bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2023–05–28
68 papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. How I caught up.
  2. Advancing reuse of genetic parts: progress and remaining challenges.
  3. Gasdermin splicing.
  4. Structures of human SGLT in the occluded state reveal conformational changes during sugar transport.
  5. Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome.
  6. Tissue repairing cytokine.
  7. IL-3 worsens MS.
  8. Platelet-derived chemokines promote skeletal muscle regeneration by guiding neutrophil recruitment to injured muscles.
  9. RNA splicing targets age-related diseases.
  10. De novo cholesterol biosynthesis in bacteria.
  11. Strand-selective base editing of human mitochondrial DNA using mitoBEs.
  12. Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide.
  13. Neutrophils contribute to fibromyalgia.
  14. The impact of rare protein coding genetic variation on adult cognitive function.
  15. Aberrant distribution of TFH cells in aged germinal centers reduces stromal cell function.
  16. Spatial dysregulation of T follicular helper cells impairs vaccine responses in aging.
  17. Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities.
  18. Vaccinia E5 is a major inhibitor of the DNA sensor cGAS.
  19. Structural basis of amine odorant perception by a mammal olfactory receptor.
  20. Tumour extracellular vesicles and particles induce liver metabolic dysfunction.
  21. Stem cell decoupling underlies impaired lymphoid development during aging.
  22. Glycolytically impaired Drosophila glial cells fuel neural metabolism via β-oxidation.
  23. Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism.
  24. B cell senescence takes guts.
  25. Dasatinib overcomes glucocorticoid resistance in B-cell acute lymphoblastic leukemia.
  26. Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis.
  27. Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA.
  28. Emerging frontiers in regenerative medicine.
  29. Proteolytic rewiring of mitochondria by LONP1 directs cell identity switching of adipocytes.
  30. Chemical-induced epigenome resetting for regeneration program activation in human cells.
  31. More human.
  32. Revealing vascular roadblocks in the brain.
  33. Mitotic bookmarking by SWI/SNF subunits.
  34. Near-lifespan longitudinal tracking of brain microvascular morphology, topology, and flow in male mice.
  35. Redefining the role of AMPK in autophagy and the energy stress response.
  36. Systematic elucidation of genetic mechanisms underlying cholesterol uptake.
  37. Host protection by two memory-like MAIT subsets.
  38. Induction of a torpor-like hypothermic and hypometabolic state in rodents by ultrasound.
  39. Coronaviral ORF6 protein mediates inter-organelle contacts and modulates host cell lipid flux for virus production.
  40. A coordinated multiorgan metabolic response contributes to human mitochondrial myopathy.
  41. Hyperphosphorylated PTEN exerts oncogenic properties.
  42. Protective Renalase-deficiency in beta cells shapes immune metabolism and function in autoimmune diabetes.
  43. Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements.
  44. Divergent metabolic programmes control two populations of MAIT cells that protect the lung.
  45. Cellular-scale proximity labeling for recording cell spatial organization in mouse tissues.
  46. Structural and functional insights into Spns2-mediated transport of sphingosine-1-phosphate.
  47. Stabilized mosaic single-cell data integration using unshared features.
  48. Rare heterozygous loss-of-function variants in the human GLP-1 receptor do not associate with cardiometabolic phenotypes.
  49. The TLR7-IRF-5 axis sensitizes memory CD4+ T cells to Fas-mediated apoptosis during HIV-1 infection.
  50. β-cell specific E2f1 deficiency impairs glucose homeostasis, β-cell identity and insulin secretion.
  51. Mitoprotease LONP1 controls white-to-beige adipocyte conversion via metabolic enzyme turnover.
  52. Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum.
  53. Gas therapy potentiates aggregation-induced emission luminogen-based photoimmunotherapy of poorly immunogenic tumors through cGAS-STING pathway activation.
  54. Integration of multi-modal single-cell data.
  55. Heat shock factor 1 (HSF1) specifically potentiates c-MYC-mediated transcription independently of the canonical heat shock response.
  56. How to effectively engage with preclinical medical learners.
  57. Activity-based directed evolution of a membrane editor in mammalian cells.
  58. Osteolectin increases bone elongation and body length by promoting growth plate chondrocyte proliferation.
  59. Combining reference genomes into a pangenome graph improves accuracy and reduces bias.
  60. Listening for neurological symptoms.
  61. Young donor hematopoietic stem cells revitalize aged or damaged bone marrow niche by transdifferentiating into functional niche cells.
  62. Genome-wide CRISPR screening of chondrocyte maturation newly implicates genes in skeletal growth and height-associated GWAS loci.
  63. Wound infiltrating adipocytes are not myofibroblasts.
  64. High-content CRISPR screening.
  65. A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST.
  66. Trogocytic molting of T cell microvilli upregulates T cell receptor surface expression and promotes clonal expansion.
  67. Learning how network structure shapes decision-making for bio-inspired computing.
  68. Dynamic BH3 profiling identifies pro-apoptotic drug combinations for the treatment of malignant pleural mesothelioma.
  1. Science. 2023 May 26. 380(6647): 866
    How I caught up.
    Emma Xu.
      
    DOI:  https://doi.org/10.1126/science.adi8191
  2. Nat Commun. 2023 May 23. 14(1): 2953
    Advancing reuse of genetic parts: progress and remaining challenges.
    Jeanet Mante, Chris J Myers.
      
    DOI:  https://doi.org/10.1038/s41467-023-38791-0
  3. Nat Immunol. 2023 May 22.
    Gasdermin splicing.
    Nicholas J Bernard.
      
    DOI:  https://doi.org/10.1038/s41590-023-01533-x
  4. Nat Commun. 2023 May 22. 14(1): 2920
    Structures of human SGLT in the occluded state reveal conformational changes during sugar transport.
    Wenhao Cui, Yange Niu, Zejian Sun, Rui Liu, Lei Chen.
      Sodium-Glucose Cotransporters (SGLT) mediate the uphill uptake of extracellular sugars and play fundamental roles in sugar metabolism. Although their structures in inward-open and outward-open conformations are emerging from structural studies, the trajectory of how SGLTs transit from the outward-facing to the inward-facing conformation remains unknown. Here, we present the cryo-EM structures of human SGLT1 and SGLT2 in the substrate-bound state. Both structures show an occluded conformation, with not only the extracellular gate but also the intracellular gate tightly sealed. The sugar substrate are caged inside a cavity surrounded by TM1, TM2, TM3, TM6, TM7, and TM10. Further structural analysis reveals the conformational changes associated with the binding and release of substrates. These structures fill a gap in our understanding of the structural mechanisms of SGLT transporters.
    DOI:  https://doi.org/10.1038/s41467-023-38720-1
  5. Nat Commun. 2023 May 23. 14(1): 2978
    Genetically encoded photocatalytic protein labeling enables spatially-resolved profiling of intracellular proteome.
    Fu Zheng, Xinyue Zhou, Peng Zou, Chenxin Yu.
      Mapping the subcellular organization of proteins is crucial for understanding their biological functions. Herein, we report a reactive oxygen species induced protein labeling and identification (RinID) method for profiling subcellular proteome in the context of living cells. Our method capitalizes on a genetically encoded photocatalyst, miniSOG, to locally generate singlet oxygen that reacts with proximal proteins. Labeled proteins are conjugated in situ with an exogenously supplied nucleophilic probe, which serves as a functional handle for subsequent affinity enrichment and mass spectrometry-based protein identification. From a panel of nucleophilic compounds, we identify biotin-conjugated aniline and propargyl amine as highly reactive probes. As a demonstration of the spatial specificity and depth of coverage in mammalian cells, we apply RinID in the mitochondrial matrix, capturing 477 mitochondrial proteins with 94% specificity. We further demonstrate the broad applicability of RinID in various subcellular compartments, including the nucleus and the endoplasmic reticulum (ER). The temporal control of RinID enables pulse-chase labeling of ER proteome in HeLa cells, which reveals substantially higher clearance rate for secreted proteins than ER resident proteins.
    DOI:  https://doi.org/10.1038/s41467-023-38565-8
  6. Nat Immunol. 2023 May 22.
    Tissue repairing cytokine.
    Ioana Visan.
      
    DOI:  https://doi.org/10.1038/s41590-023-01535-9
  7. Nat Immunol. 2023 May 22.
    IL-3 worsens MS.
    Stephanie Houston.
      
    DOI:  https://doi.org/10.1038/s41590-023-01534-w
  8. Nat Commun. 2023 May 22. 14(1): 2900
    Platelet-derived chemokines promote skeletal muscle regeneration by guiding neutrophil recruitment to injured muscles.
    Flavia A Graca, Anna Stephan, Benjamin A Minden-Birkenmaier, Abbas Shirinifard, Yong-Dong Wang, Fabio Demontis, Myriam Labelle.
      Skeletal muscle regeneration involves coordinated interactions between different cell types. Injection of platelet-rich plasma is circumstantially considered an aid to muscle repair but whether platelets promote regeneration beyond their role in hemostasis remains unexplored. Here, we find that signaling via platelet-released chemokines is an early event necessary for muscle repair in mice. Platelet depletion reduces the levels of the platelet-secreted neutrophil chemoattractants CXCL5 and CXCL7/PPBP. Consequently, early-phase neutrophil infiltration to injured muscles is impaired whereas later inflammation is exacerbated. Consistent with this model, neutrophil infiltration to injured muscles is compromised in male mice with Cxcl7-knockout platelets. Moreover, neo-angiogenesis and the re-establishment of myofiber size and muscle strength occurs optimally in control mice post-injury but not in Cxcl7ko mice and in neutrophil-depleted mice. Altogether, these findings indicate that platelet-secreted CXCL7 promotes regeneration by recruiting neutrophils to injured muscles, and that this signaling axis could be utilized therapeutically to boost muscle regeneration.
    DOI:  https://doi.org/10.1038/s41467-023-38624-0
  9. Nature. 2023 May 24.
    RNA splicing targets age-related diseases.
    Christine Evans-Pughe.
      
