bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2023–04–23
sixty papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. Slow integrin-dependent migration organizes networks of tissue-resident mast cells.
  2. Deconstructing cellular senescence in bone and beyond.
  3. People.
  4. DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age.
  5. Encephalitis and poor neuronal death-mediated control of herpes simplex virus in human inherited RIPK3 deficiency.
  6. Top Reads.
  7. Influenza virus mRNAs encode determinants for nuclear export via the cellular TREX-2 complex.
  8. The proteomic landscape of genome-wide genetic perturbations.
  9. Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis.
  10. Programmable mammalian translational modulators by CRISPR-associated proteins.
  11. Hepatocyte SREBP signaling mediates clock communication within the liver.
  12. Multi-omic underpinnings of epigenetic aging and human longevity.
  13. Complex computation from developmental priors.
  14. Single-cell genomics meets human genetics.
  15. Distinct astrocytic modulatory roles in sensory transmission during sleep, wakefulness, and arousal states in freely moving mice.
  16. A conversation with Katherine High.
  17. CX3CR1hi macrophages sustain metabolic adaptation by relieving adipose-derived stem cell senescence in visceral adipose tissue.
  18. The Chromatin Regulator Mll1 Supports T Follicular Helper Cell Differentiation by Controlling Expression of Bcl6, LEF-1, and TCF-1.
  19. Every base everywhere all at once: pangenomics comes of age.
  20. Lateral mammillary body neurons in mouse brain are disproportionately vulnerable in Alzheimer's disease.
  21. Tumor suppression by RNA surveillance.
  22. CD150-dependent hematopoietic stem cell sensing of Brucella instructs myeloid commitment.
  23. Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance.
  24. FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity.
  25. Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs.
  26. Neurons that connect without synapses.
  27. Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging.
  28. Pyruvate-supported flux through medium-chain ketothiolase promotes mitochondrial lipid tolerance in cardiac and skeletal muscles.
  29. Fructose-1,6-bisphosphatase is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness.
  30. AGGF1 therapy inhibits thoracic aortic aneurysms by enhancing integrin α7-mediated inhibition of TGF-β1 maturation and ERK1/2 signaling.
  31. Advancing cell therapy for neurodegenerative diseases.
  32. Error-related signaling in nucleus accumbens D2 receptor-expressing neurons guides inhibition-based choice behavior in mice.
  33. Science strengthened banks - but how long will stability last?
  34. Parkinson's disease-associated ATP13A2/PARK9 functions as a lysosomal H+,K+-ATPase.
  35. Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b.
  36. Temperature sensitive liposome based cancer nanomedicine enables tumour lymph node immune microenvironment remodelling.
  37. Genetics of myocardial interstitial fibrosis in the human heart and association with disease.
  38. Hybrid photoacoustic and fast super-resolution ultrasound imaging.
  39. A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates.
  40. The basolateral amygdala-anterior cingulate pathway contributes to depression-like behaviors and comorbidity with chronic pain behaviors in male mice.
  41. Tau pathology epigenetically remodels the neuron-glial cross-talk in Alzheimer's disease.
  42. The structural basis of tRNA recognition by arginyl-tRNA-protein transferase.
  43. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.
  44. DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features.
  45. Disrupting the α-synuclein-ESCRT interaction with a peptide inhibitor mitigates neurodegeneration in preclinical models of Parkinson's disease.
  46. Direct correction of haemoglobin E β-thalassaemia using base editors.
  47. Microfluidics.
  48. Autophagy supports mitochondrial metabolism through the regulation of iron homeostasis in pancreatic cancer.
  49. PI3Kβ controls immune evasion in PTEN-deficient breast tumours.
  50. HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal.
  51. Uncoupled glycerol-3-phosphate shuttle in kidney cancer reveals that cytosolic GPD is essential to support lipid synthesis.
  52. Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases.
  53. Base editor restores CD3δ-dependent SCID mutation.
  54. Gene-by-environment interactions are pervasive among natural genetic variants.
  55. RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells.
  56. Dynamic fluctuations in a bacterial metabolic network.
  57. Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers.
  58. Piezo2 regulates colonic mechanical sensitivity in a sex specific manner in mice.
  59. Structure and mechanism of the alkane-oxidizing enzyme AlkB.
  60. Engineering kinetics of TLR7/8 agonist release from bottlebrush prodrugs enables tumor-focused immune stimulation.
  1. Nat Immunol. 2023 Apr 20.
    Slow integrin-dependent migration organizes networks of tissue-resident mast cells.
    Lukas Kaltenbach, Paloma Martzloff, Sarah K Bambach, Nadim Aizarani, Michael Mihlan, Alina Gavrilov, Katharina M Glaser, Manuel Stecher, Roland Thünauer, Aude Thiriot, Klaus Heger, Katrin Kierdorf, Stephan Wienert, Ulrich H von Andrian, Marc Schmidt-Supprian, Claus Nerlov, Frederick Klauschen, Axel Roers, Marc Bajénoff, Dominic Grün, Tim Lämmermann.
      Immune cell locomotion is associated with amoeboid migration, a flexible mode of movement, which depends on rapid cycles of actin polymerization and actomyosin contraction1. Many immune cells do not necessarily require integrins, the major family of adhesion receptors in mammals, to move productively through three-dimensional tissue spaces2,3. Instead, they can use alternative strategies to transmit their actin-driven forces to the substrate, explaining their migratory adaptation to changing external environments4-6. However, whether these generalized concepts apply to all immune cells is unclear. Here, we show that the movement of mast cells (immune cells with important roles during allergy and anaphylaxis) differs fundamentally from the widely applied paradigm of interstitial immune cell migration. We identify a crucial role for integrin-dependent adhesion in controlling mast cell movement and localization to anatomical niches rich in KIT ligand, the major mast cell growth and survival factor. Our findings show that substrate-dependent haptokinesis is an important mechanism for the tissue organization of resident immune cells.
    DOI:  https://doi.org/10.1038/s41590-023-01493-2
  2. J Clin Invest. 2023 Apr 17. pii: e169069. [Epub ahead of print]133(8):
    Deconstructing cellular senescence in bone and beyond.
    Lorenz C Hofbauer, Franziska Lademann, Martina Rauner.
      Osteocytes are specialized bone cells that orchestrate skeletal remodeling. Senescent osteocytes are characterized by an activation of cyclin-dependent kinase inhibitor p16Ink4a and have been implicated in the pathogenesis of several bone loss disorders. In this issue of the JCI, Farr et al. have now shown that systemic removal of senescent cells (termed senolysis) prevented age-related bone loss at the spine and femur and mitigated bone marrow adiposity through a robust effect on osteoblasts and osteoclasts, whereas cell-specific senolysis in osteocytes alone was only partially effective. Surprisingly, transplantation of senescent fibroblasts into the peritoneum of young mice caused host osteocyte senescence associated with bone loss. This refined concept of osteocyte senescence and the effects of remote senolysis may help to develop improved senolytic strategies against multisystem aging in bone and beyond.
    DOI:  https://doi.org/10.1172/JCI169069
  3. Nat Biotechnol. 2023 Apr;41(4): 582
    People.
      
    DOI:  https://doi.org/10.1038/s41587-023-01741-8
  4. Nat Commun. 2023 04 17. 14(1): 2184
    DRAG in situ barcoding reveals an increased number of HSPCs contributing to myelopoiesis with age.
    Jos Urbanus, Jason Cosgrove, Joost B Beltman, Yuval Elhanati, Rafael A Moral, Cecile Conrad, Jeroen W van Heijst, Emilie Tubeuf, Arno Velds, Lianne Kok, Candice Merle, Jens P Magnusson, Léa Guyonnet, Jonas Frisén, Silvia Fre, Aleksandra M Walczak, Thierry Mora, Heinz Jacobs, Ton N Schumacher, Leïla Perié.
      Ageing is associated with changes in the cellular composition of the immune system. During ageing, hematopoietic stem and progenitor cells (HSPCs) that produce immune cells are thought to decline in their regenerative capacity. However, HSPC function has been mostly assessed using transplantation assays, and it remains unclear how HSPCs age in the native bone marrow niche. To address this issue, we present an in situ single cell lineage tracing technology to quantify the clonal composition and cell production of single cells in their native niche. Our results demonstrate that a pool of HSPCs with unequal output maintains myelopoiesis through overlapping waves of cell production throughout adult life. During ageing, the increased frequency of myeloid cells is explained by greater numbers of HSPCs contributing to myelopoiesis rather than the increased myeloid output of individual HSPCs. Strikingly, the myeloid output of HSPCs remains constant over time despite accumulating significant transcriptomic changes throughout adulthood. Together, these results show that, unlike emergency myelopoiesis post-transplantation, aged HSPCs in their native microenvironment do not functionally decline in their regenerative capacity.
    DOI:  https://doi.org/10.1038/s41467-023-37167-8
  5. Sci Immunol. 2023 Apr 21. 8(82): eade2860
    Encephalitis and poor neuronal death-mediated control of herpes simplex virus in human inherited RIPK3 deficiency.
    Zhiyong Liu, Eduardo J Garcia Reino, Oliver Harschnitz, Hongyan Guo, Yi-Hao Chan, Noopur V Khobrekar, Mary L Hasek, Kerry Dobbs, Darawan Rinchai, Marie Materna, Daniela Matuozzo, Danyel Lee, Paul Bastard, Jie Chen, Yoon Seung Lee, Seong K Kim, Shuxiang Zhao, Param Amin, Lazaro Lorenzo, Yoann Seeleuthner, Remi Chevalier, Laure Mazzola, Claire Gay, Jean-Louis Stephan, Baptiste Milisavljevic, Soraya Boucherit, Flore Rozenberg, Rebeca Perez de Diego, Richard D Dix, Nico Marr, Vivien Béziat, Aurelie Cobat, Mélodie Aubart, Laurent Abel, Stephane Chabrier, Gregory A Smith, Luigi D Notarangelo, Edward S Mocarski, Lorenz Studer, Jean-Laurent Casanova, Shen-Ying Zhang.
      Inborn errors of TLR3-dependent type I IFN immunity in cortical neurons underlie forebrain herpes simplex virus-1 (HSV-1) encephalitis (HSE) due to uncontrolled viral growth and subsequent cell death. We report an otherwise healthy patient with HSE who was compound heterozygous for nonsense (R422*) and frameshift (P493fs9*) RIPK3 variants. Receptor-interacting protein kinase 3 (RIPK3) is a ubiquitous cytoplasmic kinase regulating cell death outcomes, including apoptosis and necroptosis. In vitro, the R422* and P493fs9* RIPK3 proteins impaired cellular apoptosis and necroptosis upon TLR3, TLR4, or TNFR1 stimulation and ZBP1/DAI-mediated necroptotic cell death after HSV-1 infection. The patient's fibroblasts displayed no detectable RIPK3 expression. After TNFR1 or TLR3 stimulation, the patient's cells did not undergo apoptosis or necroptosis. After HSV-1 infection, the cells supported excessive viral growth despite normal induction of antiviral IFN-β and IFN-stimulated genes (ISGs). This phenotype was, nevertheless, rescued by application of exogenous type I IFN. The patient's human pluripotent stem cell (hPSC)-derived cortical neurons displayed impaired cell death and enhanced viral growth after HSV-1 infection, as did isogenic RIPK3-knockout hPSC-derived cortical neurons. Inherited RIPK3 deficiency therefore confers a predisposition to HSE by impairing the cell death-dependent control of HSV-1 in cortical neurons but not their production of or response to type I IFNs.
