bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022–10–30
seventy papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. Clonal expansion and epigenetic inheritance of long-lasting NK cell memory.
  2. Divergent clonal differentiation trajectories of T cell exhaustion.
  3. Unadjuvanted intranasal spike vaccine elicits protective mucosal immunity against sarbecoviruses.
  4. Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability.
  5. The immune synapses reveal aberrant functions of CD8 T cells during chronic HIV infection.
  6. The type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α.
  7. Thanks for the NK cell memories.
  8. On the lookout for viruses that could leap from animals into humans.
  9. Spatially resolved epigenomic profiling of single cells in complex tissues.
  10. Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR.
  11. REDD1 promotes obesity-induced metabolic dysfunction via atypical NF-κB activation.
  12. Structural mechanism of SGLT1 inhibitors.
  13. Strain level microbial detection and quantification with applications to single cell metagenomics.
  14. The N6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity.
  15. GPR97 triggers inflammatory processes in human neutrophils via a macromolecular complex upstream of PAR2 activation.
  16. Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control.
  17. Zmiz1 is required for mature β-cell function and mass expansion upon high fat feeding.
  18. How to eradicate the next pandemic disease.
  19. Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI.
  20. A noncanonical function of EIF4E limits ALDH1B1 activity and increases susceptibility to ferroptosis.
  21. Fibroblast A20 governs fibrosis susceptibility and its repression by DREAM promotes fibrosis in multiple organs.
  22. Microglia are SYK of Aβ and cell debris.
  23. Human natural killer cells confer protection against HIV-1 infection in humanized mice.
  24. Adoptive T cell therapy cures mice from active hemophagocytic lymphohistiocytosis (HLH).
  25. ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ.
  26. Microglial debris is cleared by astrocytes via C4b-facilitated phagocytosis and degraded via RUBICON-dependent noncanonical autophagy in mice.
  27. Annotation of spatially resolved single-cell data with STELLAR.
  28. Influences of rare copy-number variation on human complex traits.
  29. PTEN checkMAITs type-17 innate-like T cells.
  30. HOIP modulates the stability of GPx4 by linear ubiquitination.
  31. Intramyocardial hemorrhage drives fatty degeneration of infarcted myocardium.
  32. Multifaceted mitochondrial quality control in brown adipose tissue.
  33. Biased signaling due to oligomerization of the G protein-coupled platelet-activating factor receptor.
  34. Ornithine decarboxylase supports ILC3 responses in infectious and autoimmune colitis through positive regulation of IL-22 transcription.
  35. Pharmacological conversion of gut epithelial cells into insulin-producing cells lowers glycemia in diabetic animals.
  36. Intestine-specific removal of DAF-2 nearly doubles lifespan in Caenorhabditis elegans with little fitness cost.
  37. Preparing health-care systems for future pandemics.
  38. Subcellular localization of type IV pili regulates bacterial multicellular development.
  39. Subcellular spatial transcriptomics identifies three mechanistically different classes of localizing RNAs.
  40. Mutated lncRNA increase the risk of type 2 diabetes by promoting β cell dysfunction and insulin resistance.
  41. Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
  42. Kynurenine promotes neonatal heart regeneration by stimulating cardiomyocyte proliferation and cardiac angiogenesis.
  43. PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis.
  44. Evasion of cGAS and TRIM5 defines pandemic HIV.
  45. Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations.
  46. Revealing β-TrCP activity dynamics in live cells with a genetically encoded biosensor.
  47. Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.
  48. The Notch1/CD22 signaling axis disrupts Treg cell function in SARS-CoV2-associated multisystem inflammatory syndrome in children.
  49. Single-agent FOXO1 inhibition normalizes glycemia and induces gut β-like cells in streptozotocin-diabetic mice.
  50. Functional and metabolic alterations of gut microbiota in children with new-onset type 1 diabetes.
  51. The E3 ubiquitin ligase RNF115 regulates phagosome maturation and host response to bacterial infection.
  52. Why are some people more attractive to mosquitoes than others?
  53. Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly.
  54. Phosphorylation of RXRα mediates the effect of JNK to suppress hepatic FGF21 expression and promote metabolic syndrome.
  55. Termination of the unfolded protein response is guided by ER stress-induced HAC1 mRNA nuclear retention.
  56. Multiomics study of nonalcoholic fatty liver disease.
  57. Five ways to prepare for the next pandemic.
  58. Cftr deletion in mouse epithelial and immune cells differentially influence the intestinal microbiota.
  59. Spermidine activates mitochondrial trifunctional protein and improves antitumor immunity in mice.
  60. mTORC1 beyond anabolic metabolism: Regulation of cell death.
  61. Intergenerational nutrition benefits of India's national school feeding program: Reality or a bridge too far?
  62. An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters.
  63. A combined polygenic score of 21,293 rare and 22 common variants improves diabetes diagnosis based on hemoglobin A1C levels.
  64. Mitochondrial transplantation: opportunities and challenges in the treatment of obesity, diabetes, and nonalcoholic fatty liver disease.
  65. A SARM1/mitochondrial feedback loop drives neuropathogenesis in a Charcot-Marie-Tooth disease type 2A rat model.
  66. Gasdermin D restricts anti-tumor immunity during PD-L1 checkpoint blockade.
  67. Resolution doubling in light-sheet microscopy via oblique plane structured illumination.
  68. Metabolic control of CD47 expression through LAT2-mediated amino acid uptake promotes tumor immune evasion.
  69. Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids.
  70. Intra-islet insulin synthesis defects are associated with endoplasmic reticulum stress and loss of beta cell identity in human diabetes.
  1. Nat Immunol. 2022 Oct 26.
    Clonal expansion and epigenetic inheritance of long-lasting NK cell memory.
    Timo Rückert, Caleb A Lareau, Mir-Farzin Mashreghi, Leif S Ludwig, Chiara Romagnani.
      Clonal expansion of cells with somatically diversified receptors and their long-term maintenance as memory cells is a hallmark of adaptive immunity. Here, we studied pathogen-specific adaptation within the innate immune system, tracking natural killer (NK) cell memory to human cytomegalovirus (HCMV) infection. Leveraging single-cell multiomic maps of ex vivo NK cells and somatic mitochondrial DNA mutations as endogenous barcodes, we reveal substantial clonal expansion of adaptive NK cells in HCMV+ individuals. NK cell clonotypes were characterized by a convergent inflammatory memory signature enriched for AP1 motifs superimposed on a private set of clone-specific accessible chromatin regions. NK cell clones were stably maintained in specific epigenetic states over time, revealing that clonal inheritance of chromatin accessibility shapes the epigenetic memory repertoire. Together, we identify clonal expansion and persistence within the human innate immune system, suggesting that these mechanisms have evolved independent of antigen-receptor diversification.
    DOI:  https://doi.org/10.1038/s41590-022-01327-7
  2. Nat Immunol. 2022 Oct 26.
    Divergent clonal differentiation trajectories of T cell exhaustion.
    Bence Daniel, Kathryn E Yost, Sunnie Hsiung, Katalin Sandor, Yu Xia, Yanyan Qi, Kamir J Hiam-Galvez, Mollie Black, Colin J Raposo, Quanming Shi, Stefanie L Meier, Julia A Belk, Josephine R Giles, E John Wherry, Howard Y Chang, Takeshi Egawa, Ansuman T Satpathy.
      Chronic antigen exposure during viral infection or cancer promotes an exhausted T cell (Tex) state with reduced effector function. However, whether all antigen-specific T cell clones follow the same Tex differentiation trajectory remains unclear. Here, we generate a single-cell multiomic atlas of T cell exhaustion in murine chronic viral infection that redefines Tex phenotypic diversity, including two late-stage Tex subsets with either a terminal exhaustion (Texterm) or a killer cell lectin-like receptor-expressing cytotoxic (TexKLR) phenotype. We use paired single-cell RNA and T cell receptor sequencing to uncover clonal differentiation trajectories of Texterm-biased, TexKLR-biased or divergent clones that acquire both phenotypes. We show that high T cell receptor signaling avidity correlates with Texterm, whereas low avidity correlates with effector-like TexKLR fate. Finally, we identify similar clonal differentiation trajectories in human tumor-infiltrating lymphocytes. These findings reveal clonal heterogeneity in the T cell response to chronic antigen that influences Tex fates and persistence.
    DOI:  https://doi.org/10.1038/s41590-022-01337-5
  3. Science. 2022 Oct 27. eabo2523
    Unadjuvanted intranasal spike vaccine elicits protective mucosal immunity against sarbecoviruses.
    Tianyang Mao, Benjamin Israelow, Mario A Peña-Hernández, Alexandra Suberi, Liqun Zhou, Sophia Luyten, Melanie Reschke, Huiping Dong, Robert J Homer, W Mark Saltzman, Akiko Iwasaki.
      The SARS-CoV-2 pandemic has highlighted the need for vaccines that not only prevent disease, but also prevent transmission. Parenteral vaccines induce robust systemic immunity, but poor immunity at the respiratory mucosa. Here we describe the development of a vaccine strategy we term "prime and spike" that leverages existing immunity generated by primary vaccination (prime) to elicit mucosal immune memory within the respiratory tract using unadjuvanted intranasal spike boosters (spike). We show that prime and spike induces robust resident memory B and T cell responses, IgA at the respiratory mucosa, boosts systemic immunity, and completely protects mice with partial immunity from lethal SARS-CoV-2 infection. Using divergent spike proteins, prime and spike enables induction of cross-reactive immunity against sarbecoviruses.
    DOI:  https://doi.org/10.1126/science.abo2523
  4. Nat Commun. 2022 Oct 22. 13(1): 6301
    Epigenetic control of chromosome-associated lncRNA genes essential for replication and stability.
    Michael B Heskett, Athanasios E Vouzas, Leslie G Smith, Phillip A Yates, Christopher Boniface, Eric E Bouhassira, Paul T Spellman, David M Gilbert, Mathew J Thayer.
      ASARs are long noncoding RNA genes that control replication timing of entire human chromosomes in cis. The three known ASAR genes are located on human chromosomes 6 and 15, and are essential for chromosome integrity. To identify ASARs on all human chromosomes we utilize a set of distinctive ASAR characteristics that allow for the identification of hundreds of autosomal loci with epigenetically controlled, allele-restricted behavior in expression and replication timing of coding and noncoding genes, and is distinct from genomic imprinting. Disruption of noncoding RNA genes at five of five tested loci result in chromosome-wide delayed replication and chromosomal instability, validating their ASAR activity. In addition to the three known essential cis-acting chromosomal loci, origins, centromeres, and telomeres, we propose that all mammalian chromosomes also contain "Inactivation/Stability Centers" that display allele-restricted epigenetic regulation of protein coding and noncoding ASAR genes that are essential for replication and stability of each chromosome.
    DOI:  https://doi.org/10.1038/s41467-022-34099-7
  5. Nat Commun. 2022 Oct 28. 13(1): 6436
    The immune synapses reveal aberrant functions of CD8 T cells during chronic HIV infection.
    Nadia Anikeeva, Maria Steblyanko, Leticia Kuri-Cervantes, Marcus Buggert, Michael R Betts, Yuri Sykulev.
      Chronic HIV infection causes persistent low-grade inflammation that induces premature aging of the immune system including senescence of memory and effector CD8 T cells. To uncover the reasons of gradually diminished potency of CD8 T cells from people living with HIV, here we expose the T cells to planar lipid bilayers containing ligands for T-cell receptor and a T-cell integrins and analyze the cellular morphology, dynamics of synaptic interface formation and patterns of the cellular degranulation. We find a large fraction of phenotypically naive T cells from chronically infected people are capable to form mature synapse with focused degranulation, a signature of a differentiated T cells. Further, differentiation of aberrant naive T cells may lead to the development of anomalous effector T cells undermining their capacity to control HIV and other pathogens that could be contained otherwise.
    DOI:  https://doi.org/10.1038/s41467-022-34157-0
  6. Nat Commun. 2022 Oct 26. 13(1): 6363
    The type 1 diabetes gene TYK2 regulates β-cell development and its responses to interferon-α.
    Vikash Chandra, Hazem Ibrahim, Clémentine Halliez, Rashmi B Prasad, Federica Vecchio, Om Prakash Dwivedi, Jouni Kvist, Diego Balboa, Jonna Saarimäki-Vire, Hossam Montaser, Tom Barsby, Väinö Lithovius, Isabella Artner, Swetha Gopalakrishnan, Leif Groop, Roberto Mallone, Decio L Eizirik, Timo Otonkoski.
