bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022‒08‒28
48 papers selected by
Fawaz Alzaïd
Sorbonne Université
  1. Cutting Edge: Systemic Autoimmunity in Murine STAT3 Gain-of-Function Syndrome Is Characterized by Effector T Cell Expansion in the Absence of Overt Regulatory T Cell Dysfunction.
  2. KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress.
  3. Hepatocyte Rap1a contributes to obesity- and statin-associated hyperglycemia.
  4. Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease.
  5. Pneumolysin boosts the neuroinflammatory response to Streptococcus pneumoniae through enhanced endocytosis.
  6. Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals.
  7. Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA.
  8. Long noncoding RNA CHROMR regulates antiviral immunity in humans.
  9. Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus.
  10. The APP intracellular domain promotes LRRK2 expression to enable feed-forward neurodegenerative mechanisms in Parkinson's disease.
  11. SPICE-Met: profiling and imaging energy metabolism at the single-cell level using a fluorescent reporter mouse.
  12. Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci.
  13. Untangling the network effects of productivity and prominence among scientists.
  14. A WISP1 antibody inhibits MRTF signaling to prevent the progression of established liver fibrosis.
  15. RORγt expression in mature TH17 cells safeguards their lineage specification by inhibiting conversion to TH2 cells.
  16. Thymic mimetic cells: tolerogenic masqueraders.
  17. Leaky mitochondria.
  18. An interplay between cellular growth and atypical fusion defines morphogenesis of a modular glial niche in Drosophila.
  19. The coupling of mitoproteolysis and oxidative phosphorylation enables tracking of an active mitochondrial state through MitoTimerfluorescence.
  20. ETS1 governs pathological tissue-remodeling programs in disease-associated fibroblasts.
  21. Disease-associated oligodendrocyte responses across neurodegenerative diseases.
  22. A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes.
  23. Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.
  24. Human acute inflammatory recovery is defined by co-regulatory dynamics of white blood cell and platelet populations.
  25. Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes.
  26. Aerobic glycolysis promotes tumor immune evasion by hexokinase2-mediated phosphorylation of IκBα.
  27. Inhibition of microbial deconjugation of micellar bile acids protects against intestinal permeability and liver injury.
  28. Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19.
  29. Zeb1 sustains hematopoietic stem cell functions by suppressing mitofusin-2-mediated mitochondrial fusion.
  30. Selective TnsC recruitment enhances the fidelity of RNA-guided transposition.
  31. Lysosomal GPCR-like protein LYCHOS signals cholesterol sufficiency to mTORC1.
  32. Accurate inference of genome-wide spatial expression with iSpatial.
  33. Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.
  34. A genetic probe into the ancient and medieval history of Southern Europe and West Asia.
  35. Mammalian genome innovation through transposon domestication.
  36. ETS1 is a key transcription factor that drives RANKL-expressing, tissue-destructive fibroblasts.
  37. The genetic history of the Southern Arc: A bridge between West Asia and Europe.
  38. NAD+ metabolism drives astrocyte proinflammatory reprogramming in central nervous system autoimmunity.
  39. GLP-1-mediated delivery of tesaglitazar improves obesity and glucose metabolism in male mice.
  40. Selective suppression of melanoma lacking IFN-γ pathway by JAK inhibition depends on T cells and host TNF signaling.
  41. Mediator kinase regulates intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF.
  42. Two CTLA-4 ligands, separate pHates.
  43. Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer.
  44. Somatic ablation of IKKβ in liver and leukocytes is not tolerated in obese mice but hepatic IKKβ deletion improves fatty liver and insulin sensitivity.
  45. A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane.
  46. Uropathogenic Escherichia coli subverts mitochondrial metabolism to enable intracellular bacterial pathogenesis in urinary tract infection.
  47. Patrolling ILC3 cells monitor intestinal tissue in response to inflammation.
  48. Efficient DNA fluorescence labeling via base excision trapping.
  1. J Immunol. 2022 Aug 22. pii: ji2100920. [Epub ahead of print]
    Cutting Edge: Systemic Autoimmunity in Murine STAT3 Gain-of-Function Syndrome Is Characterized by Effector T Cell Expansion in the Absence of Overt Regulatory T Cell Dysfunction.
    Jonathan Woods, Sarah E Pemberton, Andrea D Largent, Kristy Chiang, Denny Liggitt, Mohamed Oukka, David J Rawlings, Shaun W Jackson.
      Germline gain-of-function mutations in the transcriptional factor STAT3 promote early-onset multisystemic autoimmunity. To investigate how increased STAT3 promotes systemic inflammation, we generated a transgenic knock-in strain expressing a pathogenic human mutation STAT3K392R within the endogenous murine locus. As predicted, STAT3K392R mice develop progressive lymphoid hyperplasia and systemic inflammation, mirroring the human disease. However, whereas the prevailing model holds that increased STAT3 activity drives human autoimmunity by dysregulating the balance between regulatory T cells and Th17 cell differentiation, we observed increased Th17 cells in the absence of major defects in regulatory T cell differentiation or function. In addition, STAT3K392R animals exhibited a prominent accumulation of IFN-γ-producing CD4+ and CD8+ T cells. Together, these data provide new insights into this complex human genetic syndrome and highlight the diverse cellular mechanisms by which dysregulated STAT3 activity promotes breaks in immune tolerance.
    DOI:  https://doi.org/10.4049/jimmunol.2100920
  2. Nat Commun. 2022 Aug 23. 13(1): 4941
    KLF4 recruits SWI/SNF to increase chromatin accessibility and reprogram the endothelial enhancer landscape under laminar shear stress.
    Jan-Renier Moonen, James Chappell, Minyi Shi, Tsutomu Shinohara, Dan Li, Maxwell R Mumbach, Fan Zhang, Ramesh V Nair, Joseph Nasser, Daniel H Mai, Shalina Taylor, Lingli Wang, Ross J Metzger, Howard Y Chang, Jesse M Engreitz, Michael P Snyder, Marlene Rabinovitch.
      Physiologic laminar shear stress (LSS) induces an endothelial gene expression profile that is vasculo-protective. In this report, we delineate how LSS mediates changes in the epigenetic landscape to promote this beneficial response. We show that under LSS, KLF4 interacts with the SWI/SNF nucleosome remodeling complex to increase accessibility at enhancer sites that promote the expression of homeostatic endothelial genes. By combining molecular and computational approaches we discover enhancers that loop to promoters of KLF4- and LSS-responsive genes that stabilize endothelial cells and suppress inflammation, such as BMPR2, SMAD5, and DUSP5. By linking enhancers to genes that they regulate under physiologic LSS, our work establishes a foundation for interpreting how non-coding DNA variants in these regions might disrupt protective gene expression to influence vascular disease.
    DOI:  https://doi.org/10.1038/s41467-022-32566-9
  3. Cell Rep. 2022 Aug 23. pii: S2211-1247(22)01077-4. [Epub ahead of print]40(8): 111259
    Hepatocyte Rap1a contributes to obesity- and statin-associated hyperglycemia.
    Yating Wang, Stefano Spolitu, John A Zadroga, Amesh K Sarecha, Lale Ozcan.
      Excessive hepatic glucose production contributes to the development of hyperglycemia and is a key feature of type 2 diabetes. Here, we report that activation of hepatocyte Rap1a suppresses gluconeogenic gene expression and glucose production, whereas Rap1a silencing stimulates them. Rap1a activation is suppressed in obese mouse liver, and restoring its activity improves glucose intolerance. As Rap1a's membrane localization and activation depends on its geranylgeranylation, which is inhibited by statins, we show that statin-treated hepatocytes and the human liver have lower active-Rap1a levels. Similar to Rap1a inhibition, statins stimulate hepatic gluconeogenesis and increase fasting blood glucose in obese mice. Geranylgeraniol treatment, which acts as the precursor for geranylgeranyl isoprenoids, restores Rap1a activity and improves statin-mediated glucose intolerance. Mechanistically, Rap1a activation induces actin polymerization, which suppresses gluconeogenesis by Akt-mediated FoxO1 inhibition. Thus, Rap1a regulates hepatic glucose homeostasis, and blocking its activity, via lowering geranylgeranyl isoprenoids, contributes to statin-induced glucose intolerance.
    Keywords:  CP: Metabolism; Rap1a; geranylgeranylation; gluconeogenesis; hepatic glucose production; hyperglycemia; obesity; statins; type 2 diabetes
    DOI:  https://doi.org/10.1016/j.celrep.2022.111259
  4. Nat Commun. 2022 Aug 22. 13(1): 4920
    Single cell transcriptomic analysis of the immune cell compartment in the human small intestine and in Celiac disease.
    Nader Atlasy, Anna Bujko, Espen S Bækkevold, Peter Brazda, Eva Janssen-Megens, Knut E A Lundin, Jørgen Jahnsen, Frode L Jahnsen, Hendrik G Stunnenberg.
      Celiac disease is an autoimmune disorder in which ingestion of dietary gluten triggers an immune reaction in the small intestine leading to destruction of the lining epithelium. Current treatment focusses on lifelong adherence to a gluten-free diet. Gluten-specific CD4+ T cells and cytotoxic intraepithelial CD8+ T cells have been proposed to be central in disease pathogenesis. Here we use unbiased single-cell RNA-sequencing and explore the heterogeneity of CD45+ immune cells in the human small intestine. We show altered myeloid cell transcriptomes present in active celiac lesions. CD4+ and CD8+ T cells transcriptomes show extensive changes and we define a natural intraepithelial lymphocyte population that is reduced in celiac disease. We show that the immune landscape in Celiac patients on a gluten-free diet is only partially restored compared to control samples. Altogether, we provide a single cell transcriptomic resource that can inform the immune landscape of the small intestine during Celiac disease.
    DOI:  https://doi.org/10.1038/s41467-022-32691-5
  5. Nat Commun. 2022 Aug 26. 13(1): 5032
    Pneumolysin boosts the neuroinflammatory response to Streptococcus pneumoniae through enhanced endocytosis.
    Sabrina Hupp, Christina Förtsch, Franziska Graber, Timothy J Mitchell, Asparouh I Iliev.