    DOI:  https://doi.org/10.1126/sciimmunol.ade2860
  6. J Immunol. 2023 May 01. 210(9): 1179-1180
    Top Reads.
      
    DOI:  https://doi.org/10.4049/jimmunol.2390006
  7. Nat Commun. 2023 Apr 21. 14(1): 2304
    Influenza virus mRNAs encode determinants for nuclear export via the cellular TREX-2 complex.
    Prasanna Bhat, Vasilisa Aksenova, Matthew Gazzara, Emily A Rex, Sadaf Aslam, Christina Haddad, Shengyan Gao, Matthew Esparza, Tolga Cagatay, Kimberly Batten, Sara S El Zahed, Alexei Arnaoutov, Hualin Zhong, Jerry W Shay, Blanton S Tolbert, Mary Dasso, Kristen W Lynch, Adolfo García-Sastre, Beatriz M A Fontoura.
      Nuclear export of influenza A virus (IAV) mRNAs occurs through the nuclear pore complex (NPC). Using the Auxin-Induced Degron (AID) system to rapidly degrade proteins, we show that among the nucleoporins localized at the nucleoplasmic side of the NPC, TPR is the key nucleoporin required for nuclear export of influenza virus mRNAs. TPR recruits the TRanscription and EXport complex (TREX)-2 to the NPC for exporting a subset of cellular mRNAs. By degrading components of the TREX-2 complex (GANP, Germinal-center Associated Nuclear Protein; PCID2, PCI domain containing 2), we show that influenza mRNAs require the TREX-2 complex for nuclear export and replication. Furthermore, we found that cellular mRNAs whose export is dependent on GANP have a small number of exons, a high mean exon length, long 3' UTR, and low GC content. Some of these features are shared by influenza virus mRNAs. Additionally, we identified a 45 nucleotide RNA signal from influenza virus HA mRNA that is sufficient to mediate GANP-dependent mRNA export. Thus, we report a role for the TREX-2 complex in nuclear export of influenza mRNAs and identified RNA determinants associated with the TREX-2-dependent mRNA export.
    DOI:  https://doi.org/10.1038/s41467-023-37911-0
  8. Cell. 2023 Apr 17. pii: S0092-8674(23)00300-8. [Epub ahead of print]
    The proteomic landscape of genome-wide genetic perturbations.
    Christoph B Messner, Vadim Demichev, Julia Muenzner, Simran K Aulakh, Natalie Barthel, Annika Röhl, Lucía Herrera-Domínguez, Anna-Sophia Egger, Stephan Kamrad, Jing Hou, Guihong Tan, Oliver Lemke, Enrica Calvani, Lukasz Szyrwiel, Michael Mülleder, Kathryn S Lilley, Charles Boone, Georg Kustatscher, Markus Ralser.
      Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library in Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global protein expression is driven by a complex interplay of (1) general biological properties, including translation rate, protein turnover, the formation of protein complexes, growth rate, and genome architecture, followed by (2) functional properties, such as the connectivity of a protein in genetic, metabolic, and physical interaction networks. Moreover, we show that functional proteomics complements current gene annotation strategies through the assessment of proteome profile similarity, protein covariation, and reverse proteome profiling. Thus, our study reveals principles that govern protein expression and provides a genome-spanning resource for functional annotation.
    Keywords:  Saccharomyces cerevisiae; data-independent acquisition; deletion; functional genomics; functional proteomics; gene annotation; high throughput; knockout; quantitative proteomics; systems biology
    DOI:  https://doi.org/10.1016/j.cell.2023.03.026
  9. Nat Commun. 2023 04 17. 14(1): 2194
    Ether phospholipids are required for mitochondrial reactive oxygen species homeostasis.
    Ziheng Chen, I-Lin Ho, Melinda Soeung, Er-Yen Yen, Jintan Liu, Liang Yan, Johnathon L Rose, Sanjana Srinivasan, Shan Jiang, Q Edward Chang, Ningping Feng, Jason P Gay, Qi Wang, Jing Wang, Philip L Lorenzi, Lucas J Veillon, Bo Wei, John N Weinstein, Angela K Deem, Sisi Gao, Giannicola Genovese, Andrea Viale, Wantong Yao, Costas A Lyssiotis, Joseph R Marszalek, Giulio F Draetta, Haoqiang Ying.
      Mitochondria are hubs where bioenergetics, redox homeostasis, and anabolic metabolism pathways integrate through a tightly coordinated flux of metabolites. The contributions of mitochondrial metabolism to tumor growth and therapy resistance are evident, but drugs targeting mitochondrial metabolism have repeatedly failed in the clinic. Our study in pancreatic ductal adenocarcinoma (PDAC) finds that cellular and mitochondrial lipid composition influence cancer cell sensitivity to pharmacological inhibition of electron transport chain complex I. Profiling of patient-derived PDAC models revealed that monounsaturated fatty acids (MUFAs) and MUFA-linked ether phospholipids play a critical role in maintaining ROS homeostasis. We show that ether phospholipids support mitochondrial supercomplex assembly and ROS production; accordingly, blocking de novo ether phospholipid biosynthesis sensitized PDAC cells to complex I inhibition by inducing mitochondrial ROS and lipid peroxidation. These data identify ether phospholipids as a regulator of mitochondrial redox control that contributes to the sensitivity of PDAC cells to complex I inhibition.
    DOI:  https://doi.org/10.1038/s41467-023-37924-9
  10. Nat Commun. 2023 04 19. 14(1): 2243
    Programmable mammalian translational modulators by CRISPR-associated proteins.
    Shunsuke Kawasaki, Hiroki Ono, Moe Hirosawa, Takeru Kuwabara, Shunsuke Sumi, Suji Lee, Knut Woltjen, Hirohide Saito.
      Translational modulation based on RNA-binding proteins can be used to construct artificial gene circuits, but RNA-binding proteins capable of regulating translation efficiently and orthogonally remain scarce. Here we report CARTRIDGE (Cas-Responsive Translational Regulation Integratable into Diverse Gene control) to repurpose Cas proteins as translational modulators in mammalian cells. We demonstrate that a set of Cas proteins efficiently and orthogonally repress or activate the translation of designed mRNAs that contain a Cas-binding RNA motif in the 5'-UTR. By linking multiple Cas-mediated translational modulators, we designed and built artificial circuits like logic gates, cascades, and half-subtractor circuits. Moreover, we show that various CRISPR-related technologies like anti-CRISPR and split-Cas9 platforms could be similarly repurposed to control translation. Coupling Cas-mediated translational and transcriptional regulation enhanced the complexity of synthetic circuits built by only introducing a few additional elements. Collectively, CARTRIDGE has enormous potential as a versatile molecular toolkit for mammalian synthetic biology.
    DOI:  https://doi.org/10.1038/s41467-023-37540-7
  11. J Clin Invest. 2023 Apr 17. pii: e163018. [Epub ahead of print]133(8):
    Hepatocyte SREBP signaling mediates clock communication within the liver.
    Dongyin Guan, Hosung Bae, Dishu Zhou, Ying Chen, Chunjie Jiang, Cam Mong La, Yang Xiao, Kun Zhu, Wenxiang Hu, Trang Minh Trinh, Panpan Liu, Ying Xiong, Bishuang Cai, Cholsoon Jang, Mitchell A Lazar.
      Rhythmic intraorgan communication coordinates environmental signals and the cell-intrinsic clock to maintain organ homeostasis. Hepatocyte-specific KO of core components of the molecular clock Rev-erbα and -β (Reverb-hDKO) alters cholesterol and lipid metabolism in hepatocytes as well as rhythmic gene expression in nonparenchymal cells (NPCs) of the liver. Here, we report that in fatty liver caused by diet-induced obesity (DIO), hepatocyte SREBP cleavage-activating protein (SCAP) was required for Reverb-hDKO-induced diurnal rhythmic remodeling and epigenomic reprogramming in liver macrophages (LMs). Integrative analyses of isolated hepatocytes and LMs revealed that SCAP-dependent lipidomic changes in REV-ERB-depleted hepatocytes led to the enhancement of LM metabolic rhythms. Hepatocytic loss of REV-ERBα and β (REV-ERBs) also attenuated LM rhythms via SCAP-independent polypeptide secretion. These results shed light on the signaling mechanisms by which hepatocytes regulate diurnal rhythms in NPCs in fatty liver disease caused by DIO.
    Keywords:  Epigenetics; Hepatology; Homeostasis; Metabolism
    DOI:  https://doi.org/10.1172/JCI163018
  12. Nat Commun. 2023 04 19. 14(1): 2236
    Multi-omic underpinnings of epigenetic aging and human longevity.
    Lucas A Mavromatis, Daniel B Rosoff, Andrew S Bell, Jeesun Jung, Josephin Wagner, Falk W Lohoff.
      Biological aging is accompanied by increasing morbidity, mortality, and healthcare costs; however, its molecular mechanisms are poorly understood. Here, we use multi-omic methods to integrate genomic, transcriptomic, and metabolomic data and identify biological associations with four measures of epigenetic age acceleration and a human longevity phenotype comprising healthspan, lifespan, and exceptional longevity (multivariate longevity). Using transcriptomic imputation, fine-mapping, and conditional analysis, we identify 22 high confidence associations with epigenetic age acceleration and seven with multivariate longevity. FLOT1, KPNA4, and TMX2 are novel, high confidence genes associated with epigenetic age acceleration. In parallel, cis-instrument Mendelian randomization of the druggable genome associates TPMT and NHLRC1 with epigenetic aging, supporting transcriptomic imputation findings. Metabolomics Mendelian randomization identifies a negative effect of non-high-density lipoprotein cholesterol and associated lipoproteins on multivariate longevity, but not epigenetic age acceleration. Finally, cell-type enrichment analysis implicates immune cells and precursors in epigenetic age acceleration and, more modestly, multivariate longevity. Follow-up Mendelian randomization of immune cell traits suggests lymphocyte subpopulations and lymphocytic surface molecules affect multivariate longevity and epigenetic age acceleration. Our results highlight druggable targets and biological pathways involved in aging and facilitate multi-omic comparisons of epigenetic clocks and human longevity.
    DOI:  https://doi.org/10.1038/s41467-023-37729-w
  13. Nat Commun. 2023 04 19. 14(1): 2226
    Complex computation from developmental priors.
