bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022–12–25
sixty-one papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. Commercialisation and entrepreneurship - an academic viewpoint.
  2. Exon junction complex shapes the m6A epitranscriptome.
  3. Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8+ T lymphocytes.
  4. Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease.
  5. Regulation of the alveolar regenerative niche by amphiregulin-producing regulatory T cells.
  6. Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation.
  7. Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.
  8. mTORC1 regulates a lysosome-dependent adaptive shift in intracellular lipid species.
  9. Induction of T-helper-17-cell-mediated anti-tumour immunity by pathogen-mimicking polymer nanoparticles.
  10. Glassfrogs conceal blood in their liver to maintain transparency.
  11. A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis.
  12. Loss of SUMO-specific protease 2 causes isolated glucocorticoid deficiency by blocking adrenal cortex zonal transdifferentiation in mice.
  13. Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.
  14. Innate immune signaling drives late cardiac toxicity following DNA-damaging cancer therapies.
  15. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis.
  16. Chronic exposure to synthetic food colorant Allura Red AC promotes susceptibility to experimental colitis via intestinal serotonin in mice.
  17. Rebalancing TGFβ1/BMP signals in exhausted T cells unlocks responsiveness to immune checkpoint blockade therapy.
  18. A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk.
  19. ETV3 and ETV6 enable monocyte differentiation into dendritic cells by repressing macrophage fate commitment.
  20. Multiplexed mapping of chromatin features at single-cell resolution.
  21. A brainstem integrator for self-location memory and positional homeostasis in zebrafish.
  22. Cellular sinkholes buffer membrane tension.
  23. Blocking AMPK β1 myristoylation enhances AMPK activity and protects mice from high-fat diet-induced obesity and hepatic steatosis.
  24. Endothelial cells regulate astrocyte to neural progenitor cell trans-differentiation in a mouse model of stroke.
  25. "The Times They Are A-Changin'" at Diabetes Care.
  26. Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.
  27. Aged lipid-laden microglia display impaired responses to stroke.
  28. Hypoxia drives CD39-dependent suppressor function in exhausted T cells to limit antitumor immunity.
  29. Inheritance of paternal DNA damage by histone-mediated repair restriction.
  30. Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration.
  31. Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice.
  32. Dual roles of hexokinase 2 in shaping microglial function by gating glycolytic flux and mitochondrial activity.
  33. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.
  34. Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4+ T cell reservoir.
  35. TOP READS.
  36. Chemical reaction-mediated covalent localization of bacteria.
  37. A conformation-specific nanobody targeting the nicotinamide mononucleotide-activated state of SARM1.
  38. Acute high fat diet impairs macrophage supported intestinal damage resolution.
  39. Lessons on transparency from the glassfrog.
  40. IL-17/CXCL5 signaling within the oligovascular niche mediates human and mouse white matter injury.
  41. T cell-eosinophil collaboration.
  42. STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.
  43. Adipose-targeted triiodothyronine therapy counteracts obesity-related metabolic complications and atherosclerosis with negligible side effects.
  44. Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing.
  45. Massive measles outbreak threatens India's goal to eliminate disease by 2023.
  46. Waxy lipids and waning insulin secretion.
  47. tRNA-m1A modification: a translational checkpoint for T cell expansion.
  48. Tiltable objective microscope visualizes selectivity for head motion direction and dynamics in zebrafish vestibular system.
  49. An insulin hypersecretion phenotype precedes pancreatic β cell failure in MODY3 patient-specific cells.
  50. Human β-defensin 2 ameliorates acute GVHD by limiting ileal neutrophil infiltration and restraining T cell receptor signaling.
  51. Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children.
  52. Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
  53. R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response.
  54. Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA.
  55. Machine learning assisted interferometric structured illumination microscopy for dynamic biological imaging.
  56. An αvβ3 integrin checkpoint is critical for efficient TH2 cell cytokine polarization and potentiation of antigen-specific immunity.
  57. Systemic enhancement of antitumour immunity by peritumourally implanted immunomodulatory macroporous scaffolds.
  58. Ring domains are essential for GATOR2-dependent mTORC1 activation.
  59. Targeting anti-apoptotic pathways eliminates senescent melanocytes and leads to nevi regression.
  60. Mechanism of IFT-A polymerization into trains for ciliary transport.
  61. Epigenetic clocks, aging, and cancer.
  1. Nat Commun. 2022 Dec 21. 13(1): 7859
    Commercialisation and entrepreneurship - an academic viewpoint.
      
    DOI:  https://doi.org/10.1038/s41467-022-35568-9
  2. Nat Commun. 2022 Dec 23. 13(1): 7904
    Exon junction complex shapes the m6A epitranscriptome.
    Xin Yang, Robinson Triboulet, Qi Liu, Erdem Sendinc, Richard I Gregory.
      N6-methyladenosine (m6A), the most abundant modification of mRNA, is essential for normal development and dysregulation promotes cancer. m6A is highly enriched in the 3' untranslated region (UTR) of a large subset of mRNAs to influence mRNA stability and/or translation. However, the mechanism responsible for the observed m6A distribution remains enigmatic. Here we find the exon junction complex shapes the m6A landscape by blocking METTL3-mediated m6A modification close to exon junctions within coding sequence (CDS). Depletion of EIF4A3, a core component of the EJC, causes increased METTL3 binding and m6A modification of short internal exons, and sites close to exon-exon junctions within mRNA. Reporter gene experiments further support the role of splicing and EIF4A3 deposition in controlling m6A modification via the local steric blockade of METTL3. Our results explain how characteristic patterns of m6A mRNA modification are established and uncover a role of the EJC in shaping the m6A epitranscriptome.
    DOI:  https://doi.org/10.1038/s41467-022-35643-1
  3. Nat Commun. 2022 Dec 17. 13(1): 7796
    Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8+ T lymphocytes.
    Thomas C J Tan, Van Kelly, Xiaoyan Zou, David Wright, Tony Ly, Rose Zamoyska.
      Control of mRNA translation adjusts protein production rapidly and facilitates local cellular responses to environmental conditions. Traditionally initiation of translation is considered to be a major translational control point, however, control of peptide elongation is also important. Here we show that the function of the elongation factor, eIF5a, is regulated dynamically in naïve CD8+ T cells upon activation by post-translational modification, whereupon it facilitates translation of specific subsets of proteins. eIF5a is essential for long-term survival of effector CD8+ T cells and sequencing of nascent polypeptides indicates that the production of proteins which regulate proliferation and key effector functions, particularly the production of IFNγ and less acutely TNF production and cytotoxicity, is dependent on the presence of functional eIF5a. Control of translation in multiple immune cell lineages is required to co-ordinate immune responses and these data illustrate that translational elongation contributes to post-transcriptional regulons important for the control of inflammation.
    DOI:  https://doi.org/10.1038/s41467-022-35252-y
  4. Nat Commun. 2022 Dec 22. 13(1): 7891
    Epigenome-wide meta-analysis identifies DNA methylation biomarkers associated with diabetic kidney disease.
    GENIE consortium
      Type 1 diabetes affects over nine million individuals globally, with approximately 40% developing diabetic kidney disease. Emerging evidence suggests that epigenetic alterations, such as DNA methylation, are involved in diabetic kidney disease. Here we assess differences in blood-derived genome-wide DNA methylation associated with diabetic kidney disease in 1304 carefully characterised individuals with type 1 diabetes and known renal status from two cohorts in the United Kingdom-Republic of Ireland and Finland. In the meta-analysis, we identify 32 differentially methylated CpGs in diabetic kidney disease in type 1 diabetes, 18 of which are located within genes differentially expressed in kidneys or correlated with pathological traits in diabetic kidney disease. We show that methylation at 21 of the 32 CpGs predict the development of kidney failure, extending the knowledge and potentially identifying individuals at greater risk for diabetic kidney disease in type 1 diabetes.
    DOI:  https://doi.org/10.1038/s41467-022-34963-6
  5. J Exp Med. 2023 Mar 06. pii: e20221462. [Epub ahead of print]220(3):
    Regulation of the alveolar regenerative niche by amphiregulin-producing regulatory T cells.
    Katherine A Kaiser, Lucas F Loffredo, Kenia de Los Santos-Alexis, Olivia R Ringham, Nicholas Arpaia.
      Following respiratory viral infection, regeneration of the epithelial barrier is required to preserve lung function and prevent secondary infections. Lung regulatory T (Treg) cells are critical for maintaining blood oxygenation following influenza virus infection through production of the EGFR ligand amphiregulin (Areg); however, how Treg cells engage with progenitors within the alveolar niche is unknown. Here, we describe local interactions between Treg cells and an Areg-responsive population of Col14a1+EGFR+ lung mesenchymal cells that mediate type II alveolar epithelial (AT2) cell-mediated regeneration following influenza virus infection. We propose a mechanism whereby Treg cells are deployed to sites of damage and provide pro-survival cues that support mesenchymal programming of the alveolar niche. In the absence of fibroblast EGFR signaling, we observe impaired AT2 proliferation and disrupted lung remodeling following viral clearance, uncovering a crucial immune/mesenchymal/epithelial network that guides alveolar regeneration.
    DOI:  https://doi.org/10.1084/jem.20221462
  6. Nat Commun. 2022 Dec 21. 13(1): 7791
    Huntington disease oligodendrocyte maturation deficits revealed by single-nucleus RNAseq are rescued by thiamine-biotin supplementation.
    Ryan G Lim, Osama Al-Dalahmah, Jie Wu, Maxwell P Gold, Jack C Reidling, Guomei Tang, Miriam Adam, David K Dansu, Hye-Jin Park, Patrizia Casaccia, Ricardo Miramontes, Andrea M Reyes-Ortiz, Alice Lau, Richard A Hickman, Fatima Khan, Fahad Paryani, Alice Tang, Kenneth Ofori, Emily Miyoshi, Neethu Michael, Nicolette McClure, Xena E Flowers, Jean Paul Vonsattel, Shawn Davidson, Vilas Menon, Vivek Swarup, Ernest Fraenkel, James E Goldman, Leslie M Thompson.