      In pneumococcal meningitis, bacterial growth in the cerebrospinal fluid results in lysis, the release of toxic factors, and subsequent neuroinflammation. Exposure of primary murine glia to Streptococcus pneumoniae lysates leads to strong proinflammatory cytokine and chemokine production, blocked by inhibition of the intracellular innate receptor Nod1. Lysates enhance dynamin-dependent endocytosis, and dynamin inhibition reduces neuroinflammation, blocking ligand internalization. Here we identify the cholesterol-dependent cytolysin pneumolysin as a pro-endocytotic factor in lysates, its elimination reduces their proinflammatory effect. Only pore-competent pneumolysin enhances endocytosis in a dynamin-, phosphatidylinositol-3-kinase- and potassium-dependent manner. Endocytic enhancement is limited to toxin-exposed parts of the membrane, the effect is rapid and pneumolysin permanently alters membrane dynamics. In a murine model of pneumococcal meningitis, mice treated with chlorpromazine, a neuroleptic with a complementary endocytosis inhibitory effect show reduced neuroinflammation. Thus, the dynamin-dependent endocytosis emerges as a factor in pneumococcal neuroinflammation, and its enhancement by a cytolysin represents a proinflammatory control mechanism.
    DOI:  https://doi.org/10.1038/s41467-022-32624-2
  6. Nat Commun. 2022 Aug 22. 13(1): 4923
    Whole Genome Association Study of the Plasma Metabolome Identifies Metabolites Linked to Cardiometabolic Disease in Black Individuals.
    NHLBI Trans-Omics for Precision Medicine 1 Consortium
      Integrating genetic information with metabolomics has provided new insights into genes affecting human metabolism. However, gene-metabolite integration has been primarily studied in individuals of European Ancestry, limiting the opportunity to leverage genomic diversity for discovery. In addition, these analyses have principally involved known metabolites, with the majority of the profiled peaks left unannotated. Here, we perform a whole genome association study of 2,291 metabolite peaks (known and unknown features) in 2,466 Black individuals from the Jackson Heart Study. We identify 519 locus-metabolite associations for 427 metabolite peaks and validate our findings in two multi-ethnic cohorts. A significant proportion of these associations are in ancestry specific alleles including findings in APOE, TTR and CD36. We leverage tandem mass spectrometry to annotate unknown metabolites, providing new insight into hereditary diseases including transthyretin amyloidosis and sickle cell disease. Our integrative omics approach leverages genomic diversity to provide novel insights into diverse cardiometabolic diseases.
    DOI:  https://doi.org/10.1038/s41467-022-32275-3
  7. Nat Commun. 2022 Aug 23. 13(1): 4953
    Genome-wide mutational signatures in low-coverage whole genome sequencing of cell-free DNA.
    Jonathan C M Wan, Dennis Stephens, Lingqi Luo, James R White, Caitlin M Stewart, Benoît Rousseau, Dana W Y Tsui, Luis A Diaz.
      Mutational signatures accumulate in somatic cells as an admixture of endogenous and exogenous processes that occur during an individual's lifetime. Since dividing cells release cell-free DNA (cfDNA) fragments into the circulation, we hypothesize that plasma cfDNA might reflect mutational signatures. Point mutations in plasma whole genome sequencing (WGS) are challenging to identify through conventional mutation calling due to low sequencing coverage and low mutant allele fractions. In this proof of concept study of plasma WGS at 0.3-1.5x coverage from 215 patients and 227 healthy individuals, we show that both pathological and physiological mutational signatures may be identified in plasma. By applying machine learning to mutation profiles, patients with stage I-IV cancer can be distinguished from healthy individuals with an Area Under the Curve of 0.96. Interrogating mutational processes in plasma may enable earlier cancer detection, and might enable the assessment of cancer risk and etiology.
    DOI:  https://doi.org/10.1038/s41467-022-32598-1
  8. Proc Natl Acad Sci U S A. 2022 Sep 13. 119(37): e2210321119
    Long noncoding RNA CHROMR regulates antiviral immunity in humans.
    Coen van Solingen, Yannick Cyr, Kaitlyn R Scacalossi, Maren de Vries, Tessa J Barrett, Annika de Jong, Morgane Gourvest, Tracy Zhang, Daniel Peled, Raadhika Kher, MacIntosh Cornwell, Michael A Gildea, Emily J Brown, Stephanie Fanucchi, Musa M Mhlanga, Jeffrey S Berger, Meike Dittmann, Kathryn J Moore.
      Long noncoding RNAs (lncRNAs) have emerged as critical regulators of gene expression, yet their contribution to immune regulation in humans remains poorly understood. Here, we report that the primate-specific lncRNA CHROMR is induced by influenza A virus and SARS-CoV-2 infection and coordinates the expression of interferon-stimulated genes (ISGs) that execute antiviral responses. CHROMR depletion in human macrophages reduces histone acetylation at regulatory regions of ISG loci and attenuates ISG expression in response to microbial stimuli. Mechanistically, we show that CHROMR sequesters the interferon regulatory factor (IRF)-2-dependent transcriptional corepressor IRF2BP2, thereby licensing IRF-dependent signaling and transcription of the ISG network. Consequently, CHROMR expression is essential to restrict viral infection of macrophages. Our findings identify CHROMR as a key arbitrator of antiviral innate immune signaling in humans.
    Keywords:  antiviral response; innate immune signaling; interferon-stimulated genes; lncRNA
    DOI:  https://doi.org/10.1073/pnas.2210321119
  9. Nat Commun. 2022 Aug 23. 13(1): 4951
    Covalent TCR-peptide-MHC interactions induce T cell activation and redirect T cell fate in the thymus.
    Christopher Szeto, Pirooz Zareie, Rushika C Wirasinha, Justin B Zhang, Andrea T Nguyen, Alan Riboldi-Tunnicliffe, Nicole L La Gruta, Stephanie Gras, Stephen R Daley.
      Interactions between a T cell receptor (TCR) and a peptide-major histocompatibility complex (pMHC) ligand are typically mediated by noncovalent bonds. By studying T cells expressing natural or engineered TCRs, here we describe covalent TCR-pMHC interactions that involve a cysteine-cysteine disulfide bond between the TCR and the peptide. By introducing cysteines into a known TCR-pMHC combination, we demonstrate that disulfide bond formation does not require structural rearrangement of the TCR or the peptide. We further show these disulfide bonds still form even when the initial affinity of the TCR-pMHC interaction is low. Accordingly, TCR-peptide disulfide bonds facilitate T cell activation by pMHC ligands with a wide spectrum of affinities for the TCR. Physiologically, this mechanism induces strong Zap70-dependent TCR signaling, which triggers T cell deletion or agonist selection in the thymus cortex. Covalent TCR-pMHC interactions may thus underlie a physiological T cell activation mechanism that has applications in basic immunology and potentially in immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-022-32692-4
  10. Sci Signal. 2022 Aug 23. 15(748): eabk3411
    The APP intracellular domain promotes LRRK2 expression to enable feed-forward neurodegenerative mechanisms in Parkinson's disease.
    Zhi-Wei Zhang, Haitao Tu, Mei Jiang, Sarivin Vanan, Sook Yoong Chia, Se-Eun Jang, Wuan-Ting Saw, Zhi-Wei Ong, Dong-Rui Ma, Zhi-Dong Zhou, Jie Xu, Kai-Hua Guo, Wei-Ping Yu, Shuo-Chien Ling, Richard A Margolin, Daniel G Chain, Li Zeng, Eng-King Tan.
      Gain-of-function mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are common in familial forms of Parkinson's disease (PD), which is characterized by progressive neurodegeneration that impairs motor and cognitive function. We previously demonstrated that LRRK2-mediated phosphorylation of β-amyloid precursor protein (APP) triggers the production and nuclear translocation of the APP intracellular domain (AICD). Here, we connected LRRK2 to AICD in a feed-forward cycle that enhanced LRRK2-mediated neurotoxicity. In cooperation with the transcription factor FOXO3a, AICD promoted LRRK2 expression, thus increasing the abundance of LRRK2 that promotes AICD activation. APP deficiency in LRRK2G2019S mice suppressed LRRK2 expression, LRRK2-mediated mitochondrial dysfunction, α-synuclein accumulation, and tyrosine hydroxylase (TH) loss in the brain, phenotypes associated with toxicity and loss of dopaminergic neurons in PD. Conversely, AICD overexpression increased LRRK2 expression and LRRK2-mediated neurotoxicity in LRRK2G2019S mice. In LRRK2G2019S mice or cultured dopaminergic neurons from LRRK2G2019S patients, treatment with itanapraced reduced LRRK2 expression and was neuroprotective. Itanapraced showed similar effects in a neurotoxin-induced PD mouse model, suggesting that inhibiting the AICD may also have therapeutic benefits in idiopathic PD. Our findings reveal a therapeutically targetable, feed-forward mechanism through which AICD promotes LRRK2-mediated neurotoxicity in PD.
    DOI:  https://doi.org/10.1126/scisignal.abk3411
  11. EMBO J. 2022 Aug 23. e111528
    SPICE-Met: profiling and imaging energy metabolism at the single-cell level using a fluorescent reporter mouse.
    Erica Russo, Fabrice Lemaître, Béatrice Corre, Aleksandra S Chikina, Francina Langa-Vives, Philippe Bousso.
      The regulation of cellular energy metabolism is central to most physiological and pathophysiological processes. However, most current methods have limited ability to functionally probe metabolic pathways in individual cells. Here, we describe SPICE-Met (Single-cell Profiling and Imaging of Cell Energy Metabolism), a method for profiling energy metabolism in single cells using flow cytometry or imaging. We generated a transgenic mouse expressing PercevalHR, a fluorescent reporter for cellular ATP:ADP ratio. Modulation of PercevalHR fluorescence with metabolic inhibitors was used to infer the dependence of energy metabolism on oxidative phosphorylation and glycolysis in defined cell populations identified by flow cytometry. We applied SPICE-Met to analyze T-cell memory development during vaccination. Finally, we used SPICE-Met in combination with real-time imaging to dissect the heterogeneity and plasticity of energy metabolism in single macrophages ex vivo and identify three distinct metabolic patterns. Functional probing of energy metabolism with single-cell resolution should greatly facilitate the study of immunometabolism at a steady state, during disease pathogenesis or in response to therapy.
    Keywords:  OXPHOS; energy; glycolysis; imaging; immunometabolism
    DOI:  https://doi.org/10.15252/embj.2022111528
  12. Nat Commun. 2022 Aug 24. 13(1): 4659
    Splicing QTL analysis focusing on coding sequences reveals mechanisms for disease susceptibility loci.
