bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2023‒06‒18
fifty-four papers selected by
Fawaz Alzaïd
Sorbonne Université
  1. Fibrin induces neurotoxic microglia gene programs in neurodegeneration.
  2. Mapping interindividual dynamics of innate immune response at single-cell resolution.
  3. Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis.
  4. Co-translational binding of importins to nascent proteins.
  5. Distinct neural mechanisms construct classical versus extraclassical inhibitory surrounds in an inhibitory nucleus in the midbrain attention network.
  6. Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality.
  7. TMX4-driven LINC complex disassembly and asymmetric autophagy of the nuclear envelope upon acute ER stress.
  8. Cell competition for neuron-derived trophic factor controls the turnover and lifespan of microglia.
  9. Itaconic acid underpins hepatocyte lipid metabolism in non-alcoholic fatty liver disease in male mice.
  10. Older and wiser: The benefits to neonates of aged neutrophils.
  11. Unravelling the genetic architecture of human complex traits through whole genome sequencing.
  12. Regulation of systemic metabolism by tissue-resident immune cell circuits.
  13. Embryonic vitamin D deficiency programs hematopoietic stem cells to induce type 2 diabetes.
  14. Unraveling the glycosylated immunopeptidome with HLA-Glyco.
  15. New fibroblast network connections support lymphocytic cellular service.
  16. Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection.
  17. Persistent serum protein signatures define an inflammatory subcategory of long COVID.
  18. Targeted alveolar regeneration with Frizzled-specific agonists.
  19. Neutralizing IFNγ improves safety without compromising efficacy of CAR-T cell therapy in B-cell malignancies.
  20. Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A.
  21. Losing the darkness.
  22. Chilling with cephalopods: Temperature-responsive RNA editing in octopus and squid.
  23. SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity.
  24. Transposable element evolution in mammals.
  25. Single-cell CRISPR screen for GWAS loci.
  26. Thanks for the memories: Low-avidity T cells shine against escape variants.
  27. Clonal hematopoiesis is associated with protection from Alzheimer's disease.
  28. Highly multiplexed bioactivity screening reveals human and microbiota metabolome-GPCRome interactions.
  29. Farnesyl diphosphate synthase exacerbates nonalcoholic steatohepatitis via the activation of AHR-CD36 axis.
  30. Zn2+ decoration of microtubules arrests axonal transport and displaces tau, doublecortin, and MAP2C.
  31. In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion.
  32. Human orbitofrontal cortex signals decision outcomes to sensory cortex during behavioral adaptations.
  33. xCT-mediated glutamate excretion in white adipocytes stimulates interferon-γ production by natural killer cells in obesity.
  34. Structural insight into the human SID1 transmembrane family member 2 reveals its lipid hydrolytic activity.
  35. Oyez, Oyez, Oyez!
  36. Genetic perturbation of AMP biosynthesis extends lifespan and restores metabolic health in a naturally short-lived vertebrate.
  37. HIV-1 Tat Upregulates TREM1 Expression in Human Microglia.
  38. Combining 47 human genomes into a single pangenome.
  39. Augmented temperature fluctuation aggravates muscular atrophy through the gut microbiota.
  40. An atlas of rabbit development as a model for single-cell comparative genomics.
  41. HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.
  42. Hepatic protein kinase Cbeta (PKCβ) deficiency mitigates late-onset obesity.
  43. CNK2 promotes cancer cell motility by mediating ARF6 activation downstream of AXL signalling.
  44. SEC-seq: association of molecular signatures with antibody secretion in thousands of single human plasma cells.
  45. Reversing the mitochondrial hex that bewitches NLRP3.
  46. Taurine supplement makes animals live longer - what it means for people is unclear.
  47. Recurrent infection transiently expands human tissue T cells while maintaining long-term homeostasis.
  48. Chromatin remodeling by Pol II primes efficient Pol III transcription.
  49. PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.
  50. Negativity begets longevity in T cells.
  51. Impaired histone inheritance promotes tumor progression.
  52. Hexokinase dissociation from mitochondria promotes oligomerization of VDAC that facilitates NLRP3 inflammasome assembly and activation.
  53. A highly sensitive strategy for monitoring real-time proliferation of targeted cell types in vivo.
  54. Ratiometric measurement of MAM Ca2+ dynamics using a modified CalfluxVTN.
  1. Nat Immunol. 2023 Jun 12.
    Fibrin induces neurotoxic microglia gene programs in neurodegeneration.
      
    DOI:  https://doi.org/10.1038/s41590-023-01542-w
  2. Nat Genet. 2023 Jun;55(6): 1066-1075
    Mapping interindividual dynamics of innate immune response at single-cell resolution.
    Natsuhiko Kumasaka, Raghd Rostom, Ni Huang, Krzysztof Polanski, Kerstin B Meyer, Sharad Patel, Rachel Boyd, Celine Gomez, Sam N Barnett, Nikolaos I Panousis, Jeremy Schwartzentruber, Maya Ghoussaini, Paul A Lyons, Fernando J Calero-Nieto, Berthold Göttgens, Josephine L Barnes, Kaylee B Worlock, Masahiro Yoshida, Marko Z Nikolić, Emily Stephenson, Gary Reynolds, Muzlifah Haniffa, John C Marioni, Oliver Stegle, Tzachi Hagai, Sarah A Teichmann.
      Common genetic variants across individuals modulate the cellular response to pathogens and are implicated in diverse immune pathologies, yet how they dynamically alter the response upon infection is not well understood. Here, we triggered antiviral responses in human fibroblasts from 68 healthy donors, and profiled tens of thousands of cells using single-cell RNA-sequencing. We developed GASPACHO (GAuSsian Processes for Association mapping leveraging Cell HeterOgeneity), a statistical approach designed to identify nonlinear dynamic genetic effects across transcriptional trajectories of cells. This approach identified 1,275 expression quantitative trait loci (local false discovery rate 10%) that manifested during the responses, many of which were colocalized with susceptibility loci identified by genome-wide association studies of infectious and autoimmune diseases, including the OAS1 splicing quantitative trait locus in a COVID-19 susceptibility locus. In summary, our analytical approach provides a unique framework for delineation of the genetic variants that shape a wide spectrum of transcriptional responses at single-cell resolution.
    DOI:  https://doi.org/10.1038/s41588-023-01421-y
  3. Nat Commun. 2023 Jun 13. 14(1): 3475
    Ceramide sensing by human SPT-ORMDL complex for establishing sphingolipid homeostasis.
    Tian Xie, Peng Liu, Xinyue Wu, Feitong Dong, Zike Zhang, Jian Yue, Usha Mahawar, Faheem Farooq, Hisham Vohra, Qi Fang, Wenchen Liu, Binks W Wattenberg, Xin Gong.
      The ORM/ORMDL family proteins function as regulatory subunits of the serine palmitoyltransferase (SPT) complex, which is the initiating and rate-limiting enzyme in sphingolipid biosynthesis. This complex is tightly regulated by cellular sphingolipid levels, but the sphingolipid sensing mechanism is unknown. Here we show that purified human SPT-ORMDL complexes are inhibited by the central sphingolipid metabolite ceramide. We have solved the cryo-EM structure of the SPT-ORMDL3 complex in a ceramide-bound state. Structure-guided mutational analyses reveal the essential function of this ceramide binding site for the suppression of SPT activity. Structural studies indicate that ceramide can induce and lock the N-terminus of ORMDL3 into an inhibitory conformation. Furthermore, we demonstrate that childhood amyotrophic lateral sclerosis (ALS) variants in the SPTLC1 subunit cause impaired ceramide sensing in the SPT-ORMDL3 mutants. Our work elucidates the molecular basis of ceramide sensing by the SPT-ORMDL complex for establishing sphingolipid homeostasis and indicates an important role of impaired ceramide sensing in disease development.
    DOI:  https://doi.org/10.1038/s41467-023-39274-y
  4. Nat Commun. 2023 Jun 09. 14(1): 3418
    Co-translational binding of importins to nascent proteins.
    Maximilian Seidel, Natalie Romanov, Agnieszka Obarska-Kosinska, Anja Becker, Nayara Trevisan Doimo de Azevedo, Jan Provaznik, Sankarshana R Nagaraja, Jonathan J M Landry, Vladimir Benes, Martin Beck.
      Various cellular quality control mechanisms support proteostasis. While, ribosome-associated chaperones prevent the misfolding of nascent chains during translation, importins were shown to prevent the aggregation of specific cargoes in a post-translational mechanism prior the import into the nucleoplasm. Here, we hypothesize that importins may already bind ribosome-associated cargo in a co-translational manner. We systematically measure the nascent chain association of all importins in Saccharomyces cerevisiae by selective ribosome profiling. We identify a subset of importins that bind to a wide range of nascent, often uncharacterized cargoes. This includes ribosomal proteins, chromatin remodelers and RNA binding proteins that are aggregation prone in the cytosol. We show that importins act consecutively with other ribosome-associated chaperones. Thus, the nuclear import system is directly intertwined with nascent chain folding and chaperoning.