      The complexity of affected brain regions and cell types is a challenge for Huntington's disease (HD) treatment. Here we use single nucleus RNA sequencing to investigate molecular pathology in the cortex and striatum from R6/2 mice and human HD post-mortem tissue. We identify cell type-specific and -agnostic signatures suggesting oligodendrocytes (OLs) and oligodendrocyte precursors (OPCs) are arrested in intermediate maturation states. OL-lineage regulators OLIG1 and OLIG2 are negatively correlated with CAG length in human OPCs, and ATACseq analysis of HD mouse NeuN-negative cells shows decreased accessibility regulated by OL maturation genes. The data implicates glucose and lipid metabolism in abnormal cell maturation and identify PRKCE and Thiamine Pyrophosphokinase 1 (TPK1) as central genes. Thiamine/biotin treatment of R6/1 HD mice to compensate for TPK1 dysregulation restores OL maturation and rescues neuronal pathology. Our insights into HD OL pathology spans multiple brain regions and link OL maturation deficits to abnormal thiamine metabolism.
    DOI:  https://doi.org/10.1038/s41467-022-35388-x
  7. Cell. 2022 Dec 22. pii: S0092-8674(22)01503-3. [Epub ahead of print]185(26): 4937-4953.e23
    Integrative single-cell analysis of cardiogenesis identifies developmental trajectories and non-coding mutations in congenital heart disease.
    Mohamed Ameen, Laksshman Sundaram, Mengcheng Shen, Abhimanyu Banerjee, Soumya Kundu, Surag Nair, Anna Shcherbina, Mingxia Gu, Kitchener D Wilson, Avyay Varadarajan, Nirmal Vadgama, Akshay Balsubramani, Joseph C Wu, Jesse M Engreitz, Kyle Farh, Ioannis Karakikes, Kevin C Wang, Thomas Quertermous, William J Greenleaf, Anshul Kundaje.
      To define the multi-cellular epigenomic and transcriptional landscape of cardiac cellular development, we generated single-cell chromatin accessibility maps of human fetal heart tissues. We identified eight major differentiation trajectories involving primary cardiac cell types, each associated with dynamic transcription factor (TF) activity signatures. We contrasted regulatory landscapes of iPSC-derived cardiac cell types and their in vivo counterparts, which enabled optimization of in vitro differentiation of epicardial cells. Further, we interpreted sequence based deep learning models of cell-type-resolved chromatin accessibility profiles to decipher underlying TF motif lexicons. De novo mutations predicted to affect chromatin accessibility in arterial endothelium were enriched in congenital heart disease (CHD) cases vs. controls. In vitro studies in iPSCs validated the functional impact of identified variation on the predicted developmental cell types. This work thus defines the cell-type-resolved cis-regulatory sequence determinants of heart development and identifies disruption of cell type-specific regulatory elements in CHD.
    DOI:  https://doi.org/10.1016/j.cell.2022.11.028
  8. Nat Metab. 2022 Dec;4(12): 1792-1811
    mTORC1 regulates a lysosome-dependent adaptive shift in intracellular lipid species.
    Aaron M Hosios, Meghan E Wilkinson, Molly C McNamara, Krystle C Kalafut, Margaret E Torrence, John M Asara, Brendan D Manning.
      The mechanistic target of rapamycin complex 1 (mTORC1) senses and relays environmental signals from growth factors and nutrients to metabolic networks and adaptive cellular systems to control the synthesis and breakdown of macromolecules; however, beyond inducing de novo lipid synthesis, the role of mTORC1 in controlling cellular lipid content remains poorly understood. Here we show that inhibition of mTORC1 via small molecule inhibitors or nutrient deprivation leads to the accumulation of intracellular triglycerides in both cultured cells and a mouse tumor model. The elevated triglyceride pool following mTORC1 inhibition stems from the lysosome-dependent, but autophagy-independent, hydrolysis of phospholipid fatty acids. The liberated fatty acids are available for either triglyceride synthesis or β-oxidation. Distinct from the established role of mTORC1 activation in promoting de novo lipid synthesis, our data indicate that mTORC1 inhibition triggers membrane phospholipid trafficking to the lysosome for catabolism and an adaptive shift in the use of constituent fatty acids for storage or energy production.
    DOI:  https://doi.org/10.1038/s42255-022-00706-6
  9. Nat Biomed Eng. 2022 Dec 23.
    Induction of T-helper-17-cell-mediated anti-tumour immunity by pathogen-mimicking polymer nanoparticles.
    Sejin Son, Jutaek Nam, April S Kim, Jinsung Ahn, Kyung Soo Park, May Thazin Phoo, Brett Sherren, Weiping Zou, Soo-Hong Lee, Omid C Farokhzad, Jinjun Shi, James J Moon.
      The effectivity of cancer immunotherapies is hindered by immunosuppressive tumour microenvironments that are poorly infiltrated by effector T cells and natural killer cells. In infection and autoimmune disease, the recruitment and activation of effector immune cells is coordinated by pro-inflammatory T helper 17 (TH17) cells. Here we show that pathogen-mimicking hollow nanoparticles displaying mannan (a polysaccharide that activates TH17 cells in microbial cell walls) limit the fraction of regulatory T cells and induce TH17-cell-mediated anti-tumour responses. The nanoparticles activate the pattern-recognition receptor Dectin-2 and Toll-like receptor 4 in dendritic cells, and promote the differentiation of CD4+ T cells into the TH17 phenotype. In mice, intra-tumoural administration of the nanoparticles decreased the fraction of regulatory T cells in the tumour while markedly increasing the fractions of TH17 cells (and the levels of TH17-cell-associated cytokines), CD8+ T cells, natural killer cells and M1-like macrophages. The anti-tumoural activity of the effector cells was amplified by an agonistic antibody against the co-stimulatory receptor OX40 in multiple mouse models. Nanomaterials that induce TH17-cell-mediated immune responses may have therapeutic potential.
    DOI:  https://doi.org/10.1038/s41551-022-00973-4
  10. Science. 2022 Dec 23. 378(6626): 1315-1320
    Glassfrogs conceal blood in their liver to maintain transparency.
    Carlos Taboada, Jesse Delia, Maomao Chen, Chenshuo Ma, Xiaorui Peng, Xiaoyi Zhu, Laiming Jiang, Tri Vu, Qifa Zhou, Junjie Yao, Lauren O'Connell, Sönke Johnsen.
      Transparency in animals is a complex form of camouflage involving mechanisms that reduce light scattering and absorption throughout the organism. In vertebrates, attaining transparency is difficult because their circulatory system is full of red blood cells (RBCs) that strongly attenuate light. Here, we document how glassfrogs overcome this challenge by concealing these cells from view. Using photoacoustic imaging to track RBCs in vivo, we show that resting glassfrogs increase transparency two- to threefold by removing ~89% of their RBCs from circulation and packing them within their liver. Vertebrate transparency thus requires both see-through tissues and active mechanisms that "clear" respiratory pigments from these tissues. Furthermore, glassfrogs' ability to regulate the location, density, and packing of RBCs without clotting offers insight in metabolic, hemodynamic, and blood-clot research.
    DOI:  https://doi.org/10.1126/science.abl6620
  11. Nat Commun. 2022 Dec 22. 13(1): 7851
    A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis.
    Alan E Murphy, Nathan G Skene.
      
    DOI:  https://doi.org/10.1038/s41467-022-35519-4
  12. Nat Commun. 2022 Dec 21. 13(1): 7858
    Loss of SUMO-specific protease 2 causes isolated glucocorticoid deficiency by blocking adrenal cortex zonal transdifferentiation in mice.
    Damien Dufour, Typhanie Dumontet, Isabelle Sahut-Barnola, Aude Carusi, Méline Onzon, Eric Pussard, James Jr Wilmouth, Julie Olabe, Cécily Lucas, Adrien Levasseur, Christelle Damon-Soubeyrand, Jean-Christophe Pointud, Florence Roucher-Boulez, Igor Tauveron, Guillaume Bossis, Edward T Yeh, David T Breault, Pierre Val, Anne-Marie Lefrançois-Martinez, Antoine Martinez.
      SUMOylation is a dynamic posttranslational modification, that provides fine-tuning of protein function involved in the cellular response to stress, differentiation, and tissue development. In the adrenal cortex, an emblematic endocrine organ that mediates adaptation to physiological demands, the SUMOylation gradient is inversely correlated with the gradient of cellular differentiation raising important questions about its role in functional zonation and the response to stress. Considering that SUMO-specific protease 2 (SENP2), a deSUMOylating enzyme, is upregulated by Adrenocorticotropic Hormone (ACTH)/cAMP-dependent Protein Kinase (PKA) signalling within the zona fasciculata, we generated mice with adrenal-specific Senp2 loss to address these questions. Disruption of SENP2 activity in steroidogenic cells leads to specific hypoplasia of the zona fasciculata, a blunted reponse to ACTH and isolated glucocorticoid deficiency. Mechanistically, overSUMOylation resulting from SENP2 loss shifts the balance between ACTH/PKA and WNT/β-catenin signalling leading to repression of PKA activity and ectopic activation of β-catenin. At the cellular level, this blocks transdifferentiation of β-catenin-positive zona glomerulosa cells into fasciculata cells and sensitises them to premature apoptosis. Our findings indicate that the SUMO pathway is critical for adrenal homeostasis and stress responsiveness.
    DOI:  https://doi.org/10.1038/s41467-022-35526-5
  13. Cell. 2022 Dec 22. pii: S0092-8674(22)01467-2. [Epub ahead of print]185(26): 4921-4936.e15
    Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism.
    Tommi Vatanen, Karolina S Jabbar, Terhi Ruohtula, Jarno Honkanen, Julian Avila-Pacheco, Heli Siljander, Martin Stražar, Sami Oikarinen, Heikki Hyöty, Jorma Ilonen, Caroline M Mitchell, Moran Yassour, Suvi M Virtanen, Clary B Clish, Damian R Plichta, Hera Vlamakis, Mikael Knip, Ramnik J Xavier.
      The perinatal period represents a critical window for cognitive and immune system development, promoted by maternal and infant gut microbiomes and their metabolites. Here, we tracked the co-development of microbiomes and metabolomes from late pregnancy to 1 year of age using longitudinal multi-omics data from a cohort of 70 mother-infant dyads. We discovered large-scale mother-to-infant interspecies transfer of mobile genetic elements, frequently involving genes associated with diet-related adaptations. Infant gut metabolomes were less diverse than maternal but featured hundreds of unique metabolites and microbe-metabolite associations not detected in mothers. Metabolomes and serum cytokine signatures of infants who received regular-but not extensively hydrolyzed-formula were distinct from those of exclusively breastfed infants. Taken together, our integrative analysis expands the concept of vertical transmission of the gut microbiome and provides original insights into the development of maternal and infant microbiomes and metabolomes during late pregnancy and early life.