    Kensuke Yamaguchi, Kazuyoshi Ishigaki, Akari Suzuki, Yumi Tsuchida, Haruka Tsuchiya, Shuji Sumitomo, Yasuo Nagafuchi, Fuyuki Miya, Tatsuhiko Tsunoda, Hirofumi Shoda, Keishi Fujio, Kazuhiko Yamamoto, Yuta Kochi.
      Splicing quantitative trait loci (sQTLs) are one of the major causal mechanisms in genome-wide association study (GWAS) loci, but their role in disease pathogenesis is poorly understood. One reason is the complexity of alternative splicing events producing many unknown isoforms. Here, we propose two approaches, namely integration and selection, for this complexity by focusing on protein-structure of isoforms. First, we integrate isoforms with the same coding sequence (CDS) and identify 369-601 integrated-isoform ratio QTLs (i2-rQTLs), which altered protein-structure, in six immune subsets. Second, we select CDS incomplete isoforms annotated in GENCODE and identify 175-337 isoform-ratio QTL (i-rQTL). By comprehensive long-read capture RNA-sequencing among these incomplete isoforms, we reveal 29 full-length isoforms with unannotated CDSs associated with GWAS traits. Furthermore, we show that disease-causal sQTL genes can be identified by evaluating their trans-eQTL effects. Our approaches highlight the understudied role of protein-altering sQTLs and are broadly applicable to other tissues and diseases.
    DOI:  https://doi.org/10.1038/s41467-022-32358-1
  13. Nat Commun. 2022 Aug 20. 13(1): 4907
    Untangling the network effects of productivity and prominence among scientists.
    Weihua Li, Sam Zhang, Zhiming Zheng, Skyler J Cranmer, Aaron Clauset.
      While inequalities in science are common, most efforts to understand them treat scientists as isolated individuals, ignoring the network effects of collaboration. Here, we develop models that untangle the network effects of productivity defined as paper counts, and prominence referring to high-impact publications, of individual scientists from their collaboration networks. We find that gendered differences in the productivity and prominence of mid-career researchers can be largely explained by differences in their coauthorship networks. Hence, collaboration networks act as a form of social capital, and we find evidence of their transferability from senior to junior collaborators, with benefits that decay as researchers age. Collaboration network effects can also explain a large proportion of the productivity and prominence advantages held by researchers at prestigious institutions. These results highlight a substantial role of social networks in driving inequalities in science, and suggest that collaboration networks represent an important form of unequally distributed social capital that shapes who makes what scientific discoveries.
    DOI:  https://doi.org/10.1038/s41467-022-32604-6
  14. Cell Metab. 2022 Aug 17. pii: S1550-4131(22)00308-4. [Epub ahead of print]
    A WISP1 antibody inhibits MRTF signaling to prevent the progression of established liver fibrosis.
    Ying Xi, Ryan LaCanna, Hsiao-Yen Ma, Elsa-Noah N'Diaye, Sarah Gierke, Patrick Caplazi, Meredith Sagolla, Zhiyu Huang, Laura Lucio, Alexander Arlantico, Surinder Jeet, Hans Brightbill, Claire Emson, Aaron Wong, Katrina B Morshead, Daryle J DePianto, Merone Roose-Girma, Charles Yu, Lucinda Tam, Guiquan Jia, Thirumalai R Ramalingam, Scot Marsters, Avi Ashkenazi, Si Hyun Kim, Ryan Kelly, Shuang Wu, Paul J Wolters, Ariel E Feldstein, Jason A Vander Heiden, Ning Ding.
      Fibrosis is the major risk factor associated with morbidity and mortality in patients with non-alcoholic steatohepatitis (NASH)-driven chronic liver disease. Although numerous efforts have been made to identify the mediators of the initiation of liver fibrosis, the molecular underpinnings of fibrosis progression remain poorly understood, and therapies to arrest liver fibrosis progression are elusive. Here, we identify a pathway involving WNT1-inducible signaling pathway protein 1 (WISP1) and myocardin-related transcription factor (MRTF) as a central mechanism driving liver fibrosis progression through the integrin-dependent transcriptional reprogramming of myofibroblast cytoskeleton and motility. In mice, WISP1 deficiency protects against fibrosis progression, but not fibrosis onset. Moreover, the therapeutic administration of a novel antibody blocking WISP1 halted the progression of existing liver fibrosis in NASH models. These findings implicate the WISP1-MRTF axis as a crucial determinant of liver fibrosis progression and support targeting this pathway by antibody-based therapy for the treatment of NASH fibrosis.
    Keywords:  CCN4; MRTF; NASH; WISP1; antibody therapy; fibrosis; hepatic stellate cell; liver; progression
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.009
  15. Sci Adv. 2022 Aug 26. 8(34): eabn7774
    RORγt expression in mature TH17 cells safeguards their lineage specification by inhibiting conversion to TH2 cells.
    Xinxin Chi, Wei Jin, Xiaohong Zhao, Tian Xie, Jing Shao, Xue Bai, Yu Jiang, Xiaohu Wang, Chen Dong.
      RORγt is the lineage-specific transcription factor for T helper 17 (TH17) cells and an attractive drug target for treating TH17-associated diseases. Although the critical role of RORγt in early TH17 cell differentiation has been well recognized, its function in mature TH17 cell maintenance remains largely unknown. Here, we show that genetic deletion of Rorc in mature TH17 cells inhibited their pathogenic functions. Mechanistically, loss of RORγt led to a closed chromatin configuration at key TH17-specific gene loci, particularly at the "super-enhancer" regions. Unexpectedly, RORγt directly bound and inhibited Il4 transcription, whereas pharmaceutically or genetically targeting RORγt caused spontaneous conversion of TH17 cells to TH2-like cells in vitro and in vivo. Our results thus reveal dual crucial functions of RORγt in effector TH17 cells in maintaining TH17 cell program and constraining TH2 cell conversion, offering previously unidenified considerations in therapeutic targeting of RORγt.
    DOI:  https://doi.org/10.1126/sciadv.abn7774
  16. Trends Immunol. 2022 Aug 22. pii: S1471-4906(22)00159-4. [Epub ahead of print]
    Thymic mimetic cells: tolerogenic masqueraders.
    Daniel A Michelson, Diane Mathis.
      Medullary thymic epithelial cells (mTECs) clonally delete or divert autoreactive T cells by ectopically expressing a diverse array of peripheral-tissue antigens (PTAs) within the thymus. Although thymic stromal cells with histological features of extra-thymic cell types, like myocytes or neurons, have been observed by light microscopy since the mid-1800s, most modern work on PTA expression has focused on the transcription factor Aire. Here, we highlight recent work that has refocused attention on such 'misplaced' thymic cells, referred to collectively as thymic mimetic cells. We review the molecular underpinnings of mimetic cells and their roles in establishing T cell tolerance, and we propose that mimetic cells play important roles in autoimmunity. Finally, we suggest future directions for this emerging area.
    Keywords:  Aire; T cell tolerance; Thymus; autoimmunity; transcription factor
    DOI:  https://doi.org/10.1016/j.it.2022.07.010
  17. Nat Immunol. 2022 Aug 23.
    Leaky mitochondria.
    Nick Bernard.
      
    DOI:  https://doi.org/10.1038/s41590-022-01305-z
  18. Nat Commun. 2022 Aug 25. 13(1): 4999
    An interplay between cellular growth and atypical fusion defines morphogenesis of a modular glial niche in Drosophila.
    Maria Alexandra Rujano, David Briand, Bojana Ðelić, Julie Marc, Pauline Spéder.
      Neural stem cells (NSCs) live in an intricate cellular microenvironment supporting their activity, the niche. Whilst shape and function are inseparable, the morphogenetic aspects of niche development are poorly understood. Here, we use the formation of a glial niche to investigate acquisition of architectural complexity. Cortex glia (CG) in Drosophila regulate neurogenesis and build a reticular structure around NSCs. We first show that individual CG cells grow tremendously to ensheath several NSC lineages, employing elaborate proliferative mechanisms which convert these cells into syncytia rich in cytoplasmic bridges. CG syncytia further undergo homotypic cell-cell fusion, using defined cell surface receptors and actin regulators. Cellular exchange is however dynamic in space and time. This atypical cell fusion remodels cellular borders, restructuring the CG syncytia. Ultimately, combined growth and fusion builds the multi-level architecture of the niche, and creates a modular, spatial partition of the NSC population. Our findings provide insights into how a niche forms and organises while developing intimate contacts with a stem cell population.
    DOI:  https://doi.org/10.1038/s41467-022-32685-3
  19. Redox Biol. 2022 Aug 18. pii: S2213-2317(22)00219-1. [Epub ahead of print]56 102447
    The coupling of mitoproteolysis and oxidative phosphorylation enables tracking of an active mitochondrial state through MitoTimerfluorescence.
    Yinyin Xie, Yannan Zhang, Aina Sun, Yamei Peng, Weikang Hou, Cong Xiang, Guoxin Zhang, Beibei Lai, Xiaoshuang Hou, Fangfang Zheng, Fan Wang, Geng Liu.
      The regulation of mitochondria function and health is a central node in tissue maintenance, ageing as well as the pathogenesis of various diseases. However, the maintenance of an active mitochondrial functional state and its quality control mechanisms remain incompletely understood. By studying mice with a mitochondria-targeted reporter that shifts its fluorescence from "green" to "red" with time (MitoTimer), we found MitoTimer fluorescence spectrum was heavily dependent on the oxidative metabolic state in the skeletal muscle fibers. The mitoproteolytic activity was enhanced in an energy dependent manner, and accelerated the turnover of MitoTimer protein and respiratory chain substrate, responsible for a green predominant MitoTimer fluorescence spectrum under the oxidative conditions. PGC1α, as well as anti-ageing regents promoted enhanced mitoproteolysis. In addition, cells with the green predominant mitochondria exhibited lower levels of MitoSox and protein carbonylation, indicating a favorable redox state. Thus, we identified MitoTimer as a probe for mitoproteolytic activity in vivo and found a heightened control of mitoproteolysis in the oxidative metabolic state, providing a framework for understanding the maintenance of active oxidative metabolism while limiting oxidative damages.