    DOI:  https://doi.org/10.1038/s41467-023-39150-9
  5. Nat Commun. 2023 Jun 09. 14(1): 3400
    Distinct neural mechanisms construct classical versus extraclassical inhibitory surrounds in an inhibitory nucleus in the midbrain attention network.
    Hannah M Schryver, Shreesh P Mysore.
      Inhibitory neurons in the midbrain spatial attention network, called isthmi pars magnocellularis (Imc), control stimulus selection by the sensorimotor and attentional hub, the optic tectum (OT). Here, we investigate in the barn owl how classical as well as extraclassical (global) inhibitory surrounds of Imc receptive fields (RFs), fundamental units of Imc computational function, are constructed. We find that focal, reversible blockade of GABAergic input onto Imc neurons disconnects their extraclassical inhibitory surrounds, but leaves intact their classical inhibitory surrounds. Subsequently, with paired recordings and iontophoresis, first at spatially aligned site-pairs in Imc and OT, and then, at mutually distant site-pairs within Imc, we demonstrate that classical inhibitory surrounds of Imc RFs are inherited from OT, but their extraclassical inhibitory surrounds are constructed within Imc. These results reveal key design principles of the midbrain spatial attention circuit and highlight the critical importance of competitive interactions within Imc for its operation.
    DOI:  https://doi.org/10.1038/s41467-023-39073-5
  6. Nat Commun. 2023 Jun 10. 14(1): 3453
    Deficit of homozygosity among 1.52 million individuals and genetic causes of recessive lethality.
    DBDS Genomic Consortium
      Genotypes causing pregnancy loss and perinatal mortality are depleted among living individuals and are therefore difficult to find. To explore genetic causes of recessive lethality, we searched for sequence variants with deficit of homozygosity among 1.52 million individuals from six European populations. In this study, we identified 25 genes harboring protein-altering sequence variants with a strong deficit of homozygosity (10% or less of predicted homozygotes). Sequence variants in 12 of the genes cause Mendelian disease under a recessive mode of inheritance, two under a dominant mode, but variants in the remaining 11 have not been reported to cause disease. Sequence variants with a strong deficit of homozygosity are over-represented among genes essential for growth of human cell lines and genes orthologous to mouse genes known to affect viability. The function of these genes gives insight into the genetics of intrauterine lethality. We also identified 1077 genes with homozygous predicted loss-of-function genotypes not previously described, bringing the total set of genes completely knocked out in humans to 4785.
    DOI:  https://doi.org/10.1038/s41467-023-38951-2
  7. Nat Commun. 2023 Jun 13. 14(1): 3497
    TMX4-driven LINC complex disassembly and asymmetric autophagy of the nuclear envelope upon acute ER stress.
    Marika K Kucińska, Juliette Fedry, Carmela Galli, Diego Morone, Andrea Raimondi, Tatiana Soldà, Friedrich Förster, Maurizio Molinari.
      The endoplasmic reticulum (ER) is an organelle of nucleated cells that produces proteins, lipids and oligosaccharides. ER volume and activity are increased upon induction of unfolded protein responses (UPR) and are reduced upon activation of ER-phagy programs. A specialized domain of the ER, the nuclear envelope (NE), protects the cell genome with two juxtaposed lipid bilayers, the inner and outer nuclear membranes (INM and ONM) separated by the perinuclear space (PNS). Here we report that expansion of the mammalian ER upon homeostatic perturbations results in TMX4 reductase-driven disassembly of the LINC complexes connecting INM and ONM and in ONM swelling. The physiologic distance between ONM and INM is restored, upon resolution of the ER stress, by asymmetric autophagy of the NE, which involves the LC3 lipidation machinery, the autophagy receptor SEC62 and the direct capture of ONM-derived vesicles by degradative LAMP1/RAB7-positive endolysosomes in a catabolic pathway mechanistically defined as micro-ONM-phagy.
    DOI:  https://doi.org/10.1038/s41467-023-39172-3
  8. Sci Adv. 2023 Jun 16. 9(24): eadf9790
    Cell competition for neuron-derived trophic factor controls the turnover and lifespan of microglia.
    Tao Yu, Haoyue Kuang, Xiaohai Wu, Ying Huang, Jianzhong Wang, Zilong Wen.
      Microglia are brain-resident macrophages capable of long-term maintenance through self-renewal. Yet the mechanism governing the turnover and lifespan of microglia remains unknown. In zebrafish, microglia arise from two sources, rostral blood island (RBI) and aorta-gonad-mesonephros (AGM). The RBI-derived microglia are born early but have a short lifespan and diminish in adulthood, while the AGM-derived microglia emerge later and are capable of long-term maintenance in adulthood. Here, we show that the attenuation of RBI microglia is due to their less competitiveness for neuron-derived interleukin-34 (Il34) caused by age-dependent decline of colony-stimulating factor-1 receptor a (csf1ra). Alterations of Il34/Csf1ra levels and removal of AGM microglia revamp the proportion and lifespan of RBI microglia. The csf1ra/CSF1R expression in zebrafish AGM-derived microglia and murine adult microglia also undergo age-dependent decline, leading to the elimination of aged microglia. Our study reveals cell competition as a general mechanism controlling the turnover and lifespan of microglia.
    DOI:  https://doi.org/10.1126/sciadv.adf9790
  9. Nat Metab. 2023 Jun 12.
    Itaconic acid underpins hepatocyte lipid metabolism in non-alcoholic fatty liver disease in male mice.
    Jonathan M Weiss, Erika M Palmieri, Marieli Gonzalez-Cotto, Ian A Bettencourt, Emily L Megill, Nathaniel W Snyder, Daniel W McVicar.
      Itaconate, the product of the decarboxylation of cis-aconitate, regulates numerous biological processes. We and others have revealed itaconate as a regulator of fatty acid β-oxidation, generation of mitochondrial reactive oxygen species and the metabolic interplay between resident macrophages and tumors. In the present study, we show that itaconic acid is upregulated in human non-alcoholic steatohepatitis and a mouse model of non-alcoholic fatty liver disease. Male mice deficient in the gene responsible for itaconate production (immunoresponsive gene (Irg)-1) have exacerbated lipid accumulation in the liver, glucose and insulin intolerance and mesenteric fat deposition. Treatment of mice with the itaconate derivative, 4-octyl itaconate, reverses dyslipidemia associated with high-fat diet feeding. Mechanistically, itaconate treatment of primary hepatocytes reduces lipid accumulation and increases their oxidative phosphorylation in a manner dependent upon fatty acid oxidation. We propose a model whereby macrophage-derived itaconate acts in trans upon hepatocytes to modulate the liver's ability to metabolize fatty acids.
    DOI:  https://doi.org/10.1038/s42255-023-00801-2
  10. Immunity. 2023 Jun 13. pii: S1074-7613(23)00229-7. [Epub ahead of print]56(6): 1157-1159
    Older and wiser: The benefits to neonates of aged neutrophils.
    George B Collins, Derek Gilroy.
      Neonates are relatively protected from non-neonatal pathogens by unclear mechanisms. In this issue of Immunity, Bee et al.1 show that resistance to Streptococcus pneumoniae in neonatal mice is mediated by dampened neutrophil efferocytosis, accumulation of aged neutrophils, and enhanced CD11b-dependent bacterial opsonophagocytosis.
    DOI:  https://doi.org/10.1016/j.immuni.2023.05.012
  11. Nat Commun. 2023 Jun 14. 14(1): 3520
    Unravelling the genetic architecture of human complex traits through whole genome sequencing.
    Ozvan Bocher, Cristen J Willer, Eleftheria Zeggini.
      
    DOI:  https://doi.org/10.1038/s41467-023-39259-x
  12. Immunity. 2023 Jun 13. pii: S1074-7613(23)00218-2. [Epub ahead of print]56(6): 1168-1186
    Regulation of systemic metabolism by tissue-resident immune cell circuits.
    Joey H Li, Matthew R Hepworth, Timothy E O'Sullivan.
      Recent studies have demonstrated that tissue homeostasis and metabolic function are dependent on distinct tissue-resident immune cells that form functional cell circuits with structural cells. Within these cell circuits, immune cells integrate cues from dietary contents and commensal microbes in addition to endocrine and neuronal signals present in the tissue microenvironment to regulate structural cell metabolism. These tissue-resident immune circuits can become dysregulated during inflammation and dietary overnutrition, contributing to metabolic diseases. Here, we review the evidence describing key cellular networks within and between the liver, gastrointestinal tract, and adipose tissue that control systemic metabolism and how these cell circuits become dysregulated during certain metabolic diseases. We also identify open questions in the field that have the potential to enhance our understanding of metabolic health and disease.
