bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022–11–27
sixty-nine papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo.
  2. SENP1 prevents steatohepatitis by suppressing RIPK1-driven apoptosis and inflammation.
  3. Protecting the CNS.
  4. Immunosuppressive ferroptosis.
  5. GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies.
  6. Insights into distinct signaling profiles of the µOR activated by diverse agonists.
  7. Alveolar macrophage metabolic programming via a C-type lectin receptor protects against lipo-toxicity and cell death.
  8. Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers.
  9. RNA-activated protein cleavage with a CRISPR-associated endopeptidase.
  10. Prenatal inflammation perturbs murine fetal hematopoietic development and causes persistent changes to postnatal immunity.
  11. CD47-SIRPα axis blockade in NASH promotes necroptotic hepatocyte clearance by liver macrophages and decreases hepatic fibrosis.
  12. A Multi-Omics Approach Reveals Features That Permit Robust and Widespread Regulation of IFN-Inducible Antiviral Effectors.
  13. The unknown biogeochemical impacts of drying rivers and streams.
  14. Sphingosine 1-phosphate mediates adiponectin receptor signaling essential for lipid homeostasis and embryogenesis.
  15. Transposable element-mediated rearrangements are prevalent in human genomes.
  16. iNKT cells circulate.
  17. Maintenance of Lineage Identity: Lessons from a B Cell.
  18. Spatially aware dimension reduction for spatial transcriptomics.
  19. Manipulating PP2Acα-ASK-JNK signaling to favor apoptotic over necroptotic hepatocyte fate reduces the extent of necrosis and fibrosis upon acute liver injury.
  20. circCsnk1g3- and circAnkib1-regulated interferon responses in sarcoma promote tumorigenesis by shaping the immune microenvironment.
  21. DNA mechanical flexibility controls DNA potential to activate cGAS-mediated immune surveillance.
  22. MYC multimers shield stalled replication forks from RNA polymerase.
  23. Reduced secretion of neuronal growth regulator 1 contributes to impaired adipose-neuronal crosstalk in obesity.
  24. Reversion mutations in germline BRCA1/2-mutant tumors reveal a BRCA-mediated phenotype in non-canonical histologies.
  25. mTORC1 signaling facilitates differential stem cell differentiation to shape the developing murine lung and is associated with mitochondrial capacity.
  26. The future of engineered immune cell therapies.
  27. BRAF activation by metabolic stress promotes glycolysis sensitizing NRASQ61-mutated melanomas to targeted therapy.
  28. Expanding cross-presenting dendritic cells enhances oncolytic virotherapy and is critical for long-term anti-tumor immunity.
  29. Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine.
  30. Smc5/6's multifaceted DNA binding capacities stabilize branched DNA structures.
  31. EBF1 is continuously required for stabilizing local chromatin accessibility in pro-B cells.
  32. Kinetics of mRNA nuclear export regulate innate immune response gene expression.
  33. Autophagy promotes cell survival by maintaining NAD levels.
  34. HGFAC is a ChREBP regulated hepatokine that enhances glucose and lipid homeostasis.
  35. Metabolic control of innate lymphoid cells in health and disease.
  36. A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry.
  37. The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells.
  38. Metabolic and proteomic signatures of type 2 diabetes subtypes in an Arab population.
  39. GPSM1 impairs metabolic homeostasis by controlling a pro-inflammatory pathway in macrophages.
  40. Activation of Wnt/β-catenin signaling by Zeb1 in endothelial progenitors induces vascular quiescence entry.
  41. Depletion of CD206+ M2-like macrophages induces fibro-adipogenic progenitors activation and muscle regeneration.
  42. Global landscape of replicative DNA polymerase usage in the human genome.
  43. CTLA-4 on thymic epithelial cells complements Aire for T cell central tolerance.
  44. Primate-specific transposable elements shape transcriptional networks during human development.
  45. Intronic enhancers of the human SNCA gene predominantly regulate its expression in brain in vivo.
  46. Pre-T cell receptor Self-MHC Sampling Restricts Thymocyte Dedifferentiation.
  47. Differential compartmentalization of myeloid cell phenotypes and responses towards the CNS in Alzheimer's disease.
  48. Inhaled particulate accumulation with age impairs immune function and architecture in human lung lymph nodes.
  49. Dynamic quality control machinery that operates across compartmental borders mediates the degradation of mammalian nuclear membrane proteins.
  50. Control of Gαq signaling dynamics and GPCR cross-talk by GRKs.
  51. XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation.
  52. Macrophage acetyl-CoA carboxylase regulates acute inflammation through control of glucose and lipid metabolism.
  53. Loss of MTCH-1 suppresses age-related proteostasis collapse through the inhibition of programmed cell death factors.
  54. GPCR signaling regulates severe stress-induced organismic death in Caenorhabditis elegans.
  55. A deubiquitination module essential for Treg fitness in the tumor microenvironment.
  56. SOX9 and TCF transcription factors associate to mediate Wnt/β-catenin target gene activation in colorectal cancer.
  57. Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
  58. CXCL13 is a predictive biomarker in idiopathic multicentric Castleman disease.
  59. TDP-43 safeguards the embryo genome from L1 retrotransposition.
  60. Double knockin mice show NF-κB trajectories in immune signaling and aging.
  61. Osteoblast/osteocyte-derived interleukin-11 regulates osteogenesis and systemic adipogenesis.
  62. Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T cells.
  63. A CRISPR endonuclease gene drive reveals distinct mechanisms of inheritance bias.
  64. cFLIP suppression and DR5 activation sensitize senescent cancer cells to senolysis.
  65. Rad regulation of CaV1.2 channels controls cardiac fight-or-flight response.
  66. A non-coding GWAS variant impacts anthracycline-induced cardiotoxic phenotypes in human iPSC-derived cardiomyocytes.
  67. PI(4,5)P2 diffuses freely in the plasma membrane even within high-density effector protein complexes.
  68. Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability.
  69. Adenosine deaminase acting on RNA-1 is essential for early B lymphopoiesis.
  1. Nat Commun. 2022 Nov 23. 13(1): 7204
    Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo.
    Julian C W Willis, Pedro Silva-Pinheiro, Lily Widdup, Michal Minczuk, David R Liu.
      DddA-derived cytosine base editors (DdCBEs) use programmable DNA-binding TALE repeat arrays, rather than CRISPR proteins, a split double-stranded DNA cytidine deaminase (DddA), and a uracil glycosylase inhibitor to mediate C•G-to-T•A editing in nuclear and organelle DNA. Here we report the development of zinc finger DdCBEs (ZF-DdCBEs) and the improvement of their editing performance through engineering their architectures, defining improved ZF scaffolds, and installing DddA activity-enhancing mutations. We engineer variants with improved DNA specificity by integrating four strategies to reduce off-target editing. We use optimized ZF-DdCBEs to install or correct disease-associated mutations in mitochondria and in the nucleus. Leveraging their small size, we use a single AAV9 to deliver into heart, liver, and skeletal muscle in post-natal mice ZF-DdCBEs that efficiently install disease-associated mutations. While off-target editing of ZF-DdCBEs is likely too high for therapeutic applications, these findings demonstrate a compact, all-protein base editing research tool for precise editing of organelle or nuclear DNA without double-strand DNA breaks.
    DOI:  https://doi.org/10.1038/s41467-022-34784-7
  2. Nat Commun. 2022 Nov 22. 13(1): 7153
    SENP1 prevents steatohepatitis by suppressing RIPK1-driven apoptosis and inflammation.
    Lingjie Yan, Tao Zhang, Kai Wang, Zezhao Chen, Yuanxin Yang, Bing Shan, Qi Sun, Mengmeng Zhang, Yichi Zhang, Yedan Zhong, Nan Liu, Jinyang Gu, Daichao Xu.
      Activation of RIPK1-driven cell death and inflammation play important roles in the progression of nonalcoholic steatohepatitis (NASH). However, the mechanism underlying RIPK1 activation in NASH remains unclear. Here we identified SENP1, a SUMO-specific protease, as a key endogenous inhibitor of RIPK1. SENP1 is progressively reduced in proportion to NASH severity in patients. Hepatocyte-specific SENP1-knockout mice develop spontaneous NASH-related phenotypes in a RIPK1 kinase-dependent manner. We demonstrate that SENP1 deficiency sensitizes cells to RIPK1 kinase-dependent apoptosis by promoting RIPK1 activation following TNFα stimulation. Mechanistically, SENP1 deSUMOylates RIPK1 in TNF-R1 signaling complex (TNF-RSC), keeping RIPK1 in check. Loss of SENP1 leads to SUMOylation of RIPK1, which re-orchestrates TNF-RSC and modulates the ubiquitination patterns and activity of RIPK1. Notably, genetic inhibition of RIPK1 effectively reverses disease progression in hepatocyte-specific SENP1-knockout male mice with high-fat-diet-induced nonalcoholic fatty liver. We propose that deSUMOylation of RIPK1 by SENP1 provides a pathophysiologically relevant cell death-restricting checkpoint that modulates RIPK1 activation in the pathogenesis of nonalcoholic steatohepatitis.
    DOI:  https://doi.org/10.1038/s41467-022-34993-0
  3. Nat Immunol. 2022 Nov 21.
    Protecting the CNS.
    Ioana Visan.
      
    DOI:  https://doi.org/10.1038/s41590-022-01381-1
  4. Nat Immunol. 2022 Nov 21.
    Immunosuppressive ferroptosis.
    Nicholas J Bernard.
      
    DOI:  https://doi.org/10.1038/s41590-022-01383-z
  5. Nat Commun. 2022 Nov 23. 13(1): 7209
    GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies.
    Zihuai He, Linxi Liu, Michael E Belloy, Yann Le Guen, Aaron Sossin, Xiaoxia Liu, Xinran Qi, Shiyang Ma, Prashnna K Gyawali, Tony Wyss-Coray, Hua Tang, Chiara Sabatti, Emmanuel Candès, Michael D Greicius, Iuliana Ionita-Laza.
      Recent advances in genome sequencing and imputation technologies provide an exciting opportunity to comprehensively study the contribution of genetic variants to complex phenotypes. However, our ability to translate genetic discoveries into mechanistic insights remains limited at this point. In this paper, we propose an efficient knockoff-based method, GhostKnockoff, for genome-wide association studies (GWAS) that leads to improved power and ability to prioritize putative causal variants relative to conventional GWAS approaches. The method requires only Z-scores from conventional GWAS and hence can be easily applied to enhance existing and future studies. The method can also be applied to meta-analysis of multiple GWAS allowing for arbitrary sample overlap. We demonstrate its performance using empirical simulations and two applications: (1) a meta-analysis for Alzheimer's disease comprising nine overlapping large-scale GWAS, whole-exome and whole-genome sequencing studies and (2) analysis of 1403 binary phenotypes from the UK Biobank data in 408,961 samples of European ancestry. Our results demonstrate that GhostKnockoff can identify putatively functional variants with weaker statistical effects that are missed by conventional association tests.
    DOI:  https://doi.org/10.1038/s41467-022-34932-z
  6. Nat Chem Biol. 2022 Nov 21.
    Insights into distinct signaling profiles of the µOR activated by diverse agonists.
    Qianhui Qu, Weijiao Huang, Deniz Aydin, Joseph M Paggi, Alpay B Seven, Haoqing Wang, Soumen Chakraborty, Tao Che, Jeffrey F DiBerto, Michael J Robertson, Asuka Inoue, Carl-Mikael Suomivuori, Bryan L Roth, Susruta Majumdar, Ron O Dror, Brian K Kobilka, Georgios Skiniotis.
      Drugs targeting the μ-opioid receptor (μOR) are the most effective analgesics available but are also associated with fatal respiratory depression through a pathway that remains unclear. Here we investigated the mechanistic basis of action of lofentanil (LFT) and mitragynine pseudoindoxyl (MP), two μOR agonists with different safety profiles. LFT, one of the most lethal opioids, and MP, a kratom plant derivative with reduced respiratory depression in animal studies, exhibited markedly different efficacy profiles for G protein subtype activation and β-arrestin recruitment. Cryo-EM structures of μOR-Gi1 complex with MP (2.5 Å) and LFT (3.2 Å) revealed that the two ligands engage distinct subpockets, and molecular dynamics simulations showed additional differences in the binding site that promote distinct active-state conformations on the intracellular side of the receptor where G proteins and β-arrestins bind. These observations highlight how drugs engaging different parts of the μOR orthosteric pocket can lead to distinct signaling outcomes.
    DOI:  https://doi.org/10.1038/s41589-022-01208-y
  7. Nat Commun. 2022 Nov 25. 13(1): 7272
    Alveolar macrophage metabolic programming via a C-type lectin receptor protects against lipo-toxicity and cell death.
    Michal Scur, Ahmad Bakur Mahmoud, Sayanti Dey, Farah Abdalbarri, Iona Stylianides, Daniel Medina-Luna, Gayani S Gamage, Aaron Woblistin, Alexa N M Wilson, Haggag S Zein, Ashley Stueck, Andrew Wight, Oscar A Aguilar, Francesca Di Cara, Brendon D Parsons, Mir Munir A Rahim, James R Carlyle, Andrew P Makrigiannis.