    Keywords:  gut metabolome; horizontal gene transfer; infant gut microbiome; mother-to-infant microbiome transmission
    DOI:  https://doi.org/10.1016/j.cell.2022.11.023
  14. J Exp Med. 2023 Mar 06. pii: e20220809. [Epub ahead of print]220(3):
    Innate immune signaling drives late cardiac toxicity following DNA-damaging cancer therapies.
    Achraf Shamseddine, Suchit H Patel, Valery Chavez, Zachary R Moore, Mutayyaba Adnan, Melody Di Bona, Jun Li, Chau T Dang, Lakshmi V Ramanathan, Kevin C Oeffinger, Jennifer E Liu, Richard M Steingart, Alessandra Piersigilli, Nicholas D Socci, Angel T Chan, Anthony F Yu, Samuel F Bakhoum, Adam M Schmitt.
      Late cardiac toxicity is a potentially lethal complication of cancer therapy, yet the pathogenic mechanism remains largely unknown, and few treatment options exist. Here we report DNA-damaging agents such as radiation and anthracycline chemotherapies inducing delayed cardiac inflammation following therapy due to activation of cGAS- and STING-dependent type I interferon signaling. Genetic ablation of cGAS-STING signaling in mice inhibits DNA damage-induced cardiac inflammation, rescues late cardiac functional decline, and prevents death from cardiac events. Treatment with a STING antagonist suppresses cardiac interferon signaling following DNA-damaging therapies and effectively mitigates cardiac toxicity. These results identify a therapeutically targetable, pathogenic mechanism for one of the most vexing treatment-related toxicities in cancer survivors.
    DOI:  https://doi.org/10.1084/jem.20220809
  15. Nat Genet. 2022 Dec 20.
    Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis.
    Peter Zeller, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, Alexander van Oudenaarden.
      Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.
    DOI:  https://doi.org/10.1038/s41588-022-01260-3
  16. Nat Commun. 2022 Dec 20. 13(1): 7617
    Chronic exposure to synthetic food colorant Allura Red AC promotes susceptibility to experimental colitis via intestinal serotonin in mice.
    Yun Han Kwon, Suhrid Banskota, Huaqing Wang, Laura Rossi, Jensine A Grondin, Saad A Syed, Yeganeh Yousefi, Jonathan D Schertzer, Katherine M Morrison, Michael G Wade, Alison C Holloway, Michael G Surette, Gregory R Steinberg, Waliul I Khan.
      Chemicals in food are widely used leading to significant human exposure. Allura Red AC (AR) is a highly common synthetic colorant; however, little is known about its impact on colitis. Here, we show chronic exposure of AR at a dose found in commonly consumed dietary products exacerbates experimental models of colitis in mice. While intermittent exposure is more akin to a typical human exposure, intermittent exposure to AR in mice for 12 weeks, does not influence susceptibility to colitis. However, exposure to AR during early life primes mice to heightened susceptibility to colitis. In addition, chronic exposure to AR induces mild colitis, which is associated with elevated colonic serotonin (5-hydroxytryptamine; 5-HT) levels and impairment of the epithelial barrier function via myosin light chain kinase (MLCK). Importantly, chronic exposure to AR does not influence colitis susceptibility in mice lacking tryptophan hydroxylase 1 (TPH1), the rate limiting enzyme for 5-HT biosynthesis. Cecal transfer of the perturbed gut microbiota by AR exposure worsens colitis severity in the recipient germ-free (GF) mice. Furthermore, chronic AR exposure elevates colonic 5-HT levels in naïve GF mice. Though it remains unknown whether AR has similar effects in humans, our study reveals that chronic long-term exposure to a common synthetic colorant promotes experimental colitis via colonic 5-HT in gut microbiota-dependent and -independent pathway in mice.
    DOI:  https://doi.org/10.1038/s41467-022-35309-y
  17. Nat Immunol. 2022 Dec 21.
    Rebalancing TGFβ1/BMP signals in exhausted T cells unlocks responsiveness to immune checkpoint blockade therapy.
    Abbey A Saadey, Amir Yousif, Nicole Osborne, Roya Shahinfar, Yu-Lin Chen, Brooke Laster, Meera Rajeev, Parker Bauman, Amy Webb, Hazem E Ghoneim.
      T cell dysfunctionality prevents the clearance of chronic infections and cancer. Furthermore, epigenetic programming in dysfunctional CD8+ T cells limits their response to immunotherapies, including immune checkpoint blockade (ICB). However, it is unclear which upstream signals drive acquisition of dysfunctional epigenetic programs, and whether therapeutically targeting these signals can remodel terminally dysfunctional T cells to an ICB-responsive state. Here we innovate an in vitro model system of stable human T cell dysfunction and show that chronic TGFβ1 signaling in posteffector CD8+ T cells accelerates their terminal dysfunction through stable epigenetic changes. Conversely, boosting bone morphogenetic protein (BMP) signaling while blocking TGFβ1 preserved effector and memory programs in chronically stimulated human CD8+ T cells, inducing superior responses to tumors and synergizing the ICB responses during chronic viral infection. Thus, rebalancing TGFβ1/BMP signals provides an exciting new approach to unleash dysfunctional CD8+ T cells and enhance T cell immunotherapies.
    DOI:  https://doi.org/10.1038/s41590-022-01384-y
  18. Nat Genet. 2022 Dec 21.
    A genome-wide CRISPR screen identifies CALCOCO2 as a regulator of beta cell function influencing type 2 diabetes risk.
    Antje K Rottner, Yingying Ye, Elena Navarro-Guerrero, Varsha Rajesh, Alina Pollner, Romina J Bevacqua, Jing Yang, Aliya F Spigelman, Roberta Baronio, Austin Bautista, Soren K Thomsen, James Lyon, Sameena Nawaz, Nancy Smith, Agata Wesolowska-Andersen, Jocelyn E Manning Fox, Han Sun, Seung K Kim, Daniel Ebner, Patrick E MacDonald, Anna L Gloyn.
      Identification of the genes and processes mediating genetic association signals for complex diseases represents a major challenge. As many of the genetic signals for type 2 diabetes (T2D) exert their effects through pancreatic islet-cell dysfunction, we performed a genome-wide pooled CRISPR loss-of-function screen in a human pancreatic beta cell line. We assessed the regulation of insulin content as a disease-relevant readout of beta cell function and identified 580 genes influencing this phenotype. Integration with genetic and genomic data provided experimental support for 20 candidate T2D effector transcripts including the autophagy receptor CALCOCO2. Loss of CALCOCO2 was associated with distorted mitochondria, less proinsulin-containing immature granules and accumulation of autophagosomes upon inhibition of late-stage autophagy. Carriers of T2D-associated variants at the CALCOCO2 locus further displayed altered insulin secretion. Our study highlights how cellular screens can augment existing multi-omic efforts to support mechanistic understanding and provide evidence for causal effects at genome-wide association studies loci.
    DOI:  https://doi.org/10.1038/s41588-022-01261-2
  19. Nat Immunol. 2022 Dec 21.
    ETV3 and ETV6 enable monocyte differentiation into dendritic cells by repressing macrophage fate commitment.
    Javiera Villar, Adeline Cros, Alba De Juan, Lamine Alaoui, Pierre-Emmanuel Bonte, Colleen M Lau, Ioanna Tiniakou, Boris Reizis, Elodie Segura.
      In inflamed tissues, monocytes differentiate into macrophages (mo-Macs) or dendritic cells (mo-DCs). In chronic nonresolving inflammation, mo-DCs are major drivers of pathogenic events. Manipulating monocyte differentiation would therefore be an attractive therapeutic strategy. However, how the balance of mo-DC versus mo-Mac fate commitment is regulated is not clear. In the present study, we show that the transcriptional repressors ETV3 and ETV6 control human monocyte differentiation into mo-DCs. ETV3 and ETV6 inhibit interferon (IFN)-stimulated genes; however, their action on monocyte differentiation is independent of IFN signaling. Instead, we find that ETV3 and ETV6 directly repress mo-Mac development by controlling MAFB expression. Mice deficient for Etv6 in monocytes have spontaneous expression of IFN-stimulated genes, confirming that Etv6 regulates IFN responses in vivo. Furthermore, these mice have impaired mo-DC differentiation during inflammation and reduced pathology in an experimental autoimmune encephalomyelitis model. These findings provide information about the molecular control of monocyte fate decision and identify ETV6 as a therapeutic target to redirect monocyte differentiation in inflammatory disorders.
    DOI:  https://doi.org/10.1038/s41590-022-01374-0
  20. Nat Biotechnol. 2022 Dec 19.
    Multiplexed mapping of chromatin features at single-cell resolution.
      
    DOI:  https://doi.org/10.1038/s41587-022-01589-4
  21. Cell. 2022 Dec 22. pii: S0092-8674(22)01466-0. [Epub ahead of print]185(26): 5011-5027.e20
    A brainstem integrator for self-location memory and positional homeostasis in zebrafish.
    En Yang, Maarten F Zwart, Ben James, Mikail Rubinov, Ziqiang Wei, Sujatha Narayan, Nikita Vladimirov, Brett D Mensh, James E Fitzgerald, Misha B Ahrens.
      To track and control self-location, animals integrate their movements through space. Representations of self-location are observed in the mammalian hippocampal formation, but it is unknown if positional representations exist in more ancient brain regions, how they arise from integrated self-motion, and by what pathways they control locomotion. Here, in a head-fixed, fictive-swimming, virtual-reality preparation, we exposed larval zebrafish to a variety of involuntary displacements. They tracked these displacements and, many seconds later, moved toward their earlier location through corrective swimming ("positional homeostasis"). Whole-brain functional imaging revealed a network in the medulla that stores a memory of location and induces an error signal in the inferior olive to drive future corrective swimming. Optogenetically manipulating medullary integrator cells evoked displacement-memory behavior. Ablating them, or downstream olivary neurons, abolished displacement corrections. These results reveal a multiregional hindbrain circuit in vertebrates that integrates self-motion and stores self-location to control locomotor behavior.