    Keywords:  MitoTimer; Mitoproteolysis; Muscle fiber type; Oxidative metabolism; PGC-1α
    DOI:  https://doi.org/10.1016/j.redox.2022.102447
  20. Nat Immunol. 2022 Aug 23.
    ETS1 governs pathological tissue-remodeling programs in disease-associated fibroblasts.
    Minglu Yan, Noriko Komatsu, Ryunosuke Muro, Nam Cong-Nhat Huynh, Yoshihiko Tomofuji, Yukinori Okada, Hiroshi I Suzuki, Hiroyuki Takaba, Riko Kitazawa, Sohei Kitazawa, Warunee Pluemsakunthai, Yuichi Mitsui, Takashi Satoh, Tadashi Okamura, Takeshi Nitta, Sin-Hyeog Im, Chan Johng Kim, George Kollias, Sakae Tanaka, Kazuo Okamoto, Masayuki Tsukasaki, Hiroshi Takayanagi.
      Fibroblasts, the most abundant structural cells, exert homeostatic functions but also drive disease pathogenesis. Single-cell technologies have illuminated the shared characteristics of pathogenic fibroblasts in multiple diseases including autoimmune arthritis, cancer and inflammatory colitis. However, the molecular mechanisms underlying the disease-associated fibroblast phenotypes remain largely unclear. Here, we identify ETS1 as the key transcription factor governing the pathological tissue-remodeling programs in fibroblasts. In arthritis, ETS1 drives polarization toward tissue-destructive fibroblasts by orchestrating hitherto undescribed regulatory elements of the osteoclast differentiation factor receptor activator of nuclear factor-κB ligand (RANKL) as well as matrix metalloproteinases. Fibroblast-specific ETS1 deletion resulted in ameliorated bone and cartilage damage under arthritic conditions without affecting the inflammation level. Cross-tissue fibroblast single-cell data analyses and genetic loss-of-function experiments lent support to the notion that ETS1 defines the perturbation-specific fibroblasts shared among various disease settings. These findings provide a mechanistic basis for pathogenic fibroblast polarization and have important therapeutic implications.
    DOI:  https://doi.org/10.1038/s41590-022-01285-0
  21. Cell Rep. 2022 Aug 23. pii: S2211-1247(22)01006-3. [Epub ahead of print]40(8): 111189
    Disease-associated oligodendrocyte responses across neurodegenerative diseases.
    Shristi Pandey, Kimberle Shen, Seung-Hye Lee, Yun-An A Shen, Yuanyuan Wang, Marcos Otero-García, Natalya Kotova, Stephen T Vito, Benjamin I Laufer, Dwight F Newton, Mitchell G Rezzonico, Jesse E Hanson, Joshua S Kaminker, Christopher J Bohlen, Tracy J Yuen, Brad A Friedman.
      Oligodendrocyte dysfunction has been implicated in the pathogenesis of neurodegenerative diseases, so understanding oligodendrocyte activation states would shed light on disease processes. We identify three distinct activation states of oligodendrocytes from single-cell RNA sequencing (RNA-seq) of mouse models of Alzheimer's disease (AD) and multiple sclerosis (MS): DA1 (disease-associated1, associated with immunogenic genes), DA2 (disease-associated2, associated with genes influencing survival), and IFN (associated with interferon response genes). Spatial analysis of disease-associated oligodendrocytes (DAOs) in the cuprizone model reveals that DA1 and DA2 are established outside of the lesion area during demyelination and that DA1 repopulates the lesion during remyelination. Independent meta-analysis of human single-nucleus RNA-seq datasets reveals that the transcriptional responses of MS oligodendrocytes share features with mouse models. In contrast, the oligodendrocyte activation signature observed in human AD is largely distinct from those observed in mice. This catalog of oligodendrocyte activation states (http://research-pub.gene.com/OligoLandscape/) will be important to understand disease progression and develop therapeutic interventions.
    Keywords:  Alzheimer's disease; CP: Neuroscience; data integration; demyelination; disease-associated oligodendrocytes; multiple sclerosis; oligodendrocyte; remyelination; single-cell RNA-seq; spatial analysis
    DOI:  https://doi.org/10.1016/j.celrep.2022.111189
  22. J Immunol. 2022 Aug 24. pii: ji2100537. [Epub ahead of print]
    A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes.
    Darin Salloum, Kamini Singh, Natalie R Davidson, Linlin Cao, David Kuo, Viraj R Sanghvi, Man Jiang, Maria Tello Lafoz, Agnes Viale, Gunnar Ratsch, Hans-Guido Wendel.
      The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5' untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.
    DOI:  https://doi.org/10.4049/jimmunol.2100537
  23. iScience. 2022 Aug 19. 25(8): 104850
    Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.
    Irene Söderhäll, Erik Fasterius, Charlotta Ekblom, Kenneth Söderhäll.
      Crustaceans constitute a species-rich and ecologically important animal group, and their circulating blood cells (hemocytes) are of critical importance in immunity as key players in pathogen recognition, phagocytosis, melanization, and antimicrobial defense. To gain a better understanding of the immune responses to different pathogens, it is crucial that we identify different hemocyte subpopulations with different functions and gain a better understanding of how these cells are formed. Here, we performed single-cell RNA sequencing of isolated hematopoietic tissue (HPT) cells and hemocytes from the crayfish Pacifastacus leniusculus to identify hitherto undescribed hemocyte types in the circulation and show that the circulating cells are more diversified than previously recognized. In addition, we discovered cell populations in the HPT with clear precursor characteristics as well as cells involved in iron homeostasis, representing a previously undiscovered cell type. These findings may improve our understanding of hematopoietic stem cell regulation in crustaceans and other animals.
    Keywords:  Omics; Transcriptomics; Zoology
    DOI:  https://doi.org/10.1016/j.isci.2022.104850
  24. Nat Commun. 2022 Aug 22. 13(1): 4705
    Human acute inflammatory recovery is defined by co-regulatory dynamics of white blood cell and platelet populations.
    Brody H Foy, Thoralf M Sundt, Jonathan C T Carlson, Aaron D Aguirre, John M Higgins.
      Inflammation is the physiologic reaction to cellular and tissue damage caused by trauma, ischemia, infection, and other pathologic conditions. Elevation of white blood cell count (WBC) and altered levels of other acute phase reactants are cardinal signs of inflammation, but the dynamics of these changes and their resolution are not well established. Here we studied inflammatory recovery from trauma, ischemia, and infection by tracking longitudinal dynamics of clinical laboratory measurements in hospitalized patients. We identified a universal recovery trajectory defined by exponential WBC decay and delayed linear growth of platelet count (PLT). Co-regulation of WBC-PLT dynamics is a fundamental mechanism of acute inflammatory recovery and provides a generic approach for identifying high-risk patients: 32x relative risk (RR) of adverse outcomes for cardiac surgery, 9x RR of death from COVID-19, 9x RR of death from sepsis, and 5x RR of death from myocardial infarction.
    DOI:  https://doi.org/10.1038/s41467-022-32222-2
  25. Nat Commun. 2022 Aug 23. 13(1): 4844
    Multiancestry exome sequencing reveals INHBE mutations associated with favorable fat distribution and protection from diabetes.
    Regeneron Genetics Center
      Body fat distribution is a major, heritable risk factor for cardiometabolic disease, independent of overall adiposity. Using exome-sequencing in 618,375 individuals (including 160,058 non-Europeans) from the UK, Sweden and Mexico, we identify 16 genes associated with fat distribution at exome-wide significance. We show 6-fold larger effect for fat-distribution associated rare coding variants compared with fine-mapped common alleles, enrichment for genes expressed in adipose tissue and causal genes for partial lipodystrophies, and evidence of sex-dimorphism. We describe an association with favorable fat distribution (p = 1.8 × 10-09), favorable metabolic profile and protection from type 2 diabetes (~28% lower odds; p = 0.004) for heterozygous protein-truncating mutations in INHBE, which encodes a circulating growth factor of the activin family, highly and specifically expressed in hepatocytes. Our results suggest that inhibin βE is a liver-expressed negative regulator of adipose storage whose blockade may be beneficial in fat distribution-associated metabolic disease.
    DOI:  https://doi.org/10.1038/s41467-022-32398-7
  26. Cell Metab. 2022 Aug 19. pii: S1550-4131(22)00345-X. [Epub ahead of print]
    Aerobic glycolysis promotes tumor immune evasion by hexokinase2-mediated phosphorylation of IκBα.
    Dong Guo, Yingying Tong, Xiaoming Jiang, Ying Meng, Hongfei Jiang, Linyong Du, Qingang Wu, Shan Li, Shudi Luo, Min Li, Liwei Xiao, Haiyan He, Xuxiao He, Qiujing Yu, Jing Fang, Zhimin Lu.
      High expression of PD-L1 in tumor cells contributes to tumor immune evasion. However, whether PD-L1 expression in tumor cells is regulated by the availability of nutrients is unknown. Here, we show that in human glioblastoma cells, high glucose promotes hexokinase (HK) 2 dissociation from mitochondria and its subsequent binding and phosphorylation of IκBα at T291. This leads to increased interaction between IκBα and μ-calpain protease and subsequent μ-calpain-mediated IκBα degradation and NF-κB activation-dependent transcriptional upregulation of PD-L1 expression. Expression of IκBα T291A in glioblastoma cells blocked high glucose-induced PD-L1 expression and promoted CD8+ T cell activation and infiltration into the tumor tissue, reducing brain tumor growth. Combined treatment with an HK inhibitor and an anti-PD-1 antibody eliminates tumor immune evasion and remarkably enhances the anti-tumor effect of immune checkpoint blockade. These findings elucidate a novel mechanism underlying the upregulation of PD-L1 expression mediated by aerobic glycolysis and underscore the roles of HK2 as a glucose sensor and a protein kinase in regulation of tumor immune evasion.
    Keywords:  HK2; IκBα; NF-κB; PD-L1; glycolysis; immune evasion; phosphorylation; protein kinase
    DOI:  https://doi.org/10.1016/j.cmet.2022.08.002
  27. Sci Adv. 2022 Aug 26. 8(34): eabo2794
    Inhibition of microbial deconjugation of micellar bile acids protects against intestinal permeability and liver injury.
    Darrick K Li, Snehal N Chaudhari, Yoojin Lee, Mozhdeh Sojoodi, Arijit A Adhikari, Lawrence Zukerberg, Stuti Shroff, Stephen Cole Barrett, Kenneth Tanabe, Raymond T Chung, A Sloan Devlin.