      Alveolar macrophages (AM) hold lung homeostasis intact. In addition to the defense against inhaled pathogens and deleterious inflammation, AM also maintain pulmonary surfactant homeostasis, a vital lung function that prevents pulmonary alveolar proteinosis. Signals transmitted between AM and pneumocytes of the pulmonary niche coordinate these specialized functions. However, the mechanisms that guide the metabolic homeostasis of AM remain largely elusive. We show that the NK cell-associated receptor, NKR-P1B, is expressed by AM and is essential for metabolic programming. Nkrp1b-/- mice are vulnerable to pneumococcal infection due to an age-dependent collapse in the number of AM and the formation of lipid-laden AM. The AM of Nkrp1b-/- mice show increased uptake but defective metabolism of surfactant lipids. We identify a physical relay between AM and alveolar type-II pneumocytes that is dependent on pneumocyte Clr-g expression. These findings implicate the NKR-P1B:Clr-g signaling axis in AM-pneumocyte communication as being important for maintaining metabolism in AM.
    DOI:  https://doi.org/10.1038/s41467-022-34935-w
  8. Nat Commun. 2022 Nov 19. 13(1): 7118
    Integrating transcription factor occupancy with transcriptome-wide association analysis identifies susceptibility genes in human cancers.
    Jingni He, Wanqing Wen, Alicia Beeghly, Zhishan Chen, Chen Cao, Xiao-Ou Shu, Wei Zheng, Quan Long, Xingyi Guo.
      Transcriptome-wide association studies (TWAS) have successfully discovered many putative disease susceptibility genes. However, TWAS may suffer from inaccuracy of gene expression predictions due to inclusion of non-regulatory variants. By integrating prior knowledge of susceptible transcription factor occupied elements, we develop sTF-TWAS and demonstrate that it outperforms existing TWAS approaches in both simulation and real data analyses. Under the sTF-TWAS framework, we build genetic models to predict alternative splicing and gene expression in normal breast, prostate and lung tissues from the Genotype-Tissue Expression project and apply these models to data from large genome-wide association studies (GWAS) conducted among European-ancestry populations. At Bonferroni-corrected P < 0.05, we identify 354 putative susceptibility genes for these cancers, including 189 previously unreported in GWAS loci and 45 in loci unreported by GWAS. These findings provide additional insight into the genetic susceptibility of human cancers. Additionally, we show the generalizability of the sTF-TWAS on non-cancer diseases.
    DOI:  https://doi.org/10.1038/s41467-022-34888-0
  9. Science. 2022 Nov 25. 378(6622): 874-881
    RNA-activated protein cleavage with a CRISPR-associated endopeptidase.
    Jonathan Strecker, F Esra Demircioglu, David Li, Guilhem Faure, Max E Wilkinson, Jonathan S Gootenberg, Omar O Abudayyeh, Hiroshi Nishimasu, Rhiannon K Macrae, Feng Zhang.
      In prokaryotes, CRISPR-Cas systems provide adaptive immune responses against foreign genetic elements through RNA-guided nuclease activity. Recently, additional genes with non-nuclease functions have been found in genetic association with CRISPR systems, suggesting that there may be other RNA-guided non-nucleolytic enzymes. One such gene from Desulfonema ishimotonii encodes the TPR-CHAT protease Csx29, which is associated with the CRISPR effector Cas7-11. Here, we demonstrate that this CRISPR-associated protease (CASP) exhibits programmable RNA-activated endopeptidase activity against a sigma factor inhibitor to regulate a transcriptional response. Cryo-electron microscopy of an active and substrate-bound CASP complex reveals an allosteric activation mechanism that reorganizes Csx29 catalytic residues upon target RNA binding. This work reveals an RNA-guided function in nature that can be leveraged for RNA-sensing applications in vitro and in human cells.
    DOI:  https://doi.org/10.1126/science.add7450
  10. Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01551-0. [Epub ahead of print]41(8): 111677
    Prenatal inflammation perturbs murine fetal hematopoietic development and causes persistent changes to postnatal immunity.
    Diego A López, April C Apostol, Eric J Lebish, Clint H Valencia, Mari Carmen Romero-Mulero, Polina V Pavlovich, Gloria E Hernandez, E Camilla Forsberg, Nina Cabezas-Wallscheid, Anna E Beaudin.
      Adult hematopoietic stem and progenitor cells (HSPCs) respond directly to inflammation and infection, causing both acute and persistent changes to quiescence, mobilization, and differentiation. Here we show that murine fetal HSPCs respond to prenatal inflammation in utero and that the fetal response shapes postnatal hematopoiesis and immune cell function. Heterogeneous fetal HSPCs show divergent responses to maternal immune activation (MIA), including changes in quiescence, expansion, and lineage-biased output. Single-cell transcriptomic analysis of fetal HSPCs in response to MIA reveals specific upregulation of inflammatory gene profiles in discrete, transient hematopoietic stem cell (HSC) populations that propagate expansion of lymphoid-biased progenitors. Beyond fetal development, MIA causes the inappropriate expansion and persistence of fetal lymphoid-biased progenitors postnatally, concomitant with increased cellularity and hyperresponsiveness of fetal-derived innate-like lymphocytes. Our investigation demonstrates how inflammation in utero can direct the output and function of fetal-derived immune cells by reshaping fetal HSC establishment.
    Keywords:  CP: Immunology; fetal development; hematopoiesis; heterogeneity; immunity; in utero inflammation; multipotent progenitor
    DOI:  https://doi.org/10.1016/j.celrep.2022.111677
  11. Sci Transl Med. 2022 Nov 23. 14(672): eabp8309
    CD47-SIRPα axis blockade in NASH promotes necroptotic hepatocyte clearance by liver macrophages and decreases hepatic fibrosis.
    Hongxue Shi, Xiaobo Wang, Fang Li, Brennan D Gerlach, Arif Yurdagul, Mary P Moore, Sharon Zeldin, Hanrui Zhang, Bishuang Cai, Ze Zheng, Luca Valenti, Ira Tabas.
      Necroptosis contributes to hepatocyte death in nonalcoholic steatohepatitis (NASH), but the fate and roles of necroptotic hepatocytes (necHCs) in NASH remain unknown. We show here that the accumulation of necHCs in human and mouse NASH liver is associated with an up-regulation of the "don't-eat-me" ligand CD47 on necHCs, but not on apoptotic hepatocytes, and an increase in the CD47 receptor SIRPα on liver macrophages, consistent with impaired macrophage-mediated clearance of necHCs. In vitro, necHC clearance by primary liver macrophages was enhanced by treatment with either anti-CD47 or anti-SIRPα. In a proof-of-concept mouse model of inducible hepatocyte necroptosis, anti-CD47 antibody treatment increased necHC uptake by liver macrophages and inhibited markers of hepatic stellate cell (HSC) activation, which is responsible for liver fibrogenesis. Treatment of two mouse models of diet-induced NASH with anti-CD47, anti-SIRPα, or AAV8-H1-shCD47 to silence CD47 in hepatocytes increased the uptake of necHC by liver macrophages and decreased markers of HSC activation and liver fibrosis. Anti-SIRPα treatment avoided the adverse effect of anemia found in anti-CD47-treated mice. These findings provide evidence that impaired clearance of necHCs by liver macrophages due to CD47-SIRPα up-regulation contributes to fibrotic NASH, and suggest therapeutic blockade of the CD47-SIRPα axis as a strategy to decrease the accumulation of necHCs in NASH liver and dampen the progression of hepatic fibrosis.
    DOI:  https://doi.org/10.1126/scitranslmed.abp8309
  12. J Immunol. 2022 Nov 15. 209(10): 1930-1941
    A Multi-Omics Approach Reveals Features That Permit Robust and Widespread Regulation of IFN-Inducible Antiviral Effectors.
    Loránd Göczi, Mária Csumita, Attila Horváth, Gergely Nagy, Szilárd Póliska, Matteo Pigni, Christoph Thelemann, Bence Dániel, Hamidreza Mianesaz, Tamás Varga, Kaushik Sen, Sunil K Raghav, John W Schoggins, Laszlo Nagy, Hans Acha-Orbea, Felix Meissner, Walter Reith, Lajos Széles.
      The antiviral state, an initial line of defense against viral infection, is established by a set of IFN-stimulated genes (ISGs) encoding antiviral effector proteins. The effector ISGs are transcriptionally regulated by type I IFNs mainly via activation of IFN-stimulated gene factor 3 (ISGF3). In this study, the regulatory elements of effector ISGs were characterized to determine the (epi)genetic features that enable their robust induction by type I IFNs in multiple cell types. We determined the location of regulatory elements, the DNA motifs, the occupancy of ISGF3 subunits (IRF9, STAT1, and STAT2) and other transcription factors, and the chromatin accessibility of 37 effector ISGs in murine dendritic cells. The IFN-stimulated response element (ISRE) and its tripartite version occurred most frequently in the regulatory elements of effector ISGs than in any other tested ISG subsets. Chromatin accessibility at their promoter regions was similar to most other ISGs but higher than at the promoters of inflammation-related cytokines, which were used as a reference gene set. Most effector ISGs (81.1%) had at least one ISGF3 binding region proximal to the transcription start site (TSS), and only a subset of effector ISGs (24.3%) was associated with three or more ISGF3 binding regions. The IRF9 signals were typically higher, and ISRE motifs were "stronger" (more similar to the canonical sequence) in TSS-proximal versus TSS-distal regulatory regions. Moreover, most TSS-proximal regulatory regions were accessible before stimulation in multiple cell types. Our results indicate that "strong" ISRE motifs and universally accessible promoter regions that permit robust, widespread induction are characteristic features of effector ISGs.
    DOI:  https://doi.org/10.4049/jimmunol.2200363
  13. Nat Commun. 2022 Nov 24. 13(1): 7213
    The unknown biogeochemical impacts of drying rivers and streams.
    Margaret A Zimmer, Amy J Burgin, Kendra Kaiser, Jacob Hosen.
      
    DOI:  https://doi.org/10.1038/s41467-022-34903-4
  14. Nat Commun. 2022 Nov 22. 13(1): 7162
    Sphingosine 1-phosphate mediates adiponectin receptor signaling essential for lipid homeostasis and embryogenesis.
    Mario Ruiz, Ranjan Devkota, Dimitra Panagaki, Per-Olof Bergh, Delaney Kaper, Marcus Henricsson, Ali Nik, Kasparas Petkevicius, Johanna L Höög, Mohammad Bohlooly-Y, Peter Carlsson, Jan Borén, Marc Pilon.
      Cells and organisms require proper membrane composition to function and develop. Phospholipids are the major component of membranes and are primarily acquired through the diet. Given great variability in diet composition, cells must be able to deploy mechanisms that correct deviations from optimal membrane composition and properties. Here, using lipidomics and unbiased proteomics, we found that the embryonic lethality in mice lacking the fluidity regulators Adiponectin Receptors 1 and 2 (AdipoR1/2) is associated with aberrant high saturation of the membrane phospholipids. Using mouse embryonic fibroblasts (MEFs) derived from AdipoR1/2-KO embryos, human cell lines and the model organism C. elegans we found that, mechanistically, AdipoR1/2-derived sphingosine 1-phosphate (S1P) signals in parallel through S1PR3-SREBP1 and PPARγ to sustain the expression of the fatty acid desaturase SCD and maintain membrane properties. Thus, our work identifies an evolutionary conserved pathway by which cells and organisms achieve membrane homeostasis and adapt to a variable environment.
    DOI:  https://doi.org/10.1038/s41467-022-34931-0
  15. Nat Commun. 2022 Nov 19. 13(1): 7115
    Transposable element-mediated rearrangements are prevalent in human genomes.
    Parithi Balachandran, Isha A Walawalkar, Jacob I Flores, Jacob N Dayton, Peter A Audano, Christine R Beck.
      Transposable elements constitute about half of human genomes, and their role in generating human variation through retrotransposition is broadly studied and appreciated. Structural variants mediated by transposons, which we call transposable element-mediated rearrangements (TEMRs), are less well studied, and the mechanisms leading to their formation as well as their broader impact on human diversity are poorly understood. Here, we identify 493 unique TEMRs across the genomes of three individuals. While homology directed repair is the dominant driver of TEMRs, our sequence-resolved TEMR resource allows us to identify complex inversion breakpoints, triplications or other high copy number polymorphisms, and additional complexities. TEMRs are enriched in genic loci and can create potentially important risk alleles such as a deletion in TRIM65, a known cancer biomarker and therapeutic target. These findings expand our understanding of this important class of structural variation, the mechanisms responsible for their formation, and establish them as an important driver of human diversity.
    DOI:  https://doi.org/10.1038/s41467-022-34810-8
  16. Nat Immunol. 2022 Nov 21.
    iNKT cells circulate.
    Stephanie Houston.
      
    DOI:  https://doi.org/10.1038/s41590-022-01382-0
  17. J Immunol. 2022 Dec 01. 209(11): 2073-2081
    Maintenance of Lineage Identity: Lessons from a B Cell.
    Kalina T Belcheva, Jayanta Chaudhuri.
      The maintenance of B cell identity requires active transcriptional control that enforces a B cell-specific program and suppresses alternative lineage genes. Accordingly, disrupting the B cell identity regulatory network compromises B cell function and induces cell fate plasticity by allowing derepression of alternative lineage-specific transcriptional programs. Although the B lineage is incredibly resistant to most differentiating factors, loss of just a single B lineage-specific transcription factor or the forced expression of individual non-B cell lineage transcription factors can radically disrupt B cell maintenance and allow dedifferentiation or transdifferentiation into entirely distinct lineages. B lymphocytes thereby offer an insightful and useful case study of how a specific cell lineage can maintain a stable identity throughout life and how perturbations of a single master regulator can induce cellular plasticity. In this article, we review the regulatory mechanisms that safeguard B cell identity, and we discuss how dysregulation of the B cell maintenance program can drive malignant transformation and enable therapeutic resistance.
    DOI:  https://doi.org/10.4049/jimmunol.2200497
  18. Nat Commun. 2022 Nov 23. 13(1): 7203
    Spatially aware dimension reduction for spatial transcriptomics.