    Keywords:  Ageing; Cell biology; Diseases; Non-coding RNAs
    DOI:  https://doi.org/10.1038/d41586-023-01662-1
  10. Nat Commun. 2023 May 22. 14(1): 2904
    De novo cholesterol biosynthesis in bacteria.
    Alysha K Lee, Jeremy H Wei, Paula V Welander.
      Eukaryotes produce highly modified sterols, including cholesterol, essential to eukaryotic physiology. Although few bacterial species are known to produce sterols, de novo production of cholesterol or other complex sterols in bacteria has not been reported. Here, we show that the marine myxobacterium Enhygromyxa salina produces cholesterol and provide evidence for further downstream modifications. Through bioinformatic analysis we identify a putative cholesterol biosynthesis pathway in E. salina largely homologous to the eukaryotic pathway. However, experimental evidence indicates that complete demethylation at C-4 occurs through unique bacterial proteins, distinguishing bacterial and eukaryotic cholesterol biosynthesis. Additionally, proteins from the cyanobacterium Calothrix sp. NIES-4105 are also capable of fully demethylating sterols at the C-4 position, suggesting complex sterol biosynthesis may be found in other bacterial phyla. Our results reveal an unappreciated complexity in bacterial sterol production that rivals eukaryotes and highlight the complicated evolutionary relationship between sterol biosynthesis in the bacterial and eukaryotic domains.
    DOI:  https://doi.org/10.1038/s41467-023-38638-8
  11. Nat Biotechnol. 2023 May 22.
    Strand-selective base editing of human mitochondrial DNA using mitoBEs.
    Zongyi Yi, Xiaoxue Zhang, Wei Tang, Ying Yu, Xiaoxu Wei, Xue Zhang, Wensheng Wei.
      A number of mitochondrial diseases in humans are caused by point mutations that could be corrected by base editors, but delivery of CRISPR guide RNAs into the mitochondria is difficult. In this study, we present mitochondrial DNA base editors (mitoBEs), which combine a transcription activator-like effector (TALE)-fused nickase and a deaminase for precise base editing in mitochondrial DNA. Combining mitochondria-localized, programmable TALE binding proteins with the nickase MutH or Nt.BspD6I(C) and either the single-stranded DNA-specific adenine deaminase TadA8e or the cytosine deaminase ABOBEC1 and UGI, we achieve A-to-G or C-to-T base editing with up to 77% efficiency and high specificity. We find that mitoBEs are DNA strand-selective mitochondrial base editors, with editing results more likely to be retained on the nonnicked DNA strand. Furthermore, we correct pathogenic mitochondrial DNA mutations in patient-derived cells by delivering mitoBEs encoded in circular RNAs. mitoBEs offer a precise, efficient DNA editing tool with broad applicability for therapy in mitochondrial genetic diseases.
    DOI:  https://doi.org/10.1038/s41587-023-01791-y
  12. Nat Commun. 2023 May 22. 14(1): 2929
    Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide.
    Xiaolong Li, Nishant Kumar Singh, David R Collins, Robert Ng, Angela Zhang, Pedro A Lamothe-Molina, Peter Shahinian, Shutong Xu, Kemin Tan, Alicja Piechocka-Trocha, Jonathan M Urbach, Jeffrey K Weber, Gaurav D Gaiha, Overbeck Christian Takou Mbah, Tien Huynh, Sophia Cheever, James Chen, Michael Birnbaum, Ruhong Zhou, Bruce D Walker, Jia-Huai Wang.
      Cytotoxic-T-lymphocyte (CTL) mediated control of HIV-1 is enhanced by targeting highly networked epitopes in complex with human-leukocyte-antigen-class-I (HLA-I). However, the extent to which the presenting HLA allele contributes to this process is unknown. Here we examine the CTL response to QW9, a highly networked epitope presented by the disease-protective HLA-B57 and disease-neutral HLA-B53. Despite robust targeting of QW9 in persons expressing either allele, T cell receptor (TCR) cross-recognition of the naturally occurring variant QW9_S3T is consistently reduced when presented by HLA-B53 but not by HLA-B57. Crystal structures show substantial conformational changes from QW9-HLA to QW9_S3T-HLA by both alleles. The TCR-QW9-B53 ternary complex structure manifests how the QW9-B53 can elicit effective CTLs and suggests sterically hindered cross-recognition by QW9_S3T-B53. We observe populations of cross-reactive TCRs for B57, but not B53 and also find greater peptide-HLA stability for B57 in comparison to B53. These data demonstrate differential impacts of HLAs on TCR cross-recognition and antigen presentation of a naturally arising variant, with important implications for vaccine design.
    DOI:  https://doi.org/10.1038/s41467-023-38573-8
  13. Nat Immunol. 2023 May 22.
    Neutrophils contribute to fibromyalgia.
    Laurie A Dempsey.
      
    DOI:  https://doi.org/10.1038/s41590-023-01532-y
  14. Nat Genet. 2023 May 25.
    The impact of rare protein coding genetic variation on adult cognitive function.
    Biogen Biobank Team
      Compelling evidence suggests that human cognitive function is strongly influenced by genetics. Here, we conduct a large-scale exome study to examine whether rare protein-coding variants impact cognitive function in the adult population (n = 485,930). We identify eight genes (ADGRB2, KDM5B, GIGYF1, ANKRD12, SLC8A1, RC3H2, CACNA1A and BCAS3) that are associated with adult cognitive function through rare coding variants with large effects. Rare genetic architecture for cognitive function partially overlaps with that of neurodevelopmental disorders. In the case of KDM5B we show how the genetic dosage of one of these genes may determine the variability of cognitive, behavioral and molecular traits in mice and humans. We further provide evidence that rare and common variants overlap in association signals and contribute additively to cognitive function. Our study introduces the relevance of rare coding variants for cognitive function and unveils high-impact monogenic contributions to how cognitive function is distributed in the normal adult population.
    DOI:  https://doi.org/10.1038/s41588-023-01398-8
  15. Nat Immunol. 2023 May 22.
    Aberrant distribution of TFH cells in aged germinal centers reduces stromal cell function.
      
