2), a gene whose epigenetic alterations are most highly correlated with age prediction, contributes to aging by regulating lipid metabolism. We applied artificial intelligence to predict the protein structure of ELOVL2 and the interaction with its substrate. Impaired Elovl2 function disturbs lipid synthesis with increased endoplasmic reticulum stress and mitochondrial dysfunction, leading to key aging phenotypes at both cellular and physiological level. Furthermore, restoration of mitochondrial activity can rescue age-related macular degeneration (AMD) phenotypes induced by Elovl2 deficiency in human retinal pigmental epithelial (RPE) cells; this indicates a conservative mechanism in both human and mouse. Taken together, we revealed an epigenetic-metabolism axis contributing to aging and illustrate the power of an AI-based approach in structure-function studies.
    DOI:  https://doi.org/10.1038/s41392-022-00964-6
  33. Nat Rev Immunol. 2022 May 24.
    New perspectives on the origins and heterogeneity of mast cells.
    Ashley L St John, Abhay P S Rathore, Florent Ginhoux.
      Mast cells are immune cells of the haematopoietic lineage that are now thought to have multifaceted functions during homeostasis and in various disease states. Furthermore, while mast cells have been known for a long time to contribute to allergic disease in adults, recent studies, mainly in mice, have highlighted their early origins during fetal development and potential for immune functions, including allergic responses, in early life. Our understanding of the imprinting of mast cells by particular tissues of residence and their potential for regulatory interactions with organ systems such as the peripheral immune, nervous and vascular systems is also rapidly evolving. Here, we discuss the origins of mast cells and their diverse and plastic phenotypes that are influenced by tissue residence. We explore how divergent phenotypes and functions might result from both their hard-wired 'nature' defined by their ontogeny and the 'nurture' they receive within specialized tissue microenvironments.
    DOI:  https://doi.org/10.1038/s41577-022-00731-2
  34. Nat Commun. 2022 May 26. 13(1): 2940
    Depletion of skeletal muscle satellite cells attenuates pathology in muscular dystrophy.
    Justin G Boyer, Jiuzhou Huo, Sarah Han, Julian R Havens, Vikram Prasad, Brian L Lin, David A Kass, Taejeong Song, Sakthivel Sadayappan, Ramzi J Khairallah, Christopher W Ward, Jeffery D Molkentin.
      Skeletal muscle can repair and regenerate due to resident stem cells known as satellite cells. The muscular dystrophies are progressive muscle wasting diseases underscored by chronic muscle damage that is continually repaired by satellite cell-driven regeneration. Here we generate a genetic strategy to mediate satellite cell ablation in dystrophic mouse models to investigate how satellite cells impact disease trajectory. Unexpectedly, we observe that depletion of satellite cells reduces dystrophic disease features, with improved histopathology, enhanced sarcolemmal stability and augmented muscle performance. Mechanistically, we demonstrate that satellite cells initiate expression of the myogenic transcription factor MyoD, which then induces re-expression of fetal genes in the myofibers that destabilize the sarcolemma. Indeed, MyoD re-expression in wildtype adult skeletal muscle reduces membrane stability and promotes histopathology, while MyoD inhibition in a mouse model of muscular dystrophy improved membrane stability. Taken together these observations suggest that satellite cell activation and the fetal gene program is maladaptive in chronic dystrophic skeletal muscle.
    DOI:  https://doi.org/10.1038/s41467-022-30619-7
  35. Immunology. 2022 May 25.
    CIS and TGF-β regulatory pathways influence immunity to bacterial infection.
    Timothy R McCulloch, Gustavo R Rossi, Jaring Schreuder, Gabrielle T Belz, Timothy J Wells, Fernando Souza-Fonseca-Guimaraes.
      Immunotherapy has revolutionized cancer therapy by reactivating tumor-resident cytotoxic lymphocytes. More recently, immunotherapy has emerged to restore immunity against infectious agents, including bacterial infections. Immunotherapy primarily targets inhibitory pathways in T cells, however interest in other effector populations, such as natural killer (NK) cells, is growing. We have previously discovered that NK cell metabolism, proliferation, and activation can be neutralized through the transforming growth factor (TGF)-β immunosuppressive pathway by inducing plasticity of NK cells and differentiation into innate lymphoid cell (ILC)1-like subsets. NK cells are also regulated through cytokine-inducible SH2-containing protein (CIS), which is induced by interleukin (IL)-15 and is a potent intracellular checkpoint suppressing NK cell survival and function. Targeting these two distinct pathways to restore NK cell function has shown promise in cancer models, but their application in bacterial infection remains unknown. Here, we investigate whether enhancement of NK cell function can improve anti-bacterial immunity, using Salmonella Typhimurium as a model. We identified conversion of NK cells to ILC1-like for the first time in the context of bacterial infection, where TGF-β signaling contributed to this plasticity. Future work should focus on identifying further drivers of ILC1 plasticity and its functional implication in bacterial infection models. We further describe that CIS-deficient mice displayed enhanced pro-inflammatory function and dramatically enhanced anti-bacterial immunity. Inhibition of CIS may present as a viable therapeutic option to enhance immunity towards bacterial infection.
    Keywords:  CIS; TGF-βR signaling; cellular plasticity; innate lymphoid cell 1; natural killer cells
    DOI:  https://doi.org/10.1111/imm.13516
  36. Nat Commun. 2022 May 25. 13(1): 2931
    Influence of NAFLD and bariatric surgery on hepatic and adipose tissue mitochondrial biogenesis and respiration.