    Lulu Shang, Xiang Zhou.
      Spatial transcriptomics are a collection of genomic technologies that have enabled transcriptomic profiling on tissues with spatial localization information. Analyzing spatial transcriptomic data is computationally challenging, as the data collected from various spatial transcriptomic technologies are often noisy and display substantial spatial correlation across tissue locations. Here, we develop a spatially-aware dimension reduction method, SpatialPCA, that can extract a low dimensional representation of the spatial transcriptomics data with biological signal and preserved spatial correlation structure, thus unlocking many existing computational tools previously developed in single-cell RNAseq studies for tailored analysis of spatial transcriptomics. We illustrate the benefits of SpatialPCA for spatial domain detection and explores its utility for trajectory inference on the tissue and for high-resolution spatial map construction. In the real data applications, SpatialPCA identifies key molecular and immunological signatures in a detected tumor surrounding microenvironment, including a tertiary lymphoid structure that shapes the gradual transcriptomic transition during tumorigenesis and metastasis. In addition, SpatialPCA detects the past neuronal developmental history that underlies the current transcriptomic landscape across tissue locations in the cortex.
    DOI:  https://doi.org/10.1038/s41467-022-34879-1
  19. Cell Death Dis. 2022 Nov 22. 13(11): 985
    Manipulating PP2Acα-ASK-JNK signaling to favor apoptotic over necroptotic hepatocyte fate reduces the extent of necrosis and fibrosis upon acute liver injury.
    Ke Lu, Si-Yu Shen, Ou-Yang Luo, Yue Lu, Tian-Shu Shi, Jing Wu, Qi Cheng, Hua-Jian Teng, Di Chen, Xiang Lu, Chao-Jun Li, Qing Jiang, Lei Fang, Bin Xue.
      In the widely used Carbon tetrachloride (CCl4)-induced acute liver injury (ALI) mouse model, hepatocytes are known to die from programmed cell death (PCD) processes including apoptosis and necroptosis. Both in vivo and in vitro experiments showed that CCl4 treatment could induce both apoptosis and necroptosis. Treatment of mice with the apoptosis inducer SMAC mimetic reduced necroptosis, led to less pronounced liver damage, and improved overall liver function. By LC-MS/MS, we found that PP2Acα expression was increased in ALI mice liver, and we confirmed its high expression in subacute hepatitis patients. We observed that ALI severity (including aggravated fibrogenesis) was significantly alleviated in hepatocyte-specific PP2Acα conditional knockout (PP2Acα cKO) mice. Furthermore, the relative extent of apoptosis over necroptosis was increased in the PP2Acα cKO ALI mice. Pursuing the idea that biasing the type of PCD towards apoptosis may reduce liver damage, we found that treatment of PP2Acα cKO ALI mice with the apoptosis inhibitor z-Vad-fmk increased the extent of necroptosis and caused severer damage. Mechanistically, disruption of PP2Acα prevents the dephosphorylation of pASK1(Ser967), thereby preventing the sustained activation of JNK. Inhibition of PP2Acα prevents CCl4-induced liver injury and fibrogenesis by disrupting ASK/JNK pathway mediated PCD signaling, ultimately improving liver function by biasing hepatocytes towards an apoptotic rather than necroptotic cell fate. Thus, targeting PP2A and/or ASK1 to favor apoptotic over necroptotic hepatocyte fate may represent an attractive therapeutic strategy for treating ALI.
    DOI:  https://doi.org/10.1038/s41419-022-05353-z
  20. Nat Commun. 2022 Nov 25. 13(1): 7243
    circCsnk1g3- and circAnkib1-regulated interferon responses in sarcoma promote tumorigenesis by shaping the immune microenvironment.
    Roberta Piras, Emily Y Ko, Connor Barrett, Marco De Simone, Xianzhi Lin, Marina T Broz, Fernando H G Tessaro, Mireia Castillo-Martin, Carlos Cordon-Cardo, Helen S Goodridge, Dolores Di Vizio, Mona Batish, Kate Lawrenson, Y Grace Chen, Keith Syson Chan, Jlenia Guarnerio.
      Exonic circular RNAs (circRNAs) produce predominantly non-coding RNA species that have been recently profiled in many tumors. However, their functional contribution to cancer progression is still poorly understood. Here, we identify the circRNAs expressed in soft tissue sarcoma cells and explore how the circRNAs regulate sarcoma growth in vivo. We show that circCsnk1g3 and circAnkib1 promote tumor growth by shaping a pro-tumorigenic microenvironment, possibly due to their capabilities to regulate tumor-promoting elements extrinsic to the tumor cells. Accordingly, circCsnk1g3 and circAnkib1 can control the expression of interferon-related genes and pro-inflammatory factors in the sarcoma cells, thus directing immune cell recruitment into the tumor mass, and hence their activation. Mechanistically, circRNAs may repress pro-inflammatory elements by buffering activation of the pathways mediated by RIG-I, the cytosolic viral RNA sensor. The current findings suggest that the targeting of specific circRNAs could augment the efficacy of tumor and immune response to mainstay therapies.
    DOI:  https://doi.org/10.1038/s41467-022-34872-8
  21. Nat Commun. 2022 Nov 19. 13(1): 7107
    DNA mechanical flexibility controls DNA potential to activate cGAS-mediated immune surveillance.
    Lina Wang, Siru Li, Kai Wang, Na Wang, Qiaoling Liu, Zhen Sun, Li Wang, Lulu Wang, Quentin Liu, Chengli Song, Caigang Liu, Qingkai Yang.
      DNA is well-documented to stimulate immune response. However, the nature of the DNA to activate immune surveillance is less understood. Here, we show that the activation of cyclic GMP-AMP synthase (cGAS) depends on DNA mechanical flexibility, which is controlled by DNA-sequence, -damage and -length. Consistently, DNA-sequence was shown to control cGAS activation. Structural analyses revealed that a conserved cGAS residue (mouse R222 or human R236) contributed to the DNA-flexibility detection. And the residue substitution neutralised the flexibility-controlled DNA-potential to activate cGAS, and relaxed the DNA-length specificity of cGAS. Moreover, low dose radiation was shown to mount cGAS-mediated acute immune surveillance (AIS) via repairable (reusable) DNAs in hrs. Loss of cGAS-mediated AIS decreased the regression of local and abscopal tumours in the context of focal radiation and immune checkpoint blockade. Our results build a direct link between immunosurveillance and DNA mechanical feature.
    DOI:  https://doi.org/10.1038/s41467-022-34858-6
  22. Nature. 2022 Nov 23.
    MYC multimers shield stalled replication forks from RNA polymerase.
    Daniel Solvie, Apoorva Baluapuri, Leonie Uhl, Daniel Fleischhauer, Theresa Endres, Dimitrios Papadopoulos, Amel Aziba, Abdallah Gaballa, Ivan Mikicic, Ekaterina Isaakova, Celeste Giansanti, Jennifer Jansen, Marvin Jungblut, Teresa Klein, Christina Schülein-Völk, Hans Maric, Sören Doose, Markus Sauer, Petra Beli, Andreas Rosenwald, Matthias Dobbelstein, Elmar Wolf, Martin Eilers.
      Oncoproteins of the MYC family drive the development of numerous human tumours1. In unperturbed cells, MYC proteins bind to nearly all active promoters and control transcription by RNA polymerase II2,3. MYC proteins can also coordinate transcription with DNA replication4,5 and promote the repair of transcription-associated DNA damage6, but how they exert these mechanistically diverse functions is unknown. Here we show that MYC dissociates from many of its binding sites in active promoters and forms multimeric, often sphere-like structures in response to perturbation of transcription elongation, mRNA splicing or inhibition of the proteasome. Multimerization is accompanied by a global change in the MYC interactome towards proteins involved in transcription termination and RNA processing. MYC multimers accumulate on chromatin immediately adjacent to stalled replication forks and surround FANCD2, ATR and BRCA1 proteins, which are located at stalled forks7,8. MYC multimerization is triggered in a HUWE16 and ubiquitylation-dependent manner. At active promoters, MYC multimers block antisense transcription and stabilize FANCD2 association with chromatin. This limits DNA double strand break formation during S-phase, suggesting that the multimerization of MYC enables tumour cells to proliferate under stressful conditions.
    DOI:  https://doi.org/10.1038/s41586-022-05469-4
  23. Nat Commun. 2022 Nov 25. 13(1): 7269
    Reduced secretion of neuronal growth regulator 1 contributes to impaired adipose-neuronal crosstalk in obesity.
    Elisa Duregotti, Christina M Reumiller, Ursula Mayr, Maria Hasman, Lukas E Schmidt, Sean A Burnap, Konstantinos Theofilatos, Javier Barallobre-Barreiro, Arne Beran, Maria Grandoch, Alessandro Viviano, Marjan Jahangiri, Manuel Mayr.
      While the endocrine function of white adipose tissue has been extensively explored, comparatively little is known about the secretory activity of less-investigated fat depots. Here, we use proteomics to compare the secretory profiles of male murine perivascular depots with those of canonical white and brown fat. Perivascular secretomes show enrichment for neuronal cell-adhesion molecules, reflecting a higher content of intra-parenchymal sympathetic projections compared to other adipose depots. The sympathetic innervation is reduced in the perivascular fat of obese (ob/ob) male mice, as well as in the epicardial fat of patients with obesity. Degeneration of sympathetic neurites is observed in presence of conditioned media of fat explants from ob/ob mice, that show reduced secretion of neuronal growth regulator 1. Supplementation of neuronal growth regulator 1 reverses this neurodegenerative effect, unveiling a neurotrophic role for this protein previously identified as a locus associated with human obesity. As sympathetic stimulation triggers energy-consuming processes in adipose tissue, an impaired adipose-neuronal crosstalk is likely to contribute to the disrupted metabolic homeostasis characterising obesity.
    DOI:  https://doi.org/10.1038/s41467-022-34846-w
  24. Nat Commun. 2022 Nov 23. 13(1): 7182
    Reversion mutations in germline BRCA1/2-mutant tumors reveal a BRCA-mediated phenotype in non-canonical histologies.
    Yonina R Murciano-Goroff, Alison M Schram, Ezra Y Rosen, Helen Won, Yixiao Gong, Anne Marie Noronha, Yelena Y Janjigian, Zsofia K Stadler, Jason C Chang, Soo-Ryum Yang, Diana Mandelker, Kenneth Offit, Michael F Berger, Mark T A Donoghue, Chaitanya Bandlamudi, Alexander Drilon.
      The association between loss of BRCA1/2 and a homologous recombination deficiency phenotype is lineage dependent. In BRCA-associated cancers such as breast, ovarian, pancreas and prostate, this phenotype confers sensitivity to PARP inhibitors and platinum-therapies. Somatic reversion mutations restoring BRCA1/2 function mediate resistance, and have exclusively been reported in BRCA-associated tumors. In this study, we analyze matched tumor and normal sequencing from 31,927 patients and identify 846 (2.7%) patients with germline BRCA1/2 variants across 43 different cancer types, including 11 with somatic reversion mutations. While nine are in BRCA-associated tumors, we find two reversion mutations in non-BRCA-associated histologies, namely lung and esophagogastric adenocarcinomas. Both were detected following platinum therapy. Whole exome sequencing confirms the homologous recombination deficiency phenotype of these tumors. While reversion mutations arise in all BRCA-associated cancer types, here we show that reversion mutations arising post-platinum in non-BRCA associated histologies, while rare, may indicate BRCA1/2 mediated tumorigenesis.
    DOI:  https://doi.org/10.1038/s41467-022-34109-8
  25. Nat Commun. 2022 Nov 25. 13(1): 7252
    mTORC1 signaling facilitates differential stem cell differentiation to shape the developing murine lung and is associated with mitochondrial capacity.
    Kuan Zhang, Erica Yao, Ethan Chuang, Biao Chen, Evelyn Y Chuang, Pao-Tien Chuang.
      Formation of branched organs requires sequential differentiation of stem cells. In this work, we find that the conducting airways derived from SOX2+ progenitors in the murine lungs fail to form without mTOR complex 1 (mTORC1) signaling and are replaced by lung cysts. Proximal-distal patterning through transitioning of distal SOX9+ progenitors to proximal SOX2+ cells is disrupted. Mitochondria number and ATP production are reduced. Compromised mitochondrial capacity results in a similar defect as that in mTORC1-deficient lungs. This suggests that mTORC1 promotes differentiation of SOX9+ progenitors to form the conducting airways by modulating mitochondrial capacity. Surprisingly, in all mutants, saccules are produced from lung cysts at the proper developmental time despite defective branching. SOX9+ progenitors also differentiate into alveolar epithelial type I and type II cells within saccules. These findings highlight selective utilization of energy and regulatory programs during stem cell differentiation to produce distinct structures of the mammalian lungs.
    DOI:  https://doi.org/10.1038/s41467-022-34763-y
  26. Science. 2022 Nov 25. 378(6622): 853-858
    The future of engineered immune cell therapies.
    Darrell J Irvine, Marcela V Maus, David J Mooney, Wilson W Wong.
      Immune cells are being engineered to recognize and respond to disease states, acting as a "living drug" when transferred into patients. Therapies based on engineered immune cells are now a clinical reality, with multiple engineered T cell therapies approved for treatment of hematologic malignancies. Ongoing preclinical and clinical studies are testing diverse strategies to modify the fate and function of immune cells for applications in cancer, infectious disease, and beyond. Here, we discuss current progress in treating human disease with immune cell therapeutics, emerging strategies for immune cell engineering, and challenges facing the field, with a particular emphasis on the treatment of cancer, where the most effort has been applied to date.