    DOI:  https://doi.org/10.1038/s41590-023-01520-2
  16. Nat Immunol. 2023 May 22.
    Spatial dysregulation of T follicular helper cells impairs vaccine responses in aging.
    Alyssa Silva-Cayetano, Sigrid Fra-Bido, Philippe A Robert, Silvia Innocentin, Alice R Burton, Emily M Watson, Jia Le Lee, Louise M C Webb, William S Foster, Ross C J McKenzie, Alexandre Bignon, Ine Vanderleyden, Dominik Alterauge, Julia P Lemos, Edward J Carr, Danika L Hill, Isabella Cinti, Karl Balabanian, Dirk Baumjohann, Marion Espeli, Michael Meyer-Hermann, Alice E Denton, Michelle A Linterman.
      The magnitude and quality of the germinal center (GC) response decline with age, resulting in poor vaccine-induced immunity in older individuals. A functional GC requires the co-ordination of multiple cell types across time and space, in particular across its two functionally distinct compartments: the light and dark zones. In aged mice, there is CXCR4-mediated mislocalization of T follicular helper (TFH) cells to the dark zone and a compressed network of follicular dendritic cells (FDCs) in the light zone. Here we show that TFH cell localization is critical for the quality of the antibody response and for the expansion of the FDC network upon immunization. The smaller GC and compressed FDC network in aged mice were corrected by provision of TFH cells that colocalize with FDCs using CXCR5. This demonstrates that the age-dependent defects in the GC response are reversible and shows that TFH cells support stromal cell responses to vaccines.
    DOI:  https://doi.org/10.1038/s41590-023-01519-9
  17. Nat Metab. 2023 May 22.
    Metabolic landscape of the male mouse gut identifies different niches determined by microbial activities.
    Karin H U Meier, Julian Trouillon, Hai Li, Melanie Lang, Tobias Fuhrer, Nicola Zamboni, Shinichi Sunagawa, Andrew J Macpherson, Uwe Sauer.
      Distinct niches of the mammalian gut are populated by diverse microbiota, but the contribution of spatial variation to intestinal metabolism remains unclear. Here we present a map of the longitudinal metabolome along the gut of healthy colonized and germ-free male mice. With this map, we reveal a general shift from amino acids in the small intestine to organic acids, vitamins and nucleotides in the large intestine. We compare the metabolic landscapes in colonized versus germ-free mice to disentangle the origin of many metabolites in different niches, which in some cases allows us to infer the underlying processes or identify the producing species. Beyond the known impact of diet on the small intestinal metabolic niche, distinct spatial patterns suggest specific microbial influence on the metabolome in the small intestine. Thus, we present a map of intestinal metabolism and identify metabolite-microbe associations, which provide a basis to connect the spatial occurrence of bioactive compounds to host or microorganism metabolism.
    DOI:  https://doi.org/10.1038/s42255-023-00802-1
  18. Nat Commun. 2023 May 22. 14(1): 2898
    Vaccinia E5 is a major inhibitor of the DNA sensor cGAS.
    Ning Yang, Yi Wang, Peihong Dai, Tuo Li, Christian Zierhut, Adrian Tan, Tuo Zhang, Jenny Zhaoying Xiang, Alban Ordureau, Hironori Funabiki, Zhijian Chen, Liang Deng.
      The DNA sensor cyclic GMP-AMP synthase (cGAS) is critical in host antiviral immunity. Vaccinia virus (VACV) is a large cytoplasmic DNA virus that belongs to the poxvirus family. How vaccinia virus antagonizes the cGAS-mediated cytosolic DNA-sensing pathway is not well understood. In this study, we screened 80 vaccinia genes to identify potential viral inhibitors of the cGAS/Stimulator of interferon gene (STING) pathway. We discovered that vaccinia E5 is a virulence factor and a major inhibitor of cGAS. E5 is responsible for abolishing cGAMP production during vaccinia virus (Western Reserve strain) infection of dendritic cells. E5 localizes to the cytoplasm and nucleus of infected cells. Cytosolic E5 triggers ubiquitination of cGAS and proteasome-dependent degradation via interacting with cGAS. Deleting the E5R gene from the Modified vaccinia virus Ankara (MVA) genome strongly induces type I IFN production by dendritic cells (DCs) and promotes DC maturation, and thereby improves antigen-specific T cell responses.
    DOI:  https://doi.org/10.1038/s41467-023-38514-5
  19. Nature. 2023 May 24.
    Structural basis of amine odorant perception by a mammal olfactory receptor.
    Lulu Guo, Jie Cheng, Shuo Lian, Qun Liu, Yan Lu, Yuan Zheng, Kongkai Zhu, Minghui Zhang, Yalei Kong, Chao Zhang, Naikang Rong, Yuming Zhuang, Guoxing Fang, Jingjing Jiang, Tianyao Zhang, Xiang Han, Zili Liu, Ming Xia, Shangming Liu, Lei Zhang, Stephen D Liberles, Xiao Yu, Yunfei Xu, Fan Yang, Qian Li, Jin-Peng Sun.
      Odorants are detected as smell in the nasal epithelium of mammals by two G-protein-coupled receptor families, the odorant receptors and the trace amine-associated receptors1,2 (TAARs). TAARs emerged following the divergence of jawed and jawless fish, and comprise a large monophyletic family of receptors that recognize volatile amine odorants to elicit both intraspecific and interspecific innate behaviours such as attraction and aversion3-5. Here we report cryo-electron microscopy structures of mouse TAAR9 (mTAAR9) and mTAAR9-Gs or mTAAR9-Golf trimers in complex with β-phenylethylamine, N,N-dimethylcyclohexylamine or spermidine. The mTAAR9 structures contain a deep and tight ligand-binding pocket decorated with a conserved D3.32W6.48Y7.43 motif, which is essential for amine odorant recognition. In the mTAAR9 structure, a unique disulfide bond connecting the N terminus to ECL2 is required for agonist-induced receptor activation. We identify key structural motifs of TAAR family members for detecting monoamines and polyamines and the shared sequence of different TAAR members that are responsible for recognition of the same odour chemical. We elucidate the molecular basis of mTAAR9 coupling to Gs and Golf by structural characterization and mutational analysis. Collectively, our results provide a structural basis for odorant detection, receptor activation and Golf coupling of an amine olfactory receptor.
    DOI:  https://doi.org/10.1038/s41586-023-06106-4
  20. Nature. 2023 May 24.
    Tumour extracellular vesicles and particles induce liver metabolic dysfunction.
    Gang Wang, Jianlong Li, Linda Bojmar, Haiyan Chen, Zhong Li, Gabriel C Tobias, Mengying Hu, Edwin A Homan, Serena Lucotti, Fengbo Zhao, Valentina Posada, Peter R Oxley, Michele Cioffi, Han Sang Kim, Huajuan Wang, Pernille Lauritzen, Nancy Boudreau, Zhanjun Shi, Christin E Burd, Jonathan H Zippin, James C Lo, Geoffrey S Pitt, Jonathan Hernandez, Constantinos P Zambirinis, Michael A Hollingsworth, Paul M Grandgenett, Maneesh Jain, Surinder K Batra, Dominick J DiMaio, Jean L Grem, Kelsey A Klute, Tanya M Trippett, Mikala Egeblad, Doru Paul, Jacqueline Bromberg, David Kelsen, Vinagolu K Rajasekhar, John H Healey, Irina R Matei, William R Jarnagin, Robert E Schwartz, Haiying Zhang, David Lyden.
      Cancer alters the function of multiple organs beyond those targeted by metastasis1,2. Here we show that inflammation, fatty liver and dysregulated metabolism are hallmarks of systemically affected livers in mouse models and in patients with extrahepatic metastasis. We identified tumour-derived extracellular vesicles and particles (EVPs) as crucial mediators of cancer-induced hepatic reprogramming, which could be reversed by reducing tumour EVP secretion via depletion of Rab27a. All EVP subpopulations, exosomes and principally exomeres, could dysregulate hepatic function. The fatty acid cargo of tumour EVPs-particularly palmitic acid-induced secretion of tumour necrosis factor (TNF) by Kupffer cells, generating a pro-inflammatory microenvironment, suppressing fatty acid metabolism and oxidative phosphorylation, and promoting fatty liver formation. Notably, Kupffer cell ablation or TNF blockade markedly decreased tumour-induced fatty liver generation. Tumour implantation or pre-treatment with tumour EVPs diminished cytochrome P450 gene expression and attenuated drug metabolism in a TNF-dependent manner. We also observed fatty liver and decreased cytochrome P450 expression at diagnosis in tumour-free livers of patients with pancreatic cancer who later developed extrahepatic metastasis, highlighting the clinical relevance of our findings. Notably, tumour EVP education enhanced side effects of chemotherapy, including bone marrow suppression and cardiotoxicity, suggesting that metabolic reprogramming of the liver by tumour-derived EVPs may limit chemotherapy tolerance in patients with cancer. Our results reveal how tumour-derived EVPs dysregulate hepatic function and their targetable potential, alongside TNF inhibition, for preventing fatty liver formation and enhancing the efficacy of chemotherapy.
    DOI:  https://doi.org/10.1038/s41586-023-06114-4
  21. Proc Natl Acad Sci U S A. 2023 05 30. 120(22): e2302019120
    Stem cell decoupling underlies impaired lymphoid development during aging.
    Geunhyo Jang, Stephania Contreras Castillo, Eduardo Esteva, Samik Upadhaya, Jue Feng, Nicholas M Adams, Elodie Richard, Rajeshwar Awatramani, Catherine M Sawai, Boris Reizis.
      Mammalian aging is associated with multiple defects of hematopoiesis, most prominently with the impaired development of T and B lymphocytes. This defect is thought to originate in hematopoietic stem cells (HSCs) of the bone marrow, specifically due to the age-dependent accumulation of HSCs with preferential megakaryocytic and/or myeloid potential ("myeloid bias"). Here, we tested this notion using inducible genetic labeling and tracing of HSCs in unmanipulated animals. We found that the endogenous HSC population in old mice shows reduced differentiation into all lineages including lymphoid, myeloid, and megakaryocytic. Single-cell RNA sequencing and immunophenotyping (CITE-Seq) showed that HSC progeny in old animals comprised balanced lineage spectrum including lymphoid progenitors. Lineage tracing using the aging-induced HSC marker Aldh1a1 confirmed the low contribution of old HSCs across all lineages. Competitive transplantations of total bone marrow cells with genetically marked HSCs revealed that the contribution of old HSCs was reduced, but compensated by other donor cells in myeloid cells but not in lymphocytes. Thus, the HSC population in old animals becomes globally decoupled from hematopoiesis, which cannot be compensated in lymphoid lineages. We propose that this partially compensated decoupling, rather than myeloid bias, is the primary cause of the selective impairment of lymphopoiesis in older mice.
    Keywords:  aging; hematopoietic stem cells; lymphopoiesis
    DOI:  https://doi.org/10.1073/pnas.2302019120
  22. Nat Commun. 2023 May 24. 14(1): 2996
    Glycolytically impaired Drosophila glial cells fuel neural metabolism via β-oxidation.
    Ellen McMullen, Helen Hertenstein, Katrin Strassburger, Leon Deharde, Marko Brankatschk, Stefanie Schirmeier.
      Neuronal function is highly energy demanding and thus requires efficient and constant metabolite delivery by glia. Drosophila glia are highly glycolytic and provide lactate to fuel neuronal metabolism. Flies are able to survive for several weeks in the absence of glial glycolysis. Here, we study how Drosophila glial cells maintain sufficient nutrient supply to neurons under conditions of impaired glycolysis. We show that glycolytically impaired glia rely on mitochondrial fatty acid breakdown and ketone body production to nourish neurons, suggesting that ketone bodies serve as an alternate neuronal fuel to prevent neurodegeneration. We show that in times of long-term starvation, glial degradation of absorbed fatty acids is essential to ensure survival of the fly. Further, we show that Drosophila glial cells act as a metabolic sensor and can induce mobilization of peripheral lipid stores to preserve brain metabolic homeostasis. Our study gives evidence of the importance of glial fatty acid degradation for brain function, and survival, under adverse conditions in Drosophila.
    DOI:  https://doi.org/10.1038/s41467-023-38813-x
  23. Nat Commun. 2023 May 24. 14(1): 2847
    Phospholipase D3 degrades mitochondrial DNA to regulate nucleotide signaling and APP metabolism.
    Zoë P Van Acker, Anika Perdok, Ruben Hellemans, Katherine North, Inge Vorsters, Cedric Cappel, Jonas Dehairs, Johannes V Swinnen, Ragna Sannerud, Marine Bretou, Markus Damme, Wim Annaert.
      Phospholipase D3 (PLD3) polymorphisms are linked to late-onset Alzheimer's disease (LOAD). Being a lysosomal 5'-3' exonuclease, its neuronal substrates remained unknown as well as how a defective lysosomal nucleotide catabolism connects to AD-proteinopathy. We identified mitochondrial DNA (mtDNA) as a major physiological substrate and show its manifest build-up in lysosomes of PLD3-defective cells. mtDNA accretion creates a degradative (proteolytic) bottleneck that presents at the ultrastructural level as a marked abundance of multilamellar bodies, often containing mitochondrial remnants, which correlates with increased PINK1-dependent mitophagy. Lysosomal leakage of mtDNA to the cytosol activates cGAS-STING signaling that upregulates autophagy and induces amyloid precursor C-terminal fragment (APP-CTF) and cholesterol accumulation. STING inhibition largely normalizes APP-CTF levels, whereas an APP knockout in PLD3-deficient backgrounds lowers STING activation and normalizes cholesterol biosynthesis. Collectively, we demonstrate molecular cross-talks through feedforward loops between lysosomal nucleotide turnover, cGAS-STING and APP metabolism that, when dysregulated, result in neuronal endolysosomal demise as observed in LOAD.
    DOI:  https://doi.org/10.1038/s41467-023-38501-w
  24. Nat Cell Biol. 2023 May 24.
    B cell senescence takes guts.
    Bennett G Childs, Sara I Graves, Darren J Baker.
      