      Altered host-microbe interactions and increased intestinal permeability have been implicated in disease pathogenesis. However, the mechanisms by which intestinal microbes affect epithelial barrier integrity remain unclear. Here, we investigate the impact of bacterial metabolism of host-produced bile acid (BA) metabolites on epithelial barrier integrity. We observe that rats fed a choline-deficient, l-amino acid-defined, high-fat diet (CDAHFD) exhibit reduced intestinal abundance of host-produced conjugated BAs at early time points, coinciding with increased gut permeability. We show that in vitro, conjugated BAs protect gut epithelial monolayers from damage caused by bacterially produced unconjugated BAs through micelle formation. We then demonstrate that inhibition of bacterial BA deconjugation with a small-molecule inhibitor prevents the development of pathologic intestinal permeability and hepatic inflammation in CDAHFD-fed rats. Our study identifies a signaling-independent, physicochemical mechanism for conjugated BA-mediated protection of epithelial barrier function and suggests that rational manipulation of microbial BA metabolism could be leveraged to regulate gut barrier integrity.
    DOI:  https://doi.org/10.1126/sciadv.abo2794
  28. Proc Natl Acad Sci U S A. 2022 Sep 06. 119(36): e2120680119
    Single-cell RNA sequencing uncovers the nuclear decoy lincRNA PIRAT as a regulator of systemic monocyte immunity during COVID-19.
    Marina Aznaourova, Nils Schmerer, Harshavardhan Janga, Zhenhua Zhang, Kim Pauck, Judith Bushe, Sarah M Volkers, Daniel Wendisch, Philipp Georg, Evgenia Ntini, Michelle Aillaud, Margrit Gündisch, Elisabeth Mack, Chrysanthi Skevaki, Christian Keller, Christian Bauer, Wilhelm Bertrams, Annalisa Marsico, Andrea Nist, Thorsten Stiewe, Achim D Gruber, Clemens Ruppert, Yang Li, Holger Garn, Leif E Sander, Bernd Schmeck, Leon N Schulte.
      The systemic immune response to viral infection is shaped by master transcription factors, such as NF-κB, STAT1, or PU.1. Although long noncoding RNAs (lncRNAs) have been suggested as important regulators of transcription factor activity, their contributions to the systemic immunopathologies observed during SARS-CoV-2 infection have remained unknown. Here, we employed a targeted single-cell RNA sequencing approach to reveal lncRNAs differentially expressed in blood leukocytes during severe COVID-19. Our results uncover the lncRNA PIRAT (PU.1-induced regulator of alarmin transcription) as a major PU.1 feedback-regulator in monocytes, governing the production of the alarmins S100A8/A9, key drivers of COVID-19 pathogenesis. Knockout and transgene expression, combined with chromatin-occupancy profiling, characterized PIRAT as a nuclear decoy RNA, keeping PU.1 from binding to alarmin promoters and promoting its binding to pseudogenes in naïve monocytes. NF-κB-dependent PIRAT down-regulation during COVID-19 consequently releases a transcriptional brake, fueling alarmin production. Alarmin expression is additionally enhanced by the up-regulation of the lncRNA LUCAT1, which promotes NF-κB-dependent gene expression at the expense of targets of the JAK-STAT pathway. Our results suggest a major role of nuclear noncoding RNA networks in systemic antiviral responses to SARS-CoV-2 in humans.
    Keywords:  COVID-19; PU.1; immunity; long noncoding RNA; single-cell RNA-seq
    DOI:  https://doi.org/10.1073/pnas.2120680119
  29. Cell Death Dis. 2022 Aug 25. 13(8): 735
    Zeb1 sustains hematopoietic stem cell functions by suppressing mitofusin-2-mediated mitochondrial fusion.
    Kai Zhang, Huifang Zhao, Yaru Sheng, Xinyu Chen, Penghui Xu, Jinming Wang, Zhongzhong Ji, Yuman He, Wei-Qiang Gao, Helen He Zhu.
      Metabolic status is essential in maintaining normal functions of hematopoietic stem cells (HSCs). However, how the dynamic of the mitochondrion, as a central organelle in metabolism, is molecularly regulated to orchestrate metabolism and HSC stemness remains to be elucidated. Here, we focus on the role of Zeb1, a well-characterized epithelial-to-mesenchymal transition (EMT) inducer which has been demonstrated to confer stem-cell-like characteristics in multiple cancer types in stemness regulation of HSCs. Using a Zeb1-tdTomato reporter mouse model, we find that Zeb1+Lin-Sca-1+c-Kit+ cells (Zeb1+-LSKs) represent a subset of functional long-term HSCs. Zeb1+LSKs exhibit a reduced reactive oxygen species (ROS) level, low mitochondrial mass, low mitochondrial membrane potential (MMP), and particularly small, round fragmented mitochondria. Of note, ectopic expression of Zeb1 leads to a fragmented mitochondrial morphology with a low mitochondrial metabolic status in EML cells. In addition, Zeb1-knockout (Zeb1-KO) LSKs from fetal liver display an exhausted stem-cell activity. Zeb1 deficiency results in elongated and tubulated mitochondria with increased mitochondrial mass, elevated MMP, and higher ROS production. Mechanistically, Zeb1 acts as a transcriptional suppressor on the key mitochondrial-fusion protein Mitofusin-2 (encoded by Mfn2). We highlight an important role of Zeb1 in the regulation of mitochondrial morphology in HSC and the metabolic control of HSC stemness by repressing Mfn2-mediated mitochondrial fusion.
    DOI:  https://doi.org/10.1038/s41419-022-05194-w
  30. Nature. 2022 Aug 24.
    Selective TnsC recruitment enhances the fidelity of RNA-guided transposition.
    Florian T Hoffmann, Minjoo Kim, Leslie Y Beh, Jing Wang, Phuc Leo H Vo, Diego R Gelsinger, Jerrin Thomas George, Christopher Acree, Jason T Mohabir, Israel S Fernández, Samuel H Sternberg.
      Bacterial transposons are pervasive mobile genetic elements that use distinct DNA-binding proteins for horizontal transmission. For example, Escherichia coli Tn7 homes to a specific attachment site using TnsD1, whereas CRISPR-associated transposons use type I or type V Cas effectors to insert downstream of target sites specified by guide RNAs2,3. Despite this targeting diversity, transposition invariably requires TnsB, a DDE-family transposase that catalyses DNA excision and insertion, and TnsC, a AAA+ ATPase that is thought to communicate between transposase and targeting proteins4. How TnsC mediates this communication and thereby regulates transposition fidelity has remained unclear. Here we use chromatin immunoprecipitation with sequencing to monitor in vivo formation of the type I-F RNA-guided transpososome, enabling us to resolve distinct protein recruitment events before integration. DNA targeting by the TniQ-Cascade complex is surprisingly promiscuous-hundreds of genomic off-target sites are sampled, but only a subset of those sites is licensed for TnsC and TnsB recruitment, revealing a crucial proofreading checkpoint. To advance the mechanistic understanding of interactions responsible for transpososome assembly, we determined structures of TnsC using cryogenic electron microscopy and found that ATP binding drives the formation of heptameric rings that thread DNA through the central pore, thereby positioning the substrate for downstream integration. Collectively, our results highlight the molecular specificity imparted by consecutive factor binding to genomic target sites during RNA-guided transposition, and provide a structural roadmap to guide future engineering efforts.
    DOI:  https://doi.org/10.1038/s41586-022-05059-4
  31. Science. 2022 Aug 25. eabg6621
    Lysosomal GPCR-like protein LYCHOS signals cholesterol sufficiency to mTORC1.
    Hijai R Shin, Y Rose Citron, Lei Wang, Laura Tribouillard, Claire S Goul, Robin Stipp, Yusuke Sugasawa, Aakriti Jain, Nolwenn Samson, Chun-Yan Lim, Oliver B Davis, David Castaneda-Carpio, Mingxing Qian, Daniel K Nomura, Rushika M Perera, Eunyong Park, Douglas F Covey, Mathieu Laplante, Alex S Evers, Roberto Zoncu.
      Lysosomes coordinate cellular metabolism and growth upon sensing of essential nutrients, including cholesterol. Through bioinformatic analysis of lysosomal proteomes, we identified LYsosomal CHOlesterol Signaling (LYCHOS, previously annotated as G-protein coupled receptor 155), a multidomain transmembrane protein that enables cholesterol-dependent activation of the master growth regulator, the protein kinase mechanistic Target of Rapamycin Complex 1 (mTORC1). Cholesterol bound to the N-terminal permease-like region of LYCHOS, and mutating this site impaired mTORC1 activation. At high cholesterol concentrations, LYCHOS bound to the GATOR1 complex, a GTPase-activating protein for the Rag guanosine triphosphatases, through a conserved cytoplasm-facing loop. By sequestering GATOR1, LYCHOS promotes cholesterol- and Rag-dependent recruitment of mTORC1 to lysosomes. Thus, LYCHOS functions in a lysosomal pathway for cholesterol sensing, and couples cholesterol concentrations to mTORC1-dependent anabolic signaling.
    DOI:  https://doi.org/10.1126/science.abg6621
  32. Sci Adv. 2022 Aug 26. 8(34): eabq0990
    Accurate inference of genome-wide spatial expression with iSpatial.
    Chao Zhang, Renchao Chen, Yi Zhang.
      Spatially resolved transcriptomic analyses can reveal molecular insights underlying tissue structure and context-dependent cell-cell or cell-environment interaction. Because of the current technical limitation, obtaining genome-wide spatial transcriptome at single-cell resolution is challenging. Here, we developed a new algorithm named iSpatial to derive the spatial pattern of the entire transcriptome by integrating spatial transcriptomic and single-cell RNA-seq datasets. Compared to other existing methods, iSpatial has higher accuracy in predicting gene expression and spatial distribution. Furthermore, it reduces false-positive and false-negative signals in the original datasets. By testing iSpatial with multiple spatial transcriptomic datasets, we demonstrate its wide applicability to datasets from different tissues and by different techniques. Thus, we provide a computational approach to reveal spatial organization of the entire transcriptome at single-cell resolution. With numerous high-quality datasets available in the public domain, iSpatial provides a unique way to understand the structure and function of complex tissues and disease processes.