    Keywords:  cell circuits; immunometabolism; metabolism; systems immunology; tissue homeostasis; tissue-resident
    DOI:  https://doi.org/10.1016/j.immuni.2023.05.001
  13. Nat Commun. 2023 Jun 13. 14(1): 3278
    Embryonic vitamin D deficiency programs hematopoietic stem cells to induce type 2 diabetes.
    Jisu Oh, Amy E Riek, Kevin T Bauerle, Adriana Dusso, Kyle P McNerney, Ruteja A Barve, Isra Darwech, Jennifer E Sprague, Clare Moynihan, Rong M Zhang, Greta Kutz, Ting Wang, Xiaoyun Xing, Daofeng Li, Marguerite Mrad, Nicholas M Wigge, Esmeralda Castelblanco, Alejandro Collin, Monika Bambouskova, Richard D Head, Mark S Sands, Carlos Bernal-Mizrachi.
      Environmental factors may alter the fetal genome to cause metabolic diseases. It is unknown whether embryonic immune cell programming impacts the risk of type 2 diabetes in later life. We demonstrate that transplantation of fetal hematopoietic stem cells (HSCs) made vitamin D deficient in utero induce diabetes in vitamin D-sufficient mice. Vitamin D deficiency epigenetically suppresses Jarid2 expression and activates the Mef2/PGC1a pathway in HSCs, which persists in recipient bone marrow, resulting in adipose macrophage infiltration. These macrophages secrete miR106-5p, which promotes adipose insulin resistance by repressing PIK3 catalytic and regulatory subunits and down-regulating AKT signaling. Vitamin D-deficient monocytes from human cord blood have comparable Jarid2/Mef2/PGC1a expression changes and secrete miR-106b-5p, causing adipocyte insulin resistance. These findings suggest that vitamin D deficiency during development has epigenetic consequences impacting the systemic metabolic milieu.
    DOI:  https://doi.org/10.1038/s41467-023-38849-z
  14. Nat Commun. 2023 Jun 12. 14(1): 3461
    Unraveling the glycosylated immunopeptidome with HLA-Glyco.
    Georges Bedran, Daniel A Polasky, Yi Hsiao, Fengchao Yu, Felipe da Veiga Leprevost, Javier A Alfaro, Marcin Cieslik, Alexey I Nesvizhskii.
      Recent interest in targeted therapies has been sparked by the study of MHC-associated peptides (MAPs) that undergo post-translational modifications (PTMs), particularly glycosylation. In this study, we introduce a fast computational workflow that merges the MSFragger-Glyco search algorithm with a false discovery rate control for glycopeptide analysis from mass spectrometry-based immunopeptidome data. By analyzing eight large-scale publicly available studies, we find that glycosylated MAPs are predominantly presented by MHC class II. Here, we present HLA-Glyco, a comprehensive resource containing over 3,400 human leukocyte antigen (HLA) class II N-glycopeptides from 1,049 distinct protein glycosylation sites. This resource provides valuable insights, including high levels of truncated glycans, conserved HLA-binding cores, and differences in glycosylation positional specificity between HLA allele groups. We integrate the workflow within the FragPipe computational platform and provide HLA-Glyco as a free web resource. Overall, our work provides a valuable tool and resource to aid the nascent field of glyco-immunopeptidomics.
    DOI:  https://doi.org/10.1038/s41467-023-39270-2
  15. Nat Immunol. 2023 Jun 15.
    New fibroblast network connections support lymphocytic cellular service.
    Anne L Fletcher, Kim L Good-Jacobson.
      
    DOI:  https://doi.org/10.1038/s41590-023-01537-7
  16. Nat Commun. 2023 Jun 13. 14(1): 3286
    Immune resilience despite inflammatory stress promotes longevity and favorable health outcomes including resistance to infection.
    South Texas Veterans Health Care System COVID-19 team
      Some people remain healthier throughout life than others but the underlying reasons are poorly understood. Here we hypothesize this advantage is attributable in part to optimal immune resilience (IR), defined as the capacity to preserve and/or rapidly restore immune functions that promote disease resistance (immunocompetence) and control inflammation in infectious diseases as well as other causes of inflammatory stress. We gauge IR levels with two distinct peripheral blood metrics that quantify the balance between (i) CD8+ and CD4+ T-cell levels and (ii) gene expression signatures tracking longevity-associated immunocompetence and mortality-associated inflammation. Profiles of IR metrics in ~48,500 individuals collectively indicate that some persons resist degradation of IR both during aging and when challenged with varied inflammatory stressors. With this resistance, preservation of optimal IR tracked (i) a lower risk of HIV acquisition, AIDS development, symptomatic influenza infection, and recurrent skin cancer; (ii) survival during COVID-19 and sepsis; and (iii) longevity. IR degradation is potentially reversible by decreasing inflammatory stress. Overall, we show that optimal IR is a trait observed across the age spectrum, more common in females, and aligned with a specific immunocompetence-inflammation balance linked to favorable immunity-dependent health outcomes. IR metrics and mechanisms have utility both as biomarkers for measuring immune health and for improving health outcomes.
    DOI:  https://doi.org/10.1038/s41467-023-38238-6
  17. Nat Commun. 2023 Jun 09. 14(1): 3417
    Persistent serum protein signatures define an inflammatory subcategory of long COVID.
    Aarthi Talla, Suhas V Vasaikar, Gregory Lee Szeto, Maria P Lemos, Julie L Czartoski, Hugh MacMillan, Zoe Moodie, Kristen W Cohen, Lamar B Fleming, Zachary Thomson, Lauren Okada, Lynne A Becker, Ernest M Coffey, Stephen C De Rosa, Evan W Newell, Peter J Skene, Xiaojun Li, Thomas F Bumol, M Juliana McElrath, Troy R Torgerson.
      Long COVID or post-acute sequelae of SARS-CoV-2 (PASC) is a clinical syndrome featuring diverse symptoms that can persist for months following acute SARS-CoV-2 infection. The aetiologies may include persistent inflammation, unresolved tissue damage or delayed clearance of viral protein or RNA, but the biological differences they represent are not fully understood. Here we evaluate the serum proteome in samples, longitudinally collected from 55 PASC individuals with symptoms lasting ≥60 days after onset of acute infection, in comparison to samples from symptomatically recovered SARS-CoV-2 infected and uninfected individuals. Our analysis indicates heterogeneity in PASC and identified subsets with distinct signatures of persistent inflammation. Type II interferon signaling and canonical NF-κB signaling (particularly associated with TNF), appear to be the most differentially enriched signaling pathways, distinguishing a group of patients characterized also by a persistent neutrophil activation signature. These findings help to clarify biological diversity within PASC, identify participants with molecular evidence of persistent inflammation, and highlight dominant pathways that may have diagnostic or therapeutic relevance, including a protein panel that we propose as having diagnostic utility for differentiating inflammatory and non-inflammatory PASC.
    DOI:  https://doi.org/10.1038/s41467-023-38682-4
  18. Cell. 2023 Jun 08. pii: S0092-8674(23)00541-X. [Epub ahead of print]
    Targeted alveolar regeneration with Frizzled-specific agonists.
    Ahmad N Nabhan, Joshua D Webster, Jarret J Adams, Levi Blazer, Christine Everrett, Celine Eidenschenk, Alexander Arlantico, Isabel Fleming, Hans D Brightbill, Paul J Wolters, Zora Modrusan, Somesekar Seshagiri, Stephane Angers, Sachdev S Sidhu, Kim Newton, Joseph R Arron, Vishva M Dixit.
      Wnt ligands oligomerize Frizzled (Fzd) and Lrp5/6 receptors to control the specification and activity of stem cells in many species. How Wnt signaling is selectively activated in different stem cell populations, often within the same organ, is not understood. In lung alveoli, we show that distinct Wnt receptors are expressed by epithelial (Fzd5/6), endothelial (Fzd4), and stromal (Fzd1) cells. Fzd5 is uniquely required for alveolar epithelial stem cell activity, whereas fibroblasts utilize distinct Fzd receptors. Using an expanded repertoire of Fzd-Lrp agonists, we could activate canonical Wnt signaling in alveolar epithelial stem cells via either Fzd5 or, unexpectedly, non-canonical Fzd6. A Fzd5 agonist (Fzd5ag) or Fzd6ag stimulated alveolar epithelial stem cell activity and promoted survival in mice after lung injury, but only Fzd6ag promoted an alveolar fate in airway-derived progenitors. Therefore, we identify a potential strategy for promoting regeneration without exacerbating fibrosis during lung injury.
    Keywords:  Frizzled; WNT; alveolus; lung; regeneration
    DOI:  https://doi.org/10.1016/j.cell.2023.05.022
  19. Nat Commun. 2023 Jun 09. 14(1): 3423
    Neutralizing IFNγ improves safety without compromising efficacy of CAR-T cell therapy in B-cell malignancies.