    DOI:  https://doi.org/10.1038/s41556-023-01153-5
  25. Nat Commun. 2023 May 22. 14(1): 2935
    Dasatinib overcomes glucocorticoid resistance in B-cell acute lymphoblastic leukemia.
    Jolanda Sarno, Pablo Domizi, Yuxuan Liu, Milton Merchant, Christina Bligaard Pedersen, Dorra Jedoui, Astraea Jager, Garry P Nolan, Giuseppe Gaipa, Sean C Bendall, Felice-Alessio Bava, Kara L Davis.
      Resistance to glucocorticoids (GC) is associated with an increased risk of relapse in B-cell progenitor acute lymphoblastic leukemia (BCP-ALL). Performing transcriptomic and single-cell proteomic studies in healthy B-cell progenitors, we herein identify coordination between the glucocorticoid receptor pathway with B-cell developmental pathways. Healthy pro-B cells most highly express the glucocorticoid receptor, and this developmental expression is conserved in primary BCP-ALL cells from patients at diagnosis and relapse. In-vitro and in vivo glucocorticoid treatment of primary BCP-ALL cells demonstrate that the interplay between B-cell development and the glucocorticoid pathways is crucial for GC resistance in leukemic cells. Gene set enrichment analysis in BCP-ALL cell lines surviving GC treatment show enrichment of B cell receptor signaling pathways. In addition, primary BCP-ALL cells surviving GC treatment in vitro and in vivo demonstrate a late pre-B cell phenotype with activation of PI3K/mTOR and CREB signaling. Dasatinib, a multi-kinase inhibitor, most effectively targets this active signaling in GC-resistant cells, and when combined with glucocorticoids, results in increased cell death in vitro and decreased leukemic burden and prolonged survival in an in vivo xenograft model. Targeting the active signaling through the addition of dasatinib may represent a therapeutic approach to overcome GC resistance in BCP-ALL.
    DOI:  https://doi.org/10.1038/s41467-023-38456-y
  26. Nat Commun. 2023 May 20. 14(1): 2888
    Membrane compression by synaptic vesicle exocytosis triggers ultrafast endocytosis.
    Tyler H Ogunmowo, Haoyuan Jing, Sumana Raychaudhuri, Grant F Kusick, Yuuta Imoto, Shuo Li, Kie Itoh, Ye Ma, Haani Jafri, Matthew B Dalva, Edwin R Chapman, Taekjip Ha, Shigeki Watanabe, Jian Liu.
      Compensatory endocytosis keeps the membrane surface area of secretory cells constant following exocytosis. At chemical synapses, clathrin-independent ultrafast endocytosis maintains such homeostasis. This endocytic pathway is temporally and spatially coupled to exocytosis; it initiates within 50 ms at the region immediately next to the active zone where vesicles fuse. However, the coupling mechanism is unknown. Here, we demonstrate that filamentous actin is organized as a ring, surrounding the active zone at mouse hippocampal synapses. Assuming the membrane area conservation is due to this actin ring, our theoretical model suggests that flattening of fused vesicles exerts lateral compression in the plasma membrane, resulting in rapid formation of endocytic pits at the border between the active zone and the surrounding actin-enriched region. Consistent with model predictions, our data show that ultrafast endocytosis requires sufficient compression by exocytosis of multiple vesicles and does not initiate when actin organization is disrupted, either pharmacologically or by ablation of the actin-binding protein Epsin1. Our work suggests that membrane mechanics underlie the rapid coupling of exocytosis to endocytosis at synapses.
    DOI:  https://doi.org/10.1038/s41467-023-38595-2
  27. Nat Commun. 2023 May 24. 14(1): 2987
    Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA.
    Yufeng Liang, Sydney Willey, Yu-Chieh Chung, Yi-Meng Lo, Shiqin Miao, Sarah Rundell, Li-Chun Tu, Dennis Bong.
      The most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
    DOI:  https://doi.org/10.1038/s41467-023-38579-2
  28. Science. 2023 May 26. 380(6647): 796-798
    Emerging frontiers in regenerative medicine.
    Kara L McKinley, Michael T Longaker, Shruti Naik.
      Bridging knowledge gaps could enable regenerative therapy.
    DOI:  https://doi.org/10.1126/science.add6492
  29. Nat Cell Biol. 2023 May 22.
    Proteolytic rewiring of mitochondria by LONP1 directs cell identity switching of adipocytes.
    Tingting Fu, Wanping Sun, Jiachen Xue, Zheng Zhou, Wen Wang, Qiqi Guo, Xinyi Chen, Danxia Zhou, Zhisheng Xu, Lin Liu, Liwei Xiao, Yan Mao, Likun Yang, Yujing Yin, Xue-Na Zhang, Qiangyou Wan, Bin Lu, Yuncong Chen, Min-Sheng Zhu, Philipp E Scherer, Lei Fang, Hai-Long Piao, Mengle Shao, Zhenji Gan.
      Mitochondrial proteases are emerging as key regulators of mitochondrial plasticity and acting as both protein quality surveillance and regulatory enzymes by performing highly regulated proteolytic reactions. However, it remains unclear whether the regulated mitochondrial proteolysis is mechanistically linked to cell identity switching. Here we report that cold-responsive mitochondrial proteolysis is a prerequisite for white-to-beige adipocyte cell fate programming during adipocyte thermogenic remodelling. Thermogenic stimulation selectively promotes mitochondrial proteostasis in mature white adipocytes via the mitochondrial protease LONP1. Disruption of LONP1-dependent proteolysis substantially impairs cold- or β3 adrenergic agonist-induced white-to-beige identity switching of mature adipocytes. Mechanistically, LONP1 selectively degrades succinate dehydrogenase complex iron sulfur subunit B and ensures adequate intracellular succinate levels. This alters the histone methylation status on thermogenic genes and thereby enables adipocyte cell fate programming. Finally, augmented LONP1 expression raises succinate levels and corrects ageing-related impairments in white-to-beige adipocyte conversion and adipocyte thermogenic capacity. Together, these findings reveal that LONP1 links proteolytic surveillance to mitochondrial metabolic rewiring and directs cell identity conversion during adipocyte thermogenic remodelling.
    DOI:  https://doi.org/10.1038/s41556-023-01155-3
  30. Cell Rep. 2023 May 23. pii: S2211-1247(23)00558-2. [Epub ahead of print]42(6): 112547
    Chemical-induced epigenome resetting for regeneration program activation in human cells.
    Guan Wang, Yanglu Wang, Yulin Lyu, Huanjing He, Shijia Liuyang, Jinlin Wang, Shicheng Sun, Lin Cheng, Yao Fu, Jialiang Zhu, Xinxing Zhong, Zhihan Yang, Qijing Chen, Cheng Li, Jingyang Guan, Hongkui Deng.
      Human somatic cells can be reprogrammed to pluripotent stem cells by small molecules through an intermediate stage with a regeneration signature, but how this regeneration state is induced remains largely unknown. Here, through integrated single-cell analysis of transcriptome, we demonstrate that the pathway of human chemical reprogramming with regeneration state is distinct from that of transcription-factor-mediated reprogramming. Time-course construction of chromatin landscapes unveils hierarchical histone modification remodeling underlying the regeneration program, which involved sequential enhancer recommissioning and mirrored the reversal process of regeneration potential lost in organisms as they mature. In addition, LEF1 is identified as a key upstream regulator for regeneration gene program activation. Furthermore, we reveal that regeneration program activation requires sequential enhancer silencing of somatic and proinflammatory programs. Altogether, chemical reprogramming resets the epigenome through reversal of the loss of natural regeneration, representing a distinct concept for cellular reprogramming and advancing the development of regenerative therapeutic strategies.
    Keywords:  CP: Stem cell research; activation of regeneration-like program; chemical reprogramming; enhancer recommissioning; epigenome remodeling; reboot regeneration potential
    DOI:  https://doi.org/10.1016/j.celrep.2023.112547
  31. Nature. 2023 May 24.
    More human.
    Marisca Pichette.
      
    DOI:  https://doi.org/10.1038/d41586-023-01687-6
  32. Nature. 2023 May 24.
    Revealing vascular roadblocks in the brain.
    Michael Eisenstein.
      
    Keywords:  Brain; Cardiovascular biology; Imaging; Technology
    DOI:  https://doi.org/10.1038/d41586-023-01656-z
  33. Nature. 2023 May 24.
    Mitotic bookmarking by SWI/SNF subunits.
    Zhexin Zhu, Xiaolong Chen, Ao Guo, Trishabelle Manzano, Patrick J Walsh, Kendall M Wills, Rebecca Halliburton, Sandi Radko-Juettner, Raymond D Carter, Janet F Partridge, Douglas R Green, Jinghui Zhang, Charles W M Roberts.
      For cells to initiate and sustain a differentiated state, it is necessary that a 'memory' of this state is transmitted through mitosis to the daughter cells1-3. Mammalian switch/sucrose non-fermentable (SWI/SNF) complexes (also known as Brg1/Brg-associated factors, or BAF) control cell identity by modulating chromatin architecture to regulate gene expression4-7, but whether they participate in cell fate memory is unclear. Here we provide evidence that subunits of SWI/SNF act as mitotic bookmarks to safeguard cell identity during cell division. The SWI/SNF core subunits SMARCE1 and SMARCB1 are displaced from enhancers but are bound to promoters during mitosis, and we show that this binding is required for appropriate reactivation of bound genes after mitotic exit. Ablation of SMARCE1 during a single mitosis in mouse embryonic stem cells is sufficient to disrupt gene expression, impair the occupancy of several established bookmarks at a subset of their targets and cause aberrant neural differentiation. Thus, SWI/SNF subunit SMARCE1 has a mitotic bookmarking role and is essential for heritable epigenetic fidelity during transcriptional reprogramming.
    DOI:  https://doi.org/10.1038/s41586-023-06085-6
  34. Nat Commun. 2023 May 24. 14(1): 2982
    Near-lifespan longitudinal tracking of brain microvascular morphology, topology, and flow in male mice.
    Konrad W Walek, Sabina Stefan, Jang-Hoon Lee, Pooja Puttigampala, Anna H Kim, Seong Wook Park, Paul J Marchand, Frederic Lesage, Tao Liu, Yu-Wen Alvin Huang, David A Boas, Christopher Moore, Jonghwan Lee.
      In age-related neurodegenerative diseases, pathology often develops slowly across the lifespan. As one example, in diseases such as Alzheimer's, vascular decline is believed to onset decades ahead of symptomology. However, challenges inherent in current microscopic methods make longitudinal tracking of such vascular decline difficult. Here, we describe a suite of methods for measuring brain vascular dynamics and anatomy in mice for over seven months in the same field of view. This approach is enabled by advances in optical coherence tomography (OCT) and image processing algorithms including deep learning. These integrated methods enabled us to simultaneously monitor distinct vascular properties spanning morphology, topology, and function of the microvasculature across all scales: large pial vessels, penetrating cortical vessels, and capillaries. We have demonstrated this technical capability in wild-type and 3xTg male mice. The capability will allow comprehensive and longitudinal study of a broad range of progressive vascular diseases, and normal aging, in key model systems.
    DOI:  https://doi.org/10.1038/s41467-023-38609-z
  35. Nat Commun. 2023 May 24. 14(1): 2994
    Redefining the role of AMPK in autophagy and the energy stress response.
    Ji-Man Park, Da-Hye Lee, Do-Hyung Kim.
      Autophagy maintains cellular homeostasis during low energy states. According to the current understanding, glucose-depleted cells induce autophagy through AMPK, the primary energy-sensing kinase, to acquire energy for survival. However, contrary to the prevailing concept, our study demonstrates that AMPK inhibits ULK1, the kinase responsible for autophagy initiation, thereby suppressing autophagy. We found that glucose starvation suppresses amino acid starvation-induced stimulation of ULK1-Atg14-Vps34 signaling via AMPK activation. During an energy crisis caused by mitochondrial dysfunction, the LKB1-AMPK axis inhibits ULK1 activation and autophagy induction, even under amino acid starvation. Despite its inhibitory effect, AMPK protects the ULK1-associated autophagy machinery from caspase-mediated degradation during energy deficiency, preserving the cellular ability to initiate autophagy and restore homeostasis once the stress subsides. Our findings reveal that dual functions of AMPK, restraining abrupt induction of autophagy upon energy shortage while preserving essential autophagy components, are crucial to maintain cellular homeostasis and survival during energy stress.
    DOI:  https://doi.org/10.1038/s41467-023-38401-z
  36. Cell Genom. 2023 May 10. 3(5): 100304
    Systematic elucidation of genetic mechanisms underlying cholesterol uptake.
    Marisa C Hamilton, James D Fife, Ersin Akinci, Tian Yu, Benyapa Khowpinitchai, Minsun Cha, Sammy Barkal, Thi Tun Thi, Grace H T Yeo, Juan Pablo Ramos Barroso, Matthew Jake Francoeur, Minja Velimirovic, David K Gifford, Guillaume Lettre, Haojie Yu, Christopher A Cassa, Richard I Sherwood.
      Genetic variation contributes greatly to LDL cholesterol (LDL-C) levels and coronary artery disease risk. By combining analysis of rare coding variants from the UK Biobank and genome-scale CRISPR-Cas9 knockout and activation screening, we substantially improve the identification of genes whose disruption alters serum LDL-C levels. We identify 21 genes in which rare coding variants significantly alter LDL-C levels at least partially through altered LDL-C uptake. We use co-essentiality-based gene module analysis to show that dysfunction of the RAB10 vesicle transport pathway leads to hypercholesterolemia in humans and mice by impairing surface LDL receptor levels. Further, we demonstrate that loss of function of OTX2 leads to robust reduction in serum LDL-C levels in mice and humans by increasing cellular LDL-C uptake. Altogether, we present an integrated approach that improves our understanding of the genetic regulators of LDL-C levels and provides a roadmap for further efforts to dissect complex human disease genetics.
    Keywords:  CRISPR screening; LDL cholesterol; co-essentiality; rare variant analysis
    DOI:  https://doi.org/10.1016/j.xgen.2023.100304
  37. Nat Cell Biol. 2023 May 25.
    Host protection by two memory-like MAIT subsets.
    Margarita Dominguez-Villar.
      