    Keywords:  brainstem; cerebellum; hippocampus; inferior olive; memory; motor control; navigation; neural circuits; neuroscience; path integration; zebrafish
    DOI:  https://doi.org/10.1016/j.cell.2022.11.022
  22. Nat Cell Biol. 2022 Dec 21.
    Cellular sinkholes buffer membrane tension.
    Anne K Kenworthy.
      
    DOI:  https://doi.org/10.1038/s41556-022-01032-5
  23. Cell Rep. 2022 Dec 20. pii: S2211-1247(22)01758-2. [Epub ahead of print]41(12): 111862
    Blocking AMPK β1 myristoylation enhances AMPK activity and protects mice from high-fat diet-induced obesity and hepatic steatosis.
    Katyayanee Neopane, Natalie Kozlov, Florentina Negoita, Lisa Murray-Segal, Robert Brink, Ashfaqul Hoque, Ashley J Ovens, Gavin Tjin, Luke M McAloon, Dingyi Yu, Naomi X Y Ling, Matthew J Sanders, Jonathan S Oakhill, John W Scott, Gregory R Steinberg, Kim Loh, Bruce E Kemp, Kei Sakamoto, Sandra Galic.
      AMP-activated protein kinase (AMPK) is a master regulator of cellular energy homeostasis and a therapeutic target for metabolic diseases. Co/post-translational N-myristoylation of glycine-2 (Gly2) of the AMPK β subunit has been suggested to regulate the distribution of the kinase between the cytosol and membranes through a "myristoyl switch" mechanism. However, the relevance of AMPK myristoylation for metabolic signaling in cells and in vivo is unclear. Here, we generated knockin mice with a Gly2-to-alanine point mutation of AMPKβ1 (β1-G2A). We demonstrate that non-myristoylated AMPKβ1 has reduced stability but is associated with increased kinase activity and phosphorylation of the Thr172 activation site in the AMPK α subunit. Using proximity ligation assays, we show that loss of β1 myristoylation impedes colocalization of the phosphatase PPM1A/B with AMPK in cells. Mice carrying the β1-G2A mutation have improved metabolic health with reduced adiposity, hepatic lipid accumulation, and insulin resistance under conditions of high-fat diet-induced obesity.
    Keywords:  AMPK; CP: Metabolism; adiposity; myristoylation; phosphatase; signal transduction; steatosis
    DOI:  https://doi.org/10.1016/j.celrep.2022.111862
  24. Nat Commun. 2022 Dec 19. 13(1): 7812
    Endothelial cells regulate astrocyte to neural progenitor cell trans-differentiation in a mouse model of stroke.
    Wenlu Li, Emiri T Mandeville, Violeta Durán-Laforet, Norito Fukuda, Zhanyang Yu, Yi Zheng, Aaron Held, Ji-Hyun Park, Takafumi Nakano, Masayoshi Tanaka, Jingfei Shi, Elga Esposito, Wanting Niu, Changhong Xing, Kazuhide Hayakawa, Ignacio Lizasoain, Klaus van Leyen, Xunming Ji, Brian J Wainger, Maria A Moro, Eng H Lo.
      The concept of the neurovascular unit emphasizes the importance of cell-cell signaling between neural, glial, and vascular compartments. In neurogenesis, for example, brain endothelial cells play a key role by supplying trophic support to neural progenitors. Here, we describe a surprising phenomenon where brain endothelial cells may release trans-differentiation signals that convert astrocytes into neural progenitor cells in male mice after stroke. After oxygen-glucose deprivation, brain endothelial cells release microvesicles containing pro-neural factor Ascl1 that enter into astrocytes to induce their trans-differentiation into neural progenitors. In mouse models of focal cerebral ischemia, Ascl1 is upregulated in endothelium prior to astrocytic conversion into neural progenitor cells. Injecting brain endothelial-derived microvesicles amplifies the process of astrocyte trans-differentiation. Endothelial-specific overexpression of Ascl1 increases the local conversion of astrocytes into neural progenitors and improves behavioral recovery. Our findings describe an unexpected vascular-regulated mechanism of neuroplasticity that may open up therapeutic opportunities for improving outcomes after stroke.
    DOI:  https://doi.org/10.1038/s41467-022-35498-6
  25. Diabetes Care. 2023 Jan 01. 46(1): 3-5
    "The Times They Are A-Changin'" at Diabetes Care.
    Steven E Kahn, Cheryl A M Anderson, John B Buse, Elizabeth Selvin, Sonia Y Angell, Vanita R Aroda, Jessica R Castle, Alice Y Y Cheng, Thomas Danne, Justin B Echouffo-Tcheugui, Jose C Florez, Meghana D Gadgil, Amalia Gastaldelli, Jennifer B Green, Ania M Jastreboff, Alka M Kanaya, Namratha R Kandula, Csaba P Kovesdy, Neda Laiteerapong, Kristen J Nadeau, Rodica Pop-Busui, Camille E Powe, Casey M Rebholz, Michael R Rickels, Naveed Sattar, Jonathan E Shaw, Emily K Sims, Kristina M Utzschneider, Adrian Vella, Cuilin Zhang.
      
    DOI:  https://doi.org/10.2337/dci22-0045
  26. Nat Biotechnol. 2022 Dec 19.
    Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution.
    Tim Stuart, Stephanie Hao, Bingjie Zhang, Levan Mekerishvili, Dan A Landau, Silas Maniatis, Rahul Satija, Ivan Raimondi.
      Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility and other factors. Current methods for defining chromatin states cannot measure more than one aspect in a single experiment at single-cell resolution. Here we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), an assay capable of measuring the genome-wide presence of up to three histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq uses recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk-cell and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in human immune cells. We also extend NTT-seq to enable simultaneous profiling of cell surface protein expression and multimodal chromatin states to study cells of the immune system.
    DOI:  https://doi.org/10.1038/s41587-022-01588-5
  27. EMBO Mol Med. 2022 Dec 21. e17175
    Aged lipid-laden microglia display impaired responses to stroke.
    Maria Arbaizar-Rovirosa, Jordi Pedragosa, Juan J Lozano, Carme Casal, Albert Pol, Mattia Gallizioli, Anna M Planas.
      Microglial cells of the aged brain manifest signs of dysfunction that could contribute to the worse neurological outcome of stroke in the elderly. Treatment with colony-stimulating factor 1 receptor antagonists enables transient microglia depletion that is followed by microglia repopulation after treatment interruption, causing no known harm to mice. We tested whether this strategy restored microglia function and ameliorated stroke outcome in old mice. Cerebral ischemia/reperfusion induced innate immune responses in microglia highlighted by type I interferon and metabolic changes involving lipid droplet biogenesis. Old microglia accumulated lipids under steady state and displayed exacerbated innate immune responses to stroke. Microglia repopulation in old mice reduced lipid-laden microglia, and the cells exhibited reduced inflammatory responses to ischemia. Moreover, old mice with renewed microglia showed improved motor function 2 weeks after stroke. We conclude that lipid deposits in aged microglia impair the cellular responses to ischemia and worsen functional recovery in old mice.
    Keywords:  brain; immunometabolism; ischemia; lipid droplets; microglia
    DOI:  https://doi.org/10.15252/emmm.202217175
  28. Nat Immunol. 2022 Dec 21.
    Hypoxia drives CD39-dependent suppressor function in exhausted T cells to limit antitumor immunity.
    Paolo D A Vignali, Kristin DePeaux, McLane J Watson, Chenxian Ye, B Rhodes Ford, Konstantinos Lontos, Nicole K McGaa, Nicole E Scharping, Ashley V Menk, Simon C Robson, Amanda C Poholek, Dayana B Rivadeneira, Greg M Delgoffe.
      CD8+ T cells are critical for elimination of cancer cells. Factors within the tumor microenvironment (TME) can drive these cells to a hypofunctional state known as exhaustion. The most terminally exhausted T (tTex) cells are resistant to checkpoint blockade immunotherapy and might instead limit immunotherapeutic efficacy. Here we show that intratumoral CD8+ tTex cells possess transcriptional features of CD4+Foxp3+ regulatory T cells and are similarly capable of directly suppressing T cell proliferation ex vivo. tTex cell suppression requires CD39, which generates immunosuppressive adenosine. Restricted deletion of CD39 in endogenous CD8+ T cells resulted in slowed tumor progression, improved immunotherapy responsiveness and enhanced infiltration of transferred tumor-specific T cells. CD39 is induced on tTex cells by tumor hypoxia, thus mitigation of hypoxia limits tTex suppression. Together, these data suggest tTex cells are an important regulatory population in cancer and strategies to limit their generation, reprogram their immunosuppressive state or remove them from the TME might potentiate immunotherapy.
    DOI:  https://doi.org/10.1038/s41590-022-01379-9
  29. Nature. 2022 Dec 21.
    Inheritance of paternal DNA damage by histone-mediated repair restriction.
    Siyao Wang, David H Meyer, Björn Schumacher.
      How paternal exposure to ionizing radiation affects genetic inheritance and disease risk in the offspring has been a long-standing question in radiation biology. In humans, nearly 80% of transmitted mutations arise in the paternal germline1, but the transgenerational effects of ionizing radiation exposure has remained controversial and the mechanisms are unknown. Here we show that in sex-separated Caenorhabditis elegans strains, paternal, but not maternal, exposure to ionizing radiation leads to transgenerational embryonic lethality. The offspring of irradiated males displayed various genome instability phenotypes, including DNA fragmentation, chromosomal rearrangement and aneuploidy. Paternal DNA double strand breaks were repaired by maternally provided error-prone polymerase theta-mediated end joining. Mechanistically, we show that depletion of an orthologue of human histone H1.0, HIS-24, or the heterochromatin protein HPL-1, could significantly reverse the transgenerational embryonic lethality. Removal of HIS-24 or HPL-1 reduced histone 3 lysine 9 dimethylation and enabled error-free homologous recombination repair in the germline of the F1 generation from ionizing radiation-treated P0 males, consequently improving the viability of the F2 generation. This work establishes the mechanistic underpinnings of the heritable consequences of paternal radiation exposure on the health of offspring, which may lead to congenital disorders and cancer in humans.