      Type 1 diabetes (T1D) is an autoimmune disease that results in the destruction of insulin producing pancreatic β-cells. One of the genes associated with T1D is TYK2, which encodes a Janus kinase with critical roles in type-Ι interferon (IFN-Ι) mediated intracellular signalling. To study the role of TYK2 in β-cell development and response to IFNα, we generated TYK2 knockout human iPSCs and directed them into the pancreatic endocrine lineage. Here we show that loss of TYK2 compromises the emergence of endocrine precursors by regulating KRAS expression, while mature stem cell-islets (SC-islets) function is not affected. In the SC-islets, the loss or inhibition of TYK2 prevents IFNα-induced antigen processing and presentation, including MHC Class Ι and Class ΙΙ expression, enhancing their survival against CD8+ T-cell cytotoxicity. These results identify an unsuspected role for TYK2 in β-cell development and support TYK2 inhibition in adult β-cells as a potent therapeutic target to halt T1D progression.
    DOI:  https://doi.org/10.1038/s41467-022-34069-z
  7. Nat Immunol. 2022 Oct 26.
    Thanks for the NK cell memories.
    Simon Grassmann, Joseph C Sun.
      
    DOI:  https://doi.org/10.1038/s41590-022-01336-6
  8. Nature. 2022 10;610(7933): S41
    On the lookout for viruses that could leap from animals into humans.
    Simon Makin.
      
    Keywords:  Infection; Virology
    DOI:  https://doi.org/10.1038/d41586-022-03357-5
  9. Cell. 2022 Oct 14. pii: S0092-8674(22)01254-5. [Epub ahead of print]
    Spatially resolved epigenomic profiling of single cells in complex tissues.
    Tian Lu, Cheen Euong Ang, Xiaowei Zhuang.
      The recent development of spatial omics methods has enabled single-cell profiling of the transcriptome and 3D genome organization with high spatial resolution. Expanding the repertoire of spatial omics tools, a spatially resolved single-cell epigenomics method will accelerate understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved epigenomic profiling of single cells using in situ tagmentation and transcription followed by multiplexed imaging. We demonstrated the ability to profile histone modifications marking active promoters, putative enhancers, and silent promoters in individual cells, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results suggested putative promoter-enhancer pairs and enhancer hubs regulating developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
    Keywords:  MERFISH; brain; development; enhancer; enhancer hub; enhancer-promoter interaction; epigenomic MERFISH; promoter; single-cell epigenomics; spatial epigenomic
    DOI:  https://doi.org/10.1016/j.cell.2022.09.035
  10. Nat Biotechnol. 2022 Oct 27.
    Programmable eukaryotic protein synthesis with RNA sensors by harnessing ADAR.
    Kaiyi Jiang, Jeremy Koob, Xi Dawn Chen, Rohan N Krajeski, Yifan Zhang, Verena Volf, Wenyuan Zhou, Samantha R Sgrizzi, Lukas Villiger, Jonathan S Gootenberg, Fei Chen, Omar O Abudayyeh.
      Programmable approaches to sense and respond to the presence of specific RNAs in biological systems have broad applications in research, diagnostics, and therapeutics. Here we engineer a programmable RNA-sensing technology, reprogrammable ADAR sensors (RADARS), which harnesses RNA editing by adenosine deaminases acting on RNA (ADAR) to gate translation of a cargo protein by the presence of endogenous RNA transcripts. Introduction of a stop codon in a guide upstream of the cargo makes translation contingent on binding of an endogenous transcript to the guide, leading to ADAR editing of the stop codon and allowing translational readthrough. Through systematic sensor engineering, we achieve 277 fold improvement in sensor activation and engineer RADARS with diverse cargo proteins, including luciferases, fluorescent proteins, recombinases, and caspases, enabling detection sensitivity on endogenous transcripts expressed at levels as low as 13 transcripts per million. We show that RADARS are functional as either expressed DNA or synthetic mRNA and with either exogenous or endogenous ADAR. We apply RADARS in multiple contexts, including tracking transcriptional states, RNA-sensing-induced cell death, cell-type identification, and control of synthetic mRNA translation.
    DOI:  https://doi.org/10.1038/s41587-022-01534-5
  11. Nat Commun. 2022 Oct 22. 13(1): 6303
    REDD1 promotes obesity-induced metabolic dysfunction via atypical NF-κB activation.
    Dong-Keon Lee, Taesam Kim, Junyoung Byeon, Minsik Park, Suji Kim, Joohwan Kim, Seunghwan Choi, Gihwan Lee, Chanin Park, Keun Woo Lee, Yong Jung Kwon, Jeong-Hyung Lee, Young-Guen Kwon, Young-Myeong Kim.
      Regulated in development and DNA damage response 1 (REDD1) expression is upregulated in response to metabolic imbalance and obesity. However, its role in obesity-associated complications is unclear. Here, we demonstrate that the REDD1-NF-κB axis is crucial for metabolic inflammation and dysregulation. Mice lacking Redd1 in the whole body or adipocytes exhibited restrained diet-induced obesity, inflammation, insulin resistance, and hepatic steatosis. Myeloid Redd1-deficient mice showed similar results, without restrained obesity and hepatic steatosis. Redd1-deficient adipose-derived stem cells lost their potential to differentiate into adipocytes; however, REDD1 overexpression stimulated preadipocyte differentiation and proinflammatory cytokine expression through atypical IKK-independent NF-κB activation by sequestering IκBα from the NF-κB/IκBα complex. REDD1 with mutated Lys219/220Ala, key amino acid residues for IκBα binding, could not stimulate NF-κB activation, adipogenesis, and inflammation in vitro and prevented obesity-related phenotypes in knock-in mice. The REDD1-atypical NF-κB activation axis is a therapeutic target for obesity, meta-inflammation, and metabolic complications.
    DOI:  https://doi.org/10.1038/s41467-022-34110-1
  12. Nat Commun. 2022 Oct 28. 13(1): 6440
    Structural mechanism of SGLT1 inhibitors.
    Yange Niu, Wenhao Cui, Rui Liu, Sanshan Wang, Han Ke, Xiaoguang Lei, Lei Chen.
      Sodium glucose co-transporters (SGLT) harness the electrochemical gradient of sodium to drive the uphill transport of glucose across the plasma membrane. Human SGLT1 (hSGLT1) plays a key role in sugar uptake from food and its inhibitors show promise in the treatment of several diseases. However, the inhibition mechanism for hSGLT1 remains elusive. Here, we present the cryo-EM structure of the hSGLT1-MAP17 hetero-dimeric complex in the presence of the high-affinity inhibitor LX2761. LX2761 locks the transporter in an outward-open conformation by wedging inside the substrate-binding site and the extracellular vestibule of hSGLT1. LX2761 blocks the putative water permeation pathway of hSGLT1. The structure also uncovers the conformational changes of hSGLT1 during transitions from outward-open to inward-open states.
    DOI:  https://doi.org/10.1038/s41467-022-33421-7
  13. Nat Commun. 2022 Oct 28. 13(1): 6430
    Strain level microbial detection and quantification with applications to single cell metagenomics.
    Kaiyuan Zhu, Alejandro A Schäffer, Welles Robinson, Junyan Xu, Eytan Ruppin, A Funda Ergun, Yuzhen Ye, S Cenk Sahinalp.
      Computational identification and quantification of distinct microbes from high throughput sequencing data is crucial for our understanding of human health. Existing methods either use accurate but computationally expensive alignment-based approaches or less accurate but computationally fast alignment-free approaches, which often fail to correctly assign reads to genomes. Here we introduce CAMMiQ, a combinatorial optimization framework to identify and quantify distinct genomes (specified by a database) in a metagenomic dataset. As a key methodological innovation, CAMMiQ uses substrings of variable length and those that appear in two genomes in the database, as opposed to the commonly used fixed-length, unique substrings. These substrings allow to accurately decouple mixtures of highly similar genomes resulting in higher accuracy than the leading alternatives, without requiring additional computational resources, as demonstrated on commonly used benchmarking datasets. Importantly, we show that CAMMiQ can distinguish closely related bacterial strains in simulated metagenomic and real single-cell metatranscriptomic data.
    DOI:  https://doi.org/10.1038/s41467-022-33869-7
  14. Nat Commun. 2022 Oct 28. 13(1): 6435
    The N6-methyladenosine methyltransferase METTL16 enables erythropoiesis through safeguarding genome integrity.
    Masanori Yoshinaga, Kyuho Han, David W Morgens, Takuro Horii, Ryosuke Kobayashi, Tatsuaki Tsuruyama, Fabian Hia, Shota Yasukura, Asako Kajiya, Ting Cai, Pedro H C Cruz, Alexis Vandenbon, Yutaka Suzuki, Yukio Kawahara, Izuho Hatada, Michael C Bassik, Osamu Takeuchi.
      During erythroid differentiation, the maintenance of genome integrity is key for the success of multiple rounds of cell division. However, molecular mechanisms coordinating the expression of DNA repair machinery in erythroid progenitors are poorly understood. Here, we discover that an RNA N6-methyladenosine (m6A) methyltransferase, METTL16, plays an essential role in proper erythropoiesis by safeguarding genome integrity via the control of DNA-repair-related genes. METTL16-deficient erythroblasts exhibit defective differentiation capacity, DNA damage and activation of the apoptotic program. Mechanistically, METTL16 controls m6A deposition at the structured motifs in DNA-repair-related transcripts including Brca2 and Fancm mRNAs, thereby upregulating their expression. Furthermore, a pairwise CRISPRi screen revealed that the MTR4-nuclear RNA exosome complex is involved in the regulation of METTL16 substrate mRNAs in erythroblasts. Collectively, our study uncovers that METTL16 and the MTR4-nuclear RNA exosome act as essential regulatory machinery to maintain genome integrity and erythropoiesis.
    DOI:  https://doi.org/10.1038/s41467-022-34078-y
  15. Nat Commun. 2022 Oct 27. 13(1): 6385
    GPR97 triggers inflammatory processes in human neutrophils via a macromolecular complex upstream of PAR2 activation.
    Tai-Ying Chu, Céline Zheng-Gérard, Kuan-Yeh Huang, Yu-Chi Chang, Ying-Wen Chen, Kuan-Yu I, Yu-Ling Lo, Nien-Yi Chiang, Hsin-Yi Chen, Martin Stacey, Siamon Gordon, Wen-Yi Tseng, Chiao-Yin Sun, Yen-Mu Wu, Yi-Shin Pan, Chien-Hao Huang, Chun-Yen Lin, Tse-Ching Chen, Kamel El Omari, Marilina Antonelou, Scott R Henderson, Alan Salama, Elena Seiradake, Hsi-Hsien Lin.
      Neutrophils play essential anti-microbial and inflammatory roles in host defense, however, their activities require tight regulation as dysfunction often leads to detrimental inflammatory and autoimmune diseases. Here we show that the adhesion molecule GPR97 allosterically activates CD177-associated membrane proteinase 3 (mPR3), and in conjugation with several protein interaction partners leads to neutrophil activation in humans. Crystallographic and deletion analysis of the GPR97 extracellular region identified two independent mPR3-binding domains. Mechanistically, the efficient binding and activation of mPR3 by GPR97 requires the macromolecular CD177/GPR97/PAR2/CD16b complex and induces the activation of PAR2, a G protein-coupled receptor known for its function in inflammation. Triggering PAR2 by the upstream complex leads to strong inflammatory activation, prompting anti-microbial activities and endothelial dysfunction. The role of the complex in pathologic inflammation is underscored by the finding that both GPR97 and mPR3 are upregulated on the surface of disease-associated neutrophils. In summary, we identify a PAR2 activation mechanism that directs neutrophil activation, and thus inflammation. The PR3/CD177/GPR97/PAR2/CD16b protein complex, therefore, represents a potential therapeutic target for neutrophil-mediated inflammatory diseases.
    DOI:  https://doi.org/10.1038/s41467-022-34083-1
  16. Nat Commun. 2022 Oct 27. 13(1): 6406
    Human mtRF1 terminates COX1 translation and its ablation induces mitochondrial ribosome-associated quality control.
    Franziska Nadler, Elena Lavdovskaia, Angelique Krempler, Luis Daniel Cruz-Zaragoza, Sven Dennerlein, Ricarda Richter-Dennerlein.
      Translation termination requires release factors that read a STOP codon in the decoding center and subsequently facilitate the hydrolysis of the nascent peptide chain from the peptidyl tRNA within the ribosome. In human mitochondria eleven open reading frames terminate in the standard UAA or UAG STOP codon, which can be recognized by mtRF1a, the proposed major mitochondrial release factor. However, two transcripts encoding for COX1 and ND6 terminate in the non-conventional AGA or AGG codon, respectively. How translation termination is achieved in these two cases is not known. We address this long-standing open question by showing that the non-canonical release factor mtRF1 is a specialized release factor that triggers COX1 translation termination, while mtRF1a terminates the majority of other mitochondrial translation events including the non-canonical ND6. Loss of mtRF1 leads to isolated COX deficiency and activates the mitochondrial ribosome-associated quality control accompanied by the degradation of COX1 mRNA to prevent an overload of the ribosome rescue system. Taken together, these results establish the role of mtRF1 in mitochondrial translation, which had been a mystery for decades, and lead to a comprehensive picture of translation termination in human mitochondria.