    DOI:  https://doi.org/10.1038/s41556-023-01149-1
  38. Nat Metab. 2023 May 25.
    Induction of a torpor-like hypothermic and hypometabolic state in rodents by ultrasound.
    Yaoheng Yang, Jinyun Yuan, Rachael L Field, Dezhuang Ye, Zhongtao Hu, Kevin Xu, Lu Xu, Yan Gong, Yimei Yue, Alexxai V Kravitz, Michael R Bruchas, Jianmin Cui, Jonathan R Brestoff, Hong Chen.
      Torpor is an energy-conserving state in which animals dramatically decrease their metabolic rate and body temperature to survive harsh environmental conditions. Here, we report the noninvasive, precise and safe induction of a torpor-like hypothermic and hypometabolic state in rodents by remote transcranial ultrasound stimulation at the hypothalamus preoptic area (POA). We achieve a long-lasting (>24 h) torpor-like state in mice via closed-loop feedback control of ultrasound stimulation with automated detection of body temperature. Ultrasound-induced hypothermia and hypometabolism (UIH) is triggered by activation of POA neurons, involves the dorsomedial hypothalamus as a downstream brain region and subsequent inhibition of thermogenic brown adipose tissue. Single-nucleus RNA-sequencing of POA neurons reveals TRPM2 as an ultrasound-sensitive ion channel, the knockdown of which suppresses UIH. We also demonstrate that UIH is feasible in a non-torpid animal, the rat. Our findings establish UIH as a promising technology for the noninvasive and safe induction of a torpor-like state.
    DOI:  https://doi.org/10.1038/s42255-023-00804-z
  39. EMBO J. 2023 May 23. e112542
    Coronaviral ORF6 protein mediates inter-organelle contacts and modulates host cell lipid flux for virus production.
    Mengzhen Yue, Bing Hu, Jiajia Li, Ruifeng Chen, Zhen Yuan, Hurong Xiao, Haishuang Chang, Yaming Jiu, Kun Cai, Binbin Ding.
      Lipid droplets (LDs) form inter-organelle contacts with the endoplasmic reticulum (ER) that promote their biogenesis, while LD contacts with mitochondria enhance β-oxidation of contained fatty acids. Viruses have been shown to take advantage of lipid droplets to promote viral production, but it remains unclear whether they also modulate the interactions between LDs and other organelles. Here, we showed that coronavirus ORF6 protein targets LDs and is localized to the mitochondria-LD and ER-LD contact sites, where it regulates LD biogenesis and lipolysis. At the molecular level, we find that ORF6 inserts into the LD lipid monolayer via its two amphipathic helices. ORF6 further interacts with ER membrane proteins BAP31 and USE1 to mediate ER-LDs contact formation. Additionally, ORF6 interacts with the SAM complex in the mitochondrial outer membrane to link mitochondria to LDs. In doing so, ORF6 promotes cellular lipolysis and LD biogenesis to reprogram host cell lipid flux and facilitate viral production.
    Keywords:  ORF6; endoplasmic reticulum; lipid droplets; mitochondria; organelle interaction
    DOI:  https://doi.org/10.15252/embj.2022112542
  40. EMBO Mol Med. 2023 May 24. e16951
    A coordinated multiorgan metabolic response contributes to human mitochondrial myopathy.
    Nneka Southwell, Guido Primiano, Viraj Nadkarni, Nabeel Attarwala, Emelie Beattie, Dawson Miller, Sumaitaah Alam, Irene Liparulo, Yevgeniya I Shurubor, Maria Lucia Valentino, Valerio Carelli, Serenella Servidei, Steven S Gross, Giovanni Manfredi, Qiuying Chen, Marilena D'Aurelio.
      Mitochondrial diseases are a heterogeneous group of monogenic disorders that result from impaired oxidative phosphorylation (OXPHOS). As neuromuscular tissues are highly energy-dependent, mitochondrial diseases often affect skeletal muscle. Although genetic and bioenergetic causes of OXPHOS impairment in human mitochondrial myopathies are well established, there is a limited understanding of metabolic drivers of muscle degeneration. This knowledge gap contributes to the lack of effective treatments for these disorders. Here, we discovered fundamental muscle metabolic remodeling mechanisms shared by mitochondrial disease patients and a mouse model of mitochondrial myopathy. This metabolic remodeling is triggered by a starvation-like response that evokes accelerated oxidation of amino acids through a truncated Krebs cycle. While initially adaptive, this response evolves in an integrated multiorgan catabolic signaling, lipid store mobilization, and intramuscular lipid accumulation. We show that this multiorgan feed-forward metabolic response involves leptin and glucocorticoid signaling. This study elucidates systemic metabolic dyshomeostasis mechanisms that underlie human mitochondrial myopathies and identifies potential new targets for metabolic intervention.
    Keywords:  amino acid metabolism; glucocorticoids; leptin; mitochondrial myopathy; muscle wasting
    DOI:  https://doi.org/10.15252/emmm.202216951
  41. Nat Commun. 2023 May 24. 14(1): 2983
    Hyperphosphorylated PTEN exerts oncogenic properties.
    Janine H van Ree, Karthik B Jeganathan, Raul O Fierro Velasco, Cheng Zhang, Ismail Can, Masakazu Hamada, Hu Li, Darren J Baker, Jan M van Deursen.
      PTEN is a multifaceted tumor suppressor that is highly sensitive to alterations in expression or function. The PTEN C-tail domain, which is rich in phosphorylation sites, has been implicated in PTEN stability, localization, catalytic activity, and protein interactions, but its role in tumorigenesis remains unclear. To address this, we utilized several mouse strains with nonlethal C-tail mutations. Mice homozygous for a deletion that includes S370, S380, T382 and T383 contain low PTEN levels and hyperactive AKT but are not tumor prone. Analysis of mice containing nonphosphorylatable or phosphomimetic versions of S380, a residue hyperphosphorylated in human gastric cancers, reveal that PTEN stability and ability to inhibit PI3K-AKT depends on dynamic phosphorylation-dephosphorylation of this residue. While phosphomimetic S380 drives neoplastic growth in prostate by promoting nuclear accumulation of β-catenin, nonphosphorylatable S380 is not tumorigenic. These data suggest that C-tail hyperphosphorylation creates oncogenic PTEN and is a potential target for anti-cancer therapy.
    DOI:  https://doi.org/10.1038/s41467-023-38740-x
  42. Diabetes. 2023 May 22. pii: db230030. [Epub ahead of print]
    Protective Renalase-deficiency in beta cells shapes immune metabolism and function in autoimmune diabetes.
    Kevin Bode, Tara MacDonald, Taylor Stewart, Bryhan Mendez, Erica P Cai, Noelle Morrow, Yu-Chi Lee, Peng Yi, Stephan Kissler.
      Type 1 diabetes (T1D) is caused by the immune-mediated loss of pancreatic beta cells that produce insulin. The latest advances in stem cell (SC)-beta cell differentiation methods have made a cell replacement therapy for T1D feasible. However, recurring autoimmunity would rapidly destroy transplanted SC-beta cells. A promising strategy to overcome immune rejection is to genetically engineer SC-beta cells. We previously identified Renalase (Rnls) as a novel target for beta cell protection. Here we show that Rnls deletion endows beta cells with the capacity to modulate the metabolism and function of immune cells within the local graft microenvironment. We used flow cytometry and single-cell RNA sequencing to characterize beta cell graft-infiltrating immune cells in a mouse model for T1D. Loss of Rnls within transplanted beta cells affected both the composition and the transcriptional profile of infiltrating immune cells in favor of an anti-inflammatory profile with decreased antigen presenting capacity. We propose that changes in beta cell metabolism mediate local immune regulation and that this feature could be exploited for therapeutic goals.
    DOI:  https://doi.org/10.2337/db23-0030
  43. Cell Genom. 2023 May 10. 3(5): 100291
    Resolution of structural variation in diverse mouse genomes reveals chromatin remodeling due to transposable elements.
    Ardian Ferraj, Peter A Audano, Parithi Balachandran, Anne Czechanski, Jacob I Flores, Alexander A Radecki, Varun Mosur, David S Gordon, Isha A Walawalkar, Evan E Eichler, Laura G Reinholdt, Christine R Beck.
      Diverse inbred mouse strains are important biomedical research models, yet genome characterization of many strains is fundamentally lacking in comparison with humans. In particular, catalogs of structural variants (SVs) (variants ≥ 50 bp) are incomplete, limiting the discovery of causative alleles for phenotypic variation. Here, we resolve genome-wide SVs in 20 genetically distinct inbred mice with long-read sequencing. We report 413,758 site-specific SVs affecting 13% (356 Mbp) of the mouse reference assembly, including 510 previously unannotated coding variants. We substantially improve the Mus musculus transposable element (TE) callset, and we find that TEs comprise 39% of SVs and account for 75% of altered bases. We further utilize this callset to investigate how TE heterogeneity affects mouse embryonic stem cells and find multiple TE classes that influence chromatin accessibility. Our work provides a comprehensive analysis of SVs found in diverse mouse genomes and illustrates the role of TEs in epigenetic differences.
    Keywords:  chromatin accessibility; collaborative cross; effects of structural variation; embryonic stem cells; inbred micetransposable elements; long read sequencing; mouse genomics; structural variation; whole genome assembly
    DOI:  https://doi.org/10.1016/j.xgen.2023.100291
  44. Nat Cell Biol. 2023 May 25.
    Divergent metabolic programmes control two populations of MAIT cells that protect the lung.
    Thomas Riffelmacher, Mallory Paynich Murray, Chantal Wientjens, Shilpi Chandra, Viankail Cedillo-Castelán, Ting-Fang Chou, Sara McArdle, Christopher Dillingham, Jordan Devereaux, Aaron Nilsen, Simon Brunel, David M Lewinsohn, Jeff Hasty, Gregory Seumois, Christopher A Benedict, Pandurangan Vijayanand, Mitchell Kronenberg.
      Although mucosal-associated invariant T (MAIT) cells provide rapid, innate-like responses, they are not pre-set, and memory-like responses have been described for MAIT cells following infections. The importance of metabolism for controlling these responses, however, is unknown. Here, following pulmonary immunization with a Salmonella vaccine strain, mouse MAIT cells expanded as separate CD127-Klrg1+ and CD127+Klrg1- antigen-adapted populations that differed in terms of their transcriptome, function and localization in lung tissue. These populations remained altered from steady state for months as stable, separate MAIT cell lineages with enhanced effector programmes and divergent metabolism. CD127+ MAIT cells engaged in an energetic, mitochondrial metabolic programme, which was critical for their maintenance and IL-17A synthesis. This programme was supported by high fatty acid uptake and mitochondrial oxidation and relied on highly polarized mitochondria and autophagy. After vaccination, CD127+ MAIT cells protected mice against Streptococcus pneumoniae infection. In contrast, Klrg1+ MAIT cells had dormant but ready-to-respond mitochondria and depended instead on Hif1a-driven glycolysis to survive and produce IFN-γ. They responded antigen independently and participated in protection from influenza virus. These metabolic dependencies may enable tuning of memory-like MAIT cell responses for vaccination and immunotherapies.
    DOI:  https://doi.org/10.1038/s41556-023-01152-6
  45. Sci Adv. 2023 May 26. 9(21): eadg6388
    Cellular-scale proximity labeling for recording cell spatial organization in mouse tissues.
    Xu Zhang, Qi Tang, Jiayu Sun, Yilan Guo, Shaoran Zhang, Shuyu Liang, Peng Dai, Xing Chen.
      Proximity labeling has emerged as a powerful strategy for interrogating cell-cell interactions. However, the nanometer-scale labeling radius impedes the use of current methods for indirect cell communications and makes recording cell spatial organization in tissue samples difficult. Here, we develop quinone methide-assisted identification of cell spatial organization (QMID), a chemical strategy with the labeling radius matching the cell dimension. The activating enzyme is installed on the surface of bait cells, which produces QM electrophiles that can diffuse across micrometers and label proximal prey cells independent of cell-cell contacts. In cell coculture, QMID reveals gene expression of macrophages that are regulated by spatial proximity to tumor cells. Furthermore, QMID enables labeling and isolation of proximal cells of CD4+ and CD8+ T cells in the mouse spleen, and subsequent single-cell RNA sequencing uncovers distinctive cell populations and gene expression patterns within the immune niches of specific T cell subtypes. QMID should facilitate dissecting cell spatial organization in various tissues.
    DOI:  https://doi.org/10.1126/sciadv.adg6388
  46. Cell. 2023 May 17. pii: S0092-8674(23)00457-9. [Epub ahead of print]
    Structural and functional insights into Spns2-mediated transport of sphingosine-1-phosphate.
    Hongwen Chen, Shahbaz Ahmed, Hongtu Zhao, Nadia Elghobashi-Meinhardt, Yaxin Dai, Jae Hun Kim, Jeffrey G McDonald, Xiaochun Li, Chia-Hsueh Lee.
      Sphingosine-1-phosphate (S1P) is an important signaling sphingolipid that regulates the immune system, angiogenesis, auditory function, and epithelial and endothelial barrier integrity. Spinster homolog 2 (Spns2) is an S1P transporter that exports S1P to initiate lipid signaling cascades. Modulating Spns2 activity can be beneficial in treatments of cancer, inflammation, and immune diseases. However, the transport mechanism of Spns2 and its inhibition remain unclear. Here, we present six cryo-EM structures of human Spns2 in lipid nanodiscs, including two functionally relevant intermediate conformations that link the inward- and outward-facing states, to reveal the structural basis of the S1P transport cycle. Functional analyses suggest that Spns2 exports S1P via facilitated diffusion, a mechanism distinct from other MFS lipid transporters. Finally, we show that the Spns2 inhibitor 16d attenuates the transport activity by locking Spns2 in the inward-facing state. Our work sheds light on Spns2-mediated S1P transport and aids the development of advanced Spns2 inhibitors.
    Keywords:  S1P; Spns2; cryo-EM; major facilitator superfamily; sphingolipid; uniporter
    DOI:  https://doi.org/10.1016/j.cell.2023.04.028
  47. Nat Biotechnol. 2023 May 25.
    Stabilized mosaic single-cell data integration using unshared features.
    Shila Ghazanfar, Carolina Guibentif, John C Marioni.
      Currently available single-cell omics technologies capture many unique features with different biological information content. Data integration aims to place cells, captured with different technologies, onto a common embedding to facilitate downstream analytical tasks. Current horizontal data integration techniques use a set of common features, thereby ignoring non-overlapping features and losing information. Here we introduce StabMap, a mosaic data integration technique that stabilizes mapping of single-cell data by exploiting the non-overlapping features. StabMap first infers a mosaic data topology based on shared features, then projects all cells onto supervised or unsupervised reference coordinates by traversing shortest paths along the topology. We show that StabMap performs well in various simulation contexts, facilitates 'multi-hop' mosaic data integration where some datasets do not share any features and enables the use of spatial gene expression features for mapping dissociated single-cell data onto a spatial transcriptomic reference.
    DOI:  https://doi.org/10.1038/s41587-023-01766-z
  48. J Clin Endocrinol Metab. 2023 May 26. pii: dgad290. [Epub ahead of print]
    Rare heterozygous loss-of-function variants in the human GLP-1 receptor do not associate with cardiometabolic phenotypes.
    Josefine U Melchiorsen, Kimmie V Sørensen, Jette Bork-Jensen, Hüsün S Kizilkaya, Lærke S Gasbjerg, Alexander S Hauser, Jørgen Rungby, Henrik T Sørensen, Allan Vaag, Jens S Nielsen, Oluf Pedersen, Allan Linneberg, Bolette Hartmann, Anette P Gjesing, Jens J Holst, Torben Hansen, Mette M Rosenkilde, Niels Grarup.
       CONTEXT: Impact of lost GLP-1 receptor function in human physiology.
    OBJECTIVE: Identify coding nonsynonymous GLP1R variants in Danish individuals to link their in vitro phenotypes and clinical phenotypic associations.
    METHODS: We sequenced GLP1R in 8,642 Danish individuals with type 2 diabetes or normal glucose tolerance and examined the ability of nonsynonymous variants to bind GLP-1 and to signal in transfected cells via cAMP formation and beta-arrestin recruitment. We performed a cross-sectional study between the burden of loss-of-signalling (LoS) variants and cardiometabolic phenotypes in 2,930 patients with type 2 diabetes and 5,712 participants in a population-based cohort. Furthermore, we studied the association between cardiometabolic phenotypes and the burden of the LoS variants and 60 partly overlapping predicted loss-of-function (pLoF) GLP1R variants found in 330,566 unrelated Caucasian exome-sequenced participants in the UK Biobank cohort.
    RESULTS: We identified 36 nonsynonymous variants in GLP1R of which 10 had a statistically significant loss in GLP-1-induced cAMP signalling compared to wildtype. However, no association was observed between the LoS variants and type 2 diabetes, although LoS variant carriers had a minor increased fasting plasma glucose level. Moreover, pLoF variants from the UK Biobank also did not reveal substantial cardiometabolic associations, despite a small effect on HbA1c.
    CONCLUSION: Since no homozygous LoS nor pLoF variants were identified and heterozygous carriers had similar cardiometabolic phenotype as non-carriers, we conclude that GLP-1R may be of particular importance in human physiology, due to a potential evolutionary intolerance of harmful homozygous GLP1R variants.
    Keywords:  Functional study; GLP1R; genetic association; glucagon-like peptide 1; type 2 diabetes
    DOI:  https://doi.org/10.1210/clinem/dgad290
  49. JCI Insight. 2023 May 25. pii: e167329. [Epub ahead of print]
    The TLR7-IRF-5 axis sensitizes memory CD4+ T cells to Fas-mediated apoptosis during HIV-1 infection.
    Liseth Carmona-Perez, Xavier Dagenais-Lussier, Linh Thuy Mai, Tanja Stögerer, Sharada Swaminathan, Stephane Isnard, Matthew R Rice, Betsy J Barnes, Jean Pierre Routy, Julien van Grevenynghe, Simona Stager.
      HIV-1 infection is characterized by a strong inflammatory environment, tissue disruption, and a progressive decline in CD4+ T cell count. Despite treatment with antiretroviral therapy (ART), the majority of persons living with HIV (PLWH) maintain residual levels of inflammation, low degree of immune activation, and higher sensitivity to cell death in their memory CD4+ T-cell compartment. To date, the mechanisms responsible for this high sensitivity remain elusive. We have identified the transcription factor IRF-5 to be involved in impairing the maintenance of murine CD4+ T cells in a chronic inflammatory environment. Here, we investigate whether IRF-5 also contributes to memory CD4+ T cell loss during HIV-1 infection. We show that TLR7 and IRF-5 were upregulated in memory CD4+ T cells from PLWH, when compared with naturally protected elite controllers and HIVfree participants. TLR7 was upstream of IRF-5, promoting Caspase 8 expression in CD4+ T cells from ART HIV-1+ but not from HIVfree participants. Moreover, IRF-5 and TLR7 expression inversely correlated with CD4+ T cell counts in primary HIV infection. Interestingly, the TLR7-IRF-5 axis acted synergistically with the Fas/FasL pathway, suggesting that TLR7 and IRF-5 expression in ART HIV-1+ memory CD4+ T cells represents an imprint that predisposes cells to Fas-mediated apoptosis. This predisposition could be blocked using IRF-5 inhibitory peptides. Thus, we propose IRF-5 blockade as a possible therapy to prevent memory CD4+ T cell loss in PLWH.
    Keywords:  AIDS/HIV; Apoptosis; Immunology; T cells
    DOI:  https://doi.org/10.1172/jci.insight.167329
  50. Diabetes. 2023 May 22. pii: db220604. [Epub ahead of print]
    β-cell specific E2f1 deficiency impairs glucose homeostasis, β-cell identity and insulin secretion.
    Frédérik Oger, Cyril Bourouh, Marika Elsa Friano, Emilie Courty, Laure Rolland, Xavier Gromada, Maeva Moreno, Charlène Carney, Nabil Rabhi, Emmanuelle Durand, Souhila Amanzougarene, Lionel Berberian, Mehdi Derhourhi, Etienne Blanc, Sarah Anissa Hannou, Pierre-Damien Denechaud, Zohra Benfodda, Patrick Meffre, Lluis Fajas, Julie Kerr-Conte, François Pattou, Philippe Froguel, Benoit Pourcet, Amélie Bonnefond, Patrick Collombat, Jean-Sébastien Annicotte.
      The loss of pancreatic β-cell identity emerges as an important feature of type 2 diabetes development, but the molecular mechanisms are still elusive. Here, we explore the cellautonomous role of the cell cycle regulator and transcription factor E2F1 in the maintenance of β-cell identity, insulin secretion and glucose homeostasis. We show that the β-cell-specific loss of E2f1 function in mice triggers glucose intolerance associated with defective insulin secretion, an altered endocrine cell mass, a downregulation of many β-cell genes and a concomitant increase of non-β-cell markers. Mechanistically, the epigenomic profiling of promoters of these non-β-cell upregulated genes identified an enrichment of bivalent H3K4me3/H3K27me3 or H3K27me3 marks. Conversely, promoters of downregulated genes were enriched in active chromatin H3K4me3 and H3K27ac histone marks. We find that specific E2f1 transcriptional, cistromic and epigenomic signatures are associated with these β-cell dysfunctions, with E2F1 directly regulating several β-cell genes at the chromatin level. Finally, the pharmacological inhibition of E2F transcriptional activity in human islets also impairs insulin secretion and the expression of β-cell identity genes. Our data suggest that E2F1 is critical for maintaining β-cell identity and function through a sustained control of β-cell and non β-cell transcriptional programs.
    DOI:  https://doi.org/10.2337/db22-0604
  51. Nat Cell Biol. 2023 May 24.
    Mitoprotease LONP1 controls white-to-beige adipocyte conversion via metabolic enzyme turnover.
      