    Dániel L Barabási, Taliesin Beynon, Ádám Katona, Nicolas Perez-Nieves.
      Machine learning (ML) models have long overlooked innateness: how strong pressures for survival lead to the encoding of complex behaviors in the nascent wiring of a brain. Here, we derive a neurodevelopmental encoding of artificial neural networks that considers the weight matrix of a neural network to be emergent from well-studied rules of neuronal compatibility. Rather than updating the network's weights directly, we improve task fitness by updating the neurons' wiring rules, thereby mirroring evolutionary selection on brain development. We find that our model (1) provides sufficient representational power for high accuracy on ML benchmarks while also compressing parameter count, and (2) can act as a regularizer, selecting simple circuits that provide stable and adaptive performance on metalearning tasks. In summary, by introducing neurodevelopmental considerations into ML frameworks, we not only model the emergence of innate behaviors, but also define a discovery process for structures that promote complex computations.
    DOI:  https://doi.org/10.1038/s41467-023-37980-1
  14. Nat Rev Genet. 2023 Apr 21.
    Single-cell genomics meets human genetics.
    Anna S E Cuomo, Aparna Nathan, Soumya Raychaudhuri, Daniel G MacArthur, Joseph E Powell.
      Single-cell genomic technologies are revealing the cellular composition, identities and states in tissues at unprecedented resolution. They have now scaled to the point that it is possible to query samples at the population level, across thousands of individuals. Combining single-cell information with genotype data at this scale provides opportunities to link genetic variation to the cellular processes underpinning key aspects of human biology and disease. This strategy has potential implications for disease diagnosis, risk prediction and development of therapeutic solutions. But, effectively integrating large-scale single-cell genomic data, genetic variation and additional phenotypic data will require advances in data generation and analysis methods. As single-cell genetics begins to emerge as a field in its own right, we review its current state and the challenges and opportunities ahead.
    DOI:  https://doi.org/10.1038/s41576-023-00599-5
  15. Nat Commun. 2023 04 17. 14(1): 2186
    Distinct astrocytic modulatory roles in sensory transmission during sleep, wakefulness, and arousal states in freely moving mice.
    Fushun Wang, Wei Wang, Simeng Gu, Dan Qi, Nathan A Smith, Weiguo Peng, Wei Dong, Jiajin Yuan, Binbin Zhao, Ying Mao, Peng Cao, Qing Richard Lu, Lee A Shapiro, S Stephen Yi, Erxi Wu, Jason H Huang.
      Despite extensive research on astrocytic Ca2+ in synaptic transmission, its contribution to the modulation of sensory transmission during different brain states remains largely unknown. Here, by using two-photon microscopy and whole-cell recordings, we show two distinct astrocytic Ca2+ signals in the murine barrel cortex: a small, long-lasting Ca2+ increase during sleep and a large, widespread but short-lasting Ca2+ spike when aroused. The large Ca2+ wave in aroused mice was inositol trisphosphate (IP3)-dependent, evoked by the locus coeruleus-norepinephrine system, and enhanced sensory input, contributing to reliable sensory transmission. However, the small Ca2+ transient was IP3-independent and contributed to decreased extracellular K+, hyperpolarization of the neurons, and suppression of sensory transmission. These events respond to different pharmacological inputs and contribute to distinct sleep and arousal functions by modulating the efficacy of sensory transmission. Together, our data demonstrate an important function for astrocytes in sleep and arousal states via astrocytic Ca2+ waves.
    DOI:  https://doi.org/10.1038/s41467-023-37974-z
  16. J Clin Invest. 2023 Apr 17. pii: e170663. [Epub ahead of print]133(8):
    A conversation with Katherine High.
    Ushma S Neill.
      
    DOI:  https://doi.org/10.1172/JCI170663
  17. Cell Rep. 2023 Apr 20. pii: S2211-1247(23)00435-7. [Epub ahead of print]42(5): 112424
    CX3CR1hi macrophages sustain metabolic adaptation by relieving adipose-derived stem cell senescence in visceral adipose tissue.
    Zixin Zhou, Huiying Zhang, Yan Tao, Haipeng Jie, Jingyuan Zhao, Jinhao Zang, Huijie Li, Yalin Wang, Tianci Wang, Hui Zhao, Yuan Li, Chun Guo, Faliang Zhu, Haiting Mao, Lining Zhang, Fengming Liu, Qun Wang.
      Adipose-derived stem cells (ASCs) drive healthy visceral adipose tissue (VAT) expansion via adipocyte hyperplasia. Obesity induces ASC senescence that causes VAT dysfunction and metabolic disorders. It is challenging to restrain this process by biological intervention, as mechanisms of controlling VAT ASC senescence remain unclear. We demonstrate that a population of CX3CR1hi macrophages is maintained in mouse VAT during short-term energy surplus, which sustains ASCs by restraining their senescence, driving adaptive VAT expansion and metabolic health. Long-term overnutrition induces diminishment of CX3CR1hi macrophages in mouse VAT accompanied by ASC senescence and exhaustion, while transferring CX3CR1hi macrophages restores ASC reservoir and triggers VAT beiging to alleviate the metabolic maladaptation. Mechanistically, visceral ASCs attract macrophages via MCP-1 and shape their CX3CR1hi phenotype via exosomes; these macrophages relieve ASC senescence by promoting the arginase1-eIF5A hypusination axis. These findings identify VAT CX3CR1hi macrophages as ASC supporters and unravel their therapeutic potential for metabolic maladaptation to obesity.
    Keywords:  CP: Immunology; CP: Metabolism; CX3CR1; adipose-derived stem cell; cellular senescence; macrophage; obesity; visceral adipose tissue
    DOI:  https://doi.org/10.1016/j.celrep.2023.112424
  18. J Immunol. 2023 Apr 19. pii: ji2200927. [Epub ahead of print]
    The Chromatin Regulator Mll1 Supports T Follicular Helper Cell Differentiation by Controlling Expression of Bcl6, LEF-1, and TCF-1.
    Simon Bélanger, Sonya Haupt, Caterina E Faliti, Adam Getzler, Jinyong Choi, Huitian Diao, Pabalu P Karunadharma, Nicholas A Bild, Matthew E Pipkin, Shane Crotty.
      T follicular helper (TFH) cells are essential for developing protective Ab responses following vaccination. Greater understanding of the genetic program leading to TFH differentiation is needed. Chromatin modifications are central in the control of gene expression. However, detailed knowledge of how chromatin regulators (CRs) regulate differentiation of TFH cells is limited. We screened a large short hairpin RNA library targeting all known CRs in mice and identified the histone methyltransferase mixed lineage leukemia 1 (Mll1) as a positive regulator of TFH differentiation. Loss of Mll1 expression reduced formation of TFH cells following acute viral infection or protein immunization. In addition, expression of the TFH lineage-defining transcription factor Bcl6 was reduced in the absence of Mll1. Transcriptomics analysis identified Lef1 and Tcf7 as genes dependent on Mll1 for their expression, which provides one mechanism for the regulation of TFH differentiation by Mll1. Taken together, CRs such as Mll1 substantially influence TFH differentiation.
    DOI:  https://doi.org/10.4049/jimmunol.2200927
  19. Nature. 2023 Apr;616(7957): 618-620
    Every base everywhere all at once: pangenomics comes of age.
    Michael Eisenstein.
      
    Keywords:  Computational biology and bioinformatics; DNA sequencing; Genomics; Molecular biology
    DOI:  https://doi.org/10.1038/d41586-023-01300-w
  20. Sci Transl Med. 2023 Apr 19. 15(692): eabq1019
    Lateral mammillary body neurons in mouse brain are disproportionately vulnerable in Alzheimer's disease.
    Wen-Chin Huang, Zhuyu Peng, Mitchell H Murdock, Liwang Liu, Hansruedi Mathys, Jose Davila-Velderrain, Xueqiao Jiang, Maggie Chen, Ayesha P Ng, TaeHyun Kim, Fatema Abdurrob, Fan Gao, David A Bennett, Manolis Kellis, Li-Huei Tsai.
      The neural circuits governing the induction and progression of neurodegeneration and memory impairment in Alzheimer's disease (AD) are incompletely understood. The mammillary body (MB), a subcortical node of the medial limbic circuit, is one of the first brain regions to exhibit amyloid deposition in the 5xFAD mouse model of AD. Amyloid burden in the MB correlates with pathological diagnosis of AD in human postmortem brain tissue. Whether and how MB neuronal circuitry contributes to neurodegeneration and memory deficits in AD are unknown. Using 5xFAD mice and postmortem MB samples from individuals with varying degrees of AD pathology, we identified two neuronal cell types in the MB harboring distinct electrophysiological properties and long-range projections: lateral neurons and medial neurons. lateral MB neurons harbored aberrant hyperactivity and exhibited early neurodegeneration in 5xFAD mice compared with lateral MB neurons in wild-type littermates. Inducing hyperactivity in lateral MB neurons in wild-type mice impaired performance on memory tasks, whereas attenuating aberrant hyperactivity in lateral MB neurons ameliorated memory deficits in 5xFAD mice. Our findings suggest that neurodegeneration may be a result of genetically distinct, projection-specific cellular dysfunction and that dysregulated lateral MB neurons may be causally linked to memory deficits in AD.
    DOI:  https://doi.org/10.1126/scitranslmed.abq1019
  21. Science. 2023 Apr 21. 380(6642): 240-241
    Tumor suppression by RNA surveillance.
    Robert P Fisher.
      A cyclin-dependent kinase triggers degradation of prematurely terminated RNAs.
    DOI:  https://doi.org/10.1126/science.adh4051
  22. J Exp Med. 2023 Jul 03. pii: e20210567. [Epub ahead of print]220(7):
    CD150-dependent hematopoietic stem cell sensing of Brucella instructs myeloid commitment.
    Lisiena Hysenaj, Bérengère de Laval, Vilma Arce-Gorvel, Mile Bosilkovski, Gabriela González-Espinoza, Guilhaume Debroas, Michael H Sieweke, Sandrine Sarrazin, Jean-Pierre Gorvel.
      So far, hematopoietic stem cells (HSC) are considered the source of mature immune cells, the latter being the only ones capable of mounting an immune response. Recent evidence shows HSC can also directly sense cytokines released upon infection/inflammation and pathogen-associated molecular pattern interaction while keeping a long-term memory of previously encountered signals. Direct sensing of danger signals by HSC induces early myeloid commitment, increases myeloid effector cell numbers, and contributes to an efficient immune response. Here, by using specific genetic tools on both the host and pathogen sides, we show that HSC can directly sense B. abortus pathogenic bacteria within the bone marrow via the interaction of the cell surface protein CD150 with the bacterial outer membrane protein Omp25, inducing efficient functional commitment of HSC to the myeloid lineage. This is the first demonstration of direct recognition of a live pathogen by HSC via CD150, which attests to a very early contribution of HSC to immune response.