    DOI:  https://doi.org/10.1038/s41467-022-34088-w
  17. Mol Metab. 2022 Oct 25. pii: S2212-8778(22)00190-9. [Epub ahead of print] 101621
    Zmiz1 is required for mature β-cell function and mass expansion upon high fat feeding.
    Tamadher A Alghamdi, Nicole A J Krentz, Nancy Smith, Aliya F Spigelman, Varsha Rajesh, Alok Jha, Mourad Ferdaoussi, Kunimasa Suzuki, Jing Yang, Jocelyn E Manning Fox, Han Sun, Zijie Sun, Anna L Gloyn, Patrick E MacDonald.
       OBJECTIVE: Identifying the transcripts which mediate genetic association signals for type 2 diabetes (T2D) is critical to understand disease mechanisms. Studies in pancreatic islets support the transcription factor ZMIZ1 as a transcript underlying a T2D GWAS signal, but how it influences T2D risk is unknown.
    METHODS: β-cell-specific Zmiz1 knockout (Zmiz1βKO) mice were generated and phenotypically characterised. Glucose homeostasis was assessed in Zmiz1βKO mice and their control littermates on chow diet (CD) and high fat diet (HFD). Islet morphology and function were examined by immunocytochemistry and in vitro islet function was assessed by dynamic insulin secretion assay. Transcript and protein expression were assessed by RNA sequencing and Western blotting. In islets isolated from genotyped human donors, we assessed glucose-dependent insulin secretion and islet insulin content by static incubation assay.
    RESULTS: Male and female Zmiz1βKO mice were glucose intolerant with impaired insulin secretion, compared with control littermates. Transcriptomic profiling of Zmiz1βKO islets identified over 500 differentially expressed genes including those involved in β-cell function and maturity, which we confirmed at the protein level. Upon HFD, Zmiz1βKO mice fail to expand β-cell mass and become severely diabetic. Human islets from carriers of the ZMIZ1-linked T2D-risk alleles have reduced islet insulin content and glucose-stimulated insulin secretion.
    CONCLUSIONS: β-cell Zmiz1 is required for normal glucose homeostasis. Genetic variation at the ZMIZ1 locus may influence T2D-risk by reducing islet mass expansion upon metabolic stress and the ability to maintain a mature β-cell state.
    Keywords:  diabetes; insulin; islets of Langerhans; secretion
    DOI:  https://doi.org/10.1016/j.molmet.2022.101621
  18. Nature. 2022 10;610(7933): S48-S49
    How to eradicate the next pandemic disease.
    Sam Jones.
      
    Keywords:  Diseases; History; Infection; Public health; Virology
    DOI:  https://doi.org/10.1038/d41586-022-03361-9
  19. Nat Biotechnol. 2022 Oct 27.
    Absolute quantification of single-base m6A methylation in the mammalian transcriptome using GLORI.
    Cong Liu, Hanxiao Sun, Yunpeng Yi, Weiguo Shen, Kai Li, Ye Xiao, Fei Li, Yuchen Li, Yongkang Hou, Bo Lu, Wenqing Liu, Haowei Meng, Jinying Peng, Chengqi Yi, Jing Wang.
      N6-methyladenosine (m6A) is the most abundant RNA modification in mammalian cells and the best-studied epitranscriptomic mark. Despite the development of various tools to map m6A, a transcriptome-wide method that enables absolute quantification of m6A at single-base resolution is lacking. Here we use glyoxal and nitrite-mediated deamination of unmethylated adenosines (GLORI) to develop an absolute m6A quantification method that is conceptually similar to bisulfite-sequencing-based quantification of DNA 5-methylcytosine. We apply GLORI to quantify the m6A methylomes of mouse and human cells and reveal clustered m6A modifications with differential distribution and stoichiometry. In addition, we characterize m6A dynamics under stress and examine the quantitative landscape of m6A modification in gene expression regulation. GLORI is an unbiased, convenient method for the absolute quantification of the m6A methylome.
    DOI:  https://doi.org/10.1038/s41587-022-01487-9
  20. Nat Commun. 2022 Oct 23. 13(1): 6318
    A noncanonical function of EIF4E limits ALDH1B1 activity and increases susceptibility to ferroptosis.
    Xin Chen, Jun Huang, Chunhua Yu, Jiao Liu, Wanli Gao, Jingbo Li, Xinxin Song, Zhuan Zhou, Changfeng Li, Yangchun Xie, Guido Kroemer, Jinbao Liu, Daolin Tang, Rui Kang.
      Ferroptosis is a type of lipid peroxidation-dependent cell death that is emerging as a therapeutic target for cancer. However, the mechanisms of ferroptosis during the generation and detoxification of lipid peroxidation products remain rather poorly defined. Here, we report an unexpected role for the eukaryotic translation initiation factor EIF4E as a determinant of ferroptotic sensitivity by controlling lipid peroxidation. A drug screening identified 4EGI-1 and 4E1RCat (previously known as EIF4E-EIF4G1 interaction inhibitors) as powerful inhibitors of ferroptosis. Genetic and functional studies showed that EIF4E (but not EIF4G1) promotes ferroptosis in a translation-independent manner. Using mass spectrometry and subsequent protein-protein interaction analysis, we identified EIF4E as an endogenous repressor of ALDH1B1 in mitochondria. ALDH1B1 belongs to the family of aldehyde dehydrogenases and may metabolize the aldehyde substrate 4-hydroxynonenal (4HNE) at high concentrations. Supraphysiological levels of 4HNE triggered ferroptosis, while low concentrations of 4HNE increased the cell susceptibility to classical ferroptosis inducers by activating the NOX1 pathway. Accordingly, EIF4E-dependent ALDH1B1 inhibition enhanced the anticancer activity of ferroptosis inducers in vitro and in vivo. Our results support a key function of EIF4E in orchestrating lipid peroxidation to ignite ferroptosis.
    DOI:  https://doi.org/10.1038/s41467-022-34096-w
  21. Nat Commun. 2022 Oct 26. 13(1): 6358
    Fibroblast A20 governs fibrosis susceptibility and its repression by DREAM promotes fibrosis in multiple organs.
    Wenxia Wang, Swarna Bale, Jun Wei, Bharath Yalavarthi, Dibyendu Bhattacharyya, Jing Jing Yan, Hiam Abdala-Valencia, Dan Xu, Hanshi Sun, Roberta G Marangoni, Erica Herzog, Sergejs Berdnikovs, Stephen D Miller, Amr H Sawalha, Pei-Suen Tsou, Kentaro Awaji, Takashi Yamashita, Shinichi Sato, Yoshihide Asano, Chinnaswamy Tiruppathi, Anjana Yeldandi, Bettina C Schock, Swati Bhattacharyya, John Varga.
      In addition to autoimmune and inflammatory diseases, variants of the TNFAIP3 gene encoding the ubiquitin-editing enzyme A20 are also associated with fibrosis in systemic sclerosis (SSc). However, it remains unclear how genetic factors contribute to SSc pathogenesis, and which cell types drive the disease due to SSc-specific genetic alterations. We therefore characterize the expression, function, and role of A20, and its negative transcriptional regulator DREAM, in patients with SSc and disease models. Levels of A20 are significantly reduced in SSc skin and lungs, while DREAM is elevated. In isolated fibroblasts, A20 mitigates ex vivo profibrotic responses. Mice haploinsufficient for A20, or harboring fibroblasts-specific A20 deletion, recapitulate major pathological features of SSc, whereas DREAM-null mice with elevated A20 expression are protected. In DREAM-null fibroblasts, TGF-β induces the expression of A20, compared to wild-type fibroblasts. An anti-fibrotic small molecule targeting cellular adiponectin receptors stimulates A20 expression in vitro in wild-type but not A20-deficient fibroblasts and in bleomycin-treated mice. Thus, A20 has a novel cell-intrinsic function in restraining fibroblast activation, and together with DREAM, constitutes a critical regulatory network governing the fibrotic process in SSc. A20 and DREAM represent novel druggable targets for fibrosis therapy.
    DOI:  https://doi.org/10.1038/s41467-022-33767-y
  22. Cell. 2022 Oct 27. pii: S0092-8674(22)01262-4. [Epub ahead of print]185(22): 4043-4045
    Microglia are SYK of Aβ and cell debris.
    Dorothy P Schafer, Jacob M Stillman.
      During neurodegenerative disease, resident CNS macrophages termed "microglia" assume a neuroprotective role and engulf toxic protein aggregates and cell debris. In this issue of Cell, two groups independently show how spleen tyrosine kinase (SYK) acts downstream of microglial surface receptors to propagate this neuroprotective program in vivo.
    DOI:  https://doi.org/10.1016/j.cell.2022.09.043
  23. J Clin Invest. 2022 Oct 25. pii: e162694. [Epub ahead of print]
    Human natural killer cells confer protection against HIV-1 infection in humanized mice.
    Can M Sungur, Qiankun Wang, Ayşe N Ozantürk, Hongbo Gao, Aaron J Schmitz, Marina Cella, Wayne M Yokoyama, Liang Shan.
      The role of natural killer (NK) cells against HIV-1 infections remains to be elucidated in vivo. While humanized mouse models potentially could be used to directly evaluate humans NK cell responses during HIV-1 infection, improved functional development of human NK cells in these hosts is needed. Here we report the humanized MISTRG-6-15 mouse model, in which NK cells were quick to expand and exhibit degranulation, cytotoxicity, and pro-inflammatory cytokine production in non-lymphoid organs upon HIV-1 infection, but had reduced functionality in lymphoid organs. Although HIV-1 infection induced functional impairment of NK cells, antiretroviral therapy reinvigorated NK cells in response to HIV-1 rebound after analytic treatment interruption. Moreover, a broadly neutralizing antibody PGT121 enhanced NK cell function in vivo, consistent with antibody-dependent cellular cytotoxicity. Monoclonal antibody depletion of NK cells resulted in higher viral loads in multiple non-lymphoid organs. Overall, our results in humanized MISTRG-6-15 mice demonstrated that NK cells provided direct anti-HIV-1 responses in vivo but were limited in their responses in lymphoid organs.
    Keywords:  Immunology; NK cells
    DOI:  https://doi.org/10.1172/JCI162694
  24. EMBO Mol Med. 2022 Oct 24. e16085
    Adoptive T cell therapy cures mice from active hemophagocytic lymphohistiocytosis (HLH).
    Kristoffer Weißert, Sandra Ammann, Tamara Kögl, Viviane Dettmer-Monaco, Christoph Schell, Toni Cathomen, Stephan Ehl, Peter Aichele.
      Primary hemophagocytic lymphohistiocytosis (HLH) is a hyperinflammatory syndrome caused by impaired lymphocyte cytotoxicity. First-line therapeutic regimens directed against activated immune cells or secreted cytokines show limited efficacy since they do not target the underlying immunological problem: defective lymphocyte cytotoxicity causing prolonged immune stimulation. A potential rescue strategy would be the adoptive transfer of ex vivo gene-corrected autologous T cells. However, transfusion of cytotoxicity-competent T cells under conditions of hyperinflammation may cause more harm than benefit. As a proof-of-concept for adoptive T cell therapy (ATCT) under hyperinflammatory conditions, we transferred syngeneic, cytotoxicity-competent T cells into mice with virally triggered active primary HLH. ATCT with functional syngeneic trigger-specific T cells cured Jinx mice from active HLH without life-threatening side effects and protected Perforin-deficient mice from lethal HLH progression by reconstituting cytotoxicity. Cured mice were protected long-term from HLH relapses. A threshold frequency of transferred T cells with functional differentiation was identified as a predictive biomarker for long-term survival. This study is the first proof-of-concept for ATCT in active HLH.
    Keywords:  adoptive T cell therapy; hemophagocytic lymphohistiocytosis; hyperinflammation; virus-specific T cells
    DOI:  https://doi.org/10.15252/emmm.202216085
  25. Nat Methods. 2022 Oct 24.
    ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ.
    Ian Dardani, Benjamin L Emert, Yogesh Goyal, Connie L Jiang, Amanpreet Kaur, Jasmine Lee, Sara H Rouhanifard, Gretchen M Alicea, Mitchell E Fane, Min Xiao, Meenhard Herlyn, Ashani T Weeraratna, Arjun Raj.
      RNA labeling in situ has enormous potential to visualize transcripts and quantify their levels in single cells, but it remains challenging to produce high levels of signal while also enabling multiplexed detection of multiple RNA species simultaneously. Here, we describe clampFISH 2.0, a method that uses an inverted padlock design to efficiently detect many RNA species and exponentially amplify their signals at once, while also reducing the time and cost compared with the prior clampFISH method. We leverage the increased throughput afforded by multiplexed signal amplification and sequential detection to detect 10 different RNA species in more than 1 million cells. We also show that clampFISH 2.0 works in tissue sections. We expect that the advantages offered by clampFISH 2.0 will enable many applications in spatial transcriptomics.