    DOI:  https://doi.org/10.1038/s41556-023-01161-5
  52. Nature. 2023 May 24.
    Ubiquitination regulates ER-phagy and remodelling of endoplasmic reticulum.
    Alexis González, Adriana Covarrubias-Pinto, Ramachandra M Bhaskara, Marius Glogger, Santosh K Kuncha, Audrey Xavier, Eric Seemann, Mohit Misra, Marina E Hoffmann, Bastian Bräuning, Ashwin Balakrishnan, Britta Qualmann, Volker Dötsch, Brenda A Schulman, Michael M Kessels, Christian A Hübner, Mike Heilemann, Gerhard Hummer, Ivan Dikić.
      The endoplasmic reticulum (ER) undergoes continuous remodelling via a selective autophagy pathway, known as ER-phagy1. ER-phagy receptors have a central role in this process2, but the regulatory mechanism remains largely unknown. Here we report that ubiquitination of the ER-phagy receptor FAM134B within its reticulon homology domain (RHD) promotes receptor clustering and binding to lipidated LC3B, thereby stimulating ER-phagy. Molecular dynamics (MD) simulations showed how ubiquitination perturbs the RHD structure in model bilayers and enhances membrane curvature induction. Ubiquitin molecules on RHDs mediate interactions between neighbouring RHDs to form dense receptor clusters that facilitate the large-scale remodelling of lipid bilayers. Membrane remodelling was reconstituted in vitro with liposomes and ubiquitinated FAM134B. Using super-resolution microscopy, we discovered FAM134B nanoclusters and microclusters in cells. Quantitative image analysis revealed a ubiquitin-mediated increase in FAM134B oligomerization and cluster size. We found that the E3 ligase AMFR, within multimeric ER-phagy receptor clusters, catalyses FAM134B ubiquitination and regulates the dynamic flux of ER-phagy. Our results show that ubiquitination enhances RHD functions via receptor clustering, facilitates ER-phagy and controls ER remodelling in response to cellular demands.
    DOI:  https://doi.org/10.1038/s41586-023-06089-2
  53. Nat Commun. 2023 May 23. 14(1): 2950
    Gas therapy potentiates aggregation-induced emission luminogen-based photoimmunotherapy of poorly immunogenic tumors through cGAS-STING pathway activation.
    Kaiyuan Wang, Yang Li, Xia Wang, Zhijun Zhang, Liping Cao, Xiaoyuan Fan, Bin Wan, Fengxiang Liu, Xuanbo Zhang, Zhonggui He, Yingtang Zhou, Dong Wang, Jin Sun, Xiaoyuan Chen.
      The immunologically "cold" microenvironment of triple negative breast cancer results in resistance to current immunotherapy. Here, we reveal the immunoadjuvant property of gas therapy with cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway activation to augment aggregation-induced emission (AIE)-active luminogen (AIEgen)-based photoimmunotherapy. A virus-mimicking hollow mesoporous tetrasulfide-doped organosilica is developed for co-encapsulation of AIEgen and manganese carbonyl to fabricate gas nanoadjuvant. As tetra-sulfide bonds are responsive to intratumoral glutathione, the gas nanoadjuvant achieves tumor-specific drug release, promotes photodynamic therapy, and produces hydrogen sulfide (H2S). Upon near-infrared laser irradiation, the AIEgen-mediated phototherapy triggers the burst of carbon monoxide (CO)/Mn2+. Both H2S and CO can destroy mitochondrial integrity to induce leakage of mitochondrial DNA into the cytoplasm, serving as gas immunoadjuvants to activate cGAS-STING pathway. Meanwhile, Mn2+ can sensitize cGAS to augment STING-mediated type I interferon production. Consequently, the gas nanoadjuvant potentiates photoimmunotherapy of poorly immunogenic breast tumors in female mice.
    DOI:  https://doi.org/10.1038/s41467-023-38601-7
  54. Nat Biotechnol. 2023 May 25.
    Integration of multi-modal single-cell data.
    Michelle Y Y Lee, Mingyao Li.
      