    DOI:  https://doi.org/10.1126/science.abq6990
  27. Nat Commun. 2022 Nov 19. 13(1): 7113
    BRAF activation by metabolic stress promotes glycolysis sensitizing NRASQ61-mutated melanomas to targeted therapy.
    Kimberley McGrail, Paula Granado-Martínez, Rosaura Esteve-Puig, Sara García-Ortega, Yuxin Ding, Sara Sánchez-Redondo, Berta Ferrer, Javier Hernandez-Losa, Francesc Canals, Anna Manzano, Aura Navarro-Sabaté, Ramón Bartrons, Oscar Yanes, Mileidys Pérez-Alea, Eva Muñoz-Couselo, Vicenç Garcia-Patos, Juan A Recio.
      NRAS-mutated melanoma lacks a specific line of treatment. Metabolic reprogramming is considered a novel target to control cancer; however, NRAS-oncogene contribution to this cancer hallmark is mostly unknown. Here, we show that NRASQ61-mutated melanomas specific metabolic settings mediate cell sensitivity to sorafenib upon metabolic stress. Mechanistically, these cells are dependent on glucose metabolism, in which glucose deprivation promotes a switch from CRAF to BRAF signaling. This scenario contributes to cell survival and sustains glucose metabolism through BRAF-mediated phosphorylation of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-2/3 (PFKFB2/PFKFB3). In turn, this favors the allosteric activation of phosphofructokinase-1 (PFK1), generating a feedback loop that couples glycolytic flux and the RAS signaling pathway. An in vivo treatment of NRASQ61 mutant melanomas, including patient-derived xenografts, with 2-deoxy-D-glucose (2-DG) and sorafenib effectively inhibits tumor growth. Thus, we provide evidence for NRAS-oncogene contributions to metabolic rewiring and a proof-of-principle for the treatment of NRASQ61-mutated melanoma combining metabolic stress (glycolysis inhibitors) and previously approved drugs, such as sorafenib.
    DOI:  https://doi.org/10.1038/s41467-022-34907-0
  28. Nat Commun. 2022 Nov 22. 13(1): 7149
    Expanding cross-presenting dendritic cells enhances oncolytic virotherapy and is critical for long-term anti-tumor immunity.
    Judit Svensson-Arvelund, Sara Cuadrado-Castano, Gvantsa Pantsulaia, Kristy Kim, Mark Aleynick, Linda Hammerich, Ranjan Upadhyay, Michael Yellin, Henry Marsh, Daniel Oreper, Suchit Jhunjhunwala, Christine Moussion, Miriam Merad, Brian D Brown, Adolfo García-Sastre, Joshua D Brody.
      Immunotherapies directly enhancing anti-tumor CD8+ T cell responses have yielded measurable but limited success, highlighting the need for alternatives. Anti-tumor T cell responses critically depend on antigen presenting dendritic cells (DC), and enhancing mobilization, antigen loading and activation of these cells represent an attractive possibility to potentiate T cell based therapies. Here we show that expansion of DCs by Flt3L administration impacts in situ vaccination with oncolytic Newcastle Disease Virus (NDV). Mechanistically, NDV activates DCs and sensitizes them to dying tumor cells through upregulation of dead-cell receptors and synergizes with Flt3L to promote anti-tumor CD8+ T cell cross-priming. In vivo, Flt3L-NDV in situ vaccination induces parallel amplification of virus- and tumor-specific T cells, including CD8+ T cells reactive to newly-described neoepitopes, promoting long-term tumor control. Cross-presenting conventional Type 1 DCs are indispensable for the anti-tumor, but not anti-viral, T cell response, and type I IFN-dependent CD4+ Th1 effector cells contribute to optimal anti-tumor immunity. These data demonstrate that mobilizing DCs to increase tumor antigen cross-presentation improves oncolytic virotherapy and that neoepitope-specific T cells can be induced without individualized, ex vivo manufactured vaccines.
    DOI:  https://doi.org/10.1038/s41467-022-34791-8
  29. Nat Commun. 2022 Nov 24. 13(1): 7226
    Enhanced access to the human phosphoproteome with genetically encoded phosphothreonine.
    Jack M Moen, Kyle Mohler, Svetlana Rogulina, Xiaojian Shi, Hongying Shen, Jesse Rinehart.
      Protein phosphorylation is a ubiquitous post-translational modification used to regulate cellular processes and proteome architecture by modulating protein-protein interactions. The identification of phosphorylation events through proteomic surveillance has dramatically outpaced our capacity for functional assignment using traditional strategies, which often require knowledge of the upstream kinase a priori. The development of phospho-amino-acid-specific orthogonal translation systems, evolutionarily divergent aminoacyl-tRNA synthetase and tRNA pairs that enable co-translational insertion of a phospho-amino acids, has rapidly improved our ability to assess the physiological function of phosphorylation by providing kinase-independent methods of phosphoprotein production. Despite this utility, broad deployment has been hindered by technical limitations and an inability to reconstruct complex phopho-regulatory networks. Here, we address these challenges by optimizing genetically encoded phosphothreonine translation to characterize phospho-dependent kinase activation mechanisms and, subsequently, develop a multi-level protein interaction platform to directly assess the overlap of kinase and phospho-binding protein substrate networks with phosphosite-level resolution.
    DOI:  https://doi.org/10.1038/s41467-022-34980-5
  30. Nat Commun. 2022 Nov 23. 13(1): 7179
    Smc5/6's multifaceted DNA binding capacities stabilize branched DNA structures.
    Jeremy T-H Chang, Shibai Li, Emily C Beckwitt, Thane Than, Cory Haluska, Joshua Chandanani, Michael E O'Donnell, Xiaolan Zhao, Shixin Liu.
      Smc5/6 is an evolutionarily conserved SMC complex with roles in DNA replication and repair, as well as in viral DNA restriction. Understanding its multiple functions has been hampered by a lack of mechanistic studies on how the Smc5/6 complex associates with different types of DNA. Here we address this question by simultaneously visualizing the behavior of Smc5/6 on three types of DNA, namely double-stranded (ds) DNA, single-stranded (ss) DNA, and junction DNA formed by juxtaposed ss- and dsDNA, using correlative single-molecule fluorescence and force microscopy. We find that Smc5/6 displays distinct behaviors toward different types of DNA, dynamically associating with dsDNA while stably binding to junction DNA. Mechanistically, both the Nse1-3-4 subcomplex and ATP binding enhance the complex's dsDNA association. In contrast, Smc5/6's assembly onto ssDNA emanating from junction DNA, which occurs even in the presence high-affinity ssDNA binders, is aided by Nse1-3-4, but not by ATP. Moreover, we show that Smc5/6 protects junction DNA stability by preventing ssDNA annealing. The multifaceted DNA association behaviors of Smc5/6 provide a framework for understanding its diverse functions in genome maintenance and viral DNA restriction.
    DOI:  https://doi.org/10.1038/s41467-022-34928-9
  31. Proc Natl Acad Sci U S A. 2022 Nov 29. 119(48): e2210595119
    EBF1 is continuously required for stabilizing local chromatin accessibility in pro-B cells.
    Nikolay Zolotarev, Marc Bayer, Rudolf Grosschedl.
      The establishment of de novo chromatin accessibility in lymphoid progenitors requires the "pioneering" function of transcription factor (TF) early B cell factor 1 (EBF1), which binds to naïve chromatin and induces accessibility by recruiting the BRG1 chromatin remodeler subunit. However, it remains unclear whether the function of EBF1 is continuously required for stabilizing local chromatin accessibility. To this end, we replaced EBF1 by EBF1-FKBPF36V in pro-B cells, allowing the rapid degradation by adding the degradation TAG13 (dTAG13) dimerizer. EBF1 degradation results in a loss of genome-wide EBF1 occupancy and EBF1-targeted BRG1 binding. Chromatin accessibility was rapidly diminished at EBF1-binding sites with a preference for sites whose occupancy requires the pioneering activity of the C-terminal domain of EBF1. Diminished chromatin accessibility correlated with altered gene expression. Thus, continuous activity of EBF1 is required for the stable maintenance of the transcriptional and epigenetic state of pro-B cells.
    Keywords:  B cell; BRG1; EBF1; chromatin accessibility; dTAG
    DOI:  https://doi.org/10.1073/pnas.2210595119
  32. Nat Commun. 2022 Nov 23. 13(1): 7197
    Kinetics of mRNA nuclear export regulate innate immune response gene expression.
    UCLA Ribonomics Group
      The abundance and stimulus-responsiveness of mature mRNA is thought to be determined by nuclear synthesis, processing, and cytoplasmic decay. However, the rate and efficiency of moving mRNA to the cytoplasm almost certainly contributes, but has rarely been measured. Here, we investigated mRNA export rates for innate immune genes. We generated high spatio-temporal resolution RNA-seq data from endotoxin-stimulated macrophages and parameterized a mathematical model to infer kinetic parameters with confidence intervals. We find that the effective chromatin-to-cytoplasm export rate is gene-specific, varying 100-fold: for some genes, less than 5% of synthesized transcripts arrive in the cytoplasm as mature mRNAs, while others show high export efficiency. Interestingly, effective export rates do not determine temporal gene responsiveness, but complement the wide range of mRNA decay rates; this ensures similar abundances of short- and long-lived mRNAs, which form successive innate immune response expression waves.
    DOI:  https://doi.org/10.1038/s41467-022-34635-5
  33. Dev Cell. 2022 Nov 21. pii: S1534-5807(22)00760-2. [Epub ahead of print]57(22): 2584-2598.e11
    Autophagy promotes cell survival by maintaining NAD levels.
    Tetsushi Kataura, Lucia Sedlackova, Elsje G Otten, Ruchika Kumari, David Shapira, Filippo Scialo, Rhoda Stefanatos, Kei-Ichi Ishikawa, George Kelly, Elena Seranova, Congxin Sun, Dorothea Maetzel, Niall Kenneth, Sergey Trushin, Tong Zhang, Eugenia Trushina, Charles C Bascom, Ryan Tasseff, Robert J Isfort, John E Oblong, Satomi Miwa, Michael Lazarou, Rudolf Jaenisch, Masaya Imoto, Shinji Saiki, Manolis Papamichos-Chronakis, Ravi Manjithaya, Oliver D K Maddocks, Alberto Sanz, Sovan Sarkar, Viktor I Korolchuk.
      Autophagy is an essential catabolic process that promotes the clearance of surplus or damaged intracellular components. Loss of autophagy in age-related human pathologies contributes to tissue degeneration through a poorly understood mechanism. Here, we identify an evolutionarily conserved role of autophagy from yeast to humans in the preservation of nicotinamide adenine dinucleotide (NAD) levels, which are critical for cell survival. In respiring mouse fibroblasts with autophagy deficiency, loss of mitochondrial quality control was found to trigger hyperactivation of stress responses mediated by NADases of PARP and Sirtuin families. Uncontrolled depletion of the NAD(H) pool by these enzymes ultimately contributed to mitochondrial membrane depolarization and cell death. Pharmacological and genetic interventions targeting several key elements of this cascade improved the survival of autophagy-deficient yeast, mouse fibroblasts, and human neurons. Our study provides a mechanistic link between autophagy and NAD metabolism and identifies targets for interventions in human diseases associated with autophagic, lysosomal, and mitochondrial dysfunction.
    Keywords:  DNA damage; NAD; PARP; Sirtuins; ageing; autophagy; metabolism; mitochondria; mitophagy
    DOI:  https://doi.org/10.1016/j.devcel.2022.10.008
  34. JCI Insight. 2022 Nov 22. pii: e153740. [Epub ahead of print]
    HGFAC is a ChREBP regulated hepatokine that enhances glucose and lipid homeostasis.
    Ashot Sargsyan, Ludivine Doridot, Sarah Anissa Hannou, Wenxin Tong, Harini Srinivasan, Rachael Ivison, Ruby Monn, Henry H Kou, Jonathan M Haldeman, Michelle Arlotto, Phillip J White, Paul A Grimsrud, Inna Astapova, Linus T-Y Tsai, Mark A Herman.
      Carbohydrate Responsive Element-Binding Protein (ChREBP) is a carbohydrate sensing transcription factor that regulates both adaptive and maladaptive genomic responses in coordination of systemic fuel homeostasis. Genetic variants in the ChREBP locus associate with diverse metabolic traits in humans, including circulating lipids. To identify novel ChREBP-regulated hepatokines that contribute to its systemic metabolic effects, we integrated ChREBP ChIP-seq analysis in mouse liver with human genetic and genomic data for lipid traits and identified Hepatocyte Growth Factor Activator (HGFAC) as a promising ChREBP-regulated candidate in mice and humans. HGFAC is a protease that activates the pleiotropic hormone Hepatocyte Growth Factor (HGF). We demonstrate that HGFAC KO mice have phenotypes concordant with putative loss-of-function variants in human HGFAC. Moreover, in gain- and loss-of-function genetic mouse models, we demonstrate that HGFAC enhances lipid and glucose homeostasis, which may be mediated in part through actions to activate hepatic PPARγ activity. Together, our studies show that ChREBP mediates an adaptive response to overnutrition via activation of HGFAC in the liver to preserve glucose and lipid homeostasis.
    Keywords:  Carbohydrate metabolism; Glucose metabolism; Growth factors; Metabolism
    DOI:  https://doi.org/10.1172/jci.insight.153740
  35. Nat Metab. 2022 Nov 24.
    Metabolic control of innate lymphoid cells in health and disease.
    Lei Zhou, Qingxia Lin, Gregory F Sonnenberg.