    DOI:  https://doi.org/10.1084/jem.20210567
  23. Nat Commun. 2023 Apr 20. 14(1): 2271
    Glucocorticoid activation of anti-inflammatory macrophages protects against insulin resistance.
    Giorgio Caratti, Ulrich Stifel, Bozhena Caratti, Ali J M Jamil, Kyoung-Jin Chung, Michael Kiehntopf, Markus H Gräler, Matthias Blüher, Alexander Rauch, Jan P Tuckermann.
      Insulin resistance (IR) during obesity is linked to adipose tissue macrophage (ATM)-driven inflammation of adipose tissue. Whether anti-inflammatory glucocorticoids (GCs) at physiological levels modulate IR is unclear. Here, we report that deletion of the GC receptor (GR) in myeloid cells, including macrophages in mice, aggravates obesity-related IR by enhancing adipose tissue inflammation due to decreased anti-inflammatory ATM leading to exaggerated adipose tissue lipolysis and severe hepatic steatosis. In contrast, GR deletion in Kupffer cells alone does not alter IR. Co-culture experiments show that the absence of GR in macrophages directly causes reduced phospho-AKT and glucose uptake in adipocytes, suggesting an important function of GR in ATM. GR-deficient macrophages are refractory to alternative ATM-inducing IL-4 signaling, due to reduced STAT6 chromatin loading and diminished anti-inflammatory enhancer activation. We demonstrate that GR has an important function in macrophages during obesity by limiting adipose tissue inflammation and lipolysis to promote insulin sensitivity.
    DOI:  https://doi.org/10.1038/s41467-023-37831-z
  24. Cell Metab. 2023 Apr 12. pii: S1550-4131(23)00123-7. [Epub ahead of print]
    FALCON systematically interrogates free fatty acid biology and identifies a novel mediator of lipotoxicity.
    Nicolas Wieder, Juliana Coraor Fried, Choah Kim, Eriene-Heidi Sidhom, Matthew R Brown, Jamie L Marshall, Carlos Arevalo, Moran Dvela-Levitt, Maria Kost-Alimova, Jonas Sieber, Katlyn R Gabriel, Julian Pacheco, Clary Clish, Hamdah Shafqat Abbasi, Shantanu Singh, Justine C Rutter, Martine Therrien, Haejin Yoon, Zon Weng Lai, Aaron Baublis, Renuka Subramanian, Ranjan Devkota, Jonnell Small, Vedagopuram Sreekanth, Myeonghoon Han, Donghyun Lim, Anne E Carpenter, Jason Flannick, Hilary Finucane, Marcia C Haigis, Melina Claussnitzer, Eric Sheu, Beth Stevens, Bridget K Wagner, Amit Choudhary, Jillian L Shaw, Juan Lorenzo Pablo, Anna Greka.
      Cellular exposure to free fatty acids (FFAs) is implicated in the pathogenesis of obesity-associated diseases. However, there are no scalable approaches to comprehensively assess the diverse FFAs circulating in human plasma. Furthermore, assessing how FFA-mediated processes interact with genetic risk for disease remains elusive. Here, we report the design and implementation of fatty acid library for comprehensive ontologies (FALCON), an unbiased, scalable, and multimodal interrogation of 61 structurally diverse FFAs. We identified a subset of lipotoxic monounsaturated fatty acids associated with decreased membrane fluidity. Furthermore, we prioritized genes that reflect the combined effects of harmful FFA exposure and genetic risk for type 2 diabetes (T2D). We found that c-MAF-inducing protein (CMIP) protects cells from FFA exposure by modulating Akt signaling. In sum, FALCON empowers the study of fundamental FFA biology and offers an integrative approach to identify much needed targets for diverse diseases associated with disordered FFA metabolism.
    Keywords:  CMIP; GWAS; erucic acid; kidney; lipidomics; microglia; obesity; pancreatic β cell; transcriptomics; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.cmet.2023.03.018
  25. Nat Commun. 2023 04 19. 14(1): 2229
    Mapping genomic regulation of kidney disease and traits through high-resolution and interpretable eQTLs.
    Nephrotic Syndrome Study Network (NEPTUNE)
      Expression quantitative trait locus (eQTL) studies illuminate genomic variants that regulate specific genes and contribute to fine-mapped loci discovered via genome-wide association studies (GWAS). Efforts to maximize their accuracy are ongoing. Using 240 glomerular (GLOM) and 311 tubulointerstitial (TUBE) micro-dissected samples from human kidney biopsies, we discovered 5371 GLOM and 9787 TUBE genes with at least one variant significantly associated with expression (eGene) by incorporating kidney single-nucleus open chromatin data and transcription start site distance as an "integrative prior" for Bayesian statistical fine-mapping. The use of an integrative prior resulted in higher resolution eQTLs illustrated by (1) smaller numbers of variants in credible sets with greater confidence, (2) increased enrichment of partitioned heritability for GWAS of two kidney traits, (3) an increased number of variants colocalized with the GWAS loci, and (4) enrichment of computationally predicted functional regulatory variants. A subset of variants and genes were validated experimentally in vitro and using a Drosophila nephrocyte model. More broadly, this study demonstrates that tissue-specific eQTL maps informed by single-nucleus open chromatin data have enhanced utility for diverse downstream analyses.
    DOI:  https://doi.org/10.1038/s41467-023-37691-7
  26. Science. 2023 Apr 21. 380(6642): 241-242
    Neurons that connect without synapses.
    Casey Dunn.
      The ctenophore nerve net suggests a complex evolutionary history of the animal nervous system.
    DOI:  https://doi.org/10.1126/science.adh0542
  27. Cell Stem Cell. 2023 Apr 13. pii: S1934-5909(23)00087-5. [Epub ahead of print]
    Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging.
    Ling Liu, Soochi Kim, Matthew T Buckley, Jaime M Reyes, Jengmin Kang, Lei Tian, Mingqiang Wang, Alexander Lieu, Michelle Mao, Cristina Rodriguez-Mateo, Heather D Ishak, Mira Jeong, Joseph C Wu, Margaret A Goodell, Anne Brunet, Thomas A Rando.
      Exercise has the ability to rejuvenate stem cells and improve tissue regeneration in aging animals. However, the cellular and molecular changes elicited by exercise have not been systematically studied across a broad range of cell types in stem cell compartments. We subjected young and old mice to aerobic exercise and generated a single-cell transcriptomic atlas of muscle, neural, and hematopoietic stem cells with their niche cells and progeny, complemented by whole transcriptome analysis of single myofibers. We found that exercise ameliorated the upregulation of a number of inflammatory pathways associated with old age and restored aspects of intercellular communication mediated by immune cells within these stem cell compartments. Exercise has a profound impact on the composition and transcriptomic landscape of circulating and tissue-resident immune cells. Our study provides a comprehensive view of the coordinated responses of multiple aged stem cells and niche cells to exercise at the transcriptomic level.
    Keywords:  aging; exercise; hematopoietic stem cells; inflammation; muscle stem cells; myofibers; neural stem cells; scRNA-seq; skeletal muscle; subventricular zone
    DOI:  https://doi.org/10.1016/j.stem.2023.03.016
  28. Cell Metab. 2023 Apr 11. pii: S1550-4131(23)00094-3. [Epub ahead of print]
    Pyruvate-supported flux through medium-chain ketothiolase promotes mitochondrial lipid tolerance in cardiac and skeletal muscles.
    Timothy R Koves, Guo-Fang Zhang, Michael T Davidson, Alec B Chaves, Scott B Crown, Jordan M Johnson, Dorothy H Slentz, Paul A Grimsrud, Deborah M Muoio.
      Even-chain acylcarnitine (AC) metabolites, most of which are generated as byproducts of incomplete fatty acid oxidation (FAO), are viewed as biomarkers of mitochondrial lipid stress attributable to one or more metabolic bottlenecks in the β-oxidation pathway. The origins and functional implications of FAO bottlenecks remain poorly understood. Here, we combined a sophisticated mitochondrial phenotyping platform with state-of-the-art molecular profiling tools and multiple two-state mouse models of respiratory function to uncover a mechanism that connects AC accumulation to lipid intolerance, metabolic inflexibility, and respiratory inefficiency in skeletal muscle mitochondria. These studies also identified a short-chain carbon circuit at the C4 node of FAO wherein reverse flux of glucose-derived acetyl CoA through medium-chain ketothiolase enhances lipid tolerance and redox stability in heart mitochondria by regenerating free CoA and NAD+. The findings help to explain why diminished FAO capacity, AC accumulation, and metabolic inflexibility are tightly linked to poor health outcomes.
    Keywords:  acylcarnitines; bioenergetics; exercise; fatty acid oxidation; heart; ketothiolase; metabolic flexibility; mitochondria; pyruvate; skeletal muscle
    DOI:  https://doi.org/10.1016/j.cmet.2023.03.016
  29. Cell Metab. 2023 Apr 12. pii: S1550-4131(23)00126-2. [Epub ahead of print]
    Fructose-1,6-bisphosphatase is a nonenzymatic safety valve that curtails AKT activation to prevent insulin hyperresponsiveness.
    Li Gu, Yahui Zhu, Kosuke Watari, Maiya Lee, Junlai Liu, Sofia Perez, Melinda Thai, Joshua E Mayfield, Bichen Zhang, Karina Cunha E Rocha, Fuming Li, Laura C Kim, Alexander C Jones, Igor H Wierzbicki, Xiao Liu, Alexandra C Newton, Tatiana Kisseleva, Jun Hee Lee, Wei Ying, David J Gonzalez, Alan R Saltiel, M Celeste Simon, Michael Karin.
      Insulin inhibits gluconeogenesis and stimulates glucose conversion to glycogen and lipids. How these activities are coordinated to prevent hypoglycemia and hepatosteatosis is unclear. Fructose-1,6-bisphosphatase (FBP1) is rate controlling for gluconeogenesis. However, inborn human FBP1 deficiency does not cause hypoglycemia unless accompanied by fasting or starvation, which also trigger paradoxical hepatomegaly, hepatosteatosis, and hyperlipidemia. Hepatocyte FBP1-ablated mice exhibit identical fasting-conditional pathologies along with AKT hyperactivation, whose inhibition reversed hepatomegaly, hepatosteatosis, and hyperlipidemia but not hypoglycemia. Surprisingly, fasting-mediated AKT hyperactivation is insulin dependent. Independently of its catalytic activity, FBP1 prevents insulin hyperresponsiveness by forming a stable complex with AKT, PP2A-C, and aldolase B (ALDOB), which specifically accelerates AKT dephosphorylation. Enhanced by fasting and weakened by elevated insulin, FBP1:PP2A-C:ALDOB:AKT complex formation, which is disrupted by human FBP1 deficiency mutations or a C-terminal FBP1 truncation, prevents insulin-triggered liver pathologies and maintains lipid and glucose homeostasis. Conversely, an FBP1-derived complex disrupting peptide reverses diet-induced insulin resistance.