    DOI:  https://doi.org/10.1126/sciadv.abq0990
  33. Nat Commun. 2022 Aug 26. 13(1): 5022
    Structure of the human NK cell NKR-P1:LLT1 receptor:ligand complex reveals clustering in the immune synapse.
    Jan Bláha, Tereza Skálová, Barbora Kalousková, Ondřej Skořepa, Denis Cmunt, Valéria Grobárová, Samuel Pazicky, Edita Poláchová, Celeste Abreu, Jan Stránský, Tomáš Kovaľ, Jarmila Dušková, Yuguang Zhao, Karl Harlos, Jindřich Hašek, Jan Dohnálek, Ondřej Vaněk.
      Signaling by the human C-type lectin-like receptor, natural killer (NK) cell inhibitory receptor NKR-P1, has a critical role in many immune-related diseases and cancer. C-type lectin-like receptors have weak affinities to their ligands; therefore, setting up a comprehensive model of NKR-P1-LLT1 interactions that considers the natural state of the receptor on the cell surface is necessary to understand its functions. Here we report the crystal structures of the NKR-P1 and NKR-P1:LLT1 complexes, which provides evidence that NKR-P1 forms homodimers in an unexpected arrangement to enable LLT1 binding in two modes, bridging two LLT1 molecules. These interaction clusters are suggestive of an inhibitory immune synapse. By observing the formation of these clusters in solution using SEC-SAXS analysis, by dSTORM super-resolution microscopy on the cell surface, and by following their role in receptor signaling with freshly isolated NK cells, we show that only the ligation of both LLT1 binding interfaces leads to effective NKR-P1 inhibitory signaling. In summary, our findings collectively support a model of NKR-P1:LLT1 clustering, which allows the interacting proteins to overcome weak ligand-receptor affinity and to trigger signal transduction upon cellular contact in the immune synapse.
    DOI:  https://doi.org/10.1038/s41467-022-32577-6
  34. Science. 2022 Aug 26. 377(6609): 940-951
    A genetic probe into the ancient and medieval history of Southern Europe and West Asia.
    Iosif Lazaridis, Songül Alpaslan-Roodenberg, Ayşe Acar, Ayşen Açıkkol, Anagnostis Agelarakis, Levon Aghikyan, Uğur Akyüz, Desislava Andreeva, Gojko Andrijašević, Dragana Antonović, Ian Armit, Alper Atmaca, Pavel Avetisyan, Ahmet İhsan Aytek, Krum Bacvarov, Ruben Badalyan, Stefan Bakardzhiev, Jacqueline Balen, Lorenc Bejko, Rebecca Bernardos, Andreas Bertsatos, Hanifi Biber, Ahmet Bilir, Mario Bodružić, Michelle Bonogofsky, Clive Bonsall, Dušan Borić, Nikola Borovinić, Guillermo Bravo Morante, Katharina Buttinger, Kim Callan, Francesca Candilio, Mario Carić, Olivia Cheronet, Stefan Chohadzhiev, Maria-Eleni Chovalopoulou, Stella Chryssoulaki, Ion Ciobanu, Natalija Čondić, Mihai Constantinescu, Emanuela Cristiani, Brendan J Culleton, Elizabeth Curtis, Jack Davis, Tatiana I Demcenco, Valentin Dergachev, Zafer Derin, Sylvia Deskaj, Seda Devejyan, Vojislav Djordjević, Kellie Sara Duffett Carlson, Laurie R Eccles, Nedko Elenski, Atilla Engin, Nihat Erdoğan, Sabiha Erir-Pazarcı, Daniel M Fernandes, Matthew Ferry, Suzanne Freilich, Alin Frînculeasa, Michael L Galaty, Beatriz Gamarra, Boris Gasparyan, Bisserka Gaydarska, Elif Genç, Timur Gültekin, Serkan Gündüz, Tamás Hajdu, Volker Heyd, Suren Hobosyan, Nelli Hovhannisyan, Iliya Iliev, Lora Iliev, Stanislav Iliev, İlkay İvgin, Ivor Janković, Lence Jovanova, Panagiotis Karkanas, Berna Kavaz-Kındığılı, Esra Hilal Kaya, Denise Keating, Douglas J Kennett, Seda Deniz Kesici, Anahit Khudaverdyan, Krisztián Kiss, Sinan Kılıç, Paul Klostermann, Sinem Kostak Boca Negra Valdes, Saša Kovačević, Marta Krenz-Niedbała, Maja Krznarić Škrivanko, Rovena Kurti, Pasko Kuzman, Ann Marie Lawson, Catalin Lazar, Krassimir Leshtakov, Thomas E Levy, Ioannis Liritzis, Kirsi O Lorentz, Sylwia Łukasik, Matthew Mah, Swapan Mallick, Kirsten Mandl, Kristine Martirosyan-Olshansky, Roger Matthews, Wendy Matthews, Kathleen McSweeney, Varduhi Melikyan, Adam Micco, Megan Michel, Lidija Milašinović, Alissa Mittnik, Janet M Monge, Georgi Nekhrizov, Rebecca Nicholls, Alexey G Nikitin, Vassil Nikolov, Mario Novak, Iñigo Olalde, Jonas Oppenheimer, Anna Osterholtz, Celal Özdemir, Kadir Toykan Özdoğan, Nurettin Öztürk, Nikos Papadimitriou, Niki Papakonstantinou, Anastasia Papathanasiou, Lujana Paraman, Evgeny G Paskary, Nick Patterson, Ilian Petrakiev, Levon Petrosyan, Vanya Petrova, Anna Philippa-Touchais, Ashot Piliposyan, Nada Pocuca Kuzman, Hrvoje Potrebica, Bianca Preda-Bălănică, Zrinka Premužić, T Douglas Price, Lijun Qiu, Siniša Radović, Kamal Raeuf Aziz, Petra Rajić Šikanjić, Kamal Rasheed Raheem, Sergei Razumov, Amy Richardson, Jacob Roodenberg, Rudenc Ruka, Victoria Russeva, Mustafa Şahin, Ayşegül Şarbak, Emre Savaş, Constanze Schattke, Lynne Schepartz, Tayfun Selçuk, Ayla Sevim-Erol, Michel Shamoon-Pour, Henry M Shephard, Athanasios Sideris, Angela Simalcsik, Hakob Simonyan, Vitalij Sinika, Kendra Sirak, Ghenadie Sirbu, Mario Šlaus, Andrei Soficaru, Bilal Söğüt, Arkadiusz Sołtysiak, Çilem Sönmez-Sözer, Maria Stathi, Martin Steskal, Kristin Stewardson, Sharon Stocker, Fadime Suata-Alpaslan, Alexander Suvorov, Anna Szécsényi-Nagy, Tamás Szeniczey, Nikolai Telnov, Strahil Temov, Nadezhda Todorova, Ulsi Tota, Gilles Touchais, Sevi Triantaphyllou, Atila Türker, Marina Ugarković, Todor Valchev, Fanica Veljanovska, Zlatko Videvski, Cristian Virag, Anna Wagner, Sam Walsh, Piotr Włodarczak, J Noah Workman, Aram Yardumian, Evgenii Yarovoy, Alper Yener Yavuz, Hakan Yılmaz, Fatma Zalzala, Anna Zettl, Zhao Zhang, Rafet Çavuşoğlu, Nadin Rohland, Ron Pinhasi, David Reich.
      Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.
    DOI:  https://doi.org/10.1126/science.abq0755
  35. Nat Cell Biol. 2022 Aug 25.
    Mammalian genome innovation through transposon domestication.
    Andrew J Modzelewski, Johnny Gan Chong, Ting Wang, Lin He.
      Since the discovery of transposons, their sheer abundance in host genomes has puzzled many. While historically viewed as largely harmless 'parasitic' DNAs during evolution, transposons are not a mere record of ancient genome invasion. Instead, nearly every element of transposon biology has been integrated into host biology. Here we review how host genome sequences introduced by transposon activities provide raw material for genome innovation and document the distinct evolutionary path of each species.
    DOI:  https://doi.org/10.1038/s41556-022-00970-4
  36. Nat Immunol. 2022 Aug 23.
    ETS1 is a key transcription factor that drives RANKL-expressing, tissue-destructive fibroblasts.
      
    DOI:  https://doi.org/10.1038/s41590-022-01298-9
  37. Science. 2022 Aug 26. 377(6609): eabm4247
    The genetic history of the Southern Arc: A bridge between West Asia and Europe.