    DOI:  https://doi.org/10.1038/s41587-023-01826-4
  55. Cell Rep. 2023 May 23. pii: S2211-1247(23)00568-5. [Epub ahead of print]42(6): 112557
    Heat shock factor 1 (HSF1) specifically potentiates c-MYC-mediated transcription independently of the canonical heat shock response.
    Meng Xu, Ling Lin, Babul Moni Ram, Omprakash Shriwas, Kun-Han Chuang, Siyuan Dai, Kuo-Hui Su, Zijian Tang, Chengkai Dai.
      Despite its pivotal roles in biology, how the transcriptional activity of c-MYC is tuned quantitatively remains poorly defined. Here, we show that heat shock factor 1 (HSF1), the master transcriptional regulator of the heat shock response, acts as a prime modifier of the c-MYC-mediated transcription. HSF1 deficiency diminishes c-MYC DNA binding and dampens its transcriptional activity genome wide. Mechanistically, c-MYC, MAX, and HSF1 assemble into a transcription factor complex on genomic DNAs, and surprisingly, the DNA binding of HSF1 is dispensable. Instead, HSF1 physically recruits the histone acetyltransferase general control nonderepressible 5 (GCN5), promoting histone acetylation and augmenting c-MYC transcriptional activity. Thus, we find that HSF1 specifically potentiates the c-MYC-mediated transcription, discrete from its canonical role in countering proteotoxic stress. Importantly, this mechanism of action engenders two distinct c-MYC activation states, primary and advanced, which may be important to accommodate diverse physiological and pathological conditions.
    Keywords:  CP: Molecular biology; CUT&RUN-seq; GCN5; HSF1; c-MYC; transcription factor complex
    DOI:  https://doi.org/10.1016/j.celrep.2023.112557
  56. Gastroenterology. 2023 May 18. pii: S0016-5085(23)00736-9. [Epub ahead of print]
    How to effectively engage with preclinical medical learners.
    Andrew W Tai, Justin L Sewell.
      
    Keywords:  Preclinical medical education; competency-based medical education; disparities; equity
    DOI:  https://doi.org/10.1053/j.gastro.2023.05.014
  57. Nat Chem. 2023 May 22.
    Activity-based directed evolution of a membrane editor in mammalian cells.
    Reika Tei, Saket R Bagde, J Christopher Fromme, Jeremy M Baskin.
      Cellular membranes contain numerous lipid species, and efforts to understand the biological functions of individual lipids have been stymied by a lack of approaches for controlled modulation of membrane composition in situ. Here we present a strategy for editing phospholipids, the most abundant lipids in biological membranes. Our membrane editor is based on a bacterial phospholipase D (PLD), which exchanges phospholipid head groups through hydrolysis or transphosphatidylation of phosphatidylcholine with water or exogenous alcohols. Exploiting activity-dependent directed enzyme evolution in mammalian cells, we have developed and structurally characterized a family of 'superPLDs' with up to a 100-fold enhancement in intracellular activity. We demonstrate the utility of superPLDs for both optogenetics-enabled editing of phospholipids within specific organelle membranes in live cells and biocatalytic synthesis of natural and unnatural designer phospholipids in vitro. Beyond the superPLDs, activity-based directed enzyme evolution in mammalian cells is a generalizable approach to engineer additional chemoenzymatic biomolecule editors.
    DOI:  https://doi.org/10.1038/s41557-023-01214-0
  58. Proc Natl Acad Sci U S A. 2023 05 30. 120(22): e2220159120
    Osteolectin increases bone elongation and body length by promoting growth plate chondrocyte proliferation.
    Jingzhu Zhang, Liming Du, Bethany Davis, Zhimin Gu, Junhua Lyu, Zhiyu Zhao, Jian Xu, Sean J Morrison.
      Osteolectin is a recently identified osteogenic growth factor that binds to Integrin α11 (encoded by Itga11), promoting Wnt pathway activation and osteogenic differentiation by bone marrow stromal cells. While Osteolectin and Itga11 are not required for the formation of the skeleton during fetal development, they are required for the maintenance of adult bone mass. Genome-wide association studies in humans reported a single-nucleotide variant (rs182722517) 16 kb downstream of Osteolectin associated with reduced height and plasma Osteolectin levels. In this study, we tested whether Osteolectin promotes bone elongation and found that Osteolectin-deficient mice have shorter bones than those of sex-matched littermate controls. Integrin α11 deficiency in limb mesenchymal progenitors or chondrocytes reduced growth plate chondrocyte proliferation and bone elongation. Recombinant Osteolectin injections increased femur length in juvenile mice. Human bone marrow stromal cells edited to contain the rs182722517 variant produced less Osteolectin and underwent less osteogenic differentiation than that of control cells. These studies identify Osteolectin/Integrin α11 as a regulator of bone elongation and body length in mice and humans.
    Keywords:  bone elongation; chondrocyte; integrin α11; osteogenesis; osteolectin
    DOI:  https://doi.org/10.1073/pnas.2220159120
  59. Nat Biotechnol. 2023 May 22.
    Combining reference genomes into a pangenome graph improves accuracy and reduces bias.
      
    DOI:  https://doi.org/10.1038/s41587-023-01828-2
  60. Nature. 2023 May 24.
    Listening for neurological symptoms.
    Michael Eisenstein.
      