    Keywords:  AKT; FBP1; hepatomegaly; hepatosteatosis
    DOI:  https://doi.org/10.1016/j.cmet.2023.03.021
  30. Nat Commun. 2023 Apr 20. 14(1): 2265
    AGGF1 therapy inhibits thoracic aortic aneurysms by enhancing integrin α7-mediated inhibition of TGF-β1 maturation and ERK1/2 signaling.
    Xingwen Da, Ziyan Li, Xiaofan Huang, Zuhan He, Yubing Yu, Tongtong Tian, Chengqi Xu, Yufeng Yao, Qing K Wang.
      Thoracic aortic aneurysm (TAA) is a localized or diffuse dilatation of the thoracic aortas, and causes many sudden deaths each year worldwide. However, there is no effective pharmacologic therapy. Here, we show that AGGF1 effectively blocks TAA-associated arterial inflammation and remodeling in three different mouse models (mice with transverse aortic constriction, Fbn1C1041G/+ mice, and β-aminopropionitrile-treated mice). AGGF1 expression is reduced in the ascending aortas from the three models and human TAA patients. Aggf1+/- mice and vascular smooth muscle cell (VSMC)-specific Aggf1smcKO knockout mice show aggravated TAA phenotypes. Mechanistically, AGGF1 enhances the interaction between its receptor integrin α7 and latency-associated peptide (LAP)-TGF-β1, blocks the cleavage of LAP-TGF-β1 to form mature TGF-β1, and inhibits Smad2/3 and ERK1/2 phosphorylation in VSMCs. Pirfenidone, a treatment agent for idiopathic pulmonary fibrosis, inhibits TAA-associated vascular inflammation and remodeling in wild type mice, but not in Aggf1+/- mice. In conclusion, we identify an innovative AGGF1 protein therapeutic strategy to block TAA-associated vascular inflammation and remodeling, and show that efficacy of TGF-β inhibition therapies require AGGF1.
    DOI:  https://doi.org/10.1038/s41467-023-37809-x
  31. Cell Stem Cell. 2023 Apr 14. pii: S1934-5909(23)00088-7. [Epub ahead of print]
    Advancing cell therapy for neurodegenerative diseases.
    Sally Temple.
      Cell-based therapies are being developed for various neurodegenerative diseases that affect the central nervous system (CNS). Concomitantly, the roles of individual cell types in neurodegenerative pathology are being uncovered by genetic and single-cell studies. With a greater understanding of cellular contributions to health and disease and with the arrival of promising approaches to modulate them, effective therapeutic cell products are now emerging. This review examines how the ability to generate diverse CNS cell types from stem cells, along with a deeper understanding of cell-type-specific functions and pathology, is advancing preclinical development of cell products for the treatment of neurodegenerative diseases.
    Keywords:  Alzheimer disease; GABAergic neurons; Parkinson disease; age-related macular degeneration; astrocytes; central nervous system; dopaminergic neurons; frontotemporal dementia; microglia; neurodegenerative disease; neurons; oligodendrocytes; organoids; photoreceptors; preclinical studies; progressive supranuclear palsy; retina; retinal pigment epithelium; stem cell therapy; transplantation
    DOI:  https://doi.org/10.1016/j.stem.2023.03.017
  32. Nat Commun. 2023 Apr 21. 14(1): 2284
    Error-related signaling in nucleus accumbens D2 receptor-expressing neurons guides inhibition-based choice behavior in mice.
    Tadaaki Nishioka, Suthinee Attachaipanich, Kosuke Hamaguchi, Michael Lazarus, Alban de Kerchove d'Exaerde, Tom Macpherson, Takatoshi Hikida.
      Learned associations between environmental cues and the outcomes they predict (cue-outcome associations) play a major role in behavioral control, guiding not only which responses we should perform, but also which we should inhibit, in order to achieve a specific goal. The encoding of such cue-outcome associations, as well as the performance of cue-guided choice behavior, is thought to involve dopamine D1 and D2 receptor-expressing medium spiny neurons (D1-/D2-MSNs) of the nucleus accumbens (NAc). Here, using a visual discrimination task in male mice, we assessed the role of NAc D1-/D2-MSNs in cue-guided inhibition of inappropriate responding. Cell-type specific neuronal silencing and in-vivo imaging revealed NAc D2-MSNs to contribute to inhibiting behavioral responses, with activation of NAc D2-MSNs following response errors playing an important role in optimizing future choice behavior. Our findings indicate that error-signaling by NAc D2-MSNs contributes to the ability to use environmental cues to inhibit inappropriate behavior.
    DOI:  https://doi.org/10.1038/s41467-023-38025-3
  33. Nature. 2023 Apr 19.
    Science strengthened banks - but how long will stability last?
    Mark Buchanan.
      
    DOI:  https://doi.org/10.1038/d41586-023-01291-8
  34. Nat Commun. 2023 Apr 20. 14(1): 2174
    Parkinson's disease-associated ATP13A2/PARK9 functions as a lysosomal H+,K+-ATPase.
    Takuto Fujii, Shushi Nagamori, Pattama Wiriyasermkul, Shizhou Zheng, Asaka Yago, Takahiro Shimizu, Yoshiaki Tabuchi, Tomoyuki Okumura, Tsutomu Fujii, Hiroshi Takeshima, Hideki Sakai.
      Mutations in the human ATP13A2 (PARK9), a lysosomal ATPase, cause Kufor-Rakeb Syndrome, an early-onset form of Parkinson's disease (PD). Here, we demonstrate that ATP13A2 functions as a lysosomal H+,K+-ATPase. The K+-dependent ATPase activity and the lysosomal K+-transport activity of ATP13A2 are inhibited by an inhibitor of sarco/endoplasmic reticulum Ca2+-ATPase, thapsigargin, and K+-competitive inhibitors of gastric H+,K+-ATPase, such as vonoprazan and SCH28080. Interestingly, these H+,K+-ATPase inhibitors cause lysosomal alkalinization and α-synuclein accumulation, which are pathological hallmarks of PD. Furthermore, PD-associated mutants of ATP13A2 show abnormal expression and function. Our results suggest that the H+/K+-transporting function of ATP13A2 contributes to acidification and α-synuclein degradation in lysosomes.
    DOI:  https://doi.org/10.1038/s41467-023-37815-z
  35. Nat Commun. 2023 04 19. 14(1): 2245
    Dephosphocholination by Legionella effector Lem3 functions through remodelling of the switch II region of Rab1b.
    Marietta S Kaspers, Vivian Pogenberg, Christian Pett, Stefan Ernst, Felix Ecker, Philipp Ochtrop, Michael Groll, Christian Hedberg, Aymelt Itzen.
      Bacterial pathogens often make use of post-translational modifications to manipulate host cells. Legionella pneumophila, the causative agent of Legionnaires disease, secretes the enzyme AnkX that uses cytidine diphosphate-choline to post-translationally modify the human small G-Protein Rab1 with a phosphocholine moiety at Ser76. Later in the infection, the Legionella enzyme Lem3 acts as a dephosphocholinase, hydrolytically removing the phosphocholine. While the molecular mechanism for Rab1 phosphocholination by AnkX has recently been resolved, structural insights into the activity of Lem3 remained elusive. Here, we stabilise the transient Lem3:Rab1b complex by substrate mediated covalent capture. Through crystal structures of Lem3 in the apo form and in complex with Rab1b, we reveal Lem3's catalytic mechanism, showing that it acts on Rab1 by locally unfolding it. Since Lem3 shares high structural similarity with metal-dependent protein phosphatases, our Lem3:Rab1b complex structure also sheds light on how these phosphatases recognise protein substrates.
    DOI:  https://doi.org/10.1038/s41467-023-37621-7
  36. Nat Commun. 2023 04 19. 14(1): 2248
    Temperature sensitive liposome based cancer nanomedicine enables tumour lymph node immune microenvironment remodelling.
    Shunli Fu, Lili Chang, Shujun Liu, Tong Gao, Xiao Sang, Zipeng Zhang, Weiwei Mu, Xiaoqing Liu, Shuang Liang, Han Yang, Huizhen Yang, Qingping Ma, Yongjun Liu, Na Zhang.
      Targeting tumour immunosuppressive microenvironment is a crucial strategy in immunotherapy. However, the critical role of the tumour lymph node (LN) immune microenvironment (TLIME) in the tumour immune homoeostasis is often ignored. Here, we present a nanoinducer, NIL-IM-Lip, that remodels the suppressed TLIME via simultaneously mobilizing T and NK cells. The temperature-sensitive NIL-IM-Lip is firstly delivered to tumours, then directed to the LNs following pH-sensitive shedding of NGR motif and MMP2-responsive release of IL-15. IR780 and 1-MT induces immunogenic cell death and suppress regulatory T cells simultaneously during photo-thermal stimulation. We demonstrate that combining NIL-IM-Lip with anti-PD-1 significantly enhances the effectiveness of T and NK cells, leading to greatly suppressed tumour growth in both hot and cold tumour models, with complete response in some instances. Our work thus highlights the critical role of TLIME in immunotherapy and provides proof of principle to combine LN targeting with immune checkpoint blockade in cancer immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-023-38014-6
  37. Nat Genet. 2023 Apr 20.
    Genetics of myocardial interstitial fibrosis in the human heart and association with disease.
    Victor Nauffal, Paolo Di Achille, Marcus D R Klarqvist, Jonathan W Cunningham, Matthew C Hill, James P Pirruccello, Lu-Chen Weng, Valerie N Morrill, Seung Hoan Choi, Shaan Khurshid, Samuel F Friedman, Mahan Nekoui, Carolina Roselli, Kenney Ng, Anthony A Philippakis, Puneet Batra, Patrick T Ellinor, Steven A Lubitz.
      Myocardial interstitial fibrosis is associated with cardiovascular disease and adverse prognosis. Here, to investigate the biological pathways that underlie fibrosis in the human heart, we developed a machine learning model to measure native myocardial T1 time, a marker of myocardial fibrosis, in 41,505 UK Biobank participants who underwent cardiac magnetic resonance imaging. Greater T1 time was associated with diabetes mellitus, renal disease, aortic stenosis, cardiomyopathy, heart failure, atrial fibrillation, conduction disease and rheumatoid arthritis. Genome-wide association analysis identified 11 independent loci associated with T1 time. The identified loci implicated genes involved in glucose transport (SLC2A12), iron homeostasis (HFE, TMPRSS6), tissue repair (ADAMTSL1, VEGFC), oxidative stress (SOD2), cardiac hypertrophy (MYH7B) and calcium signaling (CAMK2D). Using a transforming growth factor β1-mediated cardiac fibroblast activation assay, we found that 9 of the 11 loci consisted of genes that exhibited temporal changes in expression or open chromatin conformation supporting their biological relevance to myofibroblast cell state acquisition. By harnessing machine learning to perform large-scale quantification of myocardial interstitial fibrosis using cardiac imaging, we validate associations between cardiac fibrosis and disease, and identify new biologically relevant pathways underlying fibrosis.
