bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022‒08‒07
28 papers selected by
Fawaz Alzaïd
Sorbonne Université
  1. Genetic variants that edit risk of autoimmune diseases.
  2. RNA editing underlies genetic risk of common inflammatory diseases.
  3. Multiplex base editing to convert TAG into TAA codons in the human genome.
  4. Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis.
  5. Fate mapping of hematopoietic stem cells reveals two pathways of native thrombopoiesis.
  6. Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity.
  7. The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis.
  8. Cell-type-specific cis-eQTLs in eight human brain cell types identify novel risk genes for psychiatric and neurological disorders.
  9. Mitochondrial remodeling and ischemic protection by G protein-coupled receptor 35 agonists.
  10. An intranasal ASO therapeutic targeting SARS-CoV-2.
  11. Large-scale genome-wide association study of coronary artery disease in genetically diverse populations.
  12. Microenvironmental sensing by fibroblasts controls macrophage population size.
  13. Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex.
  14. Does immune destruction drive all forms of bone marrow failure?
  15. Maladaptive positive feedback production of ChREBPβ underlies glucotoxic β-cell failure.
  16. Single-cell transcriptome and cell type-specific molecular pathways of human non-alcoholic steatohepatitis.
  17. Viral-host interactions during splicing and nuclear export of influenza virus mRNAs.
  18. Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk.
  19. A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.
  20. The continuum of Drosophila embryonic development at single-cell resolution.
  21. Metabolic reprogramming from glycolysis to fatty acid uptake and beta-oxidation in platinum-resistant cancer cells.
  22. Nrf2 as a regulator of mitochondrial function: Energy metabolism and beyond.
  23. Intravital 3D visualization and segmentation of murine neural networks at micron resolution.
  24. Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation.
  25. Aberrant iron distribution via hepatocyte-stellate cell axis drives liver lipogenesis and fibrosis.
  26. Cellular communication network factor 1-stimulated liver macrophage efferocytosis drives hepatic stellate cell activation and liver fibrosis.
  27. ROR2 regulates self-renewal and maintenance of hair follicle stem cells.
  28. Nucleotide imbalance decouples cell growth from cell proliferation.
  1. Nature. 2022 Aug 03.
    Genetic variants that edit risk of autoimmune diseases.
    Kaur Alasoo.
      
    Keywords:  Genetics; Immunology
    DOI:  https://doi.org/10.1038/d41586-022-01641-y
  2. Nature. 2022 Aug 03.
    RNA editing underlies genetic risk of common inflammatory diseases.
    Qin Li, Michael J Gloudemans, Jonathan M Geisinger, Boming Fan, François Aguet, Tao Sun, Gokul Ramaswami, Yang I Li, Jin-Biao Ma, Jonathan K Pritchard, Stephen B Montgomery, Jin Billy Li.
      A major challenge in human genetics is to identify the molecular mechanisms of trait-associated and disease-associated variants. To achieve this, quantitative trait locus (QTL) mapping of genetic variants with intermediate molecular phenotypes such as gene expression and splicing have been widely adopted1,2. However, despite successes, the molecular basis for a considerable fraction of trait-associated and disease-associated variants remains unclear3,4. Here we show that ADAR-mediated adenosine-to-inosine RNA editing, a post-transcriptional event vital for suppressing cellular double-stranded RNA (dsRNA)-mediated innate immune interferon responses5-11, is an important potential mechanism underlying genetic variants associated with common inflammatory diseases. We identified and characterized 30,319 cis-RNA editing QTLs (edQTLs) across 49 human tissues. These edQTLs were significantly enriched in genome-wide association study signals for autoimmune and immune-mediated diseases. Colocalization analysis of edQTLs with disease risk loci further pinpointed key, putatively immunogenic dsRNAs formed by expected inverted repeat Alu elements as well as unexpected, highly over-represented cis-natural antisense transcripts. Furthermore, inflammatory disease risk variants, in aggregate, were associated with reduced editing of nearby dsRNAs and induced interferon responses in inflammatory diseases. This unique directional effect agrees with the established mechanism that lack of RNA editing by ADAR1 leads to the specific activation of the dsRNA sensor MDA5 and subsequent interferon responses and inflammation7-9. Our findings implicate cellular dsRNA editing and sensing as a previously underappreciated mechanism of common inflammatory diseases.
    DOI:  https://doi.org/10.1038/s41586-022-05052-x
  3. Nat Commun. 2022 Aug 02. 13(1): 4482
    Multiplex base editing to convert TAG into TAA codons in the human genome.