    Julie S Pedersen, Marte O Rygg, Karoline Chrøis, Elahu G Sustarsic, Zach Gerhart-Hines, Nicolai J Wever Albrechtsen, Reza R Serizawa, Viggo B Kristiansen, Astrid L Basse, Astrid E B Boilesen, Beth H Olsen, Torben Hansen, Lise Lotte Gluud, Sten Madsbad, Steen Larsen, Flemming Bendtsen, Flemming Dela.
      Impaired mitochondrial oxidative phosphorylation (OXPHOS) in liver tissue has been hypothesised to contribute to the development of nonalcoholic steatohepatitis in patients with nonalcoholic fatty liver disease (NAFLD). It is unknown whether OXPHOS capacities in human visceral (VAT) and subcutaneous adipose tissue (SAT) associate with NAFLD severity and how hepatic OXPHOS responds to improvement in NAFLD. In biopsies sampled from 62 patients with obesity undergoing bariatric surgery and nine control subjects without obesity we demonstrate that OXPHOS is reduced in VAT and SAT while increased in the liver in patients with obesity when compared with control subjects without obesity, but this was independent of NAFLD severity. In repeat liver biopsy sampling in 21 patients with obesity 12 months after bariatric surgery we found increased hepatic OXPHOS capacity and mitochondrial DNA/nuclear DNA content compared with baseline. In this work we show that obesity has an opposing association with mitochondrial respiration in adipose- and liver tissue with no overall association with NAFLD severity, however, bariatric surgery increases hepatic OXPHOS and mitochondrial biogenesis.
    DOI:  https://doi.org/10.1038/s41467-022-30629-5
  37. J Neuroinflammation. 2022 May 22. 19(1): 113
    A breakdown in microglial metabolic reprogramming causes internalization dysfunction of α-synuclein in a mouse model of Parkinson's disease.
    Jia Lu, Chenfei Wang, Xin Cheng, Ruizhi Wang, Xuehan Yan, Pengju He, Hongzhuan Chen, Zhihua Yu.
      BACKGROUND: The α-synuclein released by neurons activates microglia, which then engulfs α-synuclein for degradation via autophagy. Reactive microglia are a major pathological feature of Parkinson's disease (PD), although the exact role of microglia in the pathogenesis of PD remains unclear. Transient receptor potential vanilloid type 1 (TRPV1) channels are nonselective cation channel protein that have been proposed as neuroprotective targets in neurodegenerative diseases.METHODS: Using metabolic profiling, microglia energy metabolism was measured including oxidative phosphorylation and aerobic glycolysis. The mRFP-GFP-tagged LC3 reporter was introduced to characterize the role of TRPV1 in microglial autophagy. α-synuclein preformed fibril (PFF) TRPV1flox/flox; Cx3cr1Cre mouse model of sporadic PD were employed to study the capacity of TRPV1 activation to attenuate neurodegeneration process.
    RESULTS: We found that acute exposure to PFF caused microglial activation as a result of metabolic reprogramming from oxidative phosphorylation to aerobic glycolysis via the AKT-mTOR-HIF-1α pathway. Activated microglia eventually reached a state of chronic PFF-tolerance, accompanied by broad defects in energy metabolism. We showed that metabolic boosting by treatment with the TRPV1 agonist capsaicin rescued metabolic impairments in PFF-tolerant microglia and also defects in mitophagy caused by disruption of the AKT-mTOR-HIF-1α pathway. Capsaicin attenuated phosphorylation of α-synuclein in primary neurons by boosting phagocytosis in PFF-tolerant microglia in vitro. Finally, we found that behavioral deficits and loss of dopaminergic neurons were accelerated in the PFF TRPV1flox/flox; Cx3cr1Cre mouse model of sporadic PD. We identified defects in energy metabolism, mitophagy and phagocytosis of PFF in microglia from the substantia nigra pars compacta of TRPV1flox/flox; Cx3cr1Cre mice.
    CONCLUSION: The findings suggest that modulating microglial metabolism might be a new therapeutic strategy for PD.
    Keywords:  Autophagy; Capsaicin; Microglia; TRPV1; α-Synuclein
    DOI:  https://doi.org/10.1186/s12974-022-02484-0
  38. Sci Rep. 2022 May 25. 12(1): 8852
    Remuscularization with triiodothyronine and β1-blocker therapy reverses post-ischemic left ventricular dysfunction and adverse remodeling.
    Nikolay Bogush, Lin Tan, Emmen Naqvi, John W Calvert, Robert M Graham, W Robert Taylor, Nawazish Naqvi, Ahsan Husain.
      Renewal of the myocardium by preexisting cardiomyocytes is a powerful strategy for restoring the architecture and function of hearts injured by myocardial infarction. To advance this strategy, we show that combining two clinically approved drugs, but neither alone, muscularizes the heart through cardiomyocyte proliferation. Specifically, in adult murine cardiomyocytes, metoprolol, a cardioselective β1-adrenergic receptor blocker, when given with triiodothyronine (T3, a thyroid hormone) accentuates the ability of T3 to stimulate ERK1/2 phosphorylation and proliferative signaling by inhibiting expression of the nuclear phospho-ERK1/2-specific phosphatase, dual-specificity phosphatase-5. While short-duration metoprolol plus T3 therapy generates new heart muscle in healthy mice, in mice with myocardial infarction-induced left ventricular dysfunction and pathological remodeling, it remuscularizes the heart, restores contractile function and reverses chamber dilatation; outcomes that are enduring. If the beneficial effects of metoprolol plus T3 are replicated in humans, this therapeutic strategy has the potential to definitively address ischemic heart failure.
    DOI:  https://doi.org/10.1038/s41598-022-12723-2
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