    DOI:  https://doi.org/10.1038/s41588-023-01371-5
  38. Nat Commun. 2023 04 18. 14(1): 2191
    Hybrid photoacoustic and fast super-resolution ultrasound imaging.
    Shensheng Zhao, Jonathan Hartanto, Ritin Joseph, Cheng-Hsun Wu, Yang Zhao, Yun-Sheng Chen.
      The combination of photoacoustic (PA) imaging and ultrasound localization microscopy (ULM) with microbubbles has great potential in various fields such as oncology, neuroscience, nephrology, and immunology. Here we developed an interleaved PA/fast ULM imaging technique that enables super-resolution vascular and physiological imaging in less than 2 seconds per frame in vivo. By using sparsity-constrained (SC) optimization, we accelerated the frame rate of ULM up to 37 times with synthetic data and 28 times with in vivo data. This allows for the development of a 3D dual imaging sequence with a commonly used linear array imaging system, without the need for complicated motion correction. Using the dual imaging scheme, we demonstrated two in vivo scenarios challenging to image with either technique alone: the visualization of a dye-labeled mouse lymph node showing nearby microvasculature, and a mouse kidney microangiography with tissue oxygenation. This technique offers a powerful tool for mapping tissue physiological conditions and tracking the contrast agent biodistribution non-invasively.
    DOI:  https://doi.org/10.1038/s41467-023-37680-w
  39. Nat Commun. 2023 04 17. 14(1): 2149
    A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates.
    Payton A-B Weidenbacher, Mrinmoy Sanyal, Natalia Friedland, Shaogeng Tang, Prabhu S Arunachalam, Mengyun Hu, Ozan S Kumru, Mary Kate Morris, Jane Fontenot, Lisa Shirreff, Jonathan Do, Ya-Chen Cheng, Gayathri Vasudevan, Mark B Feinberg, Francois J Villinger, Carl Hanson, Sangeeta B Joshi, David B Volkin, Bali Pulendran, Peter S Kim.
      While the rapid development of COVID-19 vaccines has been a scientific triumph, the need remains for a globally available vaccine that provides longer-lasting immunity against present and future SARS-CoV-2 variants of concern (VOCs). Here, we describe DCFHP, a ferritin-based, protein-nanoparticle vaccine candidate that, when formulated with aluminum hydroxide as the sole adjuvant (DCFHP-alum), elicits potent and durable neutralizing antisera in non-human primates against known VOCs, including Omicron BQ.1, as well as against SARS-CoV-1. Following a booster ~one year after the initial immunization, DCFHP-alum elicits a robust anamnestic response. To enable global accessibility, we generated a cell line that can enable production of thousands of vaccine doses per liter of cell culture and show that DCFHP-alum maintains potency for at least 14 days at temperatures exceeding standard room temperature. DCFHP-alum has potential as a once-yearly (or less frequent) booster vaccine, and as a primary vaccine for pediatric use including in infants.
    DOI:  https://doi.org/10.1038/s41467-023-37417-9
  40. Nat Commun. 2023 04 17. 14(1): 2198
    The basolateral amygdala-anterior cingulate pathway contributes to depression-like behaviors and comorbidity with chronic pain behaviors in male mice.
    Léa J Becker, Clémentine Fillinger, Robin Waegaert, Sarah H Journée, Pierre Hener, Beyza Ayazgok, Muris Humo, Meltem Karatas, Maxime Thouaye, Mithil Gaikwad, Laetitia Degiorgis, Marie des Neiges Santin, Mary Mondino, Michel Barrot, El Chérif Ibrahim, Gustavo Turecki, Raoul Belzeaux, Pierre Veinante, Laura A Harsan, Sylvain Hugel, Pierre-Eric Lutz, Ipek Yalcin.
      While depression and chronic pain are frequently comorbid, underlying neuronal circuits and their psychopathological relevance remain poorly defined. Here we show in mice that hyperactivity of the neuronal pathway linking the basolateral amygdala to the anterior cingulate cortex is essential for chronic pain-induced depression. Moreover, activation of this pathway in naive male mice, in the absence of on-going pain, is sufficient to trigger depressive-like behaviors, as well as transcriptomic alterations that recapitulate core molecular features of depression in the human brain. These alterations notably impact gene modules related to myelination and the oligodendrocyte lineage. Among these, we show that Sema4a, which was significantly upregulated in both male mice and humans in the context of altered mood, is necessary for the emergence of emotional dysfunction. Overall, these results place the amygdalo-cingulate pathway at the core of pain and depression comorbidity, and unravel the role of Sema4a and impaired myelination in mood control.
    DOI:  https://doi.org/10.1038/s41467-023-37878-y
  41. Sci Adv. 2023 Apr 21. 9(16): eabq7105
    Tau pathology epigenetically remodels the neuron-glial cross-talk in Alzheimer's disease.
    Lan-Ting Zhou, Dan Liu, Hui-Cong Kang, Lu Lu, He-Zhou Huang, Wen-Qing Ai, Yang Zhou, Man-Fei Deng, Hao Li, Zhi-Qiang Liu, Wei-Feng Zhang, Ya-Zhuo Hu, Zhi-Tao Han, Hong-Hong Zhang, Jian-Jun Jia, Avijite Kumer Sarkar, Saldin Sharaydeh, Jie Wang, Heng-Ye Man, Marcel Schilling, Lars Bertram, Youming Lu, Ziyuan Guo, Ling-Qiang Zhu.
      The neuron-glia cross-talk is critical to brain homeostasis and is particularly affected by neurodegenerative diseases. How neurons manipulate the neuron-astrocyte interaction under pathological conditions, such as hyperphosphorylated tau, a pathological hallmark in Alzheimer's disease (AD), remains elusive. In this study, we identified excessively elevated neuronal expression of adenosine receptor 1 (Adora1 or A1R) in 3×Tg mice, MAPT P301L (rTg4510) mice, patients with AD, and patient-derived neurons. The up-regulation of A1R was found to be tau pathology dependent and posttranscriptionally regulated by Mef2c via miR-133a-3p. Rebuilding the miR-133a-3p/A1R signal effectively rescued synaptic and memory impairments in AD mice. Furthermore, neuronal A1R promoted the release of lipocalin 2 (Lcn2) and resulted in astrocyte activation. Last, silencing neuronal Lcn2 in AD mice ameliorated astrocyte activation and restored synaptic plasticity and learning/memory. Our findings reveal that the tau pathology remodels neuron-glial cross-talk and promotes neurodegenerative progression. Approaches targeting A1R and modulating this signaling pathway might be a potential therapeutic strategy for AD.
    DOI:  https://doi.org/10.1126/sciadv.abq7105
  42. Nat Commun. 2023 04 19. 14(1): 2232
    The structural basis of tRNA recognition by arginyl-tRNA-protein transferase.
    Thilini Abeywansha, Wei Huang, Xuan Ye, Allison Nawrocki, Xin Lan, Eckhard Jankowsky, Derek J Taylor, Yi Zhang.
      Arginyl-tRNA-protein transferase 1 (ATE1) is a master regulator of protein homeostasis, stress response, cytoskeleton maintenance, and cell migration. The diverse functions of ATE1 arise from its unique enzymatic activity to covalently attach an arginine onto its protein substrates in a tRNA-dependent manner. However, how ATE1 (and other aminoacyl-tRNA transferases) hijacks tRNA from the highly efficient ribosomal protein synthesis pathways and catalyzes the arginylation reaction remains a mystery. Here, we describe the three-dimensional structures of Saccharomyces cerevisiae ATE1 with and without its tRNA cofactor. Importantly, the putative substrate binding domain of ATE1 adopts a previously uncharacterized fold that contains an atypical zinc-binding site critical for ATE1 stability and function. The unique recognition of tRNAArg by ATE1 is coordinated through interactions with the major groove of the acceptor arm of tRNA. Binding of tRNA induces conformational changes in ATE1 that helps explain the mechanism of substrate arginylation.
    DOI:  https://doi.org/10.1038/s41467-023-38004-8
  43. Nat Commun. 2023 Apr 20. 14(1): 2131
    RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function.
    Chisa Shiraishi, Akinobu Matsumoto, Kazuya Ichihara, Taishi Yamamoto, Takeshi Yokoyama, Taisuke Mizoo, Atsushi Hatano, Masaki Matsumoto, Yoshikazu Tanaka, Eriko Matsuura-Suzuki, Shintaro Iwasaki, Shouji Matsushima, Hiroyuki Tsutsui, Keiichi I Nakayama.
      Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation.
    DOI:  https://doi.org/10.1038/s41467-023-37838-6
  44. Nat Commun. 2023 04 19. 14(1): 2230
    DeMAG predicts the effects of variants in clinically actionable genes by integrating structural and evolutionary epistatic features.
    Federica Luppino, Ivan A Adzhubei, Christopher A Cassa, Agnes Toth-Petroczy.
      Despite the increasing use of genomic sequencing in clinical practice, the interpretation of rare genetic variants remains challenging even in well-studied disease genes, resulting in many patients with Variants of Uncertain Significance (VUSs). Computational Variant Effect Predictors (VEPs) provide valuable evidence in variant assessment, but they are prone to misclassifying benign variants, contributing to false positives. Here, we develop Deciphering Mutations in Actionable Genes (DeMAG), a supervised classifier for missense variants trained using extensive diagnostic data available in 59 actionable disease genes (American College of Medical Genetics and Genomics Secondary Findings v2.0, ACMG SF v2.0). DeMAG improves performance over existing VEPs by reaching balanced specificity (82%) and sensitivity (94%) on clinical data, and includes a novel epistatic feature, the 'partners score', which leverages evolutionary and structural partnerships of residues. The 'partners score' provides a general framework for modeling epistatic interactions, integrating both clinical and functional information. We provide our tool and predictions for all missense variants in 316 clinically actionable disease genes (demag.org) to facilitate the interpretation of variants and improve clinical decision-making.
    DOI:  https://doi.org/10.1038/s41467-023-37661-z
  45. Nat Commun. 2023 04 19. 14(1): 2150
    Disrupting the α-synuclein-ESCRT interaction with a peptide inhibitor mitigates neurodegeneration in preclinical models of Parkinson's disease.
    Satra Nim, Darren M O'Hara, Carles Corbi-Verge, Albert Perez-Riba, Kazuko Fujisawa, Minesh Kapadia, Hien Chau, Federica Albanese, Grishma Pawar, Mitchell L De Snoo, Sophie G Ngana, Jisun Kim, Omar M A El-Agnaf, Enrico Rennella, Lewis E Kay, Suneil K Kalia, Lorraine V Kalia, Philip M Kim.