      Innate lymphoid cells (ILCs) are a family of predominantly tissue-resident lymphocytes that critically orchestrate immunity, inflammation, tolerance and repair at barrier surfaces of the mammalian body. Heterogeneity among ILC subsets is comparable to that of adaptive CD4+ T helper cell counterparts, and emerging studies demonstrate that ILC biology is also dictated by cellular metabolism that adapts bioenergetic requirements during activation, proliferation or cytokine production. Accumulating evidence in mouse models and human samples indicates that ILCs exhibit profound roles in shaping states of metabolic health and disease. Here we summarize and discuss our current knowledge of the cell-intrinsic and cell-extrinsic metabolic factors controlling ILC responses, as well as highlight contributions of ILCs to organismal metabolism. It is expected that continued research in this area will advance our understanding of how to manipulate ILCs or their metabolism for therapeutic strategies that benefit human health.
    DOI:  https://doi.org/10.1038/s42255-022-00685-8
  36. Nat Commun. 2022 Nov 23. 13(1): 7189
    A class-mismatched TCR bypasses MHC restriction via an unorthodox but fully functional binding geometry.
    Nishant K Singh, Jesus A Alonso, Jason R Devlin, Grant L J Keller, George I Gray, Adarsh K Chiranjivi, Sara G Foote, Lauren M Landau, Alyssa G Arbuiso, Laura I Weiss, Aaron M Rosenberg, Lance M Hellman, Michael I Nishimura, Brian M Baker.
      MHC restriction, which describes the binding of TCRs from CD4+ T cells to class II MHC proteins and TCRs from CD8+ T cells to class I MHC proteins, is a hallmark of immunology. Seemingly rare TCRs that break this paradigm exist, but mechanistic insight into their behavior is lacking. TIL1383I is a prototypical class-mismatched TCR, cloned from a CD4+ T cell but recognizing the tyrosinase tumor antigen presented by the class I MHC HLA-A2 in a fully functional manner. Here we find that TIL1383I binds this class I target with a highly atypical geometry. Despite unorthodox binding, TCR signaling, antigen specificity, and the ability to use CD8 are maintained. Structurally, a key feature of TIL1383I is an exceptionally long CDR3β loop that mediates functions that are traditionally performed separately by hypervariable and germline loops in canonical TCR structures. Our findings thus expand the range of known TCR binding geometries compatible with normal function and specificity, provide insight into the determinants of MHC restriction, and may help guide TCR selection and engineering for immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-022-34896-0
  37. Nat Commun. 2022 Nov 19. 13(1): 7099
    The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells.
    Sameera Vipat, Dipika Gupta, Sagun Jonchhe, Hele Anderspuk, Eli Rothenberg, Tatiana N Moiseeva.
      DNA polymerase epsilon (PolE) in an enzyme essential for DNA replication. Deficiencies and mutations in PolE cause severe developmental abnormalities and cancers. Paradoxically, the catalytic domain of yeast PolE catalytic subunit is dispensable for survival, and its non-catalytic essential function is linked with replicative helicase (CMG) assembly. Less is known about the PolE role in replication initiation in human cells. Here we use an auxin-inducible degron system to study the effect of POLE1 depletion on replication initiation in U2OS cells. POLE1-depleted cells were able to assemble CMG helicase and initiate DNA synthesis that failed shortly after. Expression of POLE1 non-catalytic domain rescued this defect resulting in slow, but continuous DNA synthesis. We propose a model where in human U2OS cells POLE1/POLE2 are dispensable for CMG assembly, but essential during later steps of replication initiation. Our study provides some insights into the role of PolE in replication initiation in human cells.
    DOI:  https://doi.org/10.1038/s41467-022-34911-4
  38. Nat Commun. 2022 Nov 19. 13(1): 7121
    Metabolic and proteomic signatures of type 2 diabetes subtypes in an Arab population.
    Shaza B Zaghlool, Anna Halama, Nisha Stephan, Valborg Gudmundsdottir, Vilmundur Gudnason, Lori L Jennings, Manonanthini Thangam, Emma Ahlqvist, Rayaz A Malik, Omar M E Albagha, Abdul Badi Abou-Samra, Karsten Suhre.
      Type 2 diabetes (T2D) has a heterogeneous etiology influencing its progression, treatment, and complications. A data driven cluster analysis in European individuals with T2D previously identified four subtypes: severe insulin deficient (SIDD), severe insulin resistant (SIRD), mild obesity-related (MOD), and mild age-related (MARD) diabetes. Here, the clustering approach was applied to individuals with T2D from the Qatar Biobank and validated in an independent set. Cluster-specific signatures of circulating metabolites and proteins were established, revealing subtype-specific molecular mechanisms, including activation of the complement system with features of autoimmune diabetes and reduced 1,5-anhydroglucitol in SIDD, impaired insulin signaling in SIRD, and elevated leptin and fatty acid binding protein levels in MOD. The MARD cluster was the healthiest with metabolomic and proteomic profiles most similar to the controls. We have translated the T2D subtypes to an Arab population and identified distinct molecular signatures to further our understanding of the etiology of these subtypes.
    DOI:  https://doi.org/10.1038/s41467-022-34754-z
  39. Nat Commun. 2022 Nov 25. 13(1): 7260
    GPSM1 impairs metabolic homeostasis by controlling a pro-inflammatory pathway in macrophages.
    Jing Yan, Yuemei Zhang, Hairong Yu, Yicen Zong, Daixi Wang, Jiangfei Zheng, Li Jin, Xiangtian Yu, Caizhi Liu, Yi Zhang, Feng Jiang, Rong Zhang, Xiangnan Fang, Ting Xu, Mingyu Li, Jianzhong Di, Yan Lu, Xinran Ma, Jian Zhang, Weiping Jia, Cheng Hu.
      G-protein-signaling modulator 1 (GPSM1) exhibits strong genetic association with Type 2 diabetes (T2D) and Body Mass Index in population studies. However, how GPSM1 carries out such control and in which types of cells are poorly understood. Here, we demonstrate that myeloid GPSM1 promotes metabolic inflammation to accelerate T2D and obesity development. Mice with myeloid-specific GPSM1 ablation are protected against high fat diet-induced insulin resistance, glucose dysregulation, and liver steatosis via repression of adipose tissue pro-inflammatory states. Mechanistically, GPSM1 deficiency mainly promotes TNFAIP3 transcription via the Gαi3/cAMP/PKA/CREB axis, thus inhibiting TLR4-induced NF-κB signaling in macrophages. In addition, we identify a small-molecule compound, AN-465/42243987, which suppresses the pro-inflammatory phenotype by inhibiting GPSM1 function, which could make it a candidate for metabolic therapy. Furthermore, GPSM1 expression is upregulated in visceral fat of individuals with obesity and is correlated with clinical metabolic traits. Overall, our findings identify macrophage GPSM1 as a link between metabolic inflammation and systemic homeostasis.
    DOI:  https://doi.org/10.1038/s41467-022-34998-9
  40. Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01568-6. [Epub ahead of print]41(8): 111694
    Activation of Wnt/β-catenin signaling by Zeb1 in endothelial progenitors induces vascular quiescence entry.
    Qing Cissy Yu, Ajun Geng, Christopher B Preusch, Yujie Chen, Guangdun Peng, Yishu Xu, Yingying Jia, Yi Miao, Huaqing Xue, Dong Gao, Lan Bao, Weijun Pan, Jianfeng Chen, K Christopher Garcia, Tom H Cheung, Yi Arial Zeng.
      The establishment of a functional vasculature requires endothelial cells to enter quiescence during the completion of development, otherwise pathological overgrowth occurs. How such a transition is regulated remains unclear. Here, we uncover a role of Zeb1 in defining vascular quiescence entry. During quiescence acquisition, Zeb1 increases along with the progressive decline of endothelial progenitors' activities, with Zeb1 loss resulting in endothelial overgrowth and vascular deformities. RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin sequencing (ATAC-seq) analyses reveal that Zeb1 represses Wif1, thereby activating Wnt/β-catenin signaling. Knockdown of Wif1 rescues the overgrowth induced by Zeb1 deletion. Importantly, local administration of surrogate Wnt molecules in the retina ameliorates the overgrowth defects of Zeb1 mutants. These findings show a mechanism by which Zeb1 induces quiescence of endothelial progenitors during the establishing of vascular homeostasis, providing molecular insight into the inherited neovascular pathologies associated with human ZEB1 mutations, suggesting pharmacological activation of Wnt/β-catenin signaling as a potential therapeutical approach.
    Keywords:  CP: Cell biology; CP: Molecular biology; Wnt/β-catenin signaling; Zeb1; endothelial overgrowth; endothelial progenitor; quiescence entry
    DOI:  https://doi.org/10.1016/j.celrep.2022.111694
  41. Nat Commun. 2022 Nov 21. 13(1): 7058
    Depletion of CD206+ M2-like macrophages induces fibro-adipogenic progenitors activation and muscle regeneration.
    Allah Nawaz, Muhammad Bilal, Shiho Fujisaka, Tomonobu Kado, Muhammad Rahil Aslam, Saeed Ahmed, Keisuke Okabe, Yoshiko Igarashi, Yoshiyuki Watanabe, Takahide Kuwano, Koichi Tsuneyama, Ayumi Nishimura, Yasuhiro Nishida, Seiji Yamamoto, Masakiyo Sasahara, Johji Imura, Hisashi Mori, Martin M Matzuk, Fujimi Kudo, Ichiro Manabe, Akiyoshi Uezumi, Takashi Nakagawa, Yumiko Oishi, Kazuyuki Tobe.
      Muscle regeneration requires the coordination of muscle stem cells, mesenchymal fibro-adipogenic progenitors (FAPs), and macrophages. How macrophages regulate the paracrine secretion of FAPs during the recovery process remains elusive. Herein, we systemically investigated the communication between CD206+ M2-like macrophages and FAPs during the recovery process using a transgenic mouse model. Depletion of CD206+ M2-like macrophages or deletion of CD206+ M2-like macrophages-specific TGF-β1 gene induces myogenesis and muscle regeneration. We show that depletion of CD206+ M2-like macrophages activates FAPs and activated FAPs secrete follistatin, a promyogenic factor, thereby boosting the recovery process. Conversely, deletion of the FAP-specific follistatin gene results in impaired muscle stem cell function, enhanced fibrosis, and delayed muscle regeneration. Mechanistically, CD206+ M2-like macrophages inhibit the secretion of FAP-derived follistatin via TGF-β signaling. Here we show that CD206+ M2-like macrophages constitute a microenvironment for FAPs and may regulate the myogenic potential of muscle stem/satellite cells.
    DOI:  https://doi.org/10.1038/s41467-022-34191-y
  42. Nat Commun. 2022 Nov 24. 13(1): 7221
    Global landscape of replicative DNA polymerase usage in the human genome.
    Eri Koyanagi, Yoko Kakimoto, Tamiko Minamisawa, Fumiya Yoshifuji, Toyoaki Natsume, Atsushi Higashitani, Tomoo Ogi, Antony M Carr, Masato T Kanemaki, Yasukazu Daigaku.
      The division of labour among DNA polymerase underlies the accuracy and efficiency of replication. However, the roles of replicative polymerases have not been directly established in human cells. We developed polymerase usage sequencing (Pu-seq) in HCT116 cells and mapped Polε and Polα usage genome wide. The polymerase usage profiles show Polε synthesises the leading strand and Polα contributes mainly to lagging strand synthesis. Combining the Polε and Polα profiles, we accurately predict the genome-wide pattern of fork directionality plus zones of replication initiation and termination. We confirm that transcriptional activity contributes to the pattern of initiation and termination and, by separately analysing the effect of transcription on co-directional and converging forks, demonstrate that coupled DNA synthesis of leading and lagging strands is compromised by transcription in both co-directional and convergent forks. Polymerase uncoupling is particularly evident in the vicinity of large genes, including the two most unstable common fragile sites, FRA3B and FRA3D, thus linking transcription-induced polymerase uncoupling to chromosomal instability. Together, our result demonstrated that Pu-seq in human cells provides a powerful and straightforward methodology to explore DNA polymerase usage and replication fork dynamics.
    DOI:  https://doi.org/10.1038/s41467-022-34929-8
  43. Proc Natl Acad Sci U S A. 2022 Nov 29. 119(48): e2215474119
    CTLA-4 on thymic epithelial cells complements Aire for T cell central tolerance.
    Daniel A Michelson, Christophe Benoist, Diane Mathis.
      Medullary thymic epithelial cells (mTECs) are essential for the establishment of T cell central tolerance. The transcription factor Aire plays a key role in this process, but other factors remain understudied. We found that a small population of mTECs expressed the coinhibitory receptor cytotoxic T lymphocyte-associated protein 4 (CTLA-4). These CTLA-4+ cells were detectable in perinates, peaked around young adulthood and expanded sixfold in the absence of Aire. Single-cell transcriptomics revealed CTLA-4+ mTECs to express a distinct gene signature encoding molecules associated with antigen presentation and interferon-gamma signaling. Mice conditionally lacking CTLA-4 in thymic epithelial cells had no major immunological deficiencies but displayed a mildly increased inflammatory tone and a partial defect in the generation of Foxp3+CD4+ regulatory T cells. Consequently, these mice developed modest levels of autoantibodies and lymphocytic infiltration of peripheral tissues. Thus, CTLA-4 expression in mTECs complements Aire to establish T cell central tolerance.
    Keywords:  Aire; CTLA-4; T cell; thymic epithelial cell; tolerance
    DOI:  https://doi.org/10.1073/pnas.2215474119
  44. Nat Commun. 2022 Nov 23. 13(1): 7178
    Primate-specific transposable elements shape transcriptional networks during human development.