    Iosif Lazaridis, Songül Alpaslan-Roodenberg, Ayşe Acar, Ayşen Açıkkol, Anagnostis Agelarakis, Levon Aghikyan, Uğur Akyüz, Desislava Andreeva, Gojko Andrijašević, Dragana Antonović, Ian Armit, Alper Atmaca, Pavel Avetisyan, Ahmet İhsan Aytek, Krum Bacvarov, Ruben Badalyan, Stefan Bakardzhiev, Jacqueline Balen, Lorenc Bejko, Rebecca Bernardos, Andreas Bertsatos, Hanifi Biber, Ahmet Bilir, Mario Bodružić, Michelle Bonogofsky, Clive Bonsall, Dušan Borić, Nikola Borovinić, Guillermo Bravo Morante, Katharina Buttinger, Kim Callan, Francesca Candilio, Mario Carić, Olivia Cheronet, Stefan Chohadzhiev, Maria-Eleni Chovalopoulou, Stella Chryssoulaki, Ion Ciobanu, Natalija Čondić, Mihai Constantinescu, Emanuela Cristiani, Brendan J Culleton, Elizabeth Curtis, Jack Davis, Tatiana I Demcenco, Valentin Dergachev, Zafer Derin, Sylvia Deskaj, Seda Devejyan, Vojislav Djordjević, Kellie Sara Duffett Carlson, Laurie R Eccles, Nedko Elenski, Atilla Engin, Nihat Erdoğan, Sabiha Erir-Pazarcı, Daniel M Fernandes, Matthew Ferry, Suzanne Freilich, Alin Frînculeasa, Michael L Galaty, Beatriz Gamarra, Boris Gasparyan, Bisserka Gaydarska, Elif Genç, Timur Gültekin, Serkan Gündüz, Tamás Hajdu, Volker Heyd, Suren Hobosyan, Nelli Hovhannisyan, Iliya Iliev, Lora Iliev, Stanislav Iliev, İlkay İvgin, Ivor Janković, Lence Jovanova, Panagiotis Karkanas, Berna Kavaz-Kındığılı, Esra Hilal Kaya, Denise Keating, Douglas J Kennett, Seda Deniz Kesici, Anahit Khudaverdyan, Krisztián Kiss, Sinan Kılıç, Paul Klostermann, Sinem Kostak Boca Negra Valdes, Saša Kovačević, Marta Krenz-Niedbała, Maja Krznarić Škrivanko, Rovena Kurti, Pasko Kuzman, Ann Marie Lawson, Catalin Lazar, Krassimir Leshtakov, Thomas E Levy, Ioannis Liritzis, Kirsi O Lorentz, Sylwia Łukasik, Matthew Mah, Swapan Mallick, Kirsten Mandl, Kristine Martirosyan-Olshansky, Roger Matthews, Wendy Matthews, Kathleen McSweeney, Varduhi Melikyan, Adam Micco, Megan Michel, Lidija Milašinović, Alissa Mittnik, Janet M Monge, Georgi Nekhrizov, Rebecca Nicholls, Alexey G Nikitin, Vassil Nikolov, Mario Novak, Iñigo Olalde, Jonas Oppenheimer, Anna Osterholtz, Celal Özdemir, Kadir Toykan Özdoğan, Nurettin Öztürk, Nikos Papadimitriou, Niki Papakonstantinou, Anastasia Papathanasiou, Lujana Paraman, Evgeny G Paskary, Nick Patterson, Ilian Petrakiev, Levon Petrosyan, Vanya Petrova, Anna Philippa-Touchais, Ashot Piliposyan, Nada Pocuca Kuzman, Hrvoje Potrebica, Bianca Preda-Bălănică, Zrinka Premužić, T Douglas Price, Lijun Qiu, Siniša Radović, Kamal Raeuf Aziz, Petra Rajić Šikanjić, Kamal Rasheed Raheem, Sergei Razumov, Amy Richardson, Jacob Roodenberg, Rudenc Ruka, Victoria Russeva, Mustafa Şahin, Ayşegül Şarbak, Emre Savaş, Constanze Schattke, Lynne Schepartz, Tayfun Selçuk, Ayla Sevim-Erol, Michel Shamoon-Pour, Henry M Shephard, Athanasios Sideris, Angela Simalcsik, Hakob Simonyan, Vitalij Sinika, Kendra Sirak, Ghenadie Sirbu, Mario Šlaus, Andrei Soficaru, Bilal Söğüt, Arkadiusz Sołtysiak, Çilem Sönmez-Sözer, Maria Stathi, Martin Steskal, Kristin Stewardson, Sharon Stocker, Fadime Suata-Alpaslan, Alexander Suvorov, Anna Szécsényi-Nagy, Tamás Szeniczey, Nikolai Telnov, Strahil Temov, Nadezhda Todorova, Ulsi Tota, Gilles Touchais, Sevi Triantaphyllou, Atila Türker, Marina Ugarković, Todor Valchev, Fanica Veljanovska, Zlatko Videvski, Cristian Virag, Anna Wagner, Sam Walsh, Piotr Włodarczak, J Noah Workman, Aram Yardumian, Evgenii Yarovoy, Alper Yener Yavuz, Hakan Yılmaz, Fatma Zalzala, Anna Zettl, Zhao Zhang, Rafet Çavuşoğlu, Nadin Rohland, Ron Pinhasi, David Reich.
      By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.
    DOI:  https://doi.org/10.1126/science.abm4247
  38. Proc Natl Acad Sci U S A. 2022 Aug 30. 119(35): e2211310119
    NAD+ metabolism drives astrocyte proinflammatory reprogramming in central nervous system autoimmunity.
    Tom Meyer, Dor Shimon, Sawsan Youssef, Gal Yankovitz, Adi Tessler, Tom Chernobylsky, Anat Gaoni-Yogev, Rita Perelroizen, Noga Budick-Harmelin, Lawrence Steinman, Lior Mayo.
      Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS). Astrocytes are the most abundant glial cells in the CNS, and their dysfunction contributes to the pathogenesis of MS and its animal model, experimental autoimmune encephalomyelitis (EAE). Recent advances highlight the pivotal role of cellular metabolism in programming immune responses. However, the underlying immunometabolic mechanisms that drive astrocyte pathogenicity remain elusive. Nicotinamide adenine dinucleotide (NAD+) is a vital coenzyme involved in cellular redox reactions and a substrate for NAD+-dependent enzymes. Cellular NAD+ levels are dynamically controlled by synthesis and degradation, and dysregulation of this balance has been associated with inflammation and disease. Here, we demonstrate that cell-autonomous generation of NAD+ via the salvage pathway regulates astrocyte immune function. Inhibition of nicotinamide phosphoribosyltransferase (NAMPT), a key enzyme in the salvage pathway, results in depletion of NAD+, inhibits oxidative phosphorylation, and limits astrocyte inflammatory potential. We identified CD38 as the main NADase up-regulated in reactive mouse and human astrocytes in models of neuroinflammation and MS. Genetic or pharmacological blockade of astrocyte CD38 activity augmented NAD+ levels, suppressed proinflammatory transcriptional reprogramming, impaired chemotactic potential to inflammatory monocytes, and ameliorated EAE. We found that CD38 activity is mediated via calcineurin/NFAT signaling in mouse and human reactive astrocytes. Thus, NAMPT-NAD+-CD38 circuitry in astrocytes controls their ability to meet their energy demands and drives the expression of proinflammatory transcriptional modules, contributing to CNS pathology in EAE and, potentially, MS. Our results identify candidate therapeutic targets in MS.
    Keywords:  Nicotinamide adenine dinucleotide; astrocyte; multiple sclerosis; neuroinflammation; tryptophan catabolism
    DOI:  https://doi.org/10.1073/pnas.2211310119
  39. Nat Metab. 2022 Aug;4(8): 1071-1083
    GLP-1-mediated delivery of tesaglitazar improves obesity and glucose metabolism in male mice.
    Carmelo Quarta, Kerstin Stemmer, Aaron Novikoff, Bin Yang, Felix Klingelhuber, Alex Harger, Mostafa Bakhti, Aimee Bastidas-Ponce, Eric Baugé, Jonathan E Campbell, Megan Capozzi, Christoffer Clemmensen, Gustav Collden, Perla Cota, Jon Douros, Daniel J Drucker, Barent DuBois, Annette Feuchtinger, Cristina Garcia-Caceres, Gerald Grandl, Nathalie Hennuyer, Stephan Herzig, Susanna M Hofmann, Patrick J Knerr, Konxhe Kulaj, Fanny Lalloyer, Heiko Lickert, Arek Liskiewicz, Daniela Liskiewicz, Gandhari Maity, Diego Perez-Tilve, Sneha Prakash, Miguel A Sanchez-Garrido, Qian Zhang, Bart Staels, Natalie Krahmer, Richard D DiMarchi, Matthias H Tschöp, Brian Finan, Timo D Müller.
      Dual agonists activating the peroxisome proliferator-activated receptors alpha and gamma (PPARɑ/ɣ) have beneficial effects on glucose and lipid metabolism in patients with type 2 diabetes, but their development was discontinued due to potential adverse effects. Here we report the design and preclinical evaluation of a molecule that covalently links the PPARɑ/ɣ dual-agonist tesaglitazar to a GLP-1 receptor agonist (GLP-1RA) to allow for GLP-1R-dependent cellular delivery of tesaglitazar. GLP-1RA/tesaglitazar does not differ from the pharmacokinetically matched GLP-1RA in GLP-1R signalling, but shows GLP-1R-dependent PPARɣ-retinoic acid receptor heterodimerization and enhanced improvements of body weight, food intake and glucose metabolism relative to the GLP-1RA or tesaglitazar alone in obese male mice. The conjugate fails to affect body weight and glucose metabolism in GLP-1R knockout mice and shows preserved effects in obese mice at subthreshold doses for the GLP-1RA and tesaglitazar. Liquid chromatography-mass spectrometry-based proteomics identified PPAR regulated proteins in the hypothalamus that are acutely upregulated by GLP-1RA/tesaglitazar. Our data show that GLP-1RA/tesaglitazar improves glucose control with superior efficacy to the GLP-1RA or tesaglitazar alone and suggest that this conjugate might hold therapeutic value to acutely treat hyperglycaemia and insulin resistance.
    DOI:  https://doi.org/10.1038/s42255-022-00617-6
  40. Nat Commun. 2022 Aug 25. 13(1): 5013
    Selective suppression of melanoma lacking IFN-γ pathway by JAK inhibition depends on T cells and host TNF signaling.
    Hongxing Shen, Fengyuan Huang, Xiangmin Zhang, Oluwagbemiga A Ojo, Yuebin Li, Hoa Quang Trummell, Joshua C Anderson, John Fiveash, Markus Bredel, Eddy S Yang, Christopher D Willey, Zechen Chong, James A Bonner, Lewis Zhichang Shi.
      Therapeutic resistance to immune checkpoint blockers (ICBs) in melanoma patients is a pressing issue, of which tumor loss of IFN-γ signaling genes is a major underlying mechanism. However, strategies of overcoming this resistance mechanism have been largely elusive. Moreover, given the indispensable role of tumor-infiltrating T cells (TILs) in ICBs, little is known about how tumor-intrinsic loss of IFN-γ signaling (IFNγR1KO) impacts TILs. Here, we report that IFNγR1KO melanomas have reduced infiltration and function of TILs. IFNγR1KO melanomas harbor a network of constitutively active protein tyrosine kinases centered on activated JAK1/2. Mechanistically, JAK1/2 activation is mediated by augmented mTOR. Importantly, JAK1/2 inhibition with Ruxolitinib selectively suppresses the growth of IFNγR1KO but not scrambled control melanomas, depending on T cells and host TNF. Together, our results reveal an important role of tumor-intrinsic IFN-γ signaling in shaping TILs and manifest a targeted therapy to bypass ICB resistance of melanomas defective of IFN-γ signaling.
    DOI:  https://doi.org/10.1038/s41467-022-32754-7
  41. J Clin Invest. 2022 Aug 25. pii: e158593. [Epub ahead of print]
    Mediator kinase regulates intestinal differentiation and homeostasis via the chromatin remodeling complex SWI/SNF.