    Keywords:  Alzheimer's disease; Computational biology and bioinformatics; Health care
    DOI:  https://doi.org/10.1038/d41586-023-01650-5
  61. Aging Cell. 2023 May 24. e13889
    Young donor hematopoietic stem cells revitalize aged or damaged bone marrow niche by transdifferentiating into functional niche cells.
    Na Yuan, Wen Wei, Li Ji, Jiawei Qian, Zhicong Jin, Hong Liu, Li Xu, Lei Li, Chen Zhao, Xueqin Gao, Yulong He, Mingyuan Wang, Longhai Tang, Yixuan Fang, Jianrong Wang.
      The bone marrow niche maintains hematopoietic stem cell (HSC) homeostasis and declines in function in the physiologically aging population and in patients with hematological malignancies. A fundamental question is now whether and how HSCs are able to renew or repair their niche. Here, we show that disabling HSCs based on disrupting autophagy accelerated niche aging in mice, whereas transplantation of young, but not aged or impaired, donor HSCs normalized niche cell populations and restored niche factors in host mice carrying an artificially harassed niche and in physiologically aged host mice, as well as in leukemia patients. Mechanistically, HSCs, identified using a donor lineage fluorescence-tracing system, transdifferentiate in an autophagy-dependent manner into functional niche cells in the host that include mesenchymal stromal cells and endothelial cells, previously regarded as "nonhematopoietic" sources. Our findings thus identify young donor HSCs as a primary parental source of the niche, thereby suggesting a clinical solution to revitalizing aged or damaged bone marrow hematopoietic niche.
    Keywords:  aging; hematopoiesis; hematopoietic stem cells; stem cell niche; transdifferentiation
    DOI:  https://doi.org/10.1111/acel.13889
  62. Cell Genom. 2023 May 10. 3(5): 100299
    Genome-wide CRISPR screening of chondrocyte maturation newly implicates genes in skeletal growth and height-associated GWAS loci.
    GIANT Consortium
      Alterations in the growth and maturation of chondrocytes can lead to variation in human height, including monogenic disorders of skeletal growth. We aimed to identify genes and pathways relevant to human growth by pairing human height genome-wide association studies (GWASs) with genome-wide knockout (KO) screens of growth-plate chondrocyte proliferation and maturation in vitro. We identified 145 genes that alter chondrocyte proliferation and maturation at early and/or late time points in culture, with 90% of genes validating in secondary screening. These genes are enriched in monogenic growth disorder genes and in KEGG pathways critical for skeletal growth and endochondral ossification. Further, common variants near these genes capture height heritability independent of genes computationally prioritized from GWASs. Our study emphasizes the value of functional studies in biologically relevant tissues as orthogonal datasets to refine likely causal genes from GWASs and implicates new genetic regulators of chondrocyte proliferation and maturation.
    Keywords:  chondrocyte; epiphysis; genome-wide CRISPR screen; genome-wide association studies; growth plate; height; skeletal growth
    DOI:  https://doi.org/10.1016/j.xgen.2023.100299
  63. Nat Commun. 2023 May 25. 14(1): 3020
    Wound infiltrating adipocytes are not myofibroblasts.
    Shruthi Kalgudde Gopal, Ruoxuan Dai, Ania Maria Stefanska, Meshal Ansari, Jiakuan Zhao, Pushkar Ramesh, Johannes W Bagnoli, Donovan Correa-Gallegos, Yue Lin, Simon Christ, Ilias Angelidis, Valerio Lupperger, Carsten Marr, Lindsay C Davies, Wolfgang Enard, Hans-Günther Machens, Herbert B Schiller, Dongsheng Jiang, Yuval Rinkevich.
      The origins of wound myofibroblasts and scar tissue remains unclear, but it is assumed to involve conversion of adipocytes into myofibroblasts. Here, we directly explore the potential plasticity of adipocytes and fibroblasts after skin injury. Using genetic lineage tracing and live imaging in explants and in wounded animals, we observe that injury induces a transient migratory state in adipocytes with vastly distinct cell migration patterns and behaviours from fibroblasts. Furthermore, migratory adipocytes, do not contribute to scar formation and remain non-fibrogenic in vitro, in vivo and upon transplantation into wounds in animals. Using single-cell and bulk transcriptomics we confirm that wound adipocytes do not convert into fibrogenic myofibroblasts. In summary, the injury-induced migratory adipocytes remain lineage-restricted and do not converge or reprogram into a fibrosing phenotype. These findings broadly impact basic and translational strategies in the regenerative medicine field, including clinical interventions for wound repair, diabetes, and fibrotic pathologies.
    DOI:  https://doi.org/10.1038/s41467-023-38591-6
  64. Nat Rev Methods Primers. 2022 ;pii: 9. [Epub ahead of print]2(1):
    High-content CRISPR screening.
    Christoph Bock, Paul Datlinger, Florence Chardon, Matthew A Coelho, Matthew B Dong, Keith A Lawson, Tian Lu, Laetitia Maroc, Thomas M Norman, Bicna Song, Geoff Stanley, Sidi Chen, Mathew Garnett, Wei Li, Jason Moffat, Lei S Qi, Rebecca S Shapiro, Jay Shendure, Jonathan S Weissman, Xiaowei Zhuang.
      CRISPR screens are a powerful source of biological discovery, enabling the unbiased interrogation of gene function in a wide range of applications and species. In pooled CRISPR screens, various genetically encoded perturbations are introduced into pools of cells. The targeted cells proliferate under a biological challenge such as cell competition, drug treatment or viral infection. Subsequently, the perturbation-induced effects are evaluated by sequencing-based counting of the guide RNAs that specify each perturbation. The typical results of such screens are ranked lists of genes that confer sensitivity or resistance to the biological challenge of interest. Contributing to the broad utility of CRISPR screens, adaptations of the core CRISPR technology make it possible to activate, silence or otherwise manipulate the target genes. Moreover, high-content read-outs such as single-cell RNA sequencing and spatial imaging help characterize screened cells with unprecedented detail. Dedicated software tools facilitate bioinformatic analysis and enhance reproducibility. CRISPR screening has unravelled various molecular mechanisms in basic biology, medical genetics, cancer research, immunology, infectious diseases, microbiology and other fields. This Primer describes the basic and advanced concepts of CRISPR screening and its application as a flexible and reliable method for biological discovery, biomedical research and drug development - with a special emphasis on high-content methods that make it possible to obtain detailed biological insights directly as part of the screen.
    DOI:  https://doi.org/10.1038/s43586-022-00098-7
  65. Nat Commun. 2023 May 22. 14(1): 2937
    A method for restoring signals and revealing individual macromolecule states in cryo-ET, REST.
    Haonan Zhang, Yan Li, Yanan Liu, Dongyu Li, Lin Wang, Kai Song, Keyan Bao, Ping Zhu.
      Cryo-electron tomography (cryo-ET) is widely used to explore the 3D density of biomacromolecules. However, the heavy noise and missing wedge effect prevent directly visualizing and analyzing the 3D reconstructions. Here, we introduced REST, a deep learning strategy-based method to establish the relationship between low-quality and high-quality density and transfer the knowledge to restore signals in cryo-ET. Test results on the simulated and real cryo-ET datasets show that REST performs well in denoising and compensating the missing wedge information. The application in dynamic nucleosomes, presenting either in the form of individual particles or in the context of cryo-FIB nuclei section, indicates that REST has the capability to reveal different conformations of target macromolecules without subtomogram averaging. Moreover, REST noticeably improves the reliability of particle picking. These advantages enable REST to be a powerful tool for the straightforward interpretation of target macromolecules by visual inspection of the density and of a broad range of other applications in cryo-ET, such as segmentation, particle picking, and subtomogram averaging.
    DOI:  https://doi.org/10.1038/s41467-023-38539-w
  66. Nat Commun. 2023 May 24. 14(1): 2980
    Trogocytic molting of T cell microvilli upregulates T cell receptor surface expression and promotes clonal expansion.
    Jeong-Su Park, Jun-Hyeong Kim, Won-Chang Soh, Na-Young Kim, Kyung-Sik Lee, Chang-Hyun Kim, Ik-Joo Chung, Sunjae Lee, Hye-Ran Kim, Chang-Duk Jun.
      Although T cell activation is known to involve the internalization of the T cell antigen receptor (TCR), much less is known regarding the release of TCRs following T cell interaction with cognate antigen-presenting cells. In this study, we examine the physiological mechanisms underlying TCR release following T cell activation. We show that T cell activation results in the shedding of TCRs in T cell microvilli, which involves a combined process of trogocytosis and enzymatic vesiculation, leading to the loss of membrane TCRs and microvilli-associated proteins and lipids. Surprisingly, unlike TCR internalization, this event results in the rapid upregulation of surface TCR expression and metabolic reprogramming of cholesterol and fatty acid synthesis to support cell division and survival. These results demonstrate that TCRs are lost through trogocytic 'molting' following T cell activation and highlight this mechanism as an important regulator of clonal expansion.
    DOI:  https://doi.org/10.1038/s41467-023-38707-y
  67. Nat Commun. 2023 May 23. 14(1): 2963
    Learning how network structure shapes decision-making for bio-inspired computing.
    Michael Schirner, Gustavo Deco, Petra Ritter.
      To better understand how network structure shapes intelligent behavior, we developed a learning algorithm that we used to build personalized brain network models for 650 Human Connectome Project participants. We found that participants with higher intelligence scores took more time to solve difficult problems, and that slower solvers had higher average functional connectivity. With simulations we identified a mechanistic link between functional connectivity, intelligence, processing speed and brain synchrony for trading accuracy with speed in dependence of excitation-inhibition balance. Reduced synchrony led decision-making circuits to quickly jump to conclusions, while higher synchrony allowed for better integration of evidence and more robust working memory. Strict tests were applied to ensure reproducibility and generality of the obtained results. Here, we identify links between brain structure and function that enable to learn connectome topology from noninvasive recordings and map it to inter-individual differences in behavior, suggesting broad utility for research and clinical applications.
    DOI:  https://doi.org/10.1038/s41467-023-38626-y
  68. Nat Commun. 2023 May 20. 14(1): 2897
    Dynamic BH3 profiling identifies pro-apoptotic drug combinations for the treatment of malignant pleural mesothelioma.
    Danielle S Potter, Ruochen Du, Stephan R Bohl, Kin-Hoe Chow, Keith L Ligon, Raphael Bueno, Anthony Letai.
      Malignant pleural mesothelioma (MPM) has relatively ineffective first/second-line therapy for advanced disease and only 18% five-year survival for early disease. Drug-induced mitochondrial priming measured by dynamic BH3 profiling identifies efficacious drugs in multiple disease settings. We use high throughput dynamic BH3 profiling (HTDBP) to identify drug combinations that prime primary MPM cells derived from patient tumors, which also prime patient derived xenograft (PDX) models. A navitoclax (BCL-xL/BCL-2/BCL-w antagonist) and AZD8055 (mTORC1/2 inhibitor) combination demonstrates efficacy in vivo in an MPM PDX model, validating HTDBP as an approach to identify efficacious drug combinations. Mechanistic investigation reveals AZD8055 treatment decreases MCL-1 protein levels, increases BIM protein levels, and increases MPM mitochondrial dependence on BCL-xL, which is exploited by navitoclax. Navitoclax treatment increases dependency on MCL-1 and increases BIM protein levels. These findings demonstrate that HTDBP can be used as a functional precision medicine tool to rationally construct combination drug regimens in MPM and other cancers.
    DOI:  https://doi.org/10.1038/s41467-023-38552-z
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