    Simona Manni, Francesca Del Bufalo, Pietro Merli, Domenico Alessandro Silvestris, Marika Guercio, Simona Caruso, Sofia Reddel, Laura Iaffaldano, Michele Pezzella, Stefano Di Cecca, Matilde Sinibaldi, Alessio Ottaviani, Maria Cecilia Quadraccia, Mariasole Aurigemma, Andrea Sarcinelli, Roselia Ciccone, Zeinab Abbaszadeh, Manuela Ceccarelli, Rita De Vito, Maria Chiara Lodi, Maria Giuseppina Cefalo, Angela Mastronuzzi, Biagio De Angelis, Franco Locatelli, Concetta Quintarelli.
      Chimeric antigen receptor T (CAR-T) cell therapy may achieve long-lasting remission in patients with B-cell malignancies not responding to conventional therapies. However, potentially severe and hard-to-manage side effects, including cytokine release syndrome (CRS), neurotoxicity and macrophage activation syndrome, and the lack of pathophysiological experimental models limit the applicability and development of this form of therapy. Here we present a comprehensive humanized mouse model, by which we show that IFNγ neutralization by the clinically approved monoclonal antibody, emapalumab, mitigates severe toxicity related to CAR-T cell therapy. We demonstrate that emapalumab reduces the pro-inflammatory environment in the model, thus allowing control of severe CRS and preventing brain damage, characterized by multifocal hemorrhages. Importantly, our in vitro and in vivo experiments show that IFNγ inhibition does not affect the ability of CD19-targeting CAR-T (CAR.CD19-T) cells to eradicate CD19+ lymphoma cells. Thus, our study provides evidence that anti-IFNγ treatment might reduce immune related adverse effect without compromising therapeutic success and provides rationale for an emapalumab-CAR.CD19-T cell combination therapy in humans.
    DOI:  https://doi.org/10.1038/s41467-023-38723-y
  20. Nat Commun. 2023 Jun 09. 14(1): 3391
    Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A.
    Shana Bergman, Rosemary J Cater, Ambrose Plante, Filippo Mancia, George Khelashvili.
      Major Facilitator Superfamily Domain containing 2 A (MFSD2A) is a transporter that is highly enriched at the blood-brain and blood-retinal barriers, where it mediates Na+-dependent uptake of ω-3 fatty acids in the form of lysolipids into the brain and eyes, respectively. Despite recent structural insights, it remains unclear how this process is initiated, and driven by Na+. Here, we perform Molecular Dynamics simulations which demonstrate that substrates enter outward facing MFSD2A from the outer leaflet of the membrane via lateral openings between transmembrane helices 5/8 and 2/11. The substrate headgroup enters first and engages in Na+ -bridged interactions with a conserved glutamic acid, while the tail is surrounded by hydrophobic residues. This binding mode is consistent with a "trap-and-flip" mechanism and triggers transition to an occluded conformation. Furthermore, using machine learning analysis, we identify key elements that enable these transitions. These results advance our molecular understanding of the MFSD2A transport cycle.
    DOI:  https://doi.org/10.1038/s41467-023-39088-y
  21. Science. 2023 Jun 16. 380(6650): 1116-1117
    Losing the darkness.
    Keith T Smith, Bianca Lopez, Sacha Vignieri, Brad Wible.
      
    DOI:  https://doi.org/10.1126/science.adi4552
  22. Cell. 2023 Jun 08. pii: S0092-8674(23)00540-8. [Epub ahead of print]186(12): 2518-2520
    Chilling with cephalopods: Temperature-responsive RNA editing in octopus and squid.
    Kristen M Koenig.
      The molecular mechanisms that generate the developmental and physiological complexity found within cephalopods are not well understood. In this issue of Cell, Birk et al. and Rangan and Reck-Peterson show that cephalopods differentially edit their RNA in response to temperature changes and that this editing has consequences on protein function.
    DOI:  https://doi.org/10.1016/j.cell.2023.05.021
  23. Nat Immunol. 2023 Jun 15.
    SALL1 enforces microglia-specific DNA binding and function of SMADs to establish microglia identity.
    Bethany R Fixsen, Claudia Z Han, Yi Zhou, Nathanael J Spann, Payam Saisan, Zeyang Shen, Christopher Balak, Mashito Sakai, Isidoro Cobo, Inge R Holtman, Anna S Warden, Gabriela Ramirez, Jana G Collier, Martina P Pasillas, Miao Yu, Rong Hu, Bin Li, Sarah Belhocine, David Gosselin, Nicole G Coufal, Bing Ren, Christopher K Glass.
      Spalt-like transcription factor 1 (SALL1) is a critical regulator of organogenesis and microglia identity. Here we demonstrate that disruption of a conserved microglia-specific super-enhancer interacting with the Sall1 promoter results in complete and specific loss of Sall1 expression in microglia. By determining the genomic binding sites of SALL1 and leveraging Sall1 enhancer knockout mice, we provide evidence for functional interactions between SALL1 and SMAD4 required for microglia-specific gene expression. SMAD4 binds directly to the Sall1 super-enhancer and is required for Sall1 expression, consistent with an evolutionarily conserved requirement of the TGFβ and SMAD homologs Dpp and Mad for cell-specific expression of Spalt in the Drosophila wing. Unexpectedly, SALL1 in turn promotes binding and function of SMAD4 at microglia-specific enhancers while simultaneously suppressing binding of SMAD4 to enhancers of genes that become inappropriately activated in enhancer knockout microglia, thereby enforcing microglia-specific functions of the TGFβ-SMAD signaling axis.
    DOI:  https://doi.org/10.1038/s41590-023-01528-8
  24. Nat Genet. 2023 Jun;55(6): 904
    Transposable element evolution in mammals.
    Chiara Anania.
      
    DOI:  https://doi.org/10.1038/s41588-023-01430-x
  25. Nat Genet. 2023 Jun;55(6): 904
    Single-cell CRISPR screen for GWAS loci.
    Tiago Faial.
      
    DOI:  https://doi.org/10.1038/s41588-023-01432-9
  26. Immunity. 2023 Jun 13. pii: S1074-7613(23)00230-3. [Epub ahead of print]56(6): 1160-1162
    Thanks for the memories: Low-avidity T cells shine against escape variants.
    Pirooz Zareie, Nicole L La Gruta.
      T cell responses against foreign antigens are clonally diverse, but the significance of this diversity is unclear. In this issue of Immunity, Straub et al.1 show that recruitment of low-avidity T cells during primary infection can provide protection against subsequent encounter with escape variants.
    DOI:  https://doi.org/10.1016/j.immuni.2023.05.013
  27. Nat Med. 2023 Jun 15.
    Clonal hematopoiesis is associated with protection from Alzheimer's disease.
    NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium
      Clonal hematopoiesis of indeterminate potential (CHIP) is a premalignant expansion of mutated hematopoietic stem cells. As CHIP-associated mutations are known to alter the development and function of myeloid cells, we hypothesized that CHIP may also be associated with the risk of Alzheimer's disease (AD), a disease in which brain-resident myeloid cells are thought to have a major role. To perform association tests between CHIP and AD dementia, we analyzed blood DNA sequencing data from 1,362 individuals with AD and 4,368 individuals without AD. Individuals with CHIP had a lower risk of AD dementia (meta-analysis odds ratio (OR) = 0.64, P = 3.8 × 10-5), and Mendelian randomization analyses supported a potential causal association. We observed that the same mutations found in blood were also detected in microglia-enriched fraction of the brain in seven of eight CHIP carriers. Single-nucleus chromatin accessibility profiling of brain-derived nuclei in six CHIP carriers revealed that the mutated cells comprised a large proportion of the microglial pool in the samples examined. While additional studies are required to validate the mechanistic findings, these results suggest that CHIP may have a role in attenuating the risk of AD.
    DOI:  https://doi.org/10.1038/s41591-023-02397-2
  28. Cell. 2023 Jun 08. pii: S0092-8674(23)00543-3. [Epub ahead of print]
    Highly multiplexed bioactivity screening reveals human and microbiota metabolome-GPCRome interactions.
    Haiwei Chen, Connor E Rosen, Jaime A González-Hernández, Deguang Song, Jan Potempa, Aaron M Ring, Noah W Palm.
      The human body contains thousands of metabolites derived from mammalian cells, the microbiota, food, and medical drugs. Many bioactive metabolites act through the engagement of G-protein-coupled receptors (GPCRs); however, technological limitations constrain current explorations of metabolite-GPCR interactions. Here, we developed a highly multiplexed screening technology called PRESTO-Salsa that enables simultaneous assessment of nearly all conventional GPCRs (>300 receptors) in a single well of a 96-well plate. Using PRESTO-Salsa, we screened 1,041 human-associated metabolites against the GPCRome and uncovered previously unreported endogenous, exogenous, and microbial GPCR agonists. Next, we leveraged PRESTO-Salsa to generate an atlas of microbiome-GPCR interactions across 435 human microbiome strains from multiple body sites, revealing conserved patterns of cross-tissue GPCR engagement and activation of CD97/ADGRE5 by the Porphyromonas gingivalis protease gingipain K. These studies thus establish a highly multiplexed bioactivity screening technology and expose a diverse landscape of human, diet, drug, and microbiota metabolome-GPCRome interactions.