    DOI:  https://doi.org/10.1038/s41586-022-05544-w
  30. Nature. 2022 Dec 21.
    Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration.
    Victoria Moiseeva, Andrés Cisneros, Valentina Sica, Oleg Deryagin, Yiwei Lai, Sascha Jung, Eva Andrés, Juan An, Jessica Segalés, Laura Ortet, Vera Lukesova, Giacomo Volpe, Alberto Benguria, Ana Dopazo, Salvador Aznar-Benitah, Yasuteru Urano, Antonio Del Sol, Miguel A Esteban, Yasuyuki Ohkawa, Antonio L Serrano, Eusebio Perdiguero, Pura Muñoz-Cánoves.
      Tissue regeneration requires coordination between resident stem cells and local niche cells1,2. Here we identify that senescent cells are integral components of the skeletal muscle regenerative niche that repress regeneration at all stages of life. The technical limitation of senescent-cell scarcity3 was overcome by combining single-cell transcriptomics and a senescent-cell enrichment sorting protocol. We identified and isolated different senescent cell types from damaged muscles of young and old mice. Deeper transcriptome, chromatin and pathway analyses revealed conservation of cell identity traits as well as two universal senescence hallmarks (inflammation and fibrosis) across cell type, regeneration time and ageing. Senescent cells create an aged-like inflamed niche that mirrors inflammation associated with ageing (inflammageing4) and arrests stem cell proliferation and regeneration. Reducing the burden of senescent cells, or reducing their inflammatory secretome through CD36 neutralization, accelerates regeneration in young and old mice. By contrast, transplantation of senescent cells delays regeneration. Our results provide a technique for isolating in vivo senescent cells, define a senescence blueprint for muscle, and uncover unproductive functional interactions between senescent cells and stem cells in regenerative niches that can be overcome. As senescent cells also accumulate in human muscles, our findings open potential paths for improving muscle repair throughout life.
    DOI:  https://doi.org/10.1038/s41586-022-05535-x
  31. Nat Metab. 2022 Dec;4(12): 1812-1829
    Liver RBFOX2 regulates cholesterol homeostasis via Scarb1 alternative splicing in mice.
    Helen A B Paterson, Sijia Yu, Natalia Artigas, Miguel A Prado, Nejc Haberman, Yi-Fang Wang, Andrew M Jobbins, Elena Pahita, Joao Mokochinski, Zoe Hall, Maryse Guerin, Joao A Paulo, Soon Seng Ng, Francesc Villarroya, Sheikh Tamir Rashid, Wilfried Le Goff, Boris Lenhard, Inês Cebola, Daniel Finley, Steven P Gygi, Christopher R Sibley, Santiago Vernia.
      RNA alternative splicing (AS) expands the regulatory potential of eukaryotic genomes. The mechanisms regulating liver-specific AS profiles and their contribution to liver function are poorly understood. Here, we identify a key role for the splicing factor RNA-binding Fox protein 2 (RBFOX2) in maintaining cholesterol homeostasis in a lipogenic environment in the liver. Using enhanced individual-nucleotide-resolution ultra-violet cross-linking and immunoprecipitation, we identify physiologically relevant targets of RBFOX2 in mouse liver, including the scavenger receptor class B type I (Scarb1). RBFOX2 function is decreased in the liver in diet-induced obesity, causing a Scarb1 isoform switch and alteration of hepatocyte lipid homeostasis. Our findings demonstrate that specific AS programmes actively maintain liver physiology, and underlie the lipotoxic effects of obesogenic diets when dysregulated. Splice-switching oligonucleotides targeting this network alleviate obesity-induced inflammation in the liver and promote an anti-atherogenic lipoprotein profile in the blood, underscoring the potential of isoform-specific RNA therapeutics for treating metabolism-associated diseases.
    DOI:  https://doi.org/10.1038/s42255-022-00681-y
  32. Nat Metab. 2022 Dec;4(12): 1756-1774
    Dual roles of hexokinase 2 in shaping microglial function by gating glycolytic flux and mitochondrial activity.
    Yaling Hu, Kelei Cao, Fang Wang, Weiying Wu, Weihao Mai, Liyao Qiu, Yuxiang Luo, Woo-Ping Ge, Binggui Sun, Ligen Shi, Junming Zhu, Jianmin Zhang, Zhiying Wu, Yicheng Xie, Shumin Duan, Zhihua Gao.
      Microglia continuously survey the brain parenchyma and actively shift status following stimulation. These processes demand a unique bioenergetic programme; however, little is known about the metabolic determinants in microglia. By mining large datasets and generating transgenic tools, here we show that hexokinase 2 (HK2), the most active isozyme associated with mitochondrial membrane, is selectively expressed in microglia in the brain. Genetic ablation of HK2 reduced microglial glycolytic flux and energy production, suppressed microglial repopulation, and attenuated microglial surveillance and damage-triggered migration in male mice. HK2 elevation is prominent in immune-challenged or disease-associated microglia. In ischaemic stroke models, however, HK2 deletion promoted neuroinflammation and potentiated cerebral damages. The enhanced inflammatory responses after HK2 ablation in microglia are associated with aberrant mitochondrial function and reactive oxygen species accumulation. Our study demonstrates that HK2 gates both glycolytic flux and mitochondrial activity to shape microglial functions, changes of which contribute to metabolic abnormalities and maladaptive inflammation in brain diseases.
    DOI:  https://doi.org/10.1038/s42255-022-00707-5
  33. Nat Genet. 2022 Dec 21.
    A spatially resolved atlas of the human lung characterizes a gland-associated immune niche.
    Elo Madissoon, Amanda J Oliver, Vitalii Kleshchevnikov, Anna Wilbrey-Clark, Krzysztof Polanski, Nathan Richoz, Ana Ribeiro Orsi, Lira Mamanova, Liam Bolt, Rasa Elmentaite, J Patrick Pett, Ni Huang, Chuan Xu, Peng He, Monika Dabrowska, Sophie Pritchard, Liz Tuck, Elena Prigmore, Shani Perera, Andrew Knights, Agnes Oszlanczi, Adam Hunter, Sara F Vieira, Minal Patel, Rik G H Lindeboom, Lia S Campos, Kazuhiko Matsuo, Takashi Nakayama, Masahiro Yoshida, Kaylee B Worlock, Marko Z Nikolić, Nikitas Georgakopoulos, Krishnaa T Mahbubani, Kourosh Saeb-Parsy, Omer Ali Bayraktar, Menna R Clatworthy, Oliver Stegle, Natsuhiko Kumasaka, Sarah A Teichmann, Kerstin B Meyer.
      Single-cell transcriptomics has allowed unprecedented resolution of cell types/states in the human lung, but their spatial context is less well defined. To (re)define tissue architecture of lung and airways, we profiled five proximal-to-distal locations of healthy human lungs in depth using multi-omic single cell/nuclei and spatial transcriptomics (queryable at lungcellatlas.org ). Using computational data integration and analysis, we extend beyond the suspension cell paradigm and discover macro and micro-anatomical tissue compartments including previously unannotated cell types in the epithelial, vascular, stromal and nerve bundle micro-environments. We identify and implicate peribronchial fibroblasts in lung disease. Importantly, we discover and validate a survival niche for IgA plasma cells in the airway submucosal glands (SMG). We show that gland epithelial cells recruit B cells and IgA plasma cells, and promote longevity and antibody secretion locally through expression of CCL28, APRIL and IL-6. This new 'gland-associated immune niche' has implications for respiratory health.
    DOI:  https://doi.org/10.1038/s41588-022-01243-4
  34. Nat Immunol. 2022 Dec 19.
    Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4+ T cell reservoir.
    Vincent H Wu, Jayme M L Nordin, Son Nguyen, Jaimy Joy, Felicity Mampe, Perla M Del Rio Estrada, Fernanda Torres-Ruiz, Mauricio González-Navarro, Yara Andrea Luna-Villalobos, Santiago Ávila-Ríos, Gustavo Reyes-Terán, Pablo Tebas, Luis J Montaner, Katharine J Bar, Laura A Vella, Michael R Betts.
      Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy (ART) remains a considerable impediment in research towards a cure for HIV. To address this, we developed a single-cell strategy to precisely define the unperturbed peripheral blood HIV-infected memory CD4+ T cell reservoir from ART-treated people living with HIV (ART-PLWH) via the presence of integrated accessible proviral DNA in concert with epigenetic and cell surface protein profiling. We identified profound reservoir heterogeneity within and between ART-PLWH, characterized by new and known surface markers within total and individual memory CD4+ T cell subsets. We further uncovered new epigenetic profiles and transcription factor motifs enriched in HIV-infected cells that suggest infected cells with accessible provirus, irrespective of reservoir distribution, are poised for reactivation during ART treatment. Together, our findings reveal the extensive inter- and intrapersonal cellular heterogeneity of the HIV reservoir, and establish an initial multiomic atlas to develop targeted reservoir elimination strategies.
    DOI:  https://doi.org/10.1038/s41590-022-01371-3
  35. J Immunol. 2023 Jan 01. 210(1): 1
    TOP READS.
      
    DOI:  https://doi.org/10.4049/jimmunol.2290025
  36. Nat Commun. 2022 Dec 17. 13(1): 7808
    Chemical reaction-mediated covalent localization of bacteria.
    Huilong Luo, Yanmei Chen, Xiao Kuang, Xinyue Wang, Fengmin Yang, Zhenping Cao, Lu Wang, Sisi Lin, Feng Wu, Jinyao Liu.
      Methods capable of manipulating bacterial colonization are of great significance for modulating host-microbiota relationships. Here, we describe a strategy of in-situ chemical reaction-mediated covalent localization of bacteria. Through a simple one-step imidoester reaction, primary amino groups on bacterial surface can be converted to free thiols under cytocompatible conditions. Surface thiolation is applicable to modify diverse strains and the number of introduced thiols per bacterium can be easily tuned by varying feed ratios. These chemically reactive bacteria are able to spontaneously bond with mucous layer by catalyst-free thiol-disulfide exchange between mucin-associated disulfides and newly converted thiols on bacterial surface and show thiolation level-dependent attachment. Bacteria optimized with 9.3 × 107 thiols per cell achieve 170-fold higher attachment in mucin-enriched jejunum, a challenging location for gut microbiota to colonize. As a proof-of-concept application for microbiota transplantation, covalent bonding-assisted localization of an oral probiotic in the jejunum generates an improved remission of jejunal mucositis. Our findings demonstrate that transforming bacteria with a reactive surface provides an approach to chemically control bacterial localization, which is highly desirable for developing next-generation bacterial living bioagents.