    Yuting Chen, Eriona Hysolli, Anlu Chen, Stephen Casper, Songlei Liu, Kevin Yang, Chenli Liu, George Church.
      Whole-genome recoding has been shown to enable nonstandard amino acids, biocontainment and viral resistance in bacteria. Here we take the first steps to extend this to human cells demonstrating exceptional base editing to convert TAG to TAA for 33 essential genes via a single transfection, and examine base-editing genome-wide (observing ~40 C-to-T off-target events in essential gene exons). We also introduce GRIT, a computational tool for recoding. This demonstrates the feasibility of recoding, and highly multiplex editing in mammalian cells.
    DOI:  https://doi.org/10.1038/s41467-022-31927-8
  4. Nat Commun. 2022 Aug 01. 13(1): 4464
    Xist exerts gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis.
    Tianqi Yang, Jianhong Ou, Eda Yildirim.
      X chromosome inactivation (XCI) is a dosage compensation phenomenon that occurs in females. Initiation of XCI depends on Xist RNA, which triggers silencing of one of the two X chromosomes, except for XCI escape genes that continue to be biallelically expressed. In the soma XCI is stably maintained with continuous Xist expression. How Xist impacts XCI maintenance remains an open question. Here we conditionally delete Xist in hematopoietic system of mice and report differentiation and cell cycle defects in female hematopoietic stem and progenitor cells (HSPCs). By utilizing female HSPCs and mouse embryonic fibroblasts, we find that X-linked genes show variable tolerance to Xist loss. Specifically, XCI escape genes exhibit preferential transcriptional upregulation, which associates with low H3K27me3 occupancy and high chromatin accessibility that accommodates preexisting binding of transcription factors such as Yin Yang 1 (YY1) at the basal state. We conclude that Xist is necessary for gene-specific silencing during XCI maintenance and impacts lineage-specific cell differentiation and proliferation during hematopoiesis.
    DOI:  https://doi.org/10.1038/s41467-022-32273-5
  5. Nat Commun. 2022 Aug 03. 13(1): 4504
    Fate mapping of hematopoietic stem cells reveals two pathways of native thrombopoiesis.
    Mina N F Morcos, Congxin Li, Clara M Munz, Alessandro Greco, Nicole Dressel, Susanne Reinhardt, Katrin Sameith, Andreas Dahl, Nils B Becker, Axel Roers, Thomas Höfer, Alexander Gerbaulet.
      Hematopoietic stem cells (HSCs) produce highly diverse cell lineages. Here, we chart native lineage pathways emanating from HSCs and define their physiological regulation by computationally integrating experimental approaches for fate mapping, mitotic tracking, and single-cell RNA sequencing. We find that lineages begin to split when cells leave the tip HSC population, marked by high Sca-1 and CD201 expression. Downstream, HSCs either retain high Sca-1 expression and the ability to generate lymphocytes, or irreversibly reduce Sca-1 level and enter into erythro-myelopoiesis or thrombopoiesis. Thrombopoiesis is the sum of two pathways that make comparable contributions in steady state, a long route via multipotent progenitors and CD48hi megakaryocyte progenitors (MkPs), and a short route from HSCs to developmentally distinct CD48-/lo MkPs. Enhanced thrombopoietin signaling differentially accelerates the short pathway, enabling a rapid response to increasing demand. In sum, we provide a blueprint for mapping physiological differentiation fluxes from HSCs and decipher two functionally distinct pathways of native thrombopoiesis.
    DOI:  https://doi.org/10.1038/s41467-022-31914-z
  6. Cell Stem Cell. 2022 Aug 04. pii: S1934-5909(22)00300-9. [Epub ahead of print]29(8): 1197-1212.e8
    Lipid accumulation induced by APOE4 impairs microglial surveillance of neuronal-network activity.
    Matheus B Victor, Noelle Leary, Xochitl Luna, Hiruy S Meharena, Aine Ni Scannail, P Lorenzo Bozzelli, George Samaan, Mitchell H Murdock, Djuna von Maydell, Audrey H Effenberger, Oyku Cerit, Hsin-Lan Wen, Liwang Liu, Gwyneth Welch, Maeve Bonner, Li-Huei Tsai.