    Julien Pontis, Cyril Pulver, Christopher J Playfoot, Evarist Planet, Delphine Grun, Sandra Offner, Julien Duc, Andrea Manfrin, Matthias P Lutolf, Didier Trono.
      The human genome contains more than 4.5 million inserts derived from transposable elements (TEs), the result of recurrent waves of invasion and internal propagation throughout evolution. For new TE copies to be inherited, they must become integrated in the genome of the germline or pre-implantation embryo, which requires that their source TE be expressed at these stages. Accordingly, many TEs harbor DNA binding sites for the pluripotency factors OCT4, NANOG, SOX2, and KLFs and are transiently expressed during embryonic genome activation. Here, we describe how many primate-restricted TEs have additional binding sites for lineage-specific transcription factors driving their expression during human gastrulation and later steps of fetal development. These TE integrants serve as lineage-specific enhancers fostering the transcription, amongst other targets, of KRAB-zinc finger proteins (KZFPs) of comparable evolutionary age, which in turn corral the activity of TE-embedded regulatory sequences in a similarly lineage-restricted fashion. Thus, TEs and their KZFP controllers play broad roles in shaping transcriptional networks during early human development.
    DOI:  https://doi.org/10.1038/s41467-022-34800-w
  45. Sci Adv. 2022 Nov 25. 8(47): eabq6324
    Intronic enhancers of the human SNCA gene predominantly regulate its expression in brain in vivo.
    Fubo Cheng, Wenxu Zheng, Chang Liu, Peter Antony Barbuti, Libo Yu-Taeger, Nicolas Casadei, Jeannette Huebener-Schmid, Jakob Admard, Karsten Boldt, Katrin Junger, Marius Ueffing, Henry Houlden, Manu Sharma, Rejko Kruger, Kathrin Grundmann-Hauser, Thomas Ott, Olaf Riess.
      Evidence from patients with Parkinson's disease (PD) and our previously reported α-synuclein (SNCA) transgenic rat model support the idea that increased SNCA protein is a substantial risk factor of PD pathogenesis. However, little is known about the transcription control of the human SNCA gene in the brain in vivo. Here, we identified that the DYT6 gene product THAP1 (THAP domain-containing apoptosis-associated protein 1) and its interaction partner CTCF (CCCTC-binding factor) act as transcription regulators of SNCA. THAP1 controls SNCA intronic enhancers' activities, while CTCF regulates its enhancer-promoter loop formation. The SNCA intronic enhancers present neurodevelopment-dependent activities and form enhancer clusters similar to "super-enhancers" in the brain, in which the PD-associated single-nucleotide polymorphisms are enriched. Deletion of the SNCA intronic enhancer clusters prevents the release of paused RNA polymerase II from its promoter and subsequently reduces its expression drastically in the brain, which may provide new therapeutic approaches to prevent its accumulation and thus related neurodegenerative diseases defined as synucleinopathies.
    DOI:  https://doi.org/10.1126/sciadv.abq6324
  46. Nature. 2022 Nov 21.
    Pre-T cell receptor Self-MHC Sampling Restricts Thymocyte Dedifferentiation.
    Jonathan S Duke-Cohan, Aoi Akitsu, Robert J Mallis, Cameron M Messier, Patrick H Lizotte, Jon C Aster, Wonmuk Hwang, Matthew J Lang, Ellis L Reinherz.
      Programming T lymphocytes to distinguish self from non-self is a vital, multi-step process arising in the thymus1-4. Signalling through the pre-T cell receptor (preTCR), a CD3-associated heterodimer comprising an invariant pTα chain and a clone-specific β chain, constitutes a critical early checkpoint in thymocyte development within the αβ T-cell lineage5,6. PreTCRs arrayed on double negative (DN) thymocytes, like αβ TCRs appearing on double positive (DP) thymocytes, ligate peptides bound to MHC molecules (pMHC) on thymic stroma but via a different molecular docking strategy7-10. Here we show the consequences of those distinctive interactions for thymocyte progression, using synchronized fetal thymic progenitor cultures differing in the presence or absence of pMHC on support stroma, determining single cell transcriptomes at key thymocyte developmental transitions. Although MHC negative stroma fosters αβ T lymphocyte differentiation, the absence of pMHC-preTCR interplay leads to deviant thymocyte transcriptional programming associated with dedifferentiation. Highly proliferative DN and DP subsets with antecedent characteristics of T cell lymphoblastic and myeloid malignancies emerge. Compensatory upregulation of diverse MHC class Ib proteins in B2m/H2-Ab1 MHC knockout mice partially safeguards in vivo thymocyte progression although, with ageing, disseminated DP thymic tumours may develop. Thus, beyond fostering β chain repertoire broadening for subsequent αβ TCR utilization, preTCR-pMHC interaction limits cellular plasticity to facilitate normal thymocyte differentiation and proliferation that, if absent, introduces developmental vulnerabilities.
    DOI:  https://doi.org/10.1038/s41586-022-05555-7
  47. Nat Commun. 2022 Nov 23. 13(1): 7210
    Differential compartmentalization of myeloid cell phenotypes and responses towards the CNS in Alzheimer's disease.
    Camila Fernández Zapata, Ginevra Giacomello, Eike J Spruth, Jinte Middeldorp, Gerardina Gallaccio, Adeline Dehlinger, Claudia Dames, Julia K H Leman, Roland E van Dijk, Andreas Meisel, Stephan Schlickeiser, Desiree Kunkel, Elly M Hol, Friedemann Paul, Maria Kristina Parr, Josef Priller, Chotima Böttcher.
      Myeloid cells are suggested as an important player in Alzheimer´s disease (AD). However, its continuum of phenotypic and functional changes across different body compartments and their use as a biomarker in AD remains elusive. Here, we perform multiple state-of-the-art analyses to phenotypically and metabolically characterize immune cells between peripheral blood (n = 117), cerebrospinal fluid (CSF, n = 117), choroid plexus (CP, n = 13) and brain parenchyma (n = 13). We find that CSF cells increase expression of markers involved in inflammation, phagocytosis, and metabolism. Changes in phenotype of myeloid cells from AD patients are more pronounced in CP and brain parenchyma and upon in vitro stimulation, suggesting that AD-myeloid cells are more vulnerable to environmental changes. Our findings underscore the importance of myeloid cells in AD and the detailed characterization across body compartments may serve as a resource for future studies focusing on the assessment of these cells as biomarkers in AD.
    DOI:  https://doi.org/10.1038/s41467-022-34719-2
  48. Nat Med. 2022 Nov 21.
    Inhaled particulate accumulation with age impairs immune function and architecture in human lung lymph nodes.
    Basak B Ural, Daniel P Caron, Pranay Dogra, Steven B Wells, Peter A Szabo, Tomer Granot, Takashi Senda, Maya M L Poon, Nora Lam, Puspa Thapa, Yoon Seung Lee, Masaru Kubota, Rei Matsumoto, Donna L Farber.
      Older people are particularly susceptible to infectious and neoplastic diseases of the lung and it is unclear how lifelong exposure to environmental pollutants affects respiratory immune function. In an analysis of human lymph nodes (LNs) from 84 organ donors aged 11-93 years, we found a specific age-related decline in lung-associated, but not gut-associated, LN immune function linked to the accumulation of inhaled atmospheric particulate matter. Increasing densities of particulates were found in lung-associated LNs with age, but not in the corresponding gut-associated LNs. Particulates were specifically contained within CD68+CD169- macrophages, which exhibited decreased activation, phagocytic capacity, and altered cytokine production compared with non-particulate-containing macrophages. The structures of B cell follicles and lymphatic drainage were also disrupted in lung-associated LNs with particulates. Our results reveal that the cumulative effects of environmental exposure and age may compromise immune surveillance of the lung via direct effects on immune cell function and lymphoid architecture.
    DOI:  https://doi.org/10.1038/s41591-022-02073-x
  49. Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01549-2. [Epub ahead of print]41(8): 111675
    Dynamic quality control machinery that operates across compartmental borders mediates the degradation of mammalian nuclear membrane proteins.
    Pei-Ling Tsai, Christopher J F Cameron, Maria Fernanda Forni, Renee R Wasko, Brigitte S Naughton, Valerie Horsley, Mark B Gerstein, Christian Schlieker.
      Many human diseases are caused by mutations in nuclear envelope (NE) proteins. How protein homeostasis and disease etiology are interconnected at the NE is poorly understood. Specifically, the identity of local ubiquitin ligases that facilitate ubiquitin-proteasome-dependent NE protein turnover is presently unknown. Here, we employ a short-lived, Lamin B receptor disease variant as a model substrate in a genetic screen to uncover key elements of NE protein turnover. We identify the ubiquitin-conjugating enzymes (E2s) Ube2G2 and Ube2D3, the membrane-resident ubiquitin ligases (E3s) RNF5 and HRD1, and the poorly understood protein TMEM33. RNF5, but not HRD1, requires TMEM33 both for efficient biosynthesis and function. Once synthesized, RNF5 responds dynamically to increased substrate levels at the NE by departing from the endoplasmic reticulum, where HRD1 remains confined. Thus, mammalian protein quality control machinery partitions between distinct cellular compartments to address locally changing substrate loads, establishing a robust cellular quality control system.
    Keywords:  CP: Molecular biology; CRISPR screen; ERAD; RNF5; TMEM33; nuclear envelopathies; proteasome; protein quality control; protein turnover; proteostasis; ubiquitin ligase
    DOI:  https://doi.org/10.1016/j.celrep.2022.111675
  50. Sci Adv. 2022 Nov 25. 8(47): eabq3363
    Control of Gαq signaling dynamics and GPCR cross-talk by GRKs.
    Guoqing Xiang, Amanda Acosta-Ruiz, Arthur Radoux-Mergault, Melanie Kristt, Jihye Kim, Jared D Moon, Johannes Broichhagen, Asuka Inoue, Francis S Lee, Miriam Stoeber, Jeremy S Dittman, Joshua Levitz.
      Numerous processes contribute to the regulation of G protein-coupled receptors (GPCRs), but relatively little is known about rapid mechanisms that control signaling on the seconds time scale or regulate cross-talk between receptors. Here, we reveal that the ability of some GPCR kinases (GRKs) to bind Gαq both drives acute signaling desensitization and regulates functional interactions between GPCRs. GRK2/3-mediated acute desensitization occurs within seconds, is rapidly reversible, and can occur upon local, subcellular activation. This rapid desensitization is kinase independent, insensitive to pharmacological inhibition, and generalizable across receptor families and effectors. We also find that the ability of GRK2 to bind G proteins also enables it to regulate the extent and timing of Gαq-dependent signaling cross-talk between GPCRs. Last, we find that G protein/GRK2 interactions enable a novel form of GPCR trafficking cross-talk. Together, this work reveals potent forms of Gαq-dependent GPCR regulation with wide-ranging pharmacological and physiological implications.
    DOI:  https://doi.org/10.1126/sciadv.abq3363
  51. Sci Adv. 2022 Nov 25. 8(47): eadd1466
    XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation.
    Farazul Haque, Tasuku Honjo, Nasim A Begum.
      The transcriptional coactivator Med12 regulates gene expression through its kinase module. Here, we show a kinase module-independent function of Med12 in CSR. Med12 is essential for super-enhancer activation by collaborating with p300-Jmjd6/Carm1 coactivator complexes. Med12 loss decreases H3K27 acetylation and eRNA transcription with concomitant impairment of AID-induced DNA breaks, S-S synapse formation, and 3'RR-Eμ interaction. CRISPR-dCas9-mediated enhancer activation reestablishes the epigenomic and transcriptional hallmarks of the super-enhancer and fully restores the Med12 depletion defects. Moreover, 3'RR-derived eRNAs are critical for promoting S region epigenetic regulation, synapse formation, and recruitment of Med12 and AID to the IgH locus. We find that XLID syndrome-associated Med12 mutations are defective in both 3'RR eRNA transcription and CSR, suggesting that B and neuronal cells may have cell-specific super-enhancer dysfunctions. We conclude that Med12 is essential for IgH 3'RR activation/eRNA transcription and plays a central role in AID-induced antibody gene diversification and genomic instability in B cells.
    DOI:  https://doi.org/10.1126/sciadv.add1466
  52. Sci Adv. 2022 Nov 25. 8(47): eabq1984
    Macrophage acetyl-CoA carboxylase regulates acute inflammation through control of glucose and lipid metabolism.
    Scott Yeudall, Clint M Upchurch, Philip V Seegren, Caitlin M Pavelec, Jan Greulich, Michael C Lemke, Thurl E Harris, Bimal N Desai, Kyle L Hoehn, Norbert Leitinger.
      Acetyl-CoA carboxylase (ACC) regulates lipid synthesis; however, its role in inflammatory regulation in macrophages remains unclear. We generated mice that are deficient in both ACC isoforms in myeloid cells. ACC deficiency altered the lipidomic, transcriptomic, and bioenergetic profile of bone marrow-derived macrophages, resulting in a blunted response to proinflammatory stimulation. In response to lipopolysaccharide (LPS), ACC is required for the early metabolic switch to glycolysis and remodeling of the macrophage lipidome. ACC deficiency also resulted in impaired macrophage innate immune functions, including bacterial clearance. Myeloid-specific deletion or pharmacological inhibition of ACC in mice attenuated LPS-induced expression of proinflammatory cytokines interleukin-6 (IL-6) and IL-1β, while pharmacological inhibition of ACC increased susceptibility to bacterial peritonitis in wild-type mice. Together, we identify a critical role for ACC in metabolic regulation of the innate immune response in macrophages, and thus a clinically relevant, unexpected consequence of pharmacological ACC inhibition.