    DOI:  https://doi.org/10.1038/s41467-022-35579-6
  37. Nat Commun. 2022 Dec 22. 13(1): 7898
    A conformation-specific nanobody targeting the nicotinamide mononucleotide-activated state of SARM1.
    Yun Nan Hou, Yang Cai, Wan Hua Li, Wei Ming He, Zhi Ying Zhao, Wen Jie Zhu, Qiang Wang, Xinyi Mai, Jun Liu, Hon Cheung Lee, Goran Stjepanovic, Hongmin Zhang, Yong Juan Zhao.
      Sterile alpha (SAM) and Toll/interleukin-1 receptor (TIR) motif containing 1 (SARM1) is an autoinhibitory NAD-consuming enzyme that is activated by the accumulation of nicotinamide mononucleotide (NMN) during axonal injury. Its activation mechanism is not fully understood. Here, we generate a nanobody, Nb-C6, that specifically recognizes NMN-activated SARM1. Nb-C6 stains only the activated SARM1 in cells stimulated with CZ-48, a permeant mimetic of NMN, and partially activates SARM1 in vitro and in cells. Cryo-EM of NMN/SARM1/Nb-C6 complex shows an octameric structure with ARM domains bending significantly inward and swinging out together with TIR domains. Nb-C6 binds to SAM domain of the activated SARM1 and stabilized its ARM domain. Mass spectrometry analyses indicate that the activated SARM1 in solution is highly dynamic and that the neighboring TIRs form transient dimers via the surface close to one BB loop. We show that Nb-C6 is a valuable tool for studies of SARM1 activation.
    DOI:  https://doi.org/10.1038/s41467-022-35581-y
  38. JCI Insight. 2022 Dec 20. pii: e164489. [Epub ahead of print]
    Acute high fat diet impairs macrophage supported intestinal damage resolution.
    Andrea A Hill, Myunghoo Kim, Daniel F Zegarra-Ruiz, Lin-Chun Chang, Kendra C Norwood, Adrien Assié, Wan-Jung H Wu, Michael C Renfroe, Hyo W Song, Angela M Major, Buck S Samuel, Joseph M Hyser, Randy S Longman, Gretchen E Diehl.
      Chronic exposure to high-fat diets (HFD) worsens intestinal disease pathology, but acute effects of HFD in tissue damage remain unclear. Here, we used short-term HFD feeding in a model of intestinal injury and found sustained damage with increased cecal dead neutrophil accumulation, along with dietary lipid accumulation. Neutrophil depletion rescued enhanced pathology. Macrophages from HFD treated mice showed reduced capacity to engulf dead neutrophils. Macrophage clearance of dead neutrophils activates critical barrier repair and anti-inflammatory pathways including IL10, which was lost after acute HFD feeding and intestinal injury. IL10 overexpression restored intestinal repair after HFD feeding and intestinal injury. Macrophage exposure to lipids from the HFD prevented tethering and uptake of apoptotic cells and Il10 induction. Milk fat globule-EGF factor-8 (MFGE8) is a bridging molecule that facilitates macrophage uptake of dead cells. MFGE8 also facilitates lipid uptake, and we demonstrate that dietary lipids interfere with MFGE8-mediated macrophage apoptotic neutrophil uptake and subsequent Il10 production. Our findings demonstrate that HFD promotes intestinal pathology by interfering with macrophage clearance of dead neutrophils, leading to unresolved tissue damage.
    Keywords:  Immunology; Macrophages; Neutrophils
    DOI:  https://doi.org/10.1172/jci.insight.164489
  39. Science. 2022 Dec 23. 378(6626): 1272-1273
    Lessons on transparency from the glassfrog.
    Nelly M Cruz, Richard M White.
      Transparency in glassfrogs has potential implications for human blood clotting.
    DOI:  https://doi.org/10.1126/science.adf7524
  40. Cell Rep. 2022 Dec 20. pii: S2211-1247(22)01740-5. [Epub ahead of print]41(12): 111848
    IL-17/CXCL5 signaling within the oligovascular niche mediates human and mouse white matter injury.
    Guanxi Xiao, Rosie Kumar, Yutaro Komuro, Jasmine Burguet, Visesha Kakarla, Ida Azizkhanian, Sunil A Sheth, Christopher K Williams, Xinhai R Zhang, Michal Macknicki, Andrew Brumm, Riki Kawaguchi, Phu Mai, Naoki Kaneko, Harry V Vinters, S Thomas Carmichael, Leif A Havton, Charles DeCarli, Jason D Hinman.
      Cerebral small vessel disease and brain white matter injury are worsened by cardiovascular risk factors including obesity. Molecular pathways in cerebral endothelial cells activated by chronic cerebrovascular risk factors alter cell-cell signaling, blocking endogenous and post-ischemic white matter repair. Using cell-specific translating ribosome affinity purification (RiboTag) in white matter endothelia and oligodendrocyte progenitor cells (OPCs), we identify a coordinated interleukin-chemokine signaling cascade within the oligovascular niche of subcortical white matter that is triggered by diet-induced obesity (DIO). DIO induces interleukin-17B (IL-17B) signaling that acts on the cerebral endothelia through IL-17Rb to increase both circulating and local endothelial expression of CXCL5. In white matter endothelia, CXCL5 promotes the association of OPCs with the vasculature and triggers OPC gene expression programs regulating cell migration through chemokine signaling. Targeted blockade of IL-17B reduced vessel-associated OPCs by reducing endothelial CXCL5 expression. In multiple human cohorts, blood levels of CXCL5 function as a diagnostic and prognostic biomarker of vascular cognitive impairment.
    Keywords:  CP: Immunology; CP: Neuroscience; CXCL5; IL-17; cerebral small vessel disease; high-fat diet; inflammation; obesity; stroke; white matter
    DOI:  https://doi.org/10.1016/j.celrep.2022.111848
  41. Nat Rev Immunol. 2022 Dec 21.
    T cell-eosinophil collaboration.
    Lucy Bird.
      
    DOI:  https://doi.org/10.1038/s41577-022-00832-y
  42. Nat Commun. 2022 Dec 20. 13(1): 7672
    STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.
    Hiroaki Ohishi, Seiru Shimada, Satoshi Uchino, Jieru Li, Yuko Sato, Manabu Shintani, Hitoshi Owada, Yasuyuki Ohkawa, Alexandros Pertsinidis, Takashi Yamamoto, Hiroshi Kimura, Hiroshi Ochiai.
      Transcription is a dynamic process. To detect the dynamic relationship among protein clusters of RNA polymerase II and coactivators, gene loci, and transcriptional activity, we insert an MS2 repeat, a TetO repeat, and inteins with a selection marker just downstream of the transcription start site. By optimizing the individual elements, we develop the Spliced TetO REpeAt, MS2 repeat, and INtein sandwiched reporter Gene tag (STREAMING-tag) system. Clusters of RNA polymerase II and BRD4 are observed proximal to the transcription start site of Nanog when the gene is transcribed in mouse embryonic stem cells. In contrast, clusters of MED19 and MED22 tend to be located near the transcription start site, even without transcription activity. Thus, the STREAMING-tag system reveals the spatiotemporal relationships between transcriptional activity and protein clusters near the gene. This powerful tool is useful for quantitatively understanding transcriptional regulation in living cells.
    DOI:  https://doi.org/10.1038/s41467-022-35286-2
  43. Nat Commun. 2022 Dec 20. 13(1): 7838
    Adipose-targeted triiodothyronine therapy counteracts obesity-related metabolic complications and atherosclerosis with negligible side effects.
    Kang Chen, Lai Yee Cheong, Yuan Gao, Yaming Zhang, Tianshi Feng, Qin Wang, Leigang Jin, Eric Honoré, Karen S L Lam, Weiping Wang, Xiaoyan Hui, Aimin Xu.
      Thyroid hormone (TH) is a thermogenic activator with anti-obesity potential. However, systemic TH administration has no obvious clinical benefits on weight reduction. Herein we selectively delivered triiodothyronine (T3) to adipose tissues by encapsulating T3 in liposomes modified with an adipose homing peptide (PLT3). Systemic T3 administration failed to promote thermogenesis in brown and white adipose tissues (WAT) due to a feedback suppression of sympathetic innervation. PLT3 therapy effectively obviated this feedback suppression on adrenergic inputs, and potently induced browning and thermogenesis of WAT, leading to alleviation of obesity, glucose intolerance, insulin resistance, and fatty liver in obese mice. Furthermore, PLT3 was much more effective than systemic T3 therapy in reducing hypercholesterolemia and atherosclerosis in apoE-deficient mice. These findings uncover WAT as a viable target mediating the therapeutic benefits of TH and provide a safe and efficient therapeutic strategy for obesity and its complications by delivering TH to adipose tissue.
    DOI:  https://doi.org/10.1038/s41467-022-35470-4
  44. Nat Commun. 2022 Dec 20. 13(1): 7833
    Mechanism of human Lig1 regulation by PCNA in Okazaki fragment sealing.
    Kerry Blair, Muhammad Tehseen, Vlad-Stefan Raducanu, Taha Shahid, Claudia Lancey, Fahad Rashid, Ramon Creuhet, Samir M Hamdan, Alfredo De Biasio.
      During lagging strand synthesis, DNA Ligase 1 (Lig1) cooperates with the sliding clamp PCNA to seal the nicks between Okazaki fragments generated by Pol δ and Flap endonuclease 1 (FEN1). We present several cryo-EM structures combined with functional assays, showing that human Lig1 recruits PCNA to nicked DNA using two PCNA-interacting motifs (PIPs) located at its disordered N-terminus (PIPN-term) and DNA binding domain (PIPDBD). Once Lig1 and PCNA assemble as two-stack rings encircling DNA, PIPN-term is released from PCNA and only PIPDBD is required for ligation to facilitate the substrate handoff from FEN1. Consistently, we observed that PCNA forms a defined complex with FEN1 and nicked DNA, and it recruits Lig1 to an unoccupied monomer creating a toolbelt that drives the transfer of DNA to Lig1. Collectively, our results provide a structural model on how PCNA regulates FEN1 and Lig1 during Okazaki fragments maturation.