    DOI:  https://doi.org/10.1038/s41592-022-01653-6
  26. Nat Commun. 2022 Oct 24. 13(1): 6233
    Microglial debris is cleared by astrocytes via C4b-facilitated phagocytosis and degraded via RUBICON-dependent noncanonical autophagy in mice.
    Tian Zhou, Yuxin Li, Xiaoyu Li, Fanzhuo Zeng, Yanxia Rao, Yang He, Yafei Wang, Meizhen Liu, Dali Li, Zhen Xu, Xin Zhou, Siling Du, Fugui Niu, Jiyun Peng, Xifan Mei, Sheng-Jian Ji, Yousheng Shu, Wei Lu, Feifan Guo, Tianzhun Wu, Ti-Fei Yuan, Ying Mao, Bo Peng.
      Microglia are important immune cells in the central nervous system (CNS) that undergo turnover throughout the lifespan. If microglial debris is not removed in a timely manner, accumulated debris may influence CNS function. Clearance of microglial debris is crucial for CNS homeostasis. However, underlying mechanisms remain obscure. We here investigate how dead microglia are removed. We find that although microglia can phagocytose microglial debris in vitro, the territory-dependent competition hinders the microglia-to-microglial debris engulfment in vivo. In contrast, microglial debris is mainly phagocytosed by astrocytes in the brain, facilitated by C4b opsonization. The engulfed microglial fragments are then degraded in astrocytes via RUBICON-dependent LC3-associated phagocytosis (LAP), a form of noncanonical autophagy. Interference with C4b-mediated engulfment and subsequent LAP disrupt the removal and degradation of microglial debris, respectively. Together, we elucidate the cellular and molecular mechanisms of microglial debris removal in mice, extending the knowledge on the maintenance of CNS homeostasis.
    DOI:  https://doi.org/10.1038/s41467-022-33932-3
  27. Nat Methods. 2022 Oct 24.
    Annotation of spatially resolved single-cell data with STELLAR.
    Maria Brbić, Kaidi Cao, John W Hickey, Yuqi Tan, Michael P Snyder, Garry P Nolan, Jure Leskovec.
      Accurate cell-type annotation from spatially resolved single cells is crucial to understand functional spatial biology that is the basis of tissue organization. However, current computational methods for annotating spatially resolved single-cell data are typically based on techniques established for dissociated single-cell technologies and thus do not take spatial organization into account. Here we present STELLAR, a geometric deep learning method for cell-type discovery and identification in spatially resolved single-cell datasets. STELLAR automatically assigns cells to cell types present in the annotated reference dataset and discovers novel cell types and cell states. STELLAR transfers annotations across different dissection regions, different tissues and different donors, and learns cell representations that capture higher-order tissue structures. We successfully applied STELLAR to CODEX multiplexed fluorescent microscopy data and multiplexed RNA imaging datasets. Within the Human BioMolecular Atlas Program, STELLAR has annotated 2.6 million spatially resolved single cells with dramatic time savings.
    DOI:  https://doi.org/10.1038/s41592-022-01651-8
  28. Cell. 2022 Oct 27. pii: S0092-8674(22)01247-8. [Epub ahead of print]185(22): 4233-4248.e27
    Influences of rare copy-number variation on human complex traits.
    Margaux L A Hujoel, Maxwell A Sherman, Alison R Barton, Ronen E Mukamel, Vijay G Sankaran, Chikashi Terao, Po-Ru Loh.
      The human genome contains hundreds of thousands of regions harboring copy-number variants (CNV). However, the phenotypic effects of most such polymorphisms are unknown because only larger CNVs have been ascertainable from SNP-array data generated by large biobanks. We developed a computational approach leveraging haplotype sharing in biobank cohorts to more sensitively detect CNVs. Applied to UK Biobank, this approach accounted for approximately half of all rare gene inactivation events produced by genomic structural variation. This CNV call set enabled a detailed analysis of associations between CNVs and 56 quantitative traits, identifying 269 independent associations (p < 5 × 10-8) likely to be causally driven by CNVs. Putative target genes were identifiable for nearly half of the loci, enabling insights into dosage sensitivity of these genes and uncovering several gene-trait relationships. These results demonstrate the ability of haplotype-informed analysis to provide insights into the genetic basis of human complex traits.
    Keywords:  Complex traits; Copy-number variants; Genetic associations; Haplotypes; Structural variation
    DOI:  https://doi.org/10.1016/j.cell.2022.09.028
  29. Nat Cell Biol. 2022 Oct 27.
    PTEN checkMAITs type-17 innate-like T cells.
    Nikolaos Patsoukis, Vassiliki A Boussiotis.
      
    DOI:  https://doi.org/10.1038/s41556-022-01012-9
  30. Proc Natl Acad Sci U S A. 2022 Nov;119(44): e2214227119
    HOIP modulates the stability of GPx4 by linear ubiquitination.
    Kangyun Dong, Ran Wei, Taijie Jin, Mengmeng Zhang, Jiali Shen, Huaijiang Xiang, Bing Shan, Junying Yuan, Ying Li.
      LUBAC-mediated linear ubiquitination plays a pivotal role in regulation of cell death and inflammatory pathways. Genetic deficiency in LUBAC components leads to severe immune dysfunction or embryonic lethality. LUBAC has been extensively studied for its role in mediating TNF signaling. However, Tnfr1 knockout is not able to fully rescue the embryonic lethality of LUBAC deficiency, suggesting that LUBAC may modify additional key cellular substrates in promoting cell survival. GPx4 is an important selenoprotein involved in regulating cellular redox homeostasis in defense against lipid peroxidation-mediated cell death known as ferroptosis. Here we demonstrate that LUBAC deficiency sensitizes to ferroptosis by promoting GPx4 degradation and downstream lipid peroxidation. LUBAC binds and stabilizes GPx4 by modulating its linear ubiquitination both in normal condition and under oxidative stress. Our findings identify GPx4 as a key substrate of LUBAC and a previously unrecognized role of LUBAC-mediated linear ubiquitination in regulating cellular redox status and cell death.
    Keywords:  GPx4; LUBAC; TNF; ferroptosis
    DOI:  https://doi.org/10.1073/pnas.2214227119
  31. Nat Commun. 2022 Oct 27. 13(1): 6394
    Intramyocardial hemorrhage drives fatty degeneration of infarcted myocardium.
    Ivan Cokic, Shing Fai Chan, Xingmin Guan, Anand R Nair, Hsin-Jung Yang, Ting Liu, Yinyin Chen, Diego Hernando, Jane Sykes, Richard Tang, John Butler, Alice Dohnalkova, Libor Kovarik, Robert Finney, Avinash Kali, Behzad Sharif, Louis S Bouchard, Rajesh Gupta, Mayil Singaram Krishnam, Keyur Vora, Balaji Tamarappoo, Andrew G Howarth, Andreas Kumar, Joseph Francis, Scott B Reeder, John C Wood, Frank S Prato, Rohan Dharmakumar.
      Sudden blockage of arteries supplying the heart muscle contributes to millions of heart attacks (myocardial infarction, MI) around the world. Although re-opening these arteries (reperfusion) saves MI patients from immediate death, approximately 50% of these patients go on to develop chronic heart failure (CHF) and die within a 5-year period; however, why some patients accelerate towards CHF while others do not remains unclear. Here we show, using large animal models of reperfused MI, that intramyocardial hemorrhage - the most damaging form of reperfusion injury (evident in nearly 40% of reperfused ST-elevation MI patients) - drives delayed infarct healing and is centrally responsible for continuous fatty degeneration of the infarcted myocardium contributing to adverse remodeling of the heart. Specifically, we show that the fatty degeneration of the hemorrhagic MI zone stems from iron-induced macrophage activation, lipid peroxidation, foam cell formation, ceroid production, foam cell apoptosis and iron recycling. We also demonstrate that timely reduction of iron within the hemorrhagic MI zone reduces fatty infiltration and directs the heart towards favorable remodeling. Collectively, our findings elucidate why some, but not all, MIs are destined to CHF and help define a potential therapeutic strategy to mitigate post-MI CHF independent of MI size.
    DOI:  https://doi.org/10.1038/s41467-022-33776-x
  32. Trends Cell Biol. 2022 Oct 19. pii: S0962-8924(22)00230-6. [Epub ahead of print]
    Multifaceted mitochondrial quality control in brown adipose tissue.
    Katia Aquilano, Beiyan Zhou, Jonathan R Brestoff, Daniele Lettieri-Barbato.
      Brown adipose tissue (BAT) controls mammalian core body temperature by non-shivering thermogenesis. BAT is extraordinarily rich in mitochondria, which have the peculiarity of generating heat by uncoupled respiration. Since the mitochondrial activity of BAT is subject to cycles of activation and deactivation in response to environmental temperature changes, an integrated mitochondrial quality control (MQC) system is of fundamental importance to ensure BAT physiology. Here, we provide an overview of the conventional and alternative mechanisms through which thermogenic adipocytes selectively remove damaged parts of mitochondria and how macrophages participate in the MQC system by removing extracellular mitochondrial waste to maintain the thermogenic function of BAT.
    Keywords:  adipocytes; extracellular vesicles; immune cells; metabolism; mitochondrial transfer; thermogenesis
    DOI:  https://doi.org/10.1016/j.tcb.2022.09.008
  33. Nat Commun. 2022 Oct 26. 13(1): 6365
    Biased signaling due to oligomerization of the G protein-coupled platelet-activating factor receptor.
    Junke Liu, Hengmin Tang, Chanjuan Xu, Shengnan Zhou, Xunying Zhu, Yuanyuan Li, Laurent Prézeau, Tao Xu, Jean-Philippe Pin, Philippe Rondard, Wei Ji, Jianfeng Liu.
      G protein-coupled receptors (GPCRs) are important drug targets that mediate various signaling pathways by activating G proteins and engaging β-arrestin proteins. Despite its importance for the development of therapeutics with fewer side effects, the underlying mechanism that controls the balance between these signaling modes of GPCRs remains largely unclear. Here, we show that assembly into dimers and oligomers can largely influence the signaling mode of the platelet-activating factor receptor (PAFR). Single-particle analysis results show that PAFR can form oligomers at low densities through two possible dimer interfaces. Stabilization of PAFR oligomers through cross-linking increases G protein activity, and decreases β-arrestin recruitment and agonist-induced internalization significantly. Reciprocally, β-arrestin prevents PAFR oligomerization. Our results highlight a mechanism involved in the control of receptor signaling, and thereby provide important insights into the relationship between GPCR oligomerization and downstream signaling.
    DOI:  https://doi.org/10.1038/s41467-022-34056-4
  34. Proc Natl Acad Sci U S A. 2022 Nov 08. 119(45): e2214900119
    Ornithine decarboxylase supports ILC3 responses in infectious and autoimmune colitis through positive regulation of IL-22 transcription.
    Vincent Peng, Siyan Cao, Tihana Trsan, Jennifer K Bando, Julian Avila-Pacheco, John L Cleveland, Clary Clish, Ramnik J Xavier, Marco Colonna.
      Group 3 innate lymphoid cells (ILC3s) are RORγT+ lymphocytes that are predominately enriched in mucosal tissues and produce IL-22 and IL-17A. They are the innate counterparts of Th17 cells. While Th17 lymphocytes utilize unique metabolic pathways in their differentiation program, it is unknown whether ILC3s make similar metabolic adaptations. We employed single-cell RNA sequencing and metabolomic profiling of intestinal ILC subsets to identify an enrichment of polyamine biosynthesis in ILC3s, converging on the rate-limiting enzyme ornithine decarboxylase (ODC1). In vitro and in vivo studies demonstrated that exogenous supplementation with the polyamine putrescine or its biosynthetic substrate, ornithine, enhanced ILC3 production of IL-22. Conditional deletion of ODC1 in ILC3s impaired mouse antibacterial defense against Citrobacter rodentium infection, which was associated with a decrease in anti-microbial peptide production by the intestinal epithelium. Furthermore, in a model of anti-CD40 colitis, deficiency of ODC1 in ILC3s markedly reduced the production of IL-22 and severity of inflammatory colitis. We conclude that ILC3-intrinsic polyamine biosynthesis facilitates efficient defense against enteric pathogens as well as exacerbates autoimmune colitis, thus representing an attractive target to modulate ILC3 function in intestinal disease.
    Keywords:  IL-22; enteritis; innate lymphoid cells; ornithine decarboxylase; polyamines
    DOI:  https://doi.org/10.1073/pnas.2214900119
  35. J Clin Invest. 2022 Oct 25. pii: e162720. [Epub ahead of print]
    Pharmacological conversion of gut epithelial cells into insulin-producing cells lowers glycemia in diabetic animals.
    Wen Du, Junqiang Wang, Taiyi Kuo, Liheng Wang, Wendy M McKimpson, Jinsook Son, Hitoshi Watanabe, Takumi Kitamoto, Yun-Kyoung Lee, Remi J Creusot, Lloyd E Ratner, Kasi McCune, Ya-Wen Chen, Brendan H Grubbs, Matthew E Thornton, Jason Fan, Nishat Sultana, Bryan S Diaz, Iyshwarya Balasubramanian, Nan Gao, Sandro Belvedere, Domenico Accili.