    DOI:  https://doi.org/10.1126/sciadv.abq1984
  53. Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01564-9. [Epub ahead of print]41(8): 111690
    Loss of MTCH-1 suppresses age-related proteostasis collapse through the inhibition of programmed cell death factors.
    Yahyah Aman, Annmary Paul Erinjeri, Nikolaos Tataridas-Pallas, Rhianna Williams, Rachel Wellman, Hannah Chapman, John Labbadia.
      The age-related loss of protein homeostasis (proteostasis) is at the heart of numerous neurodegenerative diseases. Therefore, finding ways to preserve proteome integrity in aged cells may be a powerful way to promote long-term health. Here, we show that reducing the activity of a highly conserved mitochondrial outer membrane protein, MTCH-1/MTCH2, suppresses age-related proteostasis collapse in Caenorhabditis elegans without disrupting development, growth, or reproduction. Loss of MTCH-1 does not influence proteostasis capacity in aged tissues through previously described pathways but instead operates by reducing CED-4 levels. This results in the sequestration of HSP-90 by inactive CED-3, which in turn leads to an increase in HSF-1 activity, transcriptional remodeling of the proteostasis network, and maintenance of proteostasis capacity with age. Together, our findings reveal a role for programmed cell death factors in determining proteome health and suggest that inhibiting MTCH-1 activity in adulthood may safeguard the aging proteome and suppress age-related diseases.
    Keywords:  CP: Cell biology; Caenorhabditis elegans; HSF-1; HSP90; MTCH-1; aging; mitochondria; molecular chaperones; programmed cell death; protein homeostasis
    DOI:  https://doi.org/10.1016/j.celrep.2022.111690
  54. Aging Cell. 2022 Nov 22. e13735
    GPCR signaling regulates severe stress-induced organismic death in Caenorhabditis elegans.
    Changnan Wang, Yong Long, Bingying Wang, Chao Zhang, Dengke K Ma.
      How an organism dies is a fundamental yet poorly understood question in biology. An organism can die of many causes, including stress-induced phenoptosis, also defined as organismic death that is regulated by its genome-encoded programs. The mechanism of stress-induced phenoptosis is still largely unknown. Here, we show that transient but severe freezing-thaw stress (FTS) in Caenorhabditis elegans induces rapid and robust phenoptosis that is regulated by G-protein coupled receptor (GPCR) signaling. RNAi screens identify the GPCR-encoding fshr-1 in mediating transcriptional responses to FTS. FSHR-1 increases ligand interaction upon FTS and activates a cyclic AMP-PKA cascade leading to a genetic program to promote organismic death under severe stress. FSHR-1/GPCR signaling up-regulates the bZIP-type transcription factor ZIP-10, linking FTS to expression of genes involved in lipid remodeling, proteostasis, and aging. A mathematical model suggests how genes may promote organismic death under severe stress conditions, potentially benefiting growth of the clonal population with individuals less stressed and more reproductively privileged. Our studies reveal the roles of FSHR-1/GPCR-mediated signaling in stress-induced gene expression and phenoptosis in C. elegans, providing empirical new insights into mechanisms of stress-induced phenoptosis with evolutionary implications.
    DOI:  https://doi.org/10.1111/acel.13735
  55. Sci Adv. 2022 Nov 25. 8(47): eabo4116
    A deubiquitination module essential for Treg fitness in the tumor microenvironment.
    Elena Montauti, Samuel E Weinberg, Peng Chu, Shuvam Chaudhuri, Nikita L Mani, Radhika Iyer, Yuanzhang Zhou, Yusi Zhang, Changhong Liu, Chen Xin, Shana Gregory, Juncheng Wei, Yana Zhang, Wantao Chen, Zhaolin Sun, Ming Yan, Deyu Fang.
      The tumor microenvironment (TME) enhances regulatory T (Treg) cell stability and immunosuppressive functions through up-regulation of lineage transcription factor Foxp3, a phenomenon known as Treg fitness or adaptation. Here, we characterize previously unknown TME-specific cellular and molecular mechanisms underlying Treg fitness. We demonstrate that TME-specific stressors including transforming growth factor-β (TGF-β), hypoxia, and nutrient deprivation selectively induce two Foxp3-specific deubiquitinases, ubiquitin-specific peptidase 22 (Usp22) and Usp21, by regulating TGF-β, HIF, and mTOR signaling, respectively, to maintain Treg fitness. Simultaneous deletion of both USPs in Treg cells largely diminishes TME-induced Foxp3 up-regulation, alters Treg metabolic signatures, impairs Treg-suppressive function, and alleviates Treg suppression on cytotoxic CD8+ T cells. Furthermore, we developed the first Usp22-specific small-molecule inhibitor, which dramatically reduced intratumoral Treg Foxp3 expression and consequently enhanced antitumor immunity. Our findings unveil previously unappreciated mechanisms underlying Treg fitness and identify Usp22 as an antitumor therapeutic target that inhibits Treg adaptability in the TME.
    DOI:  https://doi.org/10.1126/sciadv.abo4116
  56. J Biol Chem. 2022 Nov 21. pii: S0021-9258(22)01178-4. [Epub ahead of print] 102735
    SOX9 and TCF transcription factors associate to mediate Wnt/β-catenin target gene activation in colorectal cancer.
    Aravinda-Bharathi Ramakrishnan, Peter E Burby, Kavya Adiga, Ken M Cadigan.
      Activation of the Wnt/β-catenin pathway regulates gene expression by promoting the formation of a β-catenin-T cell factor (TCF) complex on target enhancers. In addition to TCFs, other transcription factors interact with the Wnt/β-catenin pathway at different levels to produce tissue-specific patterns of Wnt target gene expression. The transcription factor SOX9 potently represses many Wnt target genes by down-regulating β-catenin protein levels. Here, we find using colony formation and cell growth assays that SOX9 surprisingly promotes the proliferation of Wnt-driven colorectal cancer (CRC) cells. In contrast to how it indirectly represses Wnt targets, SOX9 directly co-occupies and activates multiple Wnt-responsive enhancers in CRC cells. Our examination of the binding site grammar of these enhancers shows the presence of TCF and SOX9 binding sites that are necessary for transcriptional activation. In addition, we identify a physical interaction between the DNA-binding domains of TCFs and SOX9 and show that TCF-SOX9 interactions are important for target gene regulation and CRC cell growth. Our work demonstrates a highly context-dependent effect of SOX9 on Wnt targets, with the presence or absence of SOX9 binding sites on Wnt-regulated enhancers determining whether they are directly activated or indirectly repressed by SOX9.
    Keywords:  Wnt pathway; Wnt signaling; colorectal cancer; enhancers; gene transcription; transcription factor
    DOI:  https://doi.org/10.1016/j.jbc.2022.102735
  57. Nat Methods. 2022 Nov 24.
    Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging.
    Christa Haase, Karin Gustafsson, Shenglin Mei, Shu-Chi Yeh, Dmitry Richter, Jelena Milosevic, Raphaël Turcotte, Peter V Kharchenko, David B Sykes, David T Scadden, Charles P Lin.
      Tissue function depends on cellular organization. While the properties of individual cells are increasingly being deciphered using powerful single-cell sequencing technologies, understanding their spatial organization and temporal evolution remains a major challenge. Here, we present Image-seq, a technology that provides single-cell transcriptional data on cells that are isolated from specific spatial locations under image guidance, thus preserving the spatial information of the target cells. It is compatible with in situ and in vivo imaging and can document the temporal and dynamic history of the cells being analyzed. Cell samples are isolated from intact tissue and processed with state-of-the-art library preparation protocols. The technique therefore combines spatial information with highly sensitive RNA sequencing readouts from individual, intact cells. We have used both high-throughput, droplet-based sequencing as well as SMARTseq-v4 library preparation to demonstrate its application to bone marrow and leukemia biology. We discovered that DPP4 is a highly upregulated gene during early progression of acute myeloid leukemia and that it marks a more proliferative subpopulation that is confined to specific bone marrow microenvironments. Furthermore, the ability of Image-seq to isolate viable, intact cells should make it compatible with a range of downstream single-cell analysis tools including multi-omics protocols.
    DOI:  https://doi.org/10.1038/s41592-022-01673-2
  58. Nat Commun. 2022 Nov 24. 13(1): 7236
    CXCL13 is a predictive biomarker in idiopathic multicentric Castleman disease.
    Sheila K Pierson, Laura Katz, Reece Williams, Melanie Mumau, Michael Gonzalez, Stacy Guzman, Ayelet Rubenstein, Ana B Oromendia, Philip Beineke, Alexander Fosså, Frits van Rhee, David C Fajgenbaum.
      Idiopathic multicentric Castleman disease (iMCD) is a rare and poorly-understood cytokine storm-driven inflammatory disorder. Interleukin-6 (IL-6) is a known disease driver in some patients, but anti-IL-6 therapy with siltuximab is not effective in all patients, and biomarkers indicating success at an early time point following treatment initiation are lacking. Here we show, by comparison of levels of 1,178 proteins in sera of healthy participants (N = 42), patients with iMCD (N = 88), and with related diseases (N = 60), a comprehensive landscape of candidate disease mediators and predictors of siltuximab response. C-X-C Motif Chemokine Ligand-13 (CXCL13) is identified and validated as the protein most prominently up-regulated in iMCD. Early and significant decrease in CXCL13 levels clearly distinguishes siltuximab responders from non-responders; a 17% reduction by day 8 following siltuximab therapy initiation is predictive of response at later time points. Our study thus suggests that CXCL13 is a predictive biomarker of response to siltuximab in iMCD.
    DOI:  https://doi.org/10.1038/s41467-022-34873-7
  59. Sci Adv. 2022 Nov 25. 8(47): eabq3806
    TDP-43 safeguards the embryo genome from L1 retrotransposition.
    Ten D Li, Kensaku Murano, Tomohiro Kitano, Youjia Guo, Lumi Negishi, Haruhiko Siomi.
      Transposable elements (TEs) are genomic parasites that propagate within the host genome and introduce mutations. Long interspersed nuclear element-1 (LINE-1 or L1) is the major TE class, which occupies nearly 20% of the mouse genome. L1 is highly active in mammalian preimplantation embryos, posing a major threat to genome integrity, but the mechanism of stage-specific protection against L1 retrotransposition is unknown. Here, we show that TAR DNA-binding protein 43 (TDP-43), mutations in which constitute a major risk factor for amyotrophic lateral sclerosis, inhibits L1 retrotransposition in mouse embryonic stem cells (mESCs) and preimplantation embryos. Knockdown of TDP-43 resulted in massive genomic L1 expansion and impaired cell growth in preimplantation embryos and ESCs. Functional analysis demonstrated that TDP-43 interacts with L1 open reading frame 1 protein (L1 ORF1p) to mediate genomic protection, and loss of this interaction led to derepression of L1 retrotransposition. Our results identify TDP-43 as a guardian of the embryonic genome.
    DOI:  https://doi.org/10.1126/sciadv.abq3806
  60. Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01556-X. [Epub ahead of print]41(8): 111682
    Double knockin mice show NF-κB trajectories in immune signaling and aging.
    Shah Md Toufiqur Rahman, Mohammad Aqdas, Erik W Martin, Francesco Tomassoni Ardori, Preeyaporn Songkiatisak, Kyu-Seon Oh, Stefan Uderhardt, Sangwon Yun, Quia C Claybourne, Ross A McDevitt, Valentina Greco, Ronald N Germain, Lino Tessarollo, Myong-Hee Sung.
      In vitro studies suggest that mapping the spatiotemporal complexity of nuclear factor κB (NF-κB) signaling is essential to understanding its function. The lack of tools to directly monitor NF-κB proteins in vivo has hindered such efforts. Here, we introduce reporter mice with the endogenous RelA (p65) or c-Rel labeled with distinct fluorescent proteins and a double knockin with both subunits labeled. Overcoming hurdles in simultaneous live-cell imaging of RelA and c-Rel, we show that quantitative features of signaling reflect the identity of activating ligands, differ between primary and immortalized cells, and shift toward c-Rel in microglia from aged brains. RelA:c-Rel heterodimer is unexpectedly depleted in the nuclei of stimulated cells. Trajectories of subunit co-expression in immune lineages reveal a reduction at key cell maturation stages. These results demonstrate the power of these reporters in gaining deeper insights into NF-κB biology, with the spectral complementarity of the labeled NF-κB proteins enabling diverse applications.
    Keywords:  CP: Immunology; NF-κB; Rela; c-Rel; endogenous knockin; fluorescence correlation spectroscopy; fluorescent fusion reporter mice; inflammatory signaling; intravital imaging; live microscopy
    DOI:  https://doi.org/10.1016/j.celrep.2022.111682
  61. Nat Commun. 2022 Nov 23. 13(1): 7194
    Osteoblast/osteocyte-derived interleukin-11 regulates osteogenesis and systemic adipogenesis.
    Bingzi Dong, Masahiro Hiasa, Yoshiki Higa, Yukiyo Ohnishi, Itsuro Endo, Takeshi Kondo, Yuichi Takashi, Maria Tsoumpra, Risa Kainuma, Shun Sawatsubashi, Hiroshi Kiyonari, Go Shioi, Hiroshi Sakaue, Tomoki Nakashima, Shigeaki Kato, Masahiro Abe, Seiji Fukumoto, Toshio Matsumoto.