    Marius V Dannappel, Danxi Zhu, Xin Sun, Hui Kheng Chua, Marle Poppelaars, Monica Suehiro, Subash Khadka, Terry Cc Lim Kam Sian, Dhanya Sooraj, Melissa Loi, Hugh Gao, Daniel Croagh, Roger J Daly, Pouya Faridi, Thomas Boyer, Ron Firestein.
      Initiation and maintenance of transcriptional states are critical for controlling normal tissue homeostasis and differentiation. Cyclin Dependent Kinases CDK8/CDK19 (Mediator kinase) are regulatory components of Mediator, a highly conserved complex that orchestrates enhancer-mediated transcriptional output. While Mediator kinase has been implicated in the transcription of genes necessary for development and growth, its function in mammals has not been well defined. Using a suite of genetically defined models and pharmacological inhibitors, we show that Cdk8/19 function in a redundant manner to regulate intestinal lineage-specification in human and mouse. Mechanistically, we find that the Mediator kinase module binds and phosphorylates key components of the chromatin remodelling complex SWI/SNF in intestinal epithelial cells. Concomitantly, SWI/SNF and MED12-Mediator co-localise at distinct lineage-specifying enhancers in a CDK8/19 dependent manner. As such, these studies reveal a novel transcriptional mechanism of intestinal cell specification, coordinated by the interaction between the chromatin remodelling complex SWI/SNF and Mediator kinase.
    Keywords:  Gastroenterology; Genetics; Molecular genetics; Mouse models; Oncogenes
    DOI:  https://doi.org/10.1172/JCI158593
  42. Nat Immunol. 2022 Aug 23.
    Two CTLA-4 ligands, separate pHates.
    Preston A Humphries, Wan-Lin Lo.
      
    DOI:  https://doi.org/10.1038/s41590-022-01296-x
  43. Sci Adv. 2022 Aug 26. 8(34): eabm4358
    Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer.
    Satyanarayan Rao, Amy L Han, Alexis Zukowski, Etana Kopin, Carol A Sartorius, Peter Kabos, Srinivas Ramachandran.
      Genome-wide binding profiles of estrogen receptor (ER) and FOXA1 reflect cancer state in ER+ breast cancer. However, routine profiling of tumor transcription factor (TF) binding is impractical in the clinic. Here, we show that plasma cell-free DNA (cfDNA) contains high-resolution ER and FOXA1 tumor binding profiles for breast cancer. Enrichment of TF footprints in plasma reflects the binding strength of the TF in originating tissue. We defined pure in vivo tumor TF signatures in plasma using ER+ breast cancer xenografts, which can distinguish xenografts with distinct ER states. Furthermore, state-specific ER-binding signatures can partition human breast tumors into groups with significantly different ER expression and mortality. Last, TF footprints in human plasma samples can identify the presence of ER+ breast cancer. Thus, plasma TF footprints enable minimally invasive mapping of the regulatory landscape of breast cancer in humans and open vast possibilities for clinical applications across multiple tumor types.
    DOI:  https://doi.org/10.1126/sciadv.abm4358
  44. FASEB J. 2022 Sep;36(9): e22512
    Somatic ablation of IKKβ in liver and leukocytes is not tolerated in obese mice but hepatic IKKβ deletion improves fatty liver and insulin sensitivity.
    Vagner Ramon R Silva, Angela Molinaro, Andrea Usseglio Gaudi, Emanuel Fryk, Claudia Sardi, Maria Hammarlund, Filip Mjörnstedt, Maria E Johansson, Barbara Becattini, Per-Anders Jansson, Giovanni Solinas.
      The kinase IKKβ controls pro-inflammatory gene expression, and its activity in the liver and leukocytes was shown to drive metabolic inflammation and insulin resistance in obesity. However, it was also proposed that liver IKKβ signaling protects obese mice from insulin resistance and endoplasmic reticulum (ER) stress by increasing XBP1s protein stability. Furthermore, mice lacking IKKβ in leukocytes display increased lethality to lipopolysaccharides. This study aims at improving our understanding of the role of IKKβ signaling in obesity. We induced IKKβ deletion in hematopoietic cells and liver of obese mice by Cre-LoxP recombination, using an INF-inducible system, or a liver-specific IKKβ deletion in obese mice by adenovirus delivery of the Cre recombinase. The histopathological, immune, and metabolic phenotype of the mice was characterized. IKKβ deletion in the liver and hematopoietic cells was not tolerated in mice with established obesity exposed to the TLR3 agonist poly(I:C) and exacerbated liver damage and ER-stress despite elevated XBP1s. By contrast, liver-specific ablation of IKKβ in obese mice reduced steatosis and improved insulin sensitivity in association with increased XBP1s protein abundance and reduced expression of de-novo lipogenesis genes. We conclude that IKKβ blockage in liver and leukocytes is not tolerated in obese mice exposed to TLR3 agonists. However, selective hepatic IKKβ ablation improves fatty liver and insulin sensitivity in association with increased XBP1s protein abundance and reduced expression of lipogenic genes.
    Keywords:  endoplasmic reticulum stress; immunometabolism; liver; metabolic inflammation
    DOI:  https://doi.org/10.1096/fj.202200694R
  45. Proc Natl Acad Sci U S A. 2022 Aug 30. 119(35): e2205425119
    A partnership between the lipid scramblase XK and the lipid transfer protein VPS13A at the plasma membrane.
    Andrés Guillén-Samander, Yumei Wu, S Sebastian Pineda, Francisco J García, Julia N Eisen, Marianna Leonzino, Berrak Ugur, Manolis Kellis, Myriam Heiman, Pietro De Camilli.
      Chorea-acanthocytosis (ChAc) and McLeod syndrome are diseases with shared clinical manifestations caused by mutations in VPS13A and XK, respectively. Key features of these conditions are the degeneration of caudate neurons and the presence of abnormally shaped erythrocytes. XK belongs to a family of plasma membrane (PM) lipid scramblases whose action results in exposure of PtdSer at the cell surface. VPS13A is an endoplasmic reticulum (ER)-anchored lipid transfer protein with a putative role in the transport of lipids at contacts of the ER with other membranes. Recently VPS13A and XK were reported to interact by still unknown mechanisms. So far, however, there is no evidence for a colocalization of the two proteins at contacts of the ER with the PM, where XK resides, as VPS13A was shown to be localized at contacts between the ER and either mitochondria or lipid droplets. Here we show that VPS13A can also localize at ER-PM contacts via the binding of its PH domain to a cytosolic loop of XK, that such interaction is regulated by an intramolecular interaction within XK, and that both VPS13A and XK are highly expressed in the caudate neurons. Binding of the PH domain of VPS13A to XK is competitive with its binding to intracellular membranes that mediate other tethering functions of VPS13A. Our findings support a model according to which VPS13A-dependent lipid transfer between the ER and the PM is coupled to lipid scrambling within the PM. They raise the possibility that defective cell surface exposure of PtdSer may be responsible for neurodegeneration.
    Keywords:  VPS13B; VPS13C; VPS13D; chorein; junctophilin
    DOI:  https://doi.org/10.1073/pnas.2205425119
  46. Nat Microbiol. 2022 Sep;7(9): 1348-1360
    Uropathogenic Escherichia coli subverts mitochondrial metabolism to enable intracellular bacterial pathogenesis in urinary tract infection.
    Connor J Beebout, Gabriella L Robertson, Bradley I Reinfeld, Alexandra M Blee, Grace H Morales, John R Brannon, Walter J Chazin, W Kimryn Rathmell, Jeffrey C Rathmell, Vivian Gama, Maria Hadjifrangiskou.
      Urinary tract infections are among the most common human bacterial infections and place a significant burden on healthcare systems due to associated morbidity, cost and antibiotic use. Despite being a facultative anaerobe, uropathogenic Escherichia coli, the primary cause of urinary tract infections, requires aerobic respiration to establish infection in the bladder. Here, by combining bacterial genetics with cell culture and murine models of infection, we demonstrate that the widely conserved respiratory quinol oxidase cytochrome bd is required for intracellular infection of urothelial cells. Through a series of genetic, biochemical and functional assays, we show that intracellular oxygen scavenging by cytochrome bd alters mitochondrial physiology by reducing the efficiency of mitochondrial respiration, stabilizing the hypoxia-inducible transcription factor HIF-1 and promoting a shift towards aerobic glycolysis. This bacterially induced rewiring of host metabolism antagonizes apoptosis, thereby protecting intracellular bacteria from urothelial cell exfoliation and preserving their replicative niche. These results reveal the metabolic basis for intracellular bacterial pathogenesis during urinary tract infection and identify subversion of mitochondrial metabolism as a bacterial strategy to facilitate persistence within the urinary tract.
    DOI:  https://doi.org/10.1038/s41564-022-01205-w
  47. Nat Immunol. 2022 Aug 24.
    Patrolling ILC3 cells monitor intestinal tissue in response to inflammation.
      
    DOI:  https://doi.org/10.1038/s41590-022-01299-8
  48. Nat Commun. 2022 Aug 26. 13(1): 5043
    Efficient DNA fluorescence labeling via base excision trapping.
    Yong Woong Jun, Emily M Harcourt, Lu Xiao, David L Wilson, Eric T Kool.
      Fluorescence labeling of DNAs is broadly useful, but methods for labeling are expensive and labor-intensive. Here we describe a general method for fluorescence labeling of oligonucleotides readily and cost-efficiently via base excision trapping (BETr), employing deaminated DNA bases to mark label positions, which are excised by base excision repair enzymes generating AP sites. Specially designed aminooxy-substituted rotor dyes trap the AP sites, yielding high emission intensities. BETr is orthogonal to DNA synthesis by polymerases, enabling multi-uracil incorporation into an amplicon and in situ BETr labeling without washing. BETr also enables labeling of dsDNA such as genomic DNA at a high labeling density in a single tube by use of nick translation. Use of two different deaminated bases facilitates two-color site-specific labeling. Use of a multi-labeled DNA construct as a bright fluorescence tag is demonstrated through the conjugation to an antibody for imaging proteins. Finally, double-strand selectivity of a repair enzyme is harnessed in sensitive reporting on the presence of a target DNA or RNA in a mixture with isothermal turnover and single nucleotide specificity. Overall, the results document a convenient and versatile method for general fluorescence labeling of DNAs.
    DOI:  https://doi.org/10.1038/s41467-022-32494-8
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