      As a highly regenerative organ, the intestine is a promising source for cellular reprogramming to replace lost pancreatic β-cells in diabetes. Gut enterochromaffin cells can be converted to insulin-producing cells by FoxO1 ablation, but their numbers are limited. In this study we report that insulin-immunoreactive cells with Paneth/goblet cell features are present in human fetal intestine. Accordingly, lineage tracing experiments show that upon genetic or pharmacologic FoxO1 ablation the Paneth/goblet lineage can also undergo conversion to the insulin lineage. We designed a screening platform in gut organoids to accurately quantitate β-like cell reprogramming and fine-tune a combination treatment to increase the efficiency of the conversion process in mice and human adult intestinal organoids. We identified a triple blockade of FOXO1, Notch, and TGFβ that, when tested in insulin-deficient STZ or NOD diabetic animals resulted in near-normalization of glucose levels, associated with the generation of intestinal insulin-producing cells. The findings illustrate a therapeutic approach to replace insulin treatment in diabetes.
    Keywords:  Beta cells; Diabetes; Endocrinology; Insulin
    DOI:  https://doi.org/10.1172/JCI162720
  36. Nat Commun. 2022 Oct 25. 13(1): 6339
    Intestine-specific removal of DAF-2 nearly doubles lifespan in Caenorhabditis elegans with little fitness cost.
    Yan-Ping Zhang, Wen-Hong Zhang, Pan Zhang, Qi Li, Yue Sun, Jia-Wen Wang, Shaobing O Zhang, Tao Cai, Cheng Zhan, Meng-Qiu Dong.
      Twenty-nine years following the breakthrough discovery that a single-gene mutation of daf-2 doubles Caenorhabditis elegans lifespan, it remains unclear where this insulin/IGF-1 receptor gene is expressed and where it acts to regulate ageing. Using knock-in fluorescent reporters, we determined that daf-2 and its downstream transcription factor daf-16 are expressed ubiquitously. Using tissue-specific targeted protein degradation, we determined that intracellular DAF-2-to-DAF-16 signaling in the intestine plays a major role in lifespan regulation, while that in the hypodermis, neurons, and germline plays a minor role. Notably, intestine-specific loss of DAF-2 activates DAF-16 in and outside the intestine, causes almost no adverse effects on development and reproduction, and extends lifespan by 94% in a way that partly requires non-intestinal DAF-16. Consistent with intestine supplying nutrients to the entire body, evidence from this and other studies suggests that altered metabolism, particularly down-regulation of protein and RNA synthesis, mediates longevity by reduction of insulin/IGF-1 signaling.
    DOI:  https://doi.org/10.1038/s41467-022-33850-4
  37. Nature. 2022 10;610(7933): S38-S40
    Preparing health-care systems for future pandemics.
    Kristina Campbell.
      
    Keywords:  Health care; Infection; Policy; Public health
    DOI:  https://doi.org/10.1038/d41586-022-03356-6
  38. Nat Commun. 2022 Oct 25. 13(1): 6334
    Subcellular localization of type IV pili regulates bacterial multicellular development.
    Courtney K Ellison, Chenyi Fei, Triana N Dalia, Ned S Wingreen, Ankur B Dalia, Joshua W Shaevitz, Zemer Gitai.
      In mammals, subcellular protein localization of factors like planar cell polarity proteins is a key driver of the multicellular organization of tissues. Bacteria also form organized multicellular communities, but these patterns are largely thought to emerge from regulation of whole-cell processes like growth, motility, cell shape, and differentiation. Here we show that a unique intracellular patterning of appendages known as type IV pili (T4P) can drive multicellular development of complex bacterial communities. Specifically, dynamic T4P appendages localize in a line along the long axis of the cell in the bacterium Acinetobacter baylyi. This long-axis localization is regulated by a functionally divergent chemosensory Pil-Chp system, and an atypical T4P protein homologue (FimV) bridges Pil-Chp signaling and T4P positioning. We further demonstrate through modeling and empirical approaches that subcellular T4P localization controls how individual cells interact with one another, independently of T4P dynamics, with different patterns of localization giving rise to distinct multicellular architectures. Our results reveal how subcellular patterning of single cells regulates the development of multicellular bacterial communities.
    DOI:  https://doi.org/10.1038/s41467-022-33564-7
  39. Nat Commun. 2022 Oct 26. 13(1): 6355
    Subcellular spatial transcriptomics identifies three mechanistically different classes of localizing RNAs.
    Lucia Cassella, Anne Ephrussi.
      Intracellular RNA localization is a widespread and dynamic phenomenon that compartmentalizes gene expression and contributes to the functional polarization of cells. Thus far, mechanisms of RNA localization identified in Drosophila have been based on a few RNAs in different tissues, and a comprehensive mechanistic analysis of RNA localization in a single tissue is lacking. Here, by subcellular spatial transcriptomics we identify RNAs localized in the apical and basal domains of the columnar follicular epithelium (FE) and we analyze the mechanisms mediating their localization. Whereas the dynein/BicD/Egl machinery controls apical RNA localization, basally-targeted RNAs require kinesin-1 to overcome a default dynein-mediated transport. Moreover, a non-canonical, translation- and dynein-dependent mechanism mediates apical localization of a subgroup of dynein-activating adaptor-encoding RNAs (BicD, Bsg25D, hook). Altogether, our study identifies at least three mechanisms underlying RNA localization in the FE, and suggests a possible link between RNA localization and dynein/dynactin/adaptor complex formation in vivo.
    DOI:  https://doi.org/10.1038/s41467-022-34004-2
  40. Cell Death Dis. 2022 Oct 27. 13(10): 904
    Mutated lncRNA increase the risk of type 2 diabetes by promoting β cell dysfunction and insulin resistance.
    Wan-Hui Guo, Qi Guo, Ya-Lin Liu, Dan-Dan Yan, Li Jin, Rong Zhang, Jing Yan, Xiang-Hang Luo, Mi Yang.
      Islet β cell dysfunction and insulin resistance are the main pathogenesis of type 2 diabetes (T2D), but the mechanism remains unclear. Here we identify a rs3819316 C > T mutation in lncRNA Reg1cp mainly expressed in islets associated with an increased risk of T2D. Analyses in 16,113 Chinese adults reveal that Mut-Reg1cp individuals had higher incidence of T2D and presented impaired insulin secretion as well as increased insulin resistance. Mice with islet β cell specific Mut-Reg1cp knock-in have more severe β cell dysfunction and insulin resistance. Mass spectrometry assay of proteins after RNA pulldown demonstrate that Mut-Reg1cp directly binds to polypyrimidine tract binding protein 1 (PTBP1), further immunofluorescence staining, western blot analysis, qPCR analysis and glucose stimulated insulin secretion test reveal that Mut-Reg1cp disrupts the stabilization of insulin mRNA by inhibiting the phosphorylation of PTBP1 in β cells. Furthermore, islet derived exosomes transfer Mut-Reg1cp into peripheral tissue, which then promote insulin resistance by inhibiting AdipoR1 translation and adiponectin signaling. Our findings identify a novel mutation in lncRNA involved in the pathogenesis of T2D, and reveal a new mechanism for the development of T2D.
    DOI:  https://doi.org/10.1038/s41419-022-05348-w
  41. Nat Biotechnol. 2022 Oct 27.
    Quantitative sequencing using BID-seq uncovers abundant pseudouridines in mammalian mRNA at base resolution.
    Qing Dai, Li-Sheng Zhang, Hui-Lung Sun, Kinga Pajdzik, Lei Yang, Chang Ye, Cheng-Wei Ju, Shun Liu, Yuru Wang, Zhong Zheng, Linda Zhang, Bryan T Harada, Xiaoyang Dou, Iryna Irkliyenko, Xinran Feng, Wen Zhang, Tao Pan, Chuan He.
      Functional characterization of pseudouridine (Ψ) in mammalian mRNA has been hampered by the lack of a quantitative method that maps Ψ in the whole transcriptome. We report bisulfite-induced deletion sequencing (BID-seq), which uses a bisulfite-mediated reaction to convert pseudouridine stoichiometrically into deletion upon reverse transcription without cytosine deamination. BID-seq enables detection of abundant Ψ sites with stoichiometry information in several human cell lines and 12 different mouse tissues using 10-20 ng input RNA. We uncover consensus sequences for Ψ in mammalian mRNA and assign different 'writer' proteins to individual Ψ deposition. Our results reveal a transcript stabilization role of Ψ sites installed by TRUB1 in human cancer cells. We also detect the presence of Ψ within stop codons of mammalian mRNA and confirm the role of Ψ in promoting stop codon readthrough in vivo. BID-seq will enable future investigations of the roles of Ψ in diverse biological processes.
    DOI:  https://doi.org/10.1038/s41587-022-01505-w
  42. Nat Commun. 2022 Oct 26. 13(1): 6371
    Kynurenine promotes neonatal heart regeneration by stimulating cardiomyocyte proliferation and cardiac angiogenesis.
    Donghong Zhang, Jinfeng Ning, Tharmarajan Ramprasath, Changjiang Yu, Xiaoxu Zheng, Ping Song, Zhonglin Xie, Ming-Hui Zou.
      Indoleamine 2,3 dioxygenase-1 (IDO1) catalyzes tryptophan-kynurenine metabolism in many inflammatory and cancer diseases. Of note, acute inflammation that occurs immediately after heart injury is essential for neonatal cardiomyocyte proliferation and heart regeneration. However, the IDO1-catalyzed tryptophan metabolism during heart regeneration is largely unexplored. Here, we find that apical neonatal mouse heart resection surgery led to rapid and consistent increases in cardiac IDO1 expression and kynurenine accumulation. Cardiac deletion of Ido1 gene or chemical inhibition of IDO1 impairs heart regeneration. Mechanistically, elevated kynurenine triggers cardiomyocyte proliferation by activating the cytoplasmic aryl hydrocarbon receptor-SRC-YAP/ERK pathway. In addition, cardiomyocyte-derived kynurenine transports to endothelial cells and stimulates cardiac angiogenesis by promoting aryl hydrocarbon receptor nuclear translocation and enhancing vascular endothelial growth factor A expression. Notably, Ahr deletion prevents indoleamine 2,3 dioxygenase -kynurenine-associated heart regeneration. In summary, increasing indoleamine 2,3 dioxygenase-derived kynurenine level promotes cardiac regeneration by functioning as an endogenous regulator of cardiomyocyte proliferation and cardiac angiogenesis.
    DOI:  https://doi.org/10.1038/s41467-022-33734-7
  43. Nat Cell Biol. 2022 Oct 27.
    PTEN directs developmental and metabolic signaling for innate-like T cell fate and tissue homeostasis.
    Daniel Bastardo Blanco, Nicole M Chapman, Jana L Raynor, Chengxian Xu, Wei Su, Anil Kc, Wei Li, Seon Ah Lim, Stefan Schattgen, Hao Shi, Isabel Risch, Yu Sun, Yogesh Dhungana, Yunjung Kim, Jun Wei, Sherri Rankin, Geoffrey Neale, Paul G Thomas, Kai Yang, Hongbo Chi.
      Phosphatase and tensin homologue (PTEN) is frequently mutated in human cancer, but its roles in lymphopoiesis and tissue homeostasis remain poorly defined. Here we show that PTEN orchestrates a two-step developmental process linking antigen receptor and IL-23-Stat3 signalling to type-17 innate-like T cell generation. Loss of PTEN leads to pronounced accumulation of mature IL-17-producing innate-like T cells in the thymus. IL-23 is essential for their accumulation, and ablation of IL-23 or IL-17 signalling rectifies the reduced survival of female PTEN-haploinsufficient mice that model human patients with PTEN mutations. Single-cell transcriptome and network analyses revealed the dynamic regulation of PTEN, mTOR and metabolic activities that accompanied type-17 cell programming. Furthermore, deletion of mTORC1 or mTORC2 blocks PTEN loss-driven type-17 cell accumulation, and this is further shaped by the Foxo1 and Stat3 pathways. Collectively, our study establishes developmental and metabolic signalling networks underpinning type-17 cell fate decisions and their functional effects at coordinating PTEN-dependent tissue homeostasis.
    DOI:  https://doi.org/10.1038/s41556-022-01011-w
  44. Nat Microbiol. 2022 Nov;7(11): 1762-1776
    Evasion of cGAS and TRIM5 defines pandemic HIV.
    Lorena Zuliani-Alvarez, Morten L Govasli, Jane Rasaiyaah, Chris Monit, Stephen O Perry, Rebecca P Sumner, Simon McAlpine-Scott, Claire Dickson, K M Rifat Faysal, Laura Hilditch, Richard J Miles, Frederic Bibollet-Ruche, Beatrice H Hahn, Till Boecking, Nikos Pinotsis, Leo C James, David A Jacques, Greg J Towers.