    Keywords:  G protein-coupled receptor (GPCR); high-throughput screening; human metabolome; microbiome; microbiota metabolites
    DOI:  https://doi.org/10.1016/j.cell.2023.05.024
  29. FASEB J. 2023 07;37(7): e23035
    Farnesyl diphosphate synthase exacerbates nonalcoholic steatohepatitis via the activation of AHR-CD36 axis.
    Jun Liu, Xinxin Zhang, Yufei Zhang, Minyi Qian, Maohui Yang, Song Yang, Lirui Wang.
      Nonalcoholic steatohepatitis (NASH) has become a major concern that threatens human health worldwide. The underlying pathogenesis was crucial but remained poorly understood. Here, we found that the expression of hepatic farnesyl diphosphate synthase (FDPS) was increased in mice and patients with NASH. Elevated FDPS levels were positively correlated with NASH severity. Overexpression of FDPS in mice provoked increased lipid accumulation, inflammation, and fibrosis, while hepatic FDPS deficiency protected mice from NASH progression. Importantly, pharmacological inhibition of FDPS with clinically used alendronate remarkably attenuated NASH-associated phenotypes in mice. Mechanistically, we demonstrated that FDPS increased its downstream product farnesyl pyrophosphate levels, which could function as an aryl hydrocarbon receptor (AHR) agonist to upregulate the expression of fatty acid translocase CD36, to accelerate the development of NASH. Collectively, these findings suggest that FDPS exacerbates NASH via AHR-CD36 axis and identify FDPS as a promising target for NASH therapy.
    Keywords:  AHR; AHR-CD36 axis; ALN; FDPS; NASH
    DOI:  https://doi.org/10.1096/fj.202300433RR
  30. J Cell Biol. 2023 Aug 07. pii: e202208121. [Epub ahead of print]222(8):
    Zn2+ decoration of microtubules arrests axonal transport and displaces tau, doublecortin, and MAP2C.
    Taylor F Minckley, Lyndsie A Salvagio, Dylan H Fudge, Kristen Verhey, Steven M Markus, Yan Qin.
      Intracellular Zn2+ concentrations increase via depolarization-mediated influx or intracellular release, but the immediate effects of Zn2+ signals on neuron function are not fully understood. By simultaneous recording of cytosolic Zn2+ and organelle motility, we find that elevated Zn2+ (IC50 ≈ 5-10 nM) reduces both lysosomal and mitochondrial motility in primary rat hippocampal neurons and HeLa cells. Using live-cell confocal microscopy and in vitro single-molecule TIRF imaging, we reveal that Zn2+ inhibits activity of motor proteins (kinesin and dynein) without disrupting their microtubule binding. Instead, Zn2+ directly binds to microtubules and selectively promotes detachment of tau, DCX, and MAP2C, but not MAP1B, MAP4, MAP7, MAP9, or p150glued. Bioinformatic predictions and structural modeling show that the Zn2+ binding sites on microtubules partially overlap with the microtubule binding sites of tau, DCX, dynein, and kinesin. Our results reveal that intraneuronal Zn2+ regulates axonal transport and microtubule-based processes by interacting with microtubules.
    DOI:  https://doi.org/10.1083/jcb.202208121
  31. Nat Commun. 2023 Jun 09. 14(1): 3386
    In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion.
    Hasan Vatandaslar, Aitor Garzia, Cindy Meyer, Svenja Godbersen, Laura T L Brandt, Esther Griesbach, Jeffrey A Chao, Thomas Tuschl, Markus Stoffel.
      System-wide cross-linking and immunoprecipitation (CLIP) approaches have unveiled regulatory mechanisms of RNA-binding proteins (RBPs) mainly in cultured cells due to limitations in the cross-linking efficiency of tissues. Here, we describe viP-CLIP (in vivo PAR-CLIP), a method capable of identifying RBP targets in mammalian tissues, thereby facilitating the functional analysis of RBP-regulatory networks in vivo. We applied viP-CLIP to mouse livers and identified Insig2 and ApoB as prominent TIAL1 target transcripts, indicating an important role of TIAL1 in cholesterol synthesis and secretion. The functional relevance of these targets was confirmed by showing that TIAL1 influences their translation in hepatocytes. Mutant Tial1 mice exhibit altered cholesterol synthesis, APOB secretion and plasma cholesterol levels. Our results demonstrate that viP-CLIP can identify physiologically relevant RBP targets by finding a factor implicated in the negative feedback regulation of cholesterol biosynthesis.
    DOI:  https://doi.org/10.1038/s41467-023-39135-8
  32. Nat Commun. 2023 Jun 15. 14(1): 3552
    Human orbitofrontal cortex signals decision outcomes to sensory cortex during behavioral adaptations.
    Bin A Wang, Maike Veismann, Abhishek Banerjee, Burkhard Pleger.
      The ability to respond flexibly to an ever-changing environment relies on the orbitofrontal cortex (OFC). However, how the OFC associates sensory information with predicted outcomes to enable flexible sensory learning in humans remains elusive. Here, we combine a probabilistic tactile reversal learning task with functional magnetic resonance imaging (fMRI) to investigate how lateral OFC (lOFC) interacts with the primary somatosensory cortex (S1) to guide flexible tactile learning in humans. fMRI results reveal that lOFC and S1 exhibit distinct task-dependent engagement: while the lOFC responds transiently to unexpected outcomes immediately following reversals, S1 is persistently engaged during re-learning. Unlike the contralateral stimulus-selective S1, activity in ipsilateral S1 mirrors the outcomes of behavior during re-learning, closely related to top-down signals from lOFC. These findings suggest that lOFC contributes to teaching signals to dynamically update representations in sensory areas, which implement computations critical for adaptive behavior.
    DOI:  https://doi.org/10.1038/s41467-023-38671-7
  33. Cell Rep. 2023 Jun 12. pii: S2211-1247(23)00647-2. [Epub ahead of print]42(6): 112636
    xCT-mediated glutamate excretion in white adipocytes stimulates interferon-γ production by natural killer cells in obesity.
    Hee-Hoon Kim, Young-Ri Shim, Ha Neul Kim, Keungmo Yang, Tom Ryu, Kyurae Kim, Sung Eun Choi, Min Jeong Kim, Chaerin Woo, Katherine Po Sin Chung, Song Hwa Hong, Hyemi Shin, Jae Myoung Suh, Youngae Jung, Geum-Sook Hwang, Won Kim, Seok-Hwan Kim, Hyuk Soo Eun, Je Kyung Seong, Won-Il Jeong.
      Obesity-mediated hypoxic stress underlies inflammation, including interferon (IFN)-γ production by natural killer (NK) cells in white adipose tissue. However, the effects of obesity on NK cell IFN-γ production remain obscure. Here, we show that hypoxia promotes xCT-mediated glutamate excretion and C-X-C motif chemokine ligand 12 (CXCL12) expression in white adipocytes, resulting in CXCR4+ NK cell recruitment. Interestingly, this spatial proximity between adipocytes and NK cells induces IFN-γ production in NK cells by stimulating metabotropic glutamate receptor 5 (mGluR5). IFN-γ then triggers inflammatory activation of macrophages and augments xCT and CXCL12 expression in adipocytes, forming a bidirectional pathway. Genetic or pharmacological inhibition of xCT, mGluR5, or IFN-γ receptor in adipocytes or NK cells alleviates obesity-related metabolic disorders in mice. Consistently, patients with obesity showed elevated levels of glutamate/mGluR5 and CXCL12/CXCR4 axes, suggesting that a bidirectional pathway between adipocytes and NK cells could be a viable therapeutic target in obesity-related metabolic disorders.
    Keywords:  CP: Immunology; CP: Metabolism; glutamate; interferon-γ; metabolic disorders; metabotropic glutamate receptor; natural killer cells; obesity
    DOI:  https://doi.org/10.1016/j.celrep.2023.112636
  34. Nat Commun. 2023 Jun 15. 14(1): 3568
    Structural insight into the human SID1 transmembrane family member 2 reveals its lipid hydrolytic activity.
    Dandan Qian, Ye Cong, Runhao Wang, Quan Chen, Chuangye Yan, Deshun Gong.