      Accumulation of α-synuclein into toxic oligomers or fibrils is implicated in dopaminergic neurodegeneration in Parkinson's disease. Here we performed a high-throughput, proteome-wide peptide screen to identify protein-protein interaction inhibitors that reduce α-synuclein oligomer levels and their associated cytotoxicity. We find that the most potent peptide inhibitor disrupts the direct interaction between the C-terminal region of α-synuclein and CHarged Multivesicular body Protein 2B (CHMP2B), a component of the Endosomal Sorting Complex Required for Transport-III (ESCRT-III). We show that α-synuclein impedes endolysosomal activity via this interaction, thereby inhibiting its own degradation. Conversely, the peptide inhibitor restores endolysosomal function and thereby decreases α-synuclein levels in multiple models, including female and male human cells harboring disease-causing α-synuclein mutations. Furthermore, the peptide inhibitor protects dopaminergic neurons from α-synuclein-mediated degeneration in hermaphroditic C. elegans and preclinical Parkinson's disease models using female rats. Thus, the α-synuclein-CHMP2B interaction is a potential therapeutic target for neurodegenerative disorders.
    DOI:  https://doi.org/10.1038/s41467-023-37464-2
  46. Nat Commun. 2023 04 19. 14(1): 2238
    Direct correction of haemoglobin E β-thalassaemia using base editors.
    Mohsin Badat, Ayesha Ejaz, Peng Hua, Siobhan Rice, Weijiao Zhang, Lance D Hentges, Christopher A Fisher, Nicholas Denny, Ron Schwessinger, Nirmani Yasara, Noemi B A Roy, Fadi Issa, Andi Roy, Paul Telfer, Jim Hughes, Sachith Mettananda, Douglas R Higgs, James O J Davies.
      Haemoglobin E (HbE) β-thalassaemia causes approximately 50% of all severe thalassaemia worldwide; equating to around 30,000 births per year. HbE β-thalassaemia is due to a point mutation in codon 26 of the human HBB gene on one allele (GAG; glutamatic acid → AAG; lysine, E26K), and any mutation causing severe β-thalassaemia on the other. When inherited together in compound heterozygosity these mutations can cause a severe thalassaemic phenotype. However, if only one allele is mutated individuals are carriers for the respective mutation and have an asymptomatic phenotype (β-thalassaemia trait). Here we describe a base editing strategy which corrects the HbE mutation either to wildtype (WT) or a normal variant haemoglobin (E26G) known as Hb Aubenas and thereby recreates the asymptomatic trait phenotype. We have achieved editing efficiencies in excess of 90% in primary human CD34 + cells. We demonstrate editing of long-term repopulating haematopoietic stem cells (LT-HSCs) using serial xenotransplantation in NSG mice. We have profiled the off-target effects using a combination of circularization for in vitro reporting of cleavage effects by sequencing (CIRCLE-seq) and deep targeted capture and have developed machine-learning based methods to predict functional effects of candidate off-target mutations.
    DOI:  https://doi.org/10.1038/s41467-023-37604-8
  47. Nat Biotechnol. 2023 Apr;41(4): 469
    Microfluidics.
      
    DOI:  https://doi.org/10.1038/s41587-023-01739-2
  48. Sci Adv. 2023 04 21. 9(16): eadf9284
    Autophagy supports mitochondrial metabolism through the regulation of iron homeostasis in pancreatic cancer.
    Subhadip Mukhopadhyay, Joel Encarnación-Rosado, Elaine Y Lin, Albert S W Sohn, Huan Zhang, Joseph D Mancias, Alec C Kimmelman.
      Pancreatic ductal adenocarcinoma (PDAC) cells maintain a high level of autophagy, allowing them to thrive in an austere microenvironment. However, the processes through which autophagy promotes PDAC growth and survival are still not fully understood. Here, we show that autophagy inhibition in PDAC alters mitochondrial function by losing succinate dehydrogenase complex iron sulfur subunit B expression by limiting the availability of the labile iron pool. PDAC uses autophagy to maintain iron homeostasis, while other tumor types assessed require macropinocytosis, with autophagy being dispensable. We observed that cancer-associated fibroblasts can provide bioavailable iron to PDAC cells, promoting resistance to autophagy ablation. To overcome this cross-talk, we used a low-iron diet and demonstrated that this augmented the response to autophagy inhibition therapy in PDAC-bearing mice. Our work highlights a critical link between autophagy, iron metabolism, and mitochondrial function that may have implications for PDAC progression.
    DOI:  https://doi.org/10.1126/sciadv.adf9284
  49. Nature. 2023 Apr 19.
    PI3Kβ controls immune evasion in PTEN-deficient breast tumours.
    Johann S Bergholz, Qiwei Wang, Qi Wang, Michelle Ramseier, Sanjay Prakadan, Weihua Wang, Rong Fang, Sheheryar Kabraji, Qian Zhou, G Kenneth Gray, Kayley Abell-Hart, Shaozhen Xie, Xiaocan Guo, Hao Gu, Thanh Von, Tao Jiang, Shuang Tang, Gordon J Freeman, Hye-Jung Kim, Alex K Shalek, Thomas M Roberts, Jean J Zhao.
      Loss of the PTEN tumour suppressor is one of the most common oncogenic drivers across all cancer types1. PTEN is the major negative regulator of PI3K signalling. The PI3Kβ isoform has been shown to play an important role in PTEN-deficient tumours, but the mechanisms underlying the importance of PI3Kβ activity remain elusive. Here, using a syngeneic genetically engineered mouse model of invasive breast cancer driven by ablation of both Pten and Trp53 (which encodes p53), we show that genetic inactivation of PI3Kβ led to a robust anti-tumour immune response that abrogated tumour growth in syngeneic immunocompetent mice, but not in immunodeficient mice. Mechanistically, PI3Kβ inactivation in the PTEN-null setting led to reduced STAT3 signalling and increased the expression of immune stimulatory molecules, thereby promoting anti-tumour immune responses. Pharmacological PI3Kβ inhibition also elicited anti-tumour immunity and synergized with immunotherapy to inhibit tumour growth. Mice with complete responses to the combined treatment displayed immune memory and rejected tumours upon re-challenge. Our findings demonstrate a molecular mechanism linking PTEN loss and STAT3 activation in cancer and suggest that PI3Kβ controls immune escape in PTEN-null tumours, providing a rationale for combining PI3Kβ inhibitors with immunotherapy for the treatment of PTEN-deficient breast cancer.
    DOI:  https://doi.org/10.1038/s41586-023-05940-w
  50. J Clin Invest. 2023 Apr 20. pii: e164317. [Epub ahead of print]
    HSV-2 triggers upregulation of MALAT1 in CD4+ T cells and promotes HIV latency reversal.
    Carl A Pierce, Lip Nam Loh, Holly R Steach, Natalia Cheshenko, Paula Preston-Hurlburt, Fengrui Zhang, Stephanie Stransky, Leah Kravets, Simone Sidoli, William M Philbrick, Michel N Nassar, Smita Krishnaswamy, Kevan C Herold, Betsy C Herold.
      HSV-2 coinfection is associated with increased HIV-1 viral loads and expanded tissue reservoirs, but the mechanisms are not well-defined. HSV-2 recurrences result in an influx of activated CD4+ T cells to sites of viral replication and an increase in activated CD4+ T cells in peripheral blood. We hypothesized that HSV-2 induces changes in these cells that facilitate HIV-1 reactivation and replication and tested this hypothesis in human CD4+ T cells and 2D10 cells, a model of HIV-1 latency. HSV-2 promoted latency reversal in HSV-2 infected and bystander 2D10 cells. Bulk and single-cell RNA sequencing studies of activated primary human CD4+ T cells identified decreased expression of HIV-1 restriction factors and increased expression of transcripts including MALAT1 that could drive HIV replication in both the HSV-2-infected and bystander cells. Transfection of 2D10 cells with VP16, an HSV-2 protein that regulates transcription, significantly upregulated MALAT1 expression, decreased trimethylation of lysine 27 on histone H3 protein, and triggered HIV latency reversal. Knockout of MALAT1 from 2D10 cells abrogated the response to VP16 and reduced the response to HSV-2 infection. These results demonstrate that HSV-2 contributes to HIV-1 reactivation through diverse mechanisms including upregulation of MALAT1 to release epigenetic silencing.
    Keywords:  AIDS/HIV; T cells; Transcription; Virology
    DOI:  https://doi.org/10.1172/JCI164317
  51. Mol Cell. 2023 Apr 20. pii: S1097-2765(23)00213-7. [Epub ahead of print]83(8): 1340-1349.e7
    Uncoupled glycerol-3-phosphate shuttle in kidney cancer reveals that cytosolic GPD is essential to support lipid synthesis.
    Cong-Hui Yao, Joon Seok Park, Kiran Kurmi, Song-Hua Hu, Giulia Notarangelo, Joseph Crowley, Heidi Jacobson, Sheng Hui, Arlene H Sharpe, Marcia C Haigis.
      The glycerol-3-phosphate shuttle (G3PS) is a major NADH shuttle that regenerates reducing equivalents in the cytosol and produces energy in the mitochondria. Here, we demonstrate that G3PS is uncoupled in kidney cancer cells where the cytosolic reaction is ∼4.5 times faster than the mitochondrial reaction. The high flux through cytosolic glycerol-3-phosphate dehydrogenase (GPD) is required to maintain redox balance and support lipid synthesis. Interestingly, inhibition of G3PS by knocking down mitochondrial GPD (GPD2) has no effect on mitochondrial respiration. Instead, loss of GPD2 upregulates cytosolic GPD on a transcriptional level and promotes cancer cell proliferation by increasing glycerol-3-phosphate supply. The proliferative advantage of GPD2 knockdown tumor can be abolished by pharmacologic inhibition of lipid synthesis. Taken together, our results suggest that G3PS is not required to run as an intact NADH shuttle but is instead truncated to support complex lipid synthesis in kidney cancer.
    Keywords:  GPD; NAD; glycerol; glycerol-3-phosphate dehydrogenase; glycerol-3-phosphate shuttle; kidney cancer; lipids; metabolism; mitochondria
    DOI:  https://doi.org/10.1016/j.molcel.2023.03.023
  52. Commun Biol. 2023 04 17. 6(1): 423
    Structure of anhydrotetracycline-bound Tet(X6) reveals the mechanism for inhibition of type 1 tetracycline destructases.
    Hirdesh Kumar, Emily E Williford, Kevin S Blake, Brett Virgin-Downey, Gautam Dantas, Timothy A Wencewicz, Niraj H Tolia.
      Inactivation of tetracycline antibiotics by tetracycline destructases (TDases) remains a clinical and agricultural threat. TDases can be classified as type 1 Tet(X)-like TDases and type 2 soil-derived TDases. Type 1 TDases are widely identified in clinical pathogens. A combination therapy of tetracycline and a TDase inhibitor is much needed to rescue the clinical efficacy of tetracyclines. Anhydrotetracycline is a pan-TDase inhibitor that inhibits both type 1 and type 2 TDases. Here, we present structural, biochemical, and phenotypic evidence that anhydrotetracycline binds in a substrate-like orientation and competitively inhibits the type 1 TDase Tet(X6) to rescue tetracycline antibiotic activity as a sacrificial substrate. Anhydrotetracycline interacting residues of Tet(X6) are conserved within type 1 TDases, indicating a conserved binding mode and mechanism of inhibition. This mode of binding and inhibition is distinct from anhydrotetracycline's inhibition of type 2 TDases. This study forms the framework for development of next-generation therapies to counteract enzymatic tetracycline resistance.