      Of the 13 known independent zoonoses of simian immunodeficiency viruses to humans, only one, leading to human immunodeficiency virus (HIV) type 1(M) has become pandemic, causing over 80 million human infections. To understand the specific features associated with pandemic human-to-human HIV spread, we compared replication of HIV-1(M) with non-pandemic HIV-(O) and HIV-2 strains in myeloid cell models. We found that non-pandemic HIV lineages replicate less well than HIV-1(M) owing to activation of cGAS and TRIM5-mediated antiviral responses. We applied phylogenetic and X-ray crystallography structural analyses to identify differences between pandemic and non-pandemic HIV capsids. We found that genetic reversal of two specific amino acid adaptations in HIV-1(M) enables activation of TRIM5, cGAS and innate immune responses. We propose a model in which the parental lineage of pandemic HIV-1(M) evolved a capsid that prevents cGAS and TRIM5 triggering, thereby allowing silent replication in myeloid cells. We hypothesize that this capsid adaptation promotes human-to-human spread through avoidance of innate immune response activation.
    DOI:  https://doi.org/10.1038/s41564-022-01247-0
  45. Commun Biol. 2022 Oct 25. 5(1): 1128
    Pooled image-base screening of mitochondria with microraft isolation distinguishes pathogenic mitofusin 2 mutations.
    Alex L Yenkin, John C Bramley, Colin L Kremitzki, Jason E Waligorski, Mariel J Liebeskind, Xinyuan E Xu, Vinay D Chandrasekaran, Maria A Vakaki, Graham W Bachman, Robi D Mitra, Jeffrey D Milbrandt, William J Buchser.
      Most human genetic variation is classified as variants of uncertain significance. While advances in genome editing have allowed innovation in pooled screening platforms, many screens deal with relatively simple readouts (viability, fluorescence) and cannot identify the complex cellular phenotypes that underlie most human diseases. In this paper, we present a generalizable functional genomics platform that combines high-content imaging, machine learning, and microraft isolation in a method termed "Raft-Seq". We highlight the efficacy of our platform by showing its ability to distinguish pathogenic point mutations of the mitochondrial regulator Mitofusin 2, even when the cellular phenotype is subtle. We also show that our platform achieves its efficacy using multiple cellular features, which can be configured on-the-fly. Raft-Seq enables a way to perform pooled screening on sets of mutations in biologically relevant cells, with the ability to physically capture any cell with a perturbed phenotype and expand it clonally, directly from the primary screen.
    DOI:  https://doi.org/10.1038/s42003-022-04089-y
  46. Nat Commun. 2022 Oct 26. 13(1): 6364
    Revealing β-TrCP activity dynamics in live cells with a genetically encoded biosensor.
    Debasish Paul, Stephen C Kales, James A Cornwell, Marwa M Afifi, Ganesha Rai, Alexey Zakharov, Anton Simeonov, Steven D Cappell.
      The F-box protein beta-transducin repeat containing protein (β-TrCP) acts as a substrate adapter for the SCF E3 ubiquitin ligase complex, plays a crucial role in cell physiology, and is often deregulated in many types of cancers. Here, we develop a fluorescent biosensor to quantitatively measure β-TrCP activity in live, single cells in real-time. We find β-TrCP remains constitutively active throughout the cell cycle and functions to maintain discreet steady-state levels of its substrates. We find no correlation between expression levels of β-TrCP and β-TrCP activity, indicating post-transcriptional regulation. A high throughput screen of small-molecules using our reporter identifies receptor-tyrosine kinase signaling as a key axis for regulating β-TrCP activity by inhibiting binding between β-TrCP and the core SCF complex. Our study introduces a method to monitor β-TrCP activity in live cells and identifies a key signaling network that regulates β-TrCP activity throughout the cell cycle.
    DOI:  https://doi.org/10.1038/s41467-022-33762-3
  47. Sci Signal. 2022 Oct 25. 15(757): eabm0808
    Host protein kinases required for SARS-CoV-2 nucleocapsid phosphorylation and viral replication.
    Tomer M Yaron, Brook E Heaton, Tyler M Levy, Jared L Johnson, Tristan X Jordan, Benjamin M Cohen, Alexander Kerelsky, Ting-Yu Lin, Katarina M Liberatore, Danielle K Bulaon, Samantha J Van Nest, Nikos Koundouros, Edward R Kastenhuber, Marisa N Mercadante, Kripa Shobana-Ganesh, Long He, Robert E Schwartz, Shuibing Chen, Harel Weinstein, Olivier Elemento, Elena Piskounova, Benjamin E Nilsson-Payant, Gina Lee, Joseph D Trimarco, Kaitlyn N Burke, Cait E Hamele, Ryan R Chaparian, Alfred T Harding, Aleksandra Tata, Xinyu Zhu, Purushothama Rao Tata, Clare M Smith, Anthony P Possemato, Sasha L Tkachev, Peter V Hornbeck, Sean A Beausoleil, Shankara K Anand, François Aguet, Gad Getz, Andrew D Davidson, Kate Heesom, Maia Kavanagh-Williamson, David A Matthews, Benjamin R tenOever, Lewis C Cantley, John Blenis, Nicholas S Heaton.
      Multiple coronaviruses have emerged independently in the past 20 years that cause lethal human diseases. Although vaccine development targeting these viruses has been accelerated substantially, there remain patients requiring treatment who cannot be vaccinated or who experience breakthrough infections. Understanding the common host factors necessary for the life cycles of coronaviruses may reveal conserved therapeutic targets. Here, we used the known substrate specificities of mammalian protein kinases to deconvolute the sequence of phosphorylation events mediated by three host protein kinase families (SRPK, GSK-3, and CK1) that coordinately phosphorylate a cluster of serine and threonine residues in the viral N protein, which is required for viral replication. We also showed that loss or inhibition of SRPK1/2, which we propose initiates the N protein phosphorylation cascade, compromised the viral replication cycle. Because these phosphorylation sites are highly conserved across coronaviruses, inhibitors of these protein kinases not only may have therapeutic potential against COVID-19 but also may be broadly useful against coronavirus-mediated diseases.
    DOI:  https://doi.org/10.1126/scisignal.abm0808
  48. J Clin Invest. 2022 Oct 25. pii: e163235. [Epub ahead of print]
    The Notch1/CD22 signaling axis disrupts Treg cell function in SARS-CoV2-associated multisystem inflammatory syndrome in children.
    Mehdi Benamar, Qian Chen, Janet Chou, Amélie M Julé, Rafik Boudra, Paola Contini, Elena Crestani, Peggy S Lai, Muyun Wang, Jason Fong, Shira Rockwitz, Pui Y Lee, Tsz Man Fion Chan, Ekin Zeynep Altun, Eda Kepenekli, Elif Karakoc-Aydiner, Ahmet Ozen, Perran Boran, Fatih Aygun, Pınar Önal, Ayse Ayzit Kilinc Sakalli, Haluk Cokugras, Metin Yusuf Gelmez, Fatma B Oktelik, Esin Cetin Aktas, Yuelin Zhong, Maria L Taylor, Katherine Irby, Natasha B Halasa, Elizabeth H Mack, Sara Signa, Ignazia Prigione, Marco Gattorno, Nicola Cotugno, Donato Amodio, Raif S Geha, Mary Beth Son, Jane W Newburger, Pankaj B Agrawal, Stefano Volpi, Paolo Palma, Ayca Kiykim, Adrienne Randolph, Gunnur Deniz, Safa Baris, Raffaele De Palma, Klaus Schmitz-Abe, Louis-Marie Charbonnier, Lauren A Henderson, Talal A Chatila.
      Multisystem inflammatory syndrome in children (MIS-C) evolves in some pediatric patients following acute infection with SARS-CoV-2 by hitherto unknown mechanisms. Whereas acute-COVID-19 severity and outcome were previously correlated with Notch4 expression on regulatory T (Treg) cells, here we show that the Treg cells in MIS-C are destabilized through a Notch1-dependent mechanism. Genetic analysis revealed that MIS-C patients were enriched in rare deleterious variants impacting inflammation and autoimmunity pathways, including dominant-negative mutations in the Notch1 regulators NUMB and NUMBL leading to Notch1 upregulation. Notch1 signaling in Treg cells induced CD22, leading to their destabilization in a mTORC1-dependent manner and to the promotion of systemic inflammation. These results establish a Notch1-CD22 signaling axis that disrupts Treg cell function in MIS-C and point to distinct immune checkpoints controlled by individual Treg cell Notch receptors that shape the inflammatory outcome in SARS-CoV-2 infection.
    Keywords:  Adaptive immunity; COVID-19; Immunology; T cells; Tolerance
    DOI:  https://doi.org/10.1172/JCI163235
  49. Mol Metab. 2022 Oct 22. pii: S2212-8778(22)00187-9. [Epub ahead of print] 101618
    Single-agent FOXO1 inhibition normalizes glycemia and induces gut β-like cells in streptozotocin-diabetic mice.
    Yun-Kyoung Lee, Wen Du, Yaohui Nie, Bryan Diaz, Nishat Sultana, Takumi Kitamoto, Rudolph L Leibel, Domenico Accili, Sandro Belvedere.
       OBJECTIVES: Insulin treatment remains the sole effective intervention for Type 1 Diabetes. Here, we investigated the therapeutic potential of converting intestinal epithelial cells to insulin-producing, glucose-responsive β-like cells by targeted inhibition of FOXO1. We have previously shown that this can be achieved by genetic ablation in gut Neurogenin3 progenitors, adenoviral or shRNA-mediated inhibition in human gut organoids, and chemical inhibition in Akita mice, a model of insulin-deficient diabetes.
    METHODS: We profiled two novel FOXO1 inhibitors in reporter gene assays, and hepatocyte gene expression studies, and in vivo pyruvate tolerance test (PTT) for their activity and specificity. We evaluated their glucose-lowering effect in mice rendered insulin-deficient by administration of streptozotocin.
    RESULTS: We provide evidence that two novel FOXO1 inhibitors, FBT432 and FBT374 have glucose-lowering and gut β-like cell-inducing properties in mice. FBT432 is also highly effective in combination with a Notch inhibitor in this model.
    CONCLUSION: The data add to a growing body of evidence suggesting that FOXO1 inhibition be pursued as an alternative treatment to insulin administration in diabetes.
    Keywords:  FOXO1 inhibitor; T1D; glucose lowering effect; gut β-like cells; insulin
    DOI:  https://doi.org/10.1016/j.molmet.2022.101618
  50. Nat Commun. 2022 Oct 26. 13(1): 6356
    Functional and metabolic alterations of gut microbiota in children with new-onset type 1 diabetes.
    Xiaoxiao Yuan, Ruirui Wang, Bing Han, ChengJun Sun, Ruimin Chen, Haiyan Wei, Linqi Chen, Hongwei Du, Guimei Li, Yu Yang, Xiaojuan Chen, Lanwei Cui, Zhenran Xu, Junfen Fu, Jin Wu, Wei Gu, Zhihong Chen, Xin Fang, Hongxiu Yang, Zhe Su, Jing Wu, Qiuyue Li, Miaoying Zhang, Yufeng Zhou, Lei Zhang, Guang Ji, Feihong Luo.
      Gut dysbiosis has been linked to type 1 diabetes (T1D); however, microbial capacity in T1D remains unclear. Here, we integratively profiled gut microbial functional and metabolic alterations in children with new-onset T1D in independent cohorts and investigated the underlying mechanisms. In T1D, the microbiota was characterized by decreased butyrate production and bile acid metabolism and increased lipopolysaccharide biosynthesis at the species, gene, and metabolite levels. The combination of 18 bacterial species and fecal metabolites provided excellently discriminatory power for T1D. Gut microbiota from children with T1D induced elevated fasting glucose levels and declined insulin sensitivity in antibiotic-treated mice. In streptozotocin-induced T1D mice, butyrate and lipopolysaccharide exerted protective and destructive effects on islet structure and function, respectively. Lipopolysaccharide aggravated the pancreatic inflammatory response, while butyrate activated Insulin1 and Insulin2 gene expression. Our study revealed perturbed microbial functional and metabolic traits in T1D, providing potential avenues for microbiome-based prevention and intervention for T1D.
    DOI:  https://doi.org/10.1038/s41467-022-33656-4
  51. EMBO J. 2022 Oct 25. e108970
    The E3 ubiquitin ligase RNF115 regulates phagosome maturation and host response to bacterial infection.
    Orsolya Bilkei-Gorzo, Tiaan Heunis, José Luis Marín-Rubio, Francesca Romana Cianfanelli, Benjamin Bernard Armando Raymond, Joseph Inns, Daniela Fabrikova, Julien Peltier, Fiona Oakley, Ralf Schmid, Anetta Härtlova, Matthias Trost.