      The systemic RNAi-defective (SID) transmembrane family member 2 (SIDT2) is a putative nucleic acid channel or transporter that plays essential roles in nucleic acid transport and lipid metabolism. Here, we report the cryo-electron microscopy (EM) structures of human SIDT2, which forms a tightly packed dimer with extensive interactions mediated by two previously uncharacterized extracellular/luminal β-strand-rich domains and the unique transmembrane domain (TMD). The TMD of each SIDT2 protomer contains eleven transmembrane helices (TMs), and no discernible nucleic acid conduction pathway has been identified within the TMD, suggesting that it may act as a transporter. Intriguingly, TM3-6 and TM9-11 form a large cavity with a putative catalytic zinc atom coordinated by three conserved histidine residues and one aspartate residue lying approximately 6 Å from the extracellular/luminal surface of the membrane. Notably, SIDT2 can hydrolyze C18 ceramide into sphingosine and fatty acid with a slow rate. The information presented advances the understanding of the structure-function relationships in the SID1 family proteins.
    DOI:  https://doi.org/10.1038/s41467-023-39335-2
  35. Nat Immunol. 2023 Jun 12.
    Oyez, Oyez, Oyez!
    Philippa M Saunders, Andrew G Brooks, Jamie Rossjohn.
      
    DOI:  https://doi.org/10.1038/s41590-023-01541-x
  36. Dev Cell. 2023 Jun 08. pii: S1534-5807(23)00248-4. [Epub ahead of print]
    Genetic perturbation of AMP biosynthesis extends lifespan and restores metabolic health in a naturally short-lived vertebrate.
    Gwendoline Astre, Tehila Atlan, Uri Goshtchevsky, Adi Oron-Gottesman, Margarita Smirnov, Kobi Shapira, Ariel Velan, Joris Deelen, Tomer Levy, Erez Y Levanon, Itamar Harel.
      During aging, the loss of metabolic homeostasis drives a myriad of pathologies. A central regulator of cellular energy, the AMP-activated protein kinase (AMPK), orchestrates organismal metabolism. However, direct genetic manipulations of the AMPK complex in mice have, so far, produced detrimental phenotypes. Here, as an alternative approach, we alter energy homeostasis by manipulating the upstream nucleotide pool. Using the turquoise killifish, we mutate APRT, a key enzyme in AMP biosynthesis, and extend the lifespan of heterozygous males. Next, we apply an integrated omics approach to show that metabolic functions are rejuvenated in old mutants, which also display a fasting-like metabolic profile and resistance to high-fat diet. At the cellular level, heterozygous cells exhibit enhanced nutrient sensitivity, reduced ATP levels, and AMPK activation. Finally, lifelong intermittent fasting abolishes the longevity benefits. Our findings suggest that perturbing AMP biosynthesis may modulate vertebrate lifespan and propose APRT as a promising target for promoting metabolic health.
    Keywords:  AMP biosynthesis; AMPK; APRT; CRISPR; aging; killifish; longevity; metabolism; nutrient sensing; sex differences
    DOI:  https://doi.org/10.1016/j.devcel.2023.05.015
  37. J Immunol. 2023 Jun 16. pii: ji2300152. [Epub ahead of print]
    HIV-1 Tat Upregulates TREM1 Expression in Human Microglia.
    Grant R Campbell, Pratima Rawat, Rachel K To, Stephen A Spector.
      Because microglia are a reservoir for HIV and are resistant to the cytopathic effects of HIV infection, they are a roadblock for any HIV cure strategy. We have previously identified that triggering receptor expressed on myeloid cells 1 (TREM1) plays a key role in human macrophage resistance to HIV-mediated cytopathogenesis. In this article, we show that HIV-infected human microglia express increased levels of TREM1 and are resistant to HIV-induced apoptosis. Moreover, upon genetic inhibition of TREM1, HIV-infected microglia undergo cell death in the absence of increased viral or proinflammatory cytokine expression or the targeting of uninfected cells. We also show that the expression of TREM1 is mediated by HIV Tat through a TLR4, TICAM1, PG-endoperoxide synthase 2, PGE synthase, and PGE2-dependent manner. These findings highlight the potential of TREM1 as a therapeutic target to eradicate HIV-infected microglia without inducing a proinflammatory response.
    DOI:  https://doi.org/10.4049/jimmunol.2300152
  38. Nat Biotechnol. 2023 Jun;41(6): 766
    Combining 47 human genomes into a single pangenome.
    Jared B Fudge.
      
    DOI:  https://doi.org/10.1038/s41587-023-01842-4
  39. Nat Commun. 2023 Jun 13. 14(1): 3494
    Augmented temperature fluctuation aggravates muscular atrophy through the gut microbiota.
    Ya Liu, Yifan Guo, Zheyu Liu, Xu Feng, Rui Zhou, Yue He, Haiyan Zhou, Hui Peng, Yan Huang.
      Large temperature difference is reported to be a risk factor for human health. However, little evidence has reported the effects of temperature fluctuation on sarcopenia, a senile disease characterized by loss of muscle mass and function. Here, we demonstrate that higher diurnal temperature range in humans has a positive correlation with the prevalence of sarcopenia. Fluctuated temperature exposure (10-25 °C) accelerates muscle atrophy and dampens exercise performance in mid-aged male mice. Interestingly, fluctuated temperature alters the microbiota composition with increased levels of Parabacteroides_distasonis, Duncaniella_dubosii and decreased levels of Candidatus_Amulumruptor, Roseburia, Eubacterium. Transplantation of fluctuated temperature-shaped microbiota replays the adverse effects on muscle function. Mechanically, we find that altered microbiota increases circulating aminoadipic acid, a lysine degradation product. Aminoadipic acid damages mitochondrial function through inhibiting mitophagy in vitro. And Eubacterium supplementation alleviates muscle atrophy and dysfunction induced by fluctuated temperature. Our results uncover the detrimental impact of fluctuated temperature on muscle function and provide a new clue for gut-muscle axis.
    DOI:  https://doi.org/10.1038/s41467-023-39171-4
  40. Nat Cell Biol. 2023 Jun 15.
    An atlas of rabbit development as a model for single-cell comparative genomics.
    Mai-Linh Nu Ton, Daniel Keitley, Bart Theeuwes, Carolina Guibentif, Jonas Ahnfelt-Rønne, Thomas Kjærgaard Andreassen, Fernando J Calero-Nieto, Ivan Imaz-Rosshandler, Blanca Pijuan-Sala, Jennifer Nichols, Èlia Benito-Gutiérrez, John C Marioni, Berthold Göttgens.
      Traditionally, the mouse has been the favoured vertebrate model for biomedical research, due to its experimental and genetic tractability. However, non-rodent embryological studies highlight that many aspects of early mouse development, such as its egg-cylinder gastrulation and method of implantation, diverge from other mammals, thus complicating inferences about human development. Like the human embryo, rabbits develop as a flat-bilaminar disc. Here we constructed a morphological and molecular atlas of rabbit development. We report transcriptional and chromatin accessibility profiles for over 180,000 single cells and high-resolution histology sections from embryos spanning gastrulation, implantation, amniogenesis and early organogenesis. Using a neighbourhood comparison pipeline, we compare the transcriptional landscape of rabbit and mouse at the scale of the entire organism. We characterize the gene regulatory programmes underlying trophoblast differentiation and identify signalling interactions involving the yolk sac mesothelium during haematopoiesis. We demonstrate how the combination of both rabbit and mouse atlases can be leveraged to extract new biological insights from sparse macaque and human data. The datasets and computational pipelines reported here set a framework for a broader cross-species approach to decipher early mammalian development, and are readily adaptable to deploy single-cell comparative genomics more broadly across biomedical research.
    DOI:  https://doi.org/10.1038/s41556-023-01174-0
  41. Immunity. 2023 Jun 08. pii: S1074-7613(23)00226-1. [Epub ahead of print]
    HLA-II immunopeptidome profiling and deep learning reveal features of antigenicity to inform antigen discovery.
    Martin Stražar, Jihye Park, Jennifer G Abelin, Hannah B Taylor, Thomas K Pedersen, Damian R Plichta, Eric M Brown, Basak Eraslan, Yuan-Mao Hung, Kayla Ortiz, Karl R Clauser, Steven A Carr, Ramnik J Xavier, Daniel B Graham.
      CD4+ T cell responses are exquisitely antigen specific and directed toward peptide epitopes displayed by human leukocyte antigen class II (HLA-II) on antigen-presenting cells. Underrepresentation of diverse alleles in ligand databases and an incomplete understanding of factors affecting antigen presentation in vivo have limited progress in defining principles of peptide immunogenicity. Here, we employed monoallelic immunopeptidomics to identify 358,024 HLA-II binders, with a particular focus on HLA-DQ and HLA-DP. We uncovered peptide-binding patterns across a spectrum of binding affinities and enrichment of structural antigen features. These aspects underpinned the development of context-aware predictor of T cell antigens (CAPTAn), a deep learning model that predicts peptide antigens based on their affinity to HLA-II and full sequence of their source proteins. CAPTAn was instrumental in discovering prevalent T cell epitopes from bacteria in the human microbiome and a pan-variant epitope from SARS-CoV-2. Together CAPTAn and associated datasets present a resource for antigen discovery and the unraveling genetic associations of HLA alleles with immunopathologies.