      Exercise results in mechanical loading of the bone and stimulates energy expenditure in the adipose tissue. It is therefore likely that the bone secretes factors to communicate with adipose tissue in response to mechanical loading. Interleukin (IL)-11 is known to be expressed in the bone, it is upregulated by mechanical loading, enhances osteogenesis and suppresses adipogenesis. Here, we show that systemic IL-11 deletion (IL-11-/-) results in reduced bone mass, suppressed bone formation response to mechanical loading, enhanced expression of Wnt inhibitors, and suppressed Wnt signaling. At the same time, the enhancement of bone resorption by mechanical unloading was unaffected. Unexpectedly, IL-11-/- mice have increased systemic adiposity and glucose intolerance. Osteoblast/osteocyte-specific IL-11 deletion in osteocalcin-Cre;IL-11fl/fl mice have reduced serum IL-11 levels, blunted bone formation under mechanical loading, and increased systemic adiposity similar to IL-11-/- mice. Adipocyte-specific IL-11 deletion in adiponectin-Cre;IL-11fl/fl did not exhibit any abnormalities. We demonstrate that osteoblast/osteocyte-derived IL-11 controls both osteogenesis and systemic adiposity in response to mechanical loading, an important insight for our understanding of osteoporosis and metabolic syndromes.
    DOI:  https://doi.org/10.1038/s41467-022-34869-3
  62. Sci Adv. 2022 Nov 25. 8(47): eadc9346
    Krüppel-like factor 4 regulates the cytolytic effector function of exhausted CD8 T cells.
    Jinwoo Nah, Rho H Seong.
      Exhausted CD8 T cells during chronic inflammatory responses against viral infections and cancer are phenotypically and functionally heterogeneous. In particular, CD8 T cells with cytolytic effector function have been recently identified among the exhausted CD8 T cell subsets. However, the regulation of their differentiation and function remains largely unknown. Here, we report that Krüppel-like factor 4 (KLF4) is a critical regulator of the exhaustion process, promoting the cytolytic effector function of exhausted CD8 T cells. KLF4-expressing CD8 T cells in exhaustion contexts showed the features of transitory effector CD8 T cells. Enforced KLF4 expression increased CD8 T cell differentiation into transitory effector subsets and enhanced their antitumor immunity. We further demonstrated that KLF4 also showed a capacity of reinvigorating exhausted CD8 T cells. Last, high KLF4 expression was positively correlated with a favorable prognosis in human patients with cancer. Our study highlights the potential impacts of KLF4 on CD8 T cell exhaustion and antitumor immune therapy.
    DOI:  https://doi.org/10.1126/sciadv.adc9346
  63. Nat Commun. 2022 Nov 21. 13(1): 7145
    A CRISPR endonuclease gene drive reveals distinct mechanisms of inheritance bias.
    Sebald A N Verkuijl, Estela Gonzalez, Ming Li, Joshua X D Ang, Nikolay P Kandul, Michelle A E Anderson, Omar S Akbari, Michael B Bonsall, Luke Alphey.
      CRISPR/Cas gene drives can bias transgene inheritance through different mechanisms. Homing drives are designed to replace a wild-type allele with a copy of a drive element on the homologous chromosome. In Aedes aegypti, the sex-determining locus is closely linked to the white gene, which was previously used as a target for a homing drive element (wGDe). Here, through an analysis using this linkage we show that in males inheritance bias of wGDe did not occur by homing, rather through increased propagation of the donor drive element. We test the same wGDe drive element with transgenes expressing Cas9 with germline regulatory elements sds3, bgcn, and nup50. We only find inheritance bias through homing, even with the identical nup50-Cas9 transgene. We propose that DNA repair outcomes may be more context dependent than anticipated and that other previously reported homing drives may, in fact, bias their inheritance through other mechanisms.
    DOI:  https://doi.org/10.1038/s41467-022-34739-y
  64. Nat Cancer. 2022 Nov 22.
    cFLIP suppression and DR5 activation sensitize senescent cancer cells to senolysis.
    Liqin Wang, Haojie Jin, Fleur Jochems, Siying Wang, Cor Lieftink, Isabel Mora Martinez, Giulia De Conti, Finn Edwards, Rodrigo Leite de Oliveira, Arnout Schepers, Yangyang Zhou, Jiaojiao Zheng, Wei Wu, Xingling Zheng, Shengxian Yuan, Jing Ling, Kathy Jastrzebski, Matheus Dos Santos Dias, Ji-Ying Song, Patrick N H Celie, Hideo Yagita, Ming Yao, Weiping Zhou, Roderick L Beijersbergen, Wenxin Qin, René Bernards.
      Senolytics, drugs that kill senescent cells, have been proposed to improve the response to pro-senescence cancer therapies; however, this remains challenging due to a lack of broadly acting senolytic drugs. Using CRISPR/Cas9-based genetic screens in different senescent cancer cell models, we identify loss of the death receptor inhibitor cFLIP as a common vulnerability of senescent cancer cells. Senescent cells are primed for apoptotic death by NF-κB-mediated upregulation of death receptor 5 (DR5) and its ligand TRAIL, but are protected from death by increased cFLIP expression. Activation of DR5 signaling by agonistic antibody, which can be enhanced further by suppression of cFLIP by BRD2 inhibition, leads to efficient killing of a variety of senescent cancer cells. Moreover, senescent cells sensitize adjacent non-senescent cells to killing by DR5 agonist through a bystander effect mediated by secretion of cytokines. We validate this 'one-two punch' cancer therapy by combining pro-senescence therapy with DR5 activation in different animal models.
    DOI:  https://doi.org/10.1038/s43018-022-00462-2
  65. Nat Cardiovasc Res. 2022 Nov;1(11): 1022-1038
    Rad regulation of CaV1.2 channels controls cardiac fight-or-flight response.
    Arianne Papa, Sergey I Zakharov, Alexander N Katchman, Jared S Kushner, Bi-Xing Chen, Lin Yang, Guoxia Liu, Alejandro Sanchez Jimenez, Robyn J Eisert, Gary A Bradshaw, Wen Dun, Shah R Ali, Aaron Rodriques, Karen Zhou, Veli Topkara, Mu Yang, John P Morrow, Emily J Tsai, Arthur Karlin, Elaine Wan, Marian Kalocsay, Geoffrey S Pitt, Henry M Colecraft, Manu Ben-Johny, Steven O Marx.
      Fight-or-flight responses involve β-adrenergic-induced increases in heart rate and contractile force. In the present study, we uncover the primary mechanism underlying the heart's innate contractile reserve. We show that four protein kinase A (PKA)-phosphorylated residues in Rad, a calcium channel inhibitor, are crucial for controlling basal calcium current and essential for β-adrenergic augmentation of calcium influx in cardiomyocytes. Even with intact PKA signaling to other proteins modulating calcium handling, preventing adrenergic activation of calcium channels in Rad-phosphosite-mutant mice (4SA-Rad) has profound physiological effects: reduced heart rate with increased pauses, reduced basal contractility, near-complete attenuation of β-adrenergic contractile response and diminished exercise capacity. Conversely, expression of mutant calcium-channel β-subunits that cannot bind 4SA-Rad is sufficient to enhance basal calcium influx and contractility to adrenergically augmented levels of wild-type mice, rescuing the failing heart phenotype of 4SA-Rad mice. Hence, disruption of interactions between Rad and calcium channels constitutes the foundation toward next-generation therapeutics specifically enhancing cardiac contractility.
    DOI:  https://doi.org/10.1038/s44161-022-00157-y
  66. Nat Commun. 2022 Nov 22. 13(1): 7171
    A non-coding GWAS variant impacts anthracycline-induced cardiotoxic phenotypes in human iPSC-derived cardiomyocytes.
    Xi Wu, Fei Shen, Guanglong Jiang, Gloria Xue, Santosh Philips, Laura Gardner, Geneva Cunningham, Casey Bales, Erica Cantor, Bryan Paul Schneider.
      Anthracyclines, widely used to treat breast cancer, have the potential for cardiotoxicity. We have previously identified and validated a germline single nucleotide polymorphism, rs28714259, associated with an increased risk of anthracycline-induced heart failure. We now provide insights into the mechanism by which rs28714259 might confer increased risk of cardiac damage. Using hiPSC-derived cardiomyocyte cell lines with either intrinsic polymorphism or CRISPR-Cas9-mediated deletion of rs28714259 locus, we demonstrate that glucocorticoid receptor signaling activated by dexamethasone pretreatment prior to doxorubicin exposure preserves cardiomyocyte viability and contractility in cardiomyocytes containing the major allele. Homozygous loss of the rs28714259 major allele diminishes dexamethasone's protective effect. We further demonstrate that the risk allele of rs28714259 disrupts glucocorticoid receptor and rs28714259 binding affinity. Finally, we highlight the activation of genes and pathways involved in cardiac hypertrophy signaling that are blocked by the risk allele, suggesting a decreased adaptive survival response to doxorubicin-related stress.
    DOI:  https://doi.org/10.1038/s41467-022-34917-y
  67. J Cell Biol. 2023 Feb 06. pii: e202204099. [Epub ahead of print]222(2):
    PI(4,5)P2 diffuses freely in the plasma membrane even within high-density effector protein complexes.
    Jonathan Pacheco, Anna C Cassidy, James P Zewe, Rachel C Wills, Gerald R V Hammond.
      The lipid phosphatidyl-D-myo-inositol-4,5-bisphosphate [PI(4,5)P2] is a master regulator of plasma membrane (PM) function. Its effector proteins regulate transport, signaling, and cytoskeletal processes that define PM structure and function. How a single type of lipid regulates so many parallel processes is unclear. We tested the hypothesis that spatially separate PI(4,5)P2 pools associate with different PM complexes. The mobility of PI(4,5)P2 was measured using biosensors by single-particle tracking. We found that PM lipids including PI(4,5)P2 diffuse rapidly (∼0.3 µm2/s) with Brownian motion, although they spend one third of their time diffusing more slowly. Surprisingly, areas of the PM occupied by PI(4,5)P2-dependent complexes did not slow PI(4,5)P2 lateral mobility. Only the spectrin and septin cytoskeletons showed reduced PI(4,5)P2 diffusion. We conclude that even structures with high densities of PI(4,5)P2 effector proteins, such as clathrin-coated pits and focal adhesions, do not corral unbound PI(4,5)P2, questioning a role for spatially segregated PI(4,5)P2 pools in organizing and regulating PM functions.
    DOI:  https://doi.org/10.1083/jcb.202204099
  68. Nat Commun. 2022 Nov 21. 13(1): 7124
    Regulome analysis in B-acute lymphoblastic leukemia exposes Core Binding Factor addiction as a therapeutic vulnerability.
    Jason P Wray, Elitza M Deltcheva, Charlotta Boiers, Simon Е Richardson, Jyoti Bikram Chhetri, John Brown, Sladjana Gagrica, Yanping Guo, Anuradha Illendula, Joost H A Martens, Hendrik G Stunnenberg, John H Bushweller, Rachael Nimmo, Tariq Enver.
      The ETV6-RUNX1 onco-fusion arises in utero, initiating a clinically silent pre-leukemic state associated with the development of pediatric B-acute lymphoblastic leukemia (B-ALL). We characterize the ETV6-RUNX1 regulome by integrating chromatin immunoprecipitation- and RNA-sequencing and show that ETV6-RUNX1 functions primarily through competition for RUNX1 binding sites and transcriptional repression. In pre-leukemia, this results in ETV6-RUNX1 antagonization of cell cycle regulation by RUNX1 as evidenced by mass cytometry analysis of B-lineage cells derived from ETV6-RUNX1 knock-in human pluripotent stem cells. In frank leukemia, knockdown of RUNX1 or its co-factor CBFβ results in cell death suggesting sustained requirement for RUNX1 activity which is recapitulated by chemical perturbation using an allosteric CBFβ-inhibitor. Strikingly, we show that RUNX1 addiction extends to other genetic subtypes of pediatric B-ALL and also adult disease. Importantly, inhibition of RUNX1 activity spares normal hematopoiesis. Our results suggest that chemical intervention in the RUNX1 program may provide a therapeutic opportunity in ALL.
    DOI:  https://doi.org/10.1038/s41467-022-34653-3
  69. Cell Rep. 2022 Nov 22. pii: S2211-1247(22)01561-3. [Epub ahead of print]41(8): 111687
    Adenosine deaminase acting on RNA-1 is essential for early B lymphopoiesis.
    Wenjing Chen, Yuxing Li, Gui-Xin Ruan, Hengjun Huang, Rui Zhang, Jing Wang, Yu Ouyang, Yan Li, Shengli Xu, Xijun Ou.
      Adenosine deaminase acting on RNA-1 (ADAR1) is a ubiquitously expressed RNA deaminase catalyzing adenosine-to-inosine editing to prevent hyperactivated cytosolic double-stranded RNA (dsRNA) response mediated by MDA5. Here, we demonstrate that ADAR1 is essential for early B lymphopoiesis from late pro-B and large pre-B cell stages onward. ADAR1 exerts its requisite role via both MDA5-dependent and -independent pathways. Interestingly, the MDA5-dependent mechanisms regulate early pro-B to large pre-B cell transition by promoting early B cell survival. In contrast, the MDA5-independent mechanisms control large pre-B to small pre-B cell transition by regulating pre-B cell receptor (pre-BCR) expression. Moreover, we show that protein kinase R (PKR) and oligoadenylate synthetase/ribonuclease (OAS/RNase) L pathways are dispensable for ADAR1's role in early B lymphopoiesis. Importantly, we demonstrate that p150 isoform of ADAR1 exclusively accounts for ADAR1's function in early B lymphopoiesis, and its conventional dsRNA-binding, but not the Z-DNA/RNA-binding or the RNA-editing, activity is required for ADAR1's function in B cell development. Thus, our findings suggest that ADAR1 regulates early B lymphopoiesis through various mechanisms.
    Keywords:  ADAR1; B cell development; CP: Immunology; MDA5; RNA editing; dsRNA binding; pre-BCR
    DOI:  https://doi.org/10.1016/j.celrep.2022.111687
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