    DOI:  https://doi.org/10.1038/s41467-022-35475-z
  45. Nature. 2022 Dec 22.
    Massive measles outbreak threatens India's goal to eliminate disease by 2023.
    Gayathri Vaidyanathan.
      
    Keywords:  Infection; Public health
    DOI:  https://doi.org/10.1038/d41586-022-04480-z
  46. Nat Cell Biol. 2022 Dec 21.
    Waxy lipids and waning insulin secretion.
    Jonathan S Bogan.
      
    DOI:  https://doi.org/10.1038/s41556-022-01036-1
  47. Cell Res. 2022 Dec 22.
    tRNA-m1A modification: a translational checkpoint for T cell expansion.
    Weike Pei, Vijay K Kuchroo.
      
    DOI:  https://doi.org/10.1038/s41422-022-00764-1
  48. Nat Commun. 2022 Dec 21. 13(1): 7622
    Tiltable objective microscope visualizes selectivity for head motion direction and dynamics in zebrafish vestibular system.
    Masashi Tanimoto, Ikuko Watakabe, Shin-Ichi Higashijima.
      Spatio-temporal information about head orientation and movement is fundamental to the sense of balance and motion. Hair cells (HCs) in otolith organs of the vestibular system transduce linear acceleration, including head tilt and vibration. Here, we build a tiltable objective microscope in which an objective lens and specimen tilt together. With in vivo Ca2+ imaging of all utricular HCs and ganglion neurons during 360° static tilt and vibration in pitch and roll axes, we reveal the direction- and static/dynamic stimulus-selective topographic responses in larval zebrafish. We find that head vibration is preferentially received by striolar HCs, whereas static tilt is preferentially transduced by extrastriolar HCs. Spatially ordered direction preference in HCs is consistent with hair-bundle polarity and is preserved in ganglion neurons through topographic innervation. Together, these results demonstrate topographically organized selectivity for direction and dynamics of head orientation/movement in the vestibular periphery.
    DOI:  https://doi.org/10.1038/s41467-022-35190-9
  49. Cell Stem Cell. 2022 Dec 19. pii: S1934-5909(22)00485-4. [Epub ahead of print]
    An insulin hypersecretion phenotype precedes pancreatic β cell failure in MODY3 patient-specific cells.
    Florian M Hermann, Maya Friis Kjærgaard, Chenglei Tian, Ulf Tiemann, Abigail Jackson, Lars Rønn Olsen, Maria Kraft, Per-Ola Carlsson, Iina M Elfving, Jarno L T Kettunen, Tiinamaija Tuomi, Ivana Novak, Henrik Semb.
      MODY3 is a monogenic hereditary form of diabetes caused by mutations in the transcription factor HNF1A. The patients progressively develop hyperglycemia due to perturbed insulin secretion, but the pathogenesis is unknown. Using patient-specific hiPSCs, we recapitulate the insulin secretion sensitivity to the membrane depolarizing agent sulfonylurea commonly observed in MODY3 patients. Unexpectedly, MODY3 patient-specific HNF1A+/R272C β cells hypersecrete insulin both in vitro and in vivo after transplantation into mice. Consistently, we identified a trend of increased birth weight in human HNF1A mutation carriers compared with healthy siblings. Reduced expression of potassium channels, specifically the KATP channel, in MODY3 β cells, increased calcium signaling, and rescue of the insulin hypersecretion phenotype by pharmacological targeting ATP-sensitive potassium channels or low-voltage-activated calcium channels suggest that more efficient membrane depolarization underlies the hypersecretion of insulin in MODY3 β cells. Our findings identify a pathogenic mechanism leading to β cell failure in MODY3.
    Keywords:  HNF1A; HNF4A; K(ATP) channel; MODY3; calcium signaling; congenital hyperinsulinemia; disease modeling; membrane potential; pancreatic β cell; patient-specific hiPSCs
    DOI:  https://doi.org/10.1016/j.stem.2022.12.001
  50. Sci Transl Med. 2022 Dec 21. 14(676): eabp9675
    Human β-defensin 2 ameliorates acute GVHD by limiting ileal neutrophil infiltration and restraining T cell receptor signaling.
    Tamina Rückert, Geoffroy Andrieux, Melanie Boerries, Kathrin Hanke-Müller, Nadine M Woessner, Stephanie Doetsch, Christoph Schell, Konrad Aumann, Julia Kolter, Annette Schmitt-Graeff, Marcel Schiff, Lukas M Braun, Eileen Haring, Sandra Kissel, Benjamin A Siranosian, Ami S Bhatt, Peter Nordkild, Jan Wehkamp, Benjamin A H Jensen, Susana Minguet, Justus Duyster, Robert Zeiser, Natalie Köhler.
      Acute graft-versus-host disease (aGVHD), which is driven by allogeneic T cells, has a high mortality rate and limited treatment options. Human β-defensin 2 (hBD-2) is an endogenous epithelial cell-derived host-defense peptide. In addition to its antimicrobial effects, hBD-2 has immunomodulatory functions thought to be mediated by CCR2 and CCR6 in myeloid cells. In this study, we analyzed the effect of recombinant hBD-2 on aGVHD development. We found that intestinal β-defensin expression was inadequately induced in response to inflammation in two independent cohorts of patients with aGVHD and in a murine aGVHD model. Treatment of mice with hBD-2 reduced GVHD severity and mortality and modulated the intestinal microbiota composition, resulting in reduced neutrophil infiltration in the ileum. Furthermore, hBD-2 treatment decreased proliferation and proinflammatory cytokine production by allogeneic T cells in vivo while preserving the beneficial graft-versus-leukemia effect. Using transcriptome and kinome profiling, we found that hBD-2 directly dampened primary murine and human allogeneic T cell proliferation, activation, and metabolism in a CCR2- and CCR6-independent manner by reducing proximal T cell receptor signaling. Furthermore, hBD-2 treatment diminished alloreactive T cell infiltration and the expression of genes involved in T cell receptor signaling in the ilea of mice with aGVHD. Together, we found that both human and murine aGVHD were characterized by a lack of intestinal β-defensin induction and that recombinant hBD-2 represents a potential therapeutic strategy to counterbalance endogenous hBD-2 deficiency.
    DOI:  https://doi.org/10.1126/scitranslmed.abp9675
  51. Science. 2022 Dec 20. eabo3627
    Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children.
    CoV-Contact Cohort§
      Multisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1, OAS2, or RNASEL in five unrelated children with MIS-C. The cytosolic dsRNA-sensing OAS1 and OAS2 generate 2'-5'-linked oligoadenylates (2-5A) that activate the ssRNA-degrading RNase L. Monocytic cell lines and primary myeloid cells with OAS1, OAS2, or RNASEL deficiencies produce excessive amounts of inflammatory cytokines upon dsRNA or SARS-CoV-2 stimulation. Exogenous 2-5A suppresses cytokine production in OAS1- but not RNase L-deficient cells. Cytokine production in RNase L-deficient cells is impaired by MDA5 or RIG-I deficiency and abolished by MAVS deficiency. Recessive OAS-RNase L deficiencies in these patients unleash the production of SARS-CoV-2-triggered, MAVS-mediated inflammatory cytokines by mononuclear phagocytes, thereby underlying MIS-C.
    DOI:  https://doi.org/10.1126/science.abo3627
  52. Nat Struct Mol Biol. 2022 Dec 22.
    Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers.
    George Spracklin, Nezar Abdennur, Maxim Imakaev, Neil Chowdhury, Sriharsa Pradhan, Leonid A Mirny, Job Dekker.
      The relationships between chromosomal compartmentalization, chromatin state and function are poorly understood. Here by profiling long-range contact frequencies in HCT116 colon cancer cells, we distinguish three silent chromatin states, comprising two types of heterochromatin and a state enriched for H3K9me2 and H2A.Z that exhibits neutral three-dimensional interaction preferences and which, to our knowledge, has not previously been characterized. We find that heterochromatin marked by H3K9me3, HP1α and HP1β correlates with strong compartmentalization. We demonstrate that disruption of DNA methyltransferase activity greatly remodels genome compartmentalization whereby domains lose H3K9me3-HP1α/β binding and acquire the neutrally interacting state while retaining late replication timing. Furthermore, we show that H3K9me3-HP1α/β heterochromatin is permissive to loop extrusion by cohesin but refractory to CTCF binding. Together, our work reveals a dynamic structural and organizational diversity of the silent portion of the genome and establishes connections between the regulation of chromatin state and chromosome organization, including an interplay between DNA methylation, compartmentalization and loop extrusion.
    DOI:  https://doi.org/10.1038/s41594-022-00892-7
  53. Nature. 2022 Dec 21.
    R-loop-derived cytoplasmic RNA-DNA hybrids activate an immune response.
    Magdalena P Crossley, Chenlin Song, Michael J Bocek, Jun-Hyuk Choi, Joseph Kousorous, Ataya Sathirachinda, Cindy Lin, Joshua R Brickner, Gongshi Bai, Hannes Lans, Wim Vermeulen, Monther Abu-Remaileh, Karlene A Cimprich.
      R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.
    DOI:  https://doi.org/10.1038/s41586-022-05545-9
  54. EMBO Rep. 2022 Dec 19. e54350
    Distinct biogenesis pathways may have led to functional divergence of the human and Drosophila Arglu1 sisRNA.
    Seow Neng Chan, Jun Wei Pek.
      Stable intronic sequence RNAs (sisRNAs) are stable, long noncoding RNAs containing intronic sequences. While sisRNAs have been found across diverse species, their level of conservation remains poorly understood. Here we report that the biogenesis and functions of a sisRNA transcribed from the highly conserved Arglu1 locus are distinct in human and Drosophila melanogaster. The Arglu1 genes in both species show similar exon-intron structures where the intron 2 is orthologous and positionally conserved. In humans, Arglu1 sisRNA retains the entire intron 2 and promotes host gene splicing. Mechanistically, Arglu1 sisRNA represses the splicing-inhibitory activity of ARGLU1 protein by binding to ARGLU1 protein and promoting its localization to nuclear speckles, away from the Arglu1 gene locus. In contrast, Drosophila dArglu1 sisRNA forms via premature cleavage of intron 2 and represses host gene splicing. This repression occurs through a local accumulation of dARGLU1 protein and inhibition of telescripting by U1 snRNPs at the dArglu1 locus. We propose that distinct biogenesis of positionally conserved Arglu1 sisRNAs in both species may have led to functional divergence.