    Keywords:  CD4(+) T cells; MHC class II; SARS-CoV-2 antigens; antigen presentation; immunopeptidomics; microbiome antigens; protein sequence models
    DOI:  https://doi.org/10.1016/j.immuni.2023.05.009
  42. J Biol Chem. 2023 Jun 12. pii: S0021-9258(23)01945-2. [Epub ahead of print] 104917
    Hepatic protein kinase Cbeta (PKCβ) deficiency mitigates late-onset obesity.
    Yaoling Shu, Nikhil Gumma, Faizule Hassan, Daniel A Branch, Lisa A Baer, Michael C Ostrowski, Kristin I Stanford, Kedryn K Baskin, Kamal D Mehta.
      Although aging is associated with progressive adiposity and decline in liver function, the underlying molecular mechanisms and metabolic interplay are incompletely understood. Here, we demonstrate that aging induces hepatic protein kinase Cbeta (PKCβ) expression, while hepatocyte PKCβ deficiency (PKCβHep-/-) in mice significantly attenuates obesity in aged mice fed a high-fat diet. Compared with control PKCβfl/fl mice, PKCβHep-/- mice showed elevated energy expenditure with augmentation of oxygen consumption and carbon dioxide production which was dependent on β3-adrenergic receptor signaling, thereby favoring negative energy balance. This effect was accompanied by induction of thermogenic genes in brown adipose tissue (BAT) and increased BAT respiratory capacity, as well as a shift to oxidative muscle fiber type with an improved mitochondrial function, thereby enhancing oxidative capacity of thermogenic tissues. Furthermore, in PKCβHep-/- mice, we determined that PKCβ overexpression in the liver mitigated elevated expression of thermogenic genes in BAT. In conclusion, our study thus establishes hepatocyte PKCβ induction as a critical component of pathophysiological energy metabolism by promoting progressive hepatic and extrahepatic metabolic derangements in energy homeostasis, contributing to late-onset obesity. These findings have potential implications for augmenting thermogenesis as a means of combating aging-induced obesity.
    Keywords:  aging; energy expenditure; high-fat and high-cholesterol diet; obesity; protein kinase Cβ; thermogenesis; β3-adrenergic signaling
    DOI:  https://doi.org/10.1016/j.jbc.2023.104917
  43. Nat Commun. 2023 Jun 15. 14(1): 3560
    CNK2 promotes cancer cell motility by mediating ARF6 activation downstream of AXL signalling.
    Guillaume Serwe, David Kachaner, Jessica Gagnon, Cédric Plutoni, Driss Lajoie, Eloïse Duramé, Malha Sahmi, Damien Garrido, Martin Lefrançois, Geneviève Arseneault, Marc K Saba-El-Leil, Sylvain Meloche, Gregory Emery, Marc Therrien.
      Cell motility is a critical feature of invasive tumour cells that is governed by complex signal transduction events. Particularly, the underlying mechanisms that bridge extracellular stimuli to the molecular machinery driving motility remain partially understood. Here, we show that the scaffold protein CNK2 promotes cancer cell migration by coupling the pro-metastatic receptor tyrosine kinase AXL to downstream activation of ARF6 GTPase. Mechanistically, AXL signalling induces PI3K-dependent recruitment of CNK2 to the plasma membrane. In turn, CNK2 stimulates ARF6 by associating with cytohesin ARF GEFs and with a novel adaptor protein called SAMD12. ARF6-GTP then controls motile forces by coordinating the respective activation and inhibition of RAC1 and RHOA GTPases. Significantly, genetic ablation of CNK2 or SAMD12 reduces metastasis in a mouse xenograft model. Together, this work identifies CNK2 and its partner SAMD12 as key components of a novel pro-motility pathway in cancer cells, which could be targeted in metastasis.
    DOI:  https://doi.org/10.1038/s41467-023-39281-z
  44. Nat Commun. 2023 Jun 15. 14(1): 3567
    SEC-seq: association of molecular signatures with antibody secretion in thousands of single human plasma cells.
    Rene Yu-Hong Cheng, Joseph de Rutte, Cade Ellis K Ito, Andee R Ott, Lucie Bosler, Wei-Ying Kuo, Jesse Liang, Brian E Hall, David J Rawlings, Dino Di Carlo, Richard G James.
      The secreted products of cells drive many functions in vivo; however, methods to link this functional information to surface markers and transcriptomes have been lacking. By accumulating secretions close to secreting cells held within cavity-containing hydrogel nanovials, we demonstrate workflows to analyze the amount of IgG secreted from single human B cells and link this information to surface markers and transcriptomes from the same cells. Measurements using flow cytometry and imaging flow cytometry corroborate the association between IgG secretion and CD38/CD138. By using oligonucleotide-labeled antibodies we find that upregulation of pathways for protein localization to the endoplasmic reticulum and mitochondrial oxidative phosphorylation are most associated with high IgG secretion, and uncover surrogate plasma cell surface markers (e.g., CD59) defined by the ability to secrete IgG. Altogether, this method links quantity of secretion with single-cell sequencing (SEC-seq) and enables researchers to fully explore the links between genome and function, laying the foundation for discoveries in immunology, stem cell biology, and beyond.
    DOI:  https://doi.org/10.1038/s41467-023-39367-8
  45. Sci Immunol. 2023 Jun 23. 8(84): eadh2967
    Reversing the mitochondrial hex that bewitches NLRP3.
    Manasa Mellacheruvu, Grace M E P Lawrence, Stefan Emming, Kate Schroder.
      Hexokinase dissociation from mitochondria triggers calcium-induced oligomerization of VDAC within the outer mitochondrial membrane, leading to NLRP3 recruitment and inflammasome signaling (see related Research Article by Baik et al.).
    DOI:  https://doi.org/10.1126/sciimmunol.adh2967
  46. Nature. 2023 Jun 09.
    Taurine supplement makes animals live longer - what it means for people is unclear.
    Myriam Vidal Valero.
      
    Keywords:  Ageing; Metabolism; Molecular biology
    DOI:  https://doi.org/10.1038/d41586-023-01910-4
  47. J Exp Med. 2023 09 04. pii: e20210692. [Epub ahead of print]220(9):
    Recurrent infection transiently expands human tissue T cells while maintaining long-term homeostasis.
    Veronica Davé, Laura E Richert-Spuhler, Tanvi Arkatkar, Lakshmi Warrier, Thepthara Pholsena, Christine Johnston, Joshua T Schiffer, Martin Prlic, Jennifer M Lund.
      Chronic viral infections are known to lead to T cell exhaustion or dysfunction. However, it remains unclear if antigen exposure episodes from periodic viral reactivation, such as herpes simplex virus type-2 (HSV-2) recrudescence, are sufficient to induce T cell dysfunction, particularly in the context of a tissue-specific localized, rather than a systemic, infection. We designed and implemented a stringent clinical surveillance protocol to longitudinally track both viral shedding and in situ tissue immune responses in a cohort of HSV+ volunteers that agreed to avoid using anti-viral therapy for the course of this study. Comparing lesion to control skin biopsies, we found that tissue T cells expanded immediately after reactivation, and then returned numerically and phenotypically to steady state. T cell responses appeared to be driven at least in part by migration of circulating T cells to the infected tissue. Our data indicate that tissue T cells are stably maintained in response to HSV reactivation, resembling a series of acute recall responses.
    DOI:  https://doi.org/10.1084/jem.20210692
  48. Nat Commun. 2023 Jun 16. 14(1): 3587
    Chromatin remodeling by Pol II primes efficient Pol III transcription.
    Carlo Yague-Sanz, Valérie Migeot, Marc Larochelle, François Bachand, Maxime Wéry, Antonin Morillon, Damien Hermand.
      The packaging of the genetic material into chromatin imposes the remodeling of this barrier to allow efficient transcription. RNA polymerase II activity is coupled with several histone modification complexes that enforce remodeling. How RNA polymerase III (Pol III) counteracts the inhibitory effect of chromatin is unknown. We report here a mechanism where RNA Polymerase II (Pol II) transcription is required to prime and maintain nucleosome depletion at Pol III loci and contributes to efficient Pol III recruitment upon re-initiation of growth from stationary phase in Fission yeast. The Pcr1 transcription factor participates in the recruitment of Pol II, which affects local histone occupancy through the associated SAGA complex and a Pol II phospho-S2 CTD / Mst2 pathway. These data expand the central role of Pol II in gene expression beyond mRNA synthesis.
    DOI:  https://doi.org/10.1038/s41467-023-39387-4
  49. EMBO J. 2023 Jun 12. e113908
    PERK signaling promotes mitochondrial elongation by remodeling membrane phosphatidic acid.