      Phagocytosis is a key process in innate immunity and homeostasis. After particle uptake, newly formed phagosomes mature by acquisition of endolysosomal enzymes. Macrophage activation by interferon gamma (IFN-γ) increases microbicidal activity, but delays phagosomal maturation by an unknown mechanism. Using quantitative proteomics, we show that phagosomal proteins harbour high levels of typical and atypical ubiquitin chain types. Moreover, phagosomal ubiquitylation of vesicle trafficking proteins is substantially enhanced upon IFN-γ activation of macrophages, suggesting a role in regulating phagosomal functions. We identified the E3 ubiquitin ligase RNF115, which is enriched on phagosomes of IFN-γ activated macrophages, as an important regulator of phagosomal maturation. Loss of RNF115 protein or ligase activity enhanced phagosomal maturation and increased cytokine responses to bacterial infection, suggesting that both innate immune signalling from the phagosome and phagolysosomal trafficking are controlled through ubiquitylation. RNF115 knock-out mice show less tissue damage in response to S. aureus infection, indicating a role of RNF115 in inflammatory responses in vivo. In conclusion, RNF115 and phagosomal ubiquitylation are important regulators of innate immune functions during bacterial infections.
    Keywords:  E3 ligase; RNF115; macrophage; phagosome; ubiquitin
    DOI:  https://doi.org/10.15252/embj.2021108970
  52. Cell. 2022 Oct 27. pii: S0092-8674(22)01263-6. [Epub ahead of print]185(22): 4040-4042
    Why are some people more attractive to mosquitoes than others?
    Jiawei Zhao, Josefina Del Mármol.
      Mosquitoes rely on their sense of smell to find humans to secure a blood meal, transmitting deadly diseases with their bite. In this issue of Cell, De Obaldía and colleagues examine why mosquitoes bite some people more than others and report an association with the level of carboxylic acids in the human skin odor.
    DOI:  https://doi.org/10.1016/j.cell.2022.09.044
  53. Nat Commun. 2022 Oct 26. 13(1): 6381
    Juxtaposition of Bub1 and Cdc20 on phosphorylated Mad1 during catalytic mitotic checkpoint complex assembly.
    Elyse S Fischer, Conny W H Yu, Johannes F Hevler, Stephen H McLaughlin, Sarah L Maslen, Albert J R Heck, Stefan M V Freund, David Barford.
      In response to improper kinetochore-microtubule attachments in mitosis, the spindle assembly checkpoint (SAC) assembles the mitotic checkpoint complex (MCC) to inhibit the anaphase-promoting complex/cyclosome, thereby delaying entry into anaphase. The MCC comprises Mad2:Cdc20:BubR1:Bub3. Its assembly is catalysed by unattached kinetochores on a Mad1:Mad2 platform. Mad1-bound closed-Mad2 (C-Mad2) recruits open-Mad2 (O-Mad2) through self-dimerization. This interaction, combined with Mps1 kinase-mediated phosphorylation of Bub1 and Mad1, accelerates MCC assembly, in a process that requires O-Mad2 to C-Mad2 conversion and concomitant binding of Cdc20. How Mad1 phosphorylation catalyses MCC assembly is poorly understood. Here, we characterized Mps1 phosphorylation of Mad1 and obtained structural insights into a phosphorylation-specific Mad1:Cdc20 interaction. This interaction, together with the Mps1-phosphorylation dependent association of Bub1 and Mad1, generates a tripartite assembly of Bub1 and Cdc20 onto the C-terminal domain of Mad1 (Mad1CTD). We additionally identify flexibility of Mad1:Mad2 that suggests how the Cdc20:Mad1CTD interaction brings the Mad2-interacting motif (MIM) of Cdc20 near O-Mad2. Thus, Mps1-dependent formation of the MCC-assembly scaffold functions to position and orient Cdc20 MIM near O-Mad2, thereby catalysing formation of C-Mad2:Cdc20.
    DOI:  https://doi.org/10.1038/s41467-022-34058-2
  54. Proc Natl Acad Sci U S A. 2022 Nov;119(44): e2210434119
    Phosphorylation of RXRα mediates the effect of JNK to suppress hepatic FGF21 expression and promote metabolic syndrome.
    Santiago Vernia, Alexandra Lee, Norman J Kennedy, Myoung Sook Han, Marta Isasa, Julie Cavanagh-Kyros, Armanda Roy, Aafreen Syed, Shanzah Chaudhry, Yvonne J K Edwards, Steven P Gygi, Guangping Gao, Roger J Davis.
      The cJun NH2-terminal kinase (JNK) signaling pathway in the liver promotes systemic changes in metabolism by regulating peroxisome proliferator-activated receptor α (PPARα)-dependent expression of the hepatokine fibroblast growth factor 21 (FGF21). Hepatocyte-specific gene ablation studies demonstrated that the Mapk9 gene (encoding JNK2) plays a key mechanistic role. Mutually exclusive inclusion of exons 7a and 7b yields expression of the isoforms JNK2α and JNK2β. Here we demonstrate that Fgf21 gene expression and metabolic regulation are primarily regulated by the JNK2α isoform. To identify relevant substrates of JNK2α, we performed a quantitative phosphoproteomic study of livers isolated from control mice, mice with JNK deficiency in hepatocytes, and mice that express only JNK2α or JNK2β in hepatocytes. We identified the JNK substrate retinoid X receptor α (RXRα) as a protein that exhibited JNK2α-promoted phosphorylation in vivo. RXRα functions as a heterodimeric partner of PPARα and may therefore mediate the effects of JNK2α signaling on Fgf21 expression. To test this hypothesis, we established mice with hepatocyte-specific expression of wild-type or mutated RXRα proteins. We found that the RXRα phosphorylation site Ser260 was required for suppression of Fgf21 gene expression. Collectively, these data establish a JNK-mediated signaling pathway that regulates hepatic Fgf21 expression.
    Keywords:  FGF21; JNK; RXRα; high-fat diet; insulin resistance
    DOI:  https://doi.org/10.1073/pnas.2210434119
  55. Nat Commun. 2022 Oct 25. 13(1): 6331
    Termination of the unfolded protein response is guided by ER stress-induced HAC1 mRNA nuclear retention.
    Laura Matabishi-Bibi, Drice Challal, Mara Barucco, Domenico Libri, Anna Babour.
      Cellular homeostasis is maintained by surveillance mechanisms that intervene at virtually every step of gene expression. In the nucleus, the yeast chromatin remodeler Isw1 holds back maturing mRNA ribonucleoparticles to prevent their untimely export, but whether this activity operates beyond quality control of mRNA biogenesis to regulate gene expression is unknown. Here, we identify the mRNA encoding the central effector of the unfolded protein response (UPR) HAC1, as an Isw1 RNA target. The direct binding of Isw1 to the 3' untranslated region of HAC1 mRNA restricts its nuclear export and is required for accurate UPR abatement. Accordingly, ISW1 inactivation sensitizes cells to endoplasmic reticulum (ER) stress while its overexpression reduces UPR induction. Our results reveal an unsuspected mechanism, in which binding of ER-stress induced Isw1 to HAC1 mRNA limits its nuclear export, providing a feedback loop that fine-tunes UPR attenuation to guarantee homeostatic adaptation to ER stress.
    DOI:  https://doi.org/10.1038/s41467-022-34133-8
  56. Nat Genet. 2022 Oct 24.
    Multiomics study of nonalcoholic fatty liver disease.
    DBDS Genomic consortium
      Nonalcoholic fatty liver (NAFL) and its sequelae are growing health problems. We performed a genome-wide association study of NAFL, cirrhosis and hepatocellular carcinoma, and integrated the findings with expression and proteomic data. For NAFL, we utilized 9,491 clinical cases and proton density fat fraction extracted from 36,116 liver magnetic resonance images. We identified 18 sequence variants associated with NAFL and 4 with cirrhosis, and found rare, protective, predicted loss-of-function variants in MTARC1 and GPAM, underscoring them as potential drug targets. We leveraged messenger RNA expression, splicing and predicted coding effects to identify 16 putative causal genes, of which many are implicated in lipid metabolism. We analyzed levels of 4,907 plasma proteins in 35,559 Icelanders and 1,459 proteins in 47,151 UK Biobank participants, identifying multiple proteins involved in disease pathogenesis. We show that proteomics can discriminate between NAFL and cirrhosis. The present study provides insights into the development of noninvasive evaluation of NAFL and new therapeutic options.
    DOI:  https://doi.org/10.1038/s41588-022-01199-5
  57. Nature. 2022 10;610(7933): S50
    Five ways to prepare for the next pandemic.
    Devi Sridhar.
      
    Keywords:  Infection; Policy; Public health
    DOI:  https://doi.org/10.1038/d41586-022-03362-8
  58. Commun Biol. 2022 Oct 26. 5(1): 1130
    Cftr deletion in mouse epithelial and immune cells differentially influence the intestinal microbiota.
    Callie E Scull, Meng Luo, Scott Jennings, Christopher M Taylor, Guoshun Wang.
      Cystic fibrosis (CF) is a life-threatening genetic disorder, caused by mutations in the CF transmembrane-conductance regulator gene (cftr) that encodes CFTR, a cAMP-activated chloride and bicarbonate channel. Clinically, CF lung disease dominates the adult patient population. However, its gastrointestinal illness claims the early morbidity and mortality, manifesting as intestinal dysbiosis, inflammation and obstruction. As CF is widely accepted as a disease of epithelial dysfunction, it is unknown whether CFTR loss-of-function in immune cells contributes to these clinical outcomes. Using cftr genetic knockout and bone marrow transplantation mouse models, we performed 16S rRNA gene sequencing of the intestinal microbes. Here we show that cftr deletion in both epithelial and immune cells collectively influence the intestinal microbiota. However, the immune defect is a major factor determining the dysbiosis in the small intestine, while the epithelial defect largely influences that in the large intestine. This finding revises the current concept by suggesting that CF epithelial defect and immune defect play differential roles in CF intestinal disease.
    DOI:  https://doi.org/10.1038/s42003-022-04101-5
  59. Science. 2022 Oct 28. 378(6618): eabj3510
    Spermidine activates mitochondrial trifunctional protein and improves antitumor immunity in mice.
    Muna Al-Habsi, Kenji Chamoto, Ken Matsumoto, Norimichi Nomura, Baihao Zhang, Yuki Sugiura, Kazuhiro Sonomura, Aprilia Maharani, Yuka Nakajima, Yibo Wu, Yayoi Nomura, Rosemary Menzies, Masaki Tajima, Koji Kitaoka, Yasuharu Haku, Sara Delghandi, Keiko Yurimoto, Fumihiko Matsuda, So Iwata, Toshihiko Ogura, Sidonia Fagarasan, Tasuku Honjo.
      Spermidine (SPD) delays age-related pathologies in various organisms. SPD supplementation overcame the impaired immunotherapy against tumors in aged mice by increasing mitochondrial function and activating CD8+ T cells. Treatment of naïve CD8+ T cells with SPD acutely enhanced fatty acid oxidation. SPD conjugated to beads bound to the mitochondrial trifunctional protein (MTP). In the MTP complex, synthesized and purified from Escherichia coli, SPD bound to the α and β subunits of MTP with strong affinity and allosterically enhanced their enzymatic activities. T cell-specific deletion of the MTP α subunit abolished enhancement of programmed cell death protein 1 (PD-1) blockade immunotherapy by SPD, indicating that MTP is required for SPD-dependent T cell activation.
    DOI:  https://doi.org/10.1126/science.abj3510
  60. J Cell Biol. 2022 Dec 05. pii: e202208103. [Epub ahead of print]221(12):
    mTORC1 beyond anabolic metabolism: Regulation of cell death.
    Jiajun Zhu, Hua Wang, Xuejun Jiang.
      The mechanistic target of rapamycin complex 1 (mTORC1), a multi-subunit protein kinase complex, interrogates growth factor signaling with cellular nutrient and energy status to control metabolic homeostasis. Activation of mTORC1 promotes biosynthesis of macromolecules, including proteins, lipids, and nucleic acids, and simultaneously suppresses catabolic processes such as lysosomal degradation of self-constituents and extracellular components. Metabolic regulation has emerged as a critical determinant of various cellular death programs, including apoptosis, pyroptosis, and ferroptosis. In this article, we review the expanding knowledge on how mTORC1 coordinates metabolic pathways to impinge on cell death regulation. We focus on the current understanding on how nutrient status and cellular signaling pathways connect mTORC1 activity with ferroptosis, an iron-dependent cell death program that has been implicated in a plethora of human diseases. In-depth understanding of the principles governing the interaction between mTORC1 and cell death pathways can ultimately guide the development of novel therapies for the treatment of relevant pathological conditions.
    DOI:  https://doi.org/10.1083/jcb.202208103
  61. Nat Commun. 2022 Oct 27. 13(1): 6351
    Intergenerational nutrition benefits of India's national school feeding program: Reality or a bridge too far?
    Harshpal Singh Sachdev, Clive Osmond, Anura V Kurpad, Tinku Thomas.