    DOI:  https://doi.org/10.1038/s42003-023-04792-4
  53. Nat Biotechnol. 2023 Apr;41(4): 470
    Base editor restores CD3δ-dependent SCID mutation.
    Jared B Fudge.
      
    DOI:  https://doi.org/10.1038/s41587-023-01768-x
  54. Cell Genom. 2023 Apr 12. 3(4): 100273
    Gene-by-environment interactions are pervasive among natural genetic variants.
    Shi-An A Chen, Alexander F Kern, Roy Moh Lik Ang, Yihua Xie, Hunter B Fraser.
      Gene-by-environment (GxE) interactions, in which a genetic variant's phenotypic effect is condition specific, are fundamental for understanding fitness landscapes and evolution but have been difficult to identify at the single-nucleotide level. Although many condition-specific quantitative trait loci (QTLs) have been mapped, these typically contain numerous inconsequential variants in linkage, precluding understanding of the causal GxE variants. Here, we introduce BARcoded Cas9 retron precise parallel editing via homology (CRISPEY-BAR), a high-throughput precision genome editing strategy, and use it to map GxE interactions of naturally occurring genetic polymorphisms impacting yeast growth. We identified hundreds of GxE variants within condition-specific QTLs, revealing unexpected genetic complexity. Moreover, we found that 93.7% of non-neutral natural variants within ergosterol biosynthesis pathway genes showed GxE interactions, including many impacting antifungal drug resistance through diverse molecular mechanisms. In sum, our results suggest an extremely complex, context-dependent fitness landscape characterized by pervasive GxE interactions while also demonstrating massively parallel genome editing as an effective means for investigating this complexity.
    Keywords:  antifungals; evolution; gene-by-environment; genome editing; quantitative genetics
    DOI:  https://doi.org/10.1016/j.xgen.2023.100273
  55. Nat Commun. 2023 Apr 21. 14(1): 2290
    RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells.
    Florisela Herrejon Chavez, Hanzhi Luo, Paolo Cifani, Alli Pine, Karen L Chu, Suhasini Joshi, Ersilia Barin, Alexandra Schurer, Mandy Chan, Kathryn Chang, Grace Y Q Han, Aspen J Pierson, Michael Xiao, Xuejing Yang, Lindsey M Kuehm, Yuning Hong, Diu T T Nguyen, Gabriela Chiosis, Alex Kentsis, Christina Leslie, Ly P Vu, Michael G Kharas.
      Tissue homeostasis is maintained after stress by engaging and activating the hematopoietic stem and progenitor compartments in the blood. Hematopoietic stem cells (HSCs) are essential for long-term repopulation after secondary transplantation. Here, using a conditional knockout mouse model, we revealed that the RNA-binding protein SYNCRIP is required for maintenance of blood homeostasis especially after regenerative stress due to defects in HSCs and progenitors. Mechanistically, we find that SYNCRIP loss results in a failure to maintain proteome homeostasis that is essential for HSC maintenance. SYNCRIP depletion results in increased protein synthesis, a dysregulated epichaperome, an accumulation of misfolded proteins and induces endoplasmic reticulum stress. Additionally, we find that SYNCRIP is required for translation of CDC42 RHO-GTPase, and loss of SYNCRIP results in defects in polarity, asymmetric segregation, and dilution of unfolded proteins. Forced expression of CDC42 recovers polarity and in vitro replating activities of HSCs. Taken together, we uncovered a post-transcriptional regulatory program that safeguards HSC self-renewal capacity and blood homeostasis.
    DOI:  https://doi.org/10.1038/s41467-023-38001-x
  56. Nat Commun. 2023 04 15. 14(1): 2173
    Dynamic fluctuations in a bacterial metabolic network.
    Shuangyu Bi, Manika Kargeti, Remy Colin, Niklas Farke, Hannes Link, Victor Sourjik.
      The operation of the central metabolism is typically assumed to be deterministic, but dynamics and high connectivity of the metabolic network make it potentially prone to generating fluctuations. However, time-resolved measurements of metabolite levels in individual cells that are required to characterize such fluctuations remained a challenge, particularly in small bacterial cells. Here we use single-cell metabolite measurements based on Förster resonance energy transfer, combined with computer simulations, to explore the real-time dynamics of the metabolic network of Escherichia coli. We observe that steplike exposure of starved E. coli to glycolytic carbon sources elicits large periodic fluctuations in the intracellular concentration of pyruvate in individual cells. These fluctuations are consistent with predicted oscillatory dynamics of E. coli metabolic network, and they are primarily controlled by biochemical reactions around the pyruvate node. Our results further indicate that fluctuations in glycolysis propagate to other cellular processes, possibly leading to temporal heterogeneity of cellular states within a population.
    DOI:  https://doi.org/10.1038/s41467-023-37957-0
  57. Nat Commun. 2023 Apr 21. 14(1): 2314
    Single-nucleus RNA-sequencing of autosomal dominant Alzheimer disease and risk variant carriers.
    Dominantly Inherited Alzheimer Network (DIAN)
      Genetic studies of Alzheimer disease (AD) have prioritized variants in genes related to the amyloid cascade, lipid metabolism, and neuroimmune modulation. However, the cell-specific effect of variants in these genes is not fully understood. Here, we perform single-nucleus RNA-sequencing (snRNA-seq) on nearly 300,000 nuclei from the parietal cortex of AD autosomal dominant (APP and PSEN1) and risk-modifying variant (APOE, TREM2 and MS4A) carriers. Within individual cell types, we capture genes commonly dysregulated across variant groups. However, specific transcriptional states are more prevalent within variant carriers. TREM2 oligodendrocytes show a dysregulated autophagy-lysosomal pathway, MS4A microglia have dysregulated complement cascade genes, and APOEε4 inhibitory neurons display signs of ferroptosis. All cell types have enriched states in autosomal dominant carriers. We leverage differential expression and single-nucleus ATAC-seq to map GWAS signals to effector cell types including the NCK2 signal to neurons in addition to the initially proposed microglia. Overall, our results provide insights into the transcriptional diversity resulting from AD genetic architecture and cellular heterogeneity. The data can be explored on the online browser ( http://web.hararilab.org/SNARE/ ).
    DOI:  https://doi.org/10.1038/s41467-023-37437-5
  58. Nat Commun. 2023 04 15. 14(1): 2158
    Piezo2 regulates colonic mechanical sensitivity in a sex specific manner in mice.
    Jonathan Madar, Namrata Tiwari, Cristina Smith, Divya Sharma, Shanwei Shen, Alsiddig Elmahdi, Liya Y Qiao.
      The mechanosensitive ion channel Piezo2 in mucosa and primary afferents transduces colonic mechanical sensation. Here we show that chemogenetic activation or nociceptor-targeted deletion of Piezo2 is sufficient to regulate colonic mechanical sensitivity in a sex dependent manner. Clozapine N-oxide-induced activation of Piezo2;hM3Dq-expressing sensory neurons evokes colonic hypersensitivity in male mice, and causes dyspnea in female mice likely due to effects on lung sensory neurons. Activation of Piezo2-expressing colonic afferent neurons also induces colonic hypersensitivity in male but not female mice. Piezo2 levels in nociceptive neurons are higher in female than in male mice. We also show that Piezo2 conditional deletion from nociceptive neurons increases body weight growth, slows colonic transits, and reduces colonic mechanosensing in female but not male mice. Piezo2 deletion blocks colonic hypersensitivity in male but not female mice. These results suggest that Piezo2 in nociceptive neurons mediates innocuous colonic mechanosensing in female mice and painful sensation in male mice, suggesting a sexual dimorphism of Piezo2 function in the colonic sensory system.
    DOI:  https://doi.org/10.1038/s41467-023-37683-7
  59. Nat Commun. 2023 04 17. 14(1): 2180
    Structure and mechanism of the alkane-oxidizing enzyme AlkB.
    Xue Guo, Jianxiu Zhang, Lei Han, Juliet Lee, Shoshana C Williams, Allison Forsberg, Yan Xu, Rachel Narehood Austin, Liang Feng.
      Alkanes are the most energy-rich form of carbon and are widely dispersed in the environment. Their transformation by microbes represents a key step in the global carbon cycle. Alkane monooxygenase (AlkB), a membrane-spanning metalloenzyme, converts straight chain alkanes to alcohols in the first step of the microbially-mediated degradation of alkanes, thereby playing a critical role in the global cycling of carbon and the bioremediation of oil. AlkB biodiversity is attributed to its ability to oxidize alkanes of various chain lengths, while individual AlkBs target a relatively narrow range. Mechanisms of substrate selectivity and catalytic activity remain elusive. Here we report the cryo-EM structure of AlkB, which provides a distinct architecture for membrane enzymes. Our structure and functional studies reveal an unexpected diiron center configuration and identify molecular determinants for substrate selectivity. These findings provide insight into the catalytic mechanism of AlkB and shed light on its function in alkane-degrading microorganisms.
    DOI:  https://doi.org/10.1038/s41467-023-37869-z
  60. Sci Adv. 2023 04 21. 9(16): eadg2239
    Engineering kinetics of TLR7/8 agonist release from bottlebrush prodrugs enables tumor-focused immune stimulation.
    Sachin H Bhagchandani, Farrukh Vohidov, Lauren E Milling, Evelyn Yuzhou Tong, Christopher M Brown, Michelle L Ramseier, Bin Liu, Timothy B Fessenden, Hung V-T Nguyen, Gavin R Kiel, Lori Won, Robert S Langer, Stefani Spranger, Alex K Shalek, Darrell J Irvine, Jeremiah A Johnson.
      Imidazoquinolines (IMDs), such as resiquimod (R848), are of great interest as potential cancer immunotherapies because of their ability to activate Toll-like receptor 7 (TLR7) and/or TLR8 on innate immune cells. Nevertheless, intravenous administration of IMDs causes severe immune-related toxicities, and attempts to improve their tissue-selective exposure while minimizing acute systemic inflammation have proven difficult. Here, using a library of R848 "bottlebrush prodrugs" (BPDs) that differ only by their R848 release kinetics, we explore how the timing of R848 exposure affects immune stimulation in vitro and in vivo. These studies led to the discovery of R848-BPDs that exhibit optimal activation kinetics to achieve potent stimulation of myeloid cells in tumors and substantial reductions in tumor growth following systemic administration in mouse syngeneic tumor models without any observable systemic toxicity. These results suggest that release kinetics can be tuned at the molecular level to provide safe yet effective systemically administered immunostimulant prodrugs for next-generation cancer immunotherapies.
    DOI:  https://doi.org/10.1126/sciadv.adg2239
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