    Valerie Perea, Christian Cole, Justine Lebeau, Vivian Dolina, Kelsey R Baron, Aparajita Madhavan, Jeffery W Kelly, Danielle A Grotjahn, R Luke Wiseman.
      Endoplasmic reticulum (ER) stress and mitochondrial dysfunction are linked in the onset and pathogenesis of numerous diseases. This has led to considerable interest in defining the mechanisms responsible for regulating mitochondria during ER stress. The PERK signaling arm of the unfolded protein response (UPR) has emerged as a prominent ER stress-responsive signaling pathway that regulates diverse aspects of mitochondrial biology. Here, we show that PERK activity promotes adaptive remodeling of mitochondrial membrane phosphatidic acid (PA) to induce protective mitochondrial elongation during acute ER stress. We find that PERK activity is required for ER stress-dependent increases in both cellular PA and YME1L-dependent degradation of the intramitochondrial PA transporter PRELID1. These two processes lead to the accumulation of PA on the outer mitochondrial membrane where it can induce mitochondrial elongation by inhibiting mitochondrial fission. Our results establish a new role for PERK in the adaptive remodeling of mitochondrial phospholipids and demonstrate that PERK-dependent PA regulation adapts organellar shape in response to ER stress.
    Keywords:  endoplasmic reticulum (ER) stress; mitochondrial morphology; phosphatidic acid; unfolded protein response (UPR)
    DOI:  https://doi.org/10.15252/embj.2023113908
  50. J Clin Invest. 2023 06 15. pii: e171027. [Epub ahead of print]133(12):
    Negativity begets longevity in T cells.
    H Alex Feldman, Hilal Cevik, Stephen N Waggoner.
      Killer immunoglobulin-like receptors (KIRs) are polymorphic receptors for human leukocyte antigens (HLAs) that provide positive or negative signals controlling lymphocyte activation. Expression of inhibitory KIRs by CD8+ T cells affects their survival and function, which is linked to improved antiviral immunity and prevention of autoimmunity. In this issue of the JCI, Zhang, Yan, and co-authors demonstrate that increased numbers of functional inhibitory KIR-HLA pairs equating to greater negative regulation promoted longer lifespans of human T cells. This effect was independent of direct signals provided to KIR-expressing T cells and was instead driven by indirect mechanisms. Since the long-term maintenance of CD8+ T cells is critical for immune readiness against cancer and infection, this discovery has implications for immunotherapy and the preservation of immune function during aging.
    DOI:  https://doi.org/10.1172/JCI171027
  51. Nat Commun. 2023 Jun 10. 14(1): 3429
    Impaired histone inheritance promotes tumor progression.
    Congcong Tian, Jiaqi Zhou, Xinran Li, Yuan Gao, Qing Wen, Xing Kang, Nan Wang, Yuan Yao, Jiuhang Jiang, Guibing Song, Tianjun Zhang, Suili Hu, JingYi Liao, Chuanhe Yu, Zhiquan Wang, Xiangyu Liu, Xinhai Pei, Kuiming Chan, Zichuan Liu, Haiyun Gan.
      Faithful inheritance of parental histones is essential to maintain epigenetic information and cellular identity during cell division. Parental histones are evenly deposited onto the replicating DNA of sister chromatids in a process dependent on the MCM2 subunit of DNA helicase. However, the impact of aberrant parental histone partition on human disease such as cancer is largely unknown. In this study, we construct a model of impaired histone inheritance by introducing MCM2-2A mutation (defective in parental histone binding) in MCF-7 breast cancer cells. The resulting impaired histone inheritance reprograms the histone modification landscapes of progeny cells, especially the repressive histone mark H3K27me3. Lower H3K27me3 levels derepress the expression of genes associated with development, cell proliferation, and epithelial to mesenchymal transition. These epigenetic changes confer fitness advantages to some newly emerged subclones and consequently promote tumor growth and metastasis after orthotopic implantation. In summary, our results indicate that impaired inheritance of parental histones can drive tumor progression.
    DOI:  https://doi.org/10.1038/s41467-023-39185-y
  52. Sci Immunol. 2023 Jun 23. 8(84): eade7652
    Hexokinase dissociation from mitochondria promotes oligomerization of VDAC that facilitates NLRP3 inflammasome assembly and activation.
    Sung Hoon Baik, V Krishnan Ramanujan, Courtney Becker, Sarah Fett, David M Underhill, Andrea J Wolf.
      NLRP3 inflammasome activation is a highly regulated process for controlling secretion of the potent inflammatory cytokines IL-1β and IL-18 that are essential during bacterial infection, sterile inflammation, and disease, including colitis, diabetes, Alzheimer's disease, and atherosclerosis. Diverse stimuli activate the NLRP3 inflammasome, and unifying upstream signals has been challenging to identify. Here, we report that a common upstream step in NLRP3 inflammasome activation is the dissociation of the glycolytic enzyme hexokinase 2 from the voltage-dependent anion channel (VDAC) in the outer membrane of mitochondria. Hexokinase 2 dissociation from VDAC triggers activation of inositol triphosphate receptors, leading to release of calcium from the ER, which is taken up by mitochondria. This influx of calcium into mitochondria leads to oligomerization of VDAC, which is known to form a macromolecule-sized pore in the outer membranes of mitochondria that allows proteins and mitochondrial DNA (mtDNA), often associated with apoptosis and inflammation, respectively, to exit the mitochondria. We observe that VDAC oligomers aggregate with NLRP3 during initial assembly of the multiprotein oligomeric NLRP3 inflammasome complex. We also find that mtDNA is necessary for NLRP3 association with VDAC oligomers. These data, together with other recent work, help to paint a more complete picture of the pathway leading to NLRP3 inflammasome activation.
    DOI:  https://doi.org/10.1126/sciimmunol.ade7652
  53. Nat Commun. 2023 Jun 14. 14(1): 3253
    A highly sensitive strategy for monitoring real-time proliferation of targeted cell types in vivo.
    Hiroto Sugawara, Junta Imai, Junpei Yamamoto, Tomohito Izumi, Yohei Kawana, Akira Endo, Masato Kohata, Junro Seike, Haremaru Kubo, Hiroshi Komamura, Yuichiro Munakata, Yoichiro Asai, Shinichiro Hosaka, Shojiro Sawada, Shinjiro Kodama, Kei Takahashi, Keizo Kaneko, Hideki Katagiri.
      Cell proliferation processes play pivotal roles in timely adaptation to many biological situations. Herein, we establish a highly sensitive and simple strategy by which time-series showing the proliferation of a targeted cell type can be quantitatively monitored in vivo in the same individuals. We generate mice expressing a secreted type of luciferase only in cells producing Cre under the control of the Ki67 promoter. Crossing these with tissue-specific Cre-expressing mice allows us to monitor the proliferation time course of pancreatic β-cells, which are few in number and weakly proliferative, by measuring plasma luciferase activity. Physiological time courses, during obesity development, pregnancy and juvenile growth, as well as diurnal variation, of β-cell proliferation, are clearly detected. Moreover, this strategy can be utilized for highly sensitive ex vivo screening for proliferative factors for targeted cells. Thus, these technologies may contribute to advancements in broad areas of biological and medical research.
    DOI:  https://doi.org/10.1038/s41467-023-38897-5
  54. Nat Commun. 2023 Jun 16. 14(1): 3586
    Ratiometric measurement of MAM Ca2+ dynamics using a modified CalfluxVTN.
    Eunbyul Cho, Youngsik Woo, Yeongjun Suh, Bo Kyoung Suh, Soo Jeong Kim, Truong Thi My Nhung, Jin Yeong Yoo, Tran Diem Nghi, Su Been Lee, Dong Jin Mun, Sang Ki Park.
      Mitochondria-associated ER membrane (MAM) is a structure where these calcium-regulating organelles form close physical contact sites for efficient Ca2+ crosstalk. Despite the central importance of MAM Ca2+ dynamics in diverse biological processes, directly and specifically measuring Ca2+ concentrations inside MAM is technically challenging. Here, we develop MAM-Calflux, a MAM-specific BRET-based Ca2+ indicator. The successful application of the bimolecular fluorescence complementation (BiFC) concept highlights Ca2+-responsive BRET signals in MAM. The BiFC strategy imparts dual functionality as a Ca2+ indicator and quantitative structural marker specific for MAM. As a ratiometric Ca2+ indicator, MAM-Calflux estimates steady-state MAM Ca2+ levels. Finally, it enables the visualization of uneven intracellular distribution of MAM Ca2+ and the elucidation of abnormally accumulated MAM Ca2+ from the neurons of Parkinson's disease mouse model in both steady-state and stimulated conditions. Therefore, we propose that MAM-Calflux can be a versatile tool for ratiometrically measuring dynamic inter-organellar Ca2+ communication.
    DOI:  https://doi.org/10.1038/s41467-023-39343-2
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