      
    DOI:  https://doi.org/10.1038/s41467-022-33338-1
  62. Genes Dev. 2022 Oct 27.
    An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters.
    Chitvan Mittal, Olivia Lang, William K M Lai, B Franklin Pugh.
      Genome-wide, little is understood about how proteins organize at inducible promoters before and after induction and to what extent inducible and constitutive architectures depend on cofactors. We report that sequence-specific transcription factors and their tethered cofactors (e.g., SAGA [Spt-Ada-Gcn5-acetyltransferase], Mediator, TUP, NuA4, SWI/SNF, and RPD3-L) are generally bound to promoters prior to induction ("poised"), rather than recruited upon induction, whereas induction recruits the preinitiation complex (PIC) to DNA. Through depletion and/or deletion experiments, we show that SAGA does not function at constitutive promoters, although a SAGA-independent Gcn5 acetylates +1 nucleosomes there. When inducible promoters are poised, SAGA catalyzes +1 nucleosome acetylation but not PIC assembly. When induced, SAGA catalyzes acetylation, deubiquitylation, and PIC assembly. Surprisingly, SAGA mediates induction by creating a PIC that allows TFIID (transcription factor II-D) to stably associate, rather than creating a completely TFIID-independent PIC, as generally thought. These findings suggest that inducible systems, where present, are integrated with constitutive systems.
    Keywords:  ChIP-seq; SAGA; Saccharomyces; gene regulation; genomics; transcription preinitiation complex
    DOI:  https://doi.org/10.1101/gad.350026.122
  63. Nat Genet. 2022 Oct 24.
    A combined polygenic score of 21,293 rare and 22 common variants improves diabetes diagnosis based on hemoglobin A1C levels.
    AMP-T2D-GENES Consortium
      Polygenic scores (PGSs) combine the effects of common genetic variants1,2 to predict risk or treatment strategies for complex diseases3-7. Adding rare variation to PGSs has largely unknown benefits and is methodically challenging. Here, we developed a method for constructing rare variant PGSs and applied it to calculate genetically modified hemoglobin A1C thresholds for type 2 diabetes (T2D) diagnosis7-10. The resultant rare variant PGS is highly polygenic (21,293 variants across 154 genes), depends on ultra-rare variants (72.7% observed in fewer than three people) and identifies significantly more undiagnosed T2D cases than expected by chance (odds ratio = 2.71; P = 1.51 × 10-6). A PGS combining common and rare variants is expected to identify 4.9 million misdiagnosed T2D cases in the United States-nearly 1.5-fold more than the common variant PGS alone. These results provide a method for constructing complex trait PGSs from rare variants and suggest that rare variants will augment common variants in precision medicine approaches for common disease.
    DOI:  https://doi.org/10.1038/s41588-022-01200-1
  64. J Transl Med. 2022 Oct 22. 20(1): 483
    Mitochondrial transplantation: opportunities and challenges in the treatment of obesity, diabetes, and nonalcoholic fatty liver disease.
    Yifei Chen, Fuji Yang, Ying Chu, Zhihua Yun, Yongmin Yan, Jianhua Jin.
      Metabolic diseases, including obesity, diabetes, and nonalcoholic fatty liver disease (NAFLD), are rising in both incidence and prevalence and remain a major global health and socioeconomic burden in the twenty-first century. Despite an increasing understanding of these diseases, the lack of effective treatments remains an ongoing challenge. Mitochondria are key players in intracellular energy production, calcium homeostasis, signaling, and apoptosis. Emerging evidence shows that mitochondrial dysfunction participates in the pathogeneses of metabolic diseases. Exogenous supplementation with healthy mitochondria is emerging as a promising therapeutic approach to treating these diseases. This article reviews recent advances in the use of mitochondrial transplantation therapy (MRT) in such treatment.
    Keywords:  Diabetes; Extracellular vesicles; Mitochondrial transfer; Nonalcoholic fatty liver disease; Obesity
    DOI:  https://doi.org/10.1186/s12967-022-03693-0
  65. J Clin Invest. 2022 Oct 26. pii: e161566. [Epub ahead of print]
    A SARM1/mitochondrial feedback loop drives neuropathogenesis in a Charcot-Marie-Tooth disease type 2A rat model.
    Yurie Yamada, Amy Strickland, Yo Sasaki, A Joseph Bloom, Aaron DiAntonio, Jeffrey Milbrandt.
      Charcot-Marie-Tooth disease (CMT) type 2A is an axonal neuropathy caused by mutations in the mitofusin 2 (MFN2) gene. MFN2 mutations result in profound mitochondrial abnormalities, but the mechanism underlying axonal pathology is unknown. SARM1, the central executioner of axon degeneration, can induce neuropathy and is activated by dysfunctional mitochondria. We tested the role of SARM1 in a rat model carrying a dominant CMT2A mutation (Mfn2H361Y) that exhibits progressive dying-back axonal degeneration, NMJ abnormalities, muscle atrophy, and mitochondrial abnormalities, all hallmarks of the human disease. We generated Sarm1 knockout and Mfn2H361Y, Sarm1 double mutant rats and find that deletion of Sarm1 rescues axonal, synaptic, muscle, and functional phenotypes, demonstrating that SARM1 is responsible for much of the neuropathology in this model. Despite the presence of mutant MFN2 protein in these double mutant rats, loss of SARM1 also dramatically suppressed many mitochondrial defects, including the number, size, and cristae density defects of synaptic mitochondria. This surprising finding indicates that dysfunctional mitochondria activate SARM1, and activated SARM1 feeds back on mitochondria to exacerbate mitochondrial pathology. As such, this work identifies SARM1 inhibition as an exciting therapeutic candidate for the treatment of CMT2A and other neurodegenerative diseases with prominent mitochondrial pathology.
    Keywords:  Neurodegeneration; Neurological disorders; Neuromuscular disease; Neuroscience
    DOI:  https://doi.org/10.1172/JCI161566
  66. Cell Rep. 2022 Oct 25. pii: S2211-1247(22)01409-7. [Epub ahead of print]41(4): 111553
    Gasdermin D restricts anti-tumor immunity during PD-L1 checkpoint blockade.
    Yuying Jiang, Yongbing Yang, Yingchao Hu, Rui Yang, Jiajia Huang, Yi Liu, Yuqing Wu, Sheng Li, Chunmei Ma, Fiachra Humphries, Bingwei Wang, Xi Wang, Zhibin Hu, Shuo Yang.
      Tumor microenvironments (TMEs) require co-operation of innate and adaptive immune cells, which influence tumor progression and immunotherapy. Caspase-activated gasdermins facilitate tumor death and promote anti-tumor immunity. How pyroptosis in immune cells affects the TME remains unclear. TME expression of gasdermin D (GSDMD) is highly expressed in antigen-presenting cells (APCs) and correlates with immune checkpoint signatures. Through conditional deletion of GSDMD, we demonstrate that GSDMD in TME APCs restricts anti-tumor immunity during PD-L1 inhibition. Loss of GSDMD in APCs enhances interferon-stimulated genes (ISGs), thereby promoting CD8+ T cell activation in a cGAS-dependent manner. Moreover, pharmacological inhibition of GSDMD-mediated pyroptosis and PD-L1 improve anti-tumor immunity, highlighting the potential of combining GSDMD/PD-L1 inhibition for immunotherapy as a therapeutic strategy.
    Keywords:  CP: Cancer; CP: Immunology; GSDMD; anti-tumor immunity; macrophage/DC
    DOI:  https://doi.org/10.1016/j.celrep.2022.111553
  67. Nat Methods. 2022 Oct 24.
    Resolution doubling in light-sheet microscopy via oblique plane structured illumination.
    Bingying Chen, Bo-Jui Chang, Philippe Roudot, Felix Zhou, Etai Sapoznik, Madeleine Marlar-Pavey, James B Hayes, Peter T Brown, Chih-Wei Zeng, Talley Lambert, Jonathan R Friedman, Chun-Li Zhang, Dylan T Burnette, Douglas P Shepherd, Kevin M Dean, Reto P Fiolka.
      Structured illumination microscopy (SIM) doubles the spatial resolution of a fluorescence microscope without requiring high laser powers or specialized fluorophores. However, the excitation of out-of-focus fluorescence can accelerate photobleaching and phototoxicity. In contrast, light-sheet fluorescence microscopy (LSFM) largely avoids exciting out-of-focus fluorescence, thereby enabling volumetric imaging with low photobleaching and intrinsic optical sectioning. Combining SIM with LSFM would enable gentle three-dimensional (3D) imaging at doubled resolution. However, multiple orientations of the illumination pattern, which are needed for isotropic resolution doubling in SIM, are challenging to implement in a light-sheet format. Here we show that multidirectional structured illumination can be implemented in oblique plane microscopy, an LSFM technique that uses a single objective for excitation and detection, in a straightforward manner. We demonstrate isotropic lateral resolution below 150 nm, combined with lower phototoxicity compared to traditional SIM systems and volumetric acquisition speed exceeding 1 Hz.
    DOI:  https://doi.org/10.1038/s41592-022-01635-8
  68. Nat Commun. 2022 Oct 23. 13(1): 6308
    Metabolic control of CD47 expression through LAT2-mediated amino acid uptake promotes tumor immune evasion.
    Zenan Wang, Binghao Li, Shan Li, Wenlong Lin, Zhan Wang, Shengdong Wang, Weida Chen, Wei Shi, Tao Chen, Hao Zhou, Eloy Yinwang, Wenkan Zhang, Haochen Mou, Xupeng Chai, Jiahao Zhang, Zhimin Lu, Zhaoming Ye.
      Chemotherapy elicits tumor immune evasion with poorly characterized mechanisms. Here, we demonstrate that chemotherapy markedly enhances the expression levels of CD47 in osteosarcoma tissues, which are positively associated with patient mortality. We reveal that macrophages in response to chemotherapy secrete interleukin-18, which in turn upregulates expression of L-amino acid transporter 2 (LAT2) in tumor cells for substantially enhanced uptakes of leucine and glutamine, two potent stimulators of mTORC1. The increased levels of leucine and enhanced glutaminolysis activate mTORC1 and subsequent c-Myc-mediated transcription of CD47. Depletion of LAT2 or treatment of tumor cells with a LAT inhibitor downregulates CD47 with enhanced macrophage infiltration and phagocytosis of tumor cells, and sensitizes osteosarcoma to doxorubicin treatment in mice. These findings unveil a mutual regulation between macrophage and tumor cells that plays a critical role in tumor immune evasion and underscore the potential to intervene with the LAT2-mediated amino acid uptake for improving cancer therapies.
    DOI:  https://doi.org/10.1038/s41467-022-34064-4
  69. Nat Commun. 2022 Oct 26. 13(1): 6368
    Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids.
    Carl J Schiltz, Jennifer R Wilson, Christopher J Hosford, Myfanwy C Adams, Stephanie E Preising, Stacy L DeBlasio, Hannah J MacLeod, Joyce Van Eck, Michelle L Heck, Joshua S Chappie.
      Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain (NRTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the NRTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV NRTD can act as an inhibitor of virus transmission and identify NRTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus NRTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.
    DOI:  https://doi.org/10.1038/s41467-022-33979-2
  70. Diabetologia. 2022 Oct 25.
    Intra-islet insulin synthesis defects are associated with endoplasmic reticulum stress and loss of beta cell identity in human diabetes.
    Noemi Brusco, Guido Sebastiani, Gianfranco Di Giuseppe, Giada Licata, Giuseppina E Grieco, Daniela Fignani, Laura Nigi, Caterina Formichi, Elena Aiello, Stefano Auddino, Giuseppe Quero, Chiara M A Cefalo, Francesca Cinti, Andrea Mari, Pietro M Ferraro, Alfredo Pontecorvi, Sergio Alfieri, Andrea Giaccari, Francesco Dotta, Teresa Mezza.
       AIMS/HYPOTHESIS: Endoplasmic reticulum (ER) stress and beta cell dedifferentiation both play leading roles in impaired insulin secretion in overt type 2 diabetes. Whether and how these factors are related in the natural history of the disease remains, however, unclear.
    METHODS: In this study, we analysed pancreas biopsies from a cohort of metabolically characterised living donors to identify defects in in situ insulin synthesis and intra-islet expression of ER stress and beta cell phenotype markers.
    RESULTS: We provide evidence that in situ altered insulin processing is closely connected to in vivo worsening of beta cell function. Further, activation of ER stress genes reflects the alteration of insulin processing in situ. Using a combination of 17 different markers, we characterised individual pancreatic islets from normal glucose tolerant, impaired glucose tolerant and type 2 diabetic participants and reconstructed disease progression.
    CONCLUSIONS/INTERPRETATION: Our study suggests that increased beta cell workload is accompanied by a progressive increase in ER stress with defects in insulin synthesis and loss of beta cell identity.
    Keywords:  Dedifferentiation; ER stress; Pancreatic islets; Proinsulin; Type 2 diabetes
    DOI:  https://doi.org/10.1007/s00125-022-05814-2
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