    Keywords:  Arglu1; autoregulation; orthologous intron; positional conservation; sisRNA
    DOI:  https://doi.org/10.15252/embr.202154350
  55. Nat Commun. 2022 Dec 21. 13(1): 7836
    Machine learning assisted interferometric structured illumination microscopy for dynamic biological imaging.
    Edward N Ward, Lisa Hecker, Charles N Christensen, Jacob R Lamb, Meng Lu, Luca Mascheroni, Chyi Wei Chung, Anna Wang, Christopher J Rowlands, Gabriele S Kaminski Schierle, Clemens F Kaminski.
      Structured Illumination Microscopy, SIM, is one of the most powerful optical imaging methods available to visualize biological environments at subcellular resolution. Its limitations stem from a difficulty of imaging in multiple color channels at once, which reduces imaging speed. Furthermore, there is substantial experimental complexity in setting up SIM systems, preventing a widespread adoption. Here, we present Machine-learning Assisted, Interferometric Structured Illumination Microscopy, MAI-SIM, as an easy-to-implement method for live cell super-resolution imaging at high speed and in multiple colors. The instrument is based on an interferometer design in which illumination patterns are generated, rotated, and stepped in phase through movement of a single galvanometric mirror element. The design is robust, flexible, and works for all wavelengths. We complement the unique properties of the microscope with an open source machine-learning toolbox that permits real-time reconstructions to be performed, providing instant visualization of super-resolved images from live biological samples.
    DOI:  https://doi.org/10.1038/s41467-022-35307-0
  56. Nat Immunol. 2022 Dec 22.
    An αvβ3 integrin checkpoint is critical for efficient TH2 cell cytokine polarization and potentiation of antigen-specific immunity.
    Aydan C H Szeto, Ana C F Ferreira, Jonathan Mannion, Paula A Clark, Meera Sivasubramaniam, Morgan W D Heycock, Alastair Crisp, Helen E Jolin, Patrycja Kozik, Martin D Knolle, Andrew N J McKenzie.
      Naive CD4+ T lymphocytes initially undergo antigen-specific activation to promote a broad-spectrum response before adopting bespoke cytokine expression profiles shaped by intercellular microenvironmental cues, resulting in pathogen-focused modular cytokine responses. Interleukin (IL)-4-induced Gata3 upregulation is important for the helper type 2 T cell (TH2 cell) polarization associated with anti-helminth immunity and misdirected allergic inflammation. Whether additional microenvironmental factors participate is unclear. Using whole mouse-genome CRISPR-Cas9 screens, we discovered a previously unappreciated role for αvβ3 integrin in TH2 cell differentiation. Low-level αvβ3 expression by naive CD4+ T cells contributed to pan-T cell activation by promoting T-T cell clustering and IL-2/CD25/STAT5 signaling. Subsequently, IL-4/Gata3-induced selective upregulation of αvβ3 licensed intercellular αvβ3-Thy1 interactions among TH2 cells, enhanced mammalian target of rapamycin (mTOR) signaling, supported differentiation and promoted IL-5/IL-13 production. In mice, αvβ3 was required for efficient, allergen-driven, antigen-specific lung TH2 cell responses. Thus, αvβ3-expressing TH2 cells form multicellular factories to propagate and amplify TH2 cell responses.
    DOI:  https://doi.org/10.1038/s41590-022-01378-w
  57. Nat Biomed Eng. 2022 Dec 22.
    Systemic enhancement of antitumour immunity by peritumourally implanted immunomodulatory macroporous scaffolds.
    Fatemeh S Majedi, Mohammad Mahdi Hasani-Sadrabadi, Timothy J Thauland, Sundeep G Keswani, Song Li, Louis-S Bouchard, Manish J Butte.
      A tumour microenvironment abundant in regulatory T (Treg) cells aids solid tumours to evade clearance by effector T cells. Systemic strategies to suppress Treg cells or to augment immunity can elicit autoimmune side effects, cytokine storms and other toxicities. Here we report the design, fabrication and therapeutic performance of a biodegradable macroporous scaffold, implanted peritumourally, that releases a small-molecule inhibitor of transforming growth factor β to suppress Treg cells, chemokines to attract effector T cells and antibodies to stimulate them. In two mouse models of aggressive tumours, the implant boosted the recruitment and activation of effector T cells into the tumour and depleted it of Treg cells, which resulted in an 'immunological abscopal effect' on distant metastases and in the establishment of long-term memory that impeded tumour recurrence. We also show that the scaffold can be used to deliver tumour-antigen-specific T cells into the tumour. Peritumourally implanted immunomodulatory scaffolds may represent a general strategy to enhance T-cell immunity and avoid the toxicities of systemic therapies.
    DOI:  https://doi.org/10.1038/s41551-022-00977-0
  58. Mol Cell. 2022 Dec 08. pii: S1097-2765(22)01134-0. [Epub ahead of print]
    Ring domains are essential for GATOR2-dependent mTORC1 activation.
    Cong Jiang, Xiaoming Dai, Shaohui He, Hongfei Zhou, Lan Fang, Jianping Guo, Songlei Liu, Tao Zhang, Weijuan Pan, Haihong Yu, Tianmin Fu, Dali Li, Hiroyuki Inuzuka, Ping Wang, Jianru Xiao, Wenyi Wei.
      The GATOR2-GATOR1 signaling axis is essential for amino-acid-dependent mTORC1 activation. However, the molecular function of the GATOR2 complex remains unknown. Here, we report that disruption of the Ring domains of Mios, WDR24, or WDR59 completely impedes amino-acid-mediated mTORC1 activation. Mechanistically, via interacting with Ring domains of WDR59 and WDR24, the Ring domain of Mios acts as a hub to maintain GATOR2 integrity, disruption of which leads to self-ubiquitination of WDR24. Physiologically, leucine stimulation dissociates Sestrin2 from the Ring domain of WDR24 and confers its availability to UBE2D3 and subsequent ubiquitination of NPRL2, contributing to GATOR2-mediated GATOR1 inactivation. As such, WDR24 ablation or Ring deletion prevents mTORC1 activation, leading to severe growth defects and embryonic lethality at E10.5 in mice. Hence, our findings demonstrate that Ring domains are essential for GATOR2 to transmit amino acid availability to mTORC1 and further reveal the essentiality of nutrient sensing during embryonic development.
    Keywords:  Gator1; Gator2; NPRL2; Sestrin; WDR24; amino acid sensing; mTOR; ubiquitination
    DOI:  https://doi.org/10.1016/j.molcel.2022.11.021
  59. Nat Commun. 2022 Dec 23. 13(1): 7923
    Targeting anti-apoptotic pathways eliminates senescent melanocytes and leads to nevi regression.
    Jaskaren Kohli, Chen Ge, Eleni Fitsiou, Miriam Doepner, Simone M Brandenburg, William J Faller, Todd W Ridky, Marco Demaria.
      Human melanocytic nevi (moles) result from a brief period of clonal expansion of melanocytes. As a cellular defensive mechanism against oncogene-induced hyperplasia, nevus-resident melanocytes enter a senescent state of stable cell cycle arrest. Senescent melanocytes can persist for months in mice and years in humans with a risk to escape the senescent state and progress to melanoma. The mechanisms providing prolonged survival of senescent melanocytes remain poorly understood. Here, we show that senescent melanocytes in culture and in nevi express high level of the anti-apoptotic BCL-2 family member BCL-W but remain insensitive to the pan-BCL-2 inhibitor ABT-263. We demonstrate that resistance to ABT-263 is driven by mTOR-mediated enhanced translation of another anti-apoptotic member, MCL-1. Strikingly, the combination of ABT-263 and MCL-1 inhibitors results in synthetic lethality to senescent melanocytes, and its topical application sufficient to eliminate nevi in male mice. These data highlight the important role of redundant anti-apoptotic mechanisms for the survival advantage of senescent melanocytes, and the proof-of-concept for a non-invasive combination therapy for nevi removal.
    DOI:  https://doi.org/10.1038/s41467-022-35657-9
  60. Cell. 2022 Dec 22. pii: S0092-8674(22)01508-2. [Epub ahead of print]185(26): 4986-4998.e12
    Mechanism of IFT-A polymerization into trains for ciliary transport.
    Shimi Meleppattu, Haixia Zhou, Jin Dai, Miao Gui, Alan Brown.
      Intraflagellar transport (IFT) is the highly conserved process by which proteins are transported along ciliary microtubules by a train-like polymeric assembly of IFT-A and IFT-B complexes. IFT-A is sandwiched between IFT-B and the ciliary membrane, consistent with its putative role in transporting transmembrane and membrane-associated cargoes. Here, we have used single-particle analysis electron cryomicroscopy (cryo-EM) to determine structures of native IFT-A complexes. We show that subcomplex rearrangements enable IFT-A to polymerize laterally on anterograde IFT trains, revealing a cooperative assembly mechanism. Surprisingly, we discover that binding of IFT-A to IFT-B shields the preferred lipid-binding interface from the ciliary membrane but orients an interconnected network of β-propeller domains with the capacity to accommodate diverse cargoes toward the ciliary membrane. This work provides a mechanistic basis for understanding IFT-train assembly and cargo interactions.
    Keywords:  cilia; cryo-EM; cryo-ET; flagella; intraflagellar transport; lipid binding; microtubule; molecular transport; vesicle
    DOI:  https://doi.org/10.1016/j.cell.2022.11.033
  61. Science. 2022 Dec 23. 378(6626): 1276-1277
    Epigenetic clocks, aging, and cancer.
    Sarah E Johnstone, Vadim N Gladyshev, Martin J Aryee, Bradley E Bernstein.
      Global methylation changes in aging cells affect cancer risk and tissue homeostasis.
    DOI:  https://doi.org/10.1126/science.abn4009
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