      Apolipoprotein E4 (APOE4) is the greatest known genetic risk factor for developing sporadic Alzheimer's disease. How the interaction of APOE4 microglia with neurons differs from microglia expressing the disease-neutral APOE3 allele remains unknown. Here, we employ CRISPR-edited induced pluripotent stem cells (iPSCs) to dissect the impact of APOE4 in neuron-microglia communication. Our results reveal that APOE4 induces a lipid-accumulated state that renders microglia weakly responsive to neuronal activity. By examining the transcriptional signatures of APOE3 versus APOE4 microglia in response to neuronal conditioned media, we established that neuronal cues differentially induce a lipogenic program in APOE4 microglia that exacerbates pro-inflammatory signals. Through decreased uptake of extracellular fatty acids and lipoproteins, we identified that APOE4 microglia disrupts the coordinated activity of neuronal ensembles. These findings suggest that abnormal neuronal network-level disturbances observed in Alzheimer's disease patients harboring APOE4 may in part be triggered by impairment in lipid homeostasis in non-neuronal cells.
    Keywords:  APOE; Alzheimer’s risk variant; GIRKs; calcium dynamics; forebrain spheroids; lipid droplet; microglia; network-activity; stem cells
    DOI:  https://doi.org/10.1016/j.stem.2022.07.005
  7. Immunity. 2022 Aug 03. pii: S1074-7613(22)00335-1. [Epub ahead of print]
    The transcription factor FoxP3 can fold into two dimerization states with divergent implications for regulatory T cell function and immune homeostasis.
    Fangwei Leng, Wenxiang Zhang, Ricardo N Ramirez, Juliette Leon, Yi Zhong, Lifei Hou, Koichi Yuki, Joris van der Veeken, Alexander Y Rudensky, Christophe Benoist, Sun Hur.
      FoxP3 is an essential transcription factor (TF) for immunologic homeostasis, but how it utilizes the common forkhead DNA-binding domain (DBD) to perform its unique function remains poorly understood. We here demonstrated that unlike other known forkhead TFs, FoxP3 formed a head-to-head dimer using a unique linker (Runx1-binding region [RBR]) preceding the forkhead domain. Head-to-head dimerization conferred distinct DNA-binding specificity and created a docking site for the cofactor Runx1. RBR was also important for proper folding of the forkhead domain, as truncation of RBR induced domain-swap dimerization of forkhead, which was previously considered the physiological form of FoxP3. Rather, swap-dimerization impaired FoxP3 function, as demonstrated with the disease-causing mutation R337Q, whereas a swap-suppressive mutation largely rescued R337Q-mediated functional impairment. Altogether, our findings suggest that FoxP3 can fold into two distinct dimerization states: head-to-head dimerization representing functional specialization of an ancient DBD and swap dimerization associated with impaired functions.
    Keywords:  Foxp3; IPEX; Runx1; Treg; forkhead; homodimer; transcription factor
    DOI:  https://doi.org/10.1016/j.immuni.2022.07.002
  8. Nat Neurosci. 2022 Aug;25(8): 1104-1112
    Cell-type-specific cis-eQTLs in eight human brain cell types identify novel risk genes for psychiatric and neurological disorders.
    Julien Bryois, Daniela Calini, Will Macnair, Lynette Foo, Eduard Urich, Ward Ortmann, Victor Alejandro Iglesias, Suresh Selvaraj, Erik Nutma, Manuel Marzin, Sandra Amor, Anna Williams, Gonçalo Castelo-Branco, Vilas Menon, Philip De Jager, Dheeraj Malhotra.
      To date, most expression quantitative trait loci (eQTL) studies, which investigate how genetic variants contribute to gene expression, have been performed in heterogeneous brain tissues rather than specific cell types. In this study, we performed an eQTL analysis using single-nuclei RNA sequencing from 192 individuals in eight brain cell types derived from the prefrontal cortex, temporal cortex and white matter. We identified 7,607 eGenes, a substantial fraction (46%, 3,537/7,607) of which show cell-type-specific effects, with strongest effects in microglia. Cell-type-level eQTLs affected more constrained genes and had larger effect sizes than tissue-level eQTLs. Integration of brain cell type eQTLs with genome-wide association studies (GWAS) revealed novel relationships between expression and disease risk for neuropsychiatric and neurodegenerative diseases. For most GWAS loci, a single gene co-localized in a single cell type, providing new clues into disease etiology. Our findings demonstrate substantial contrast in genetic regulation of gene expression among brain cell types and reveal potential mechanisms by which disease risk genes influence brain disorders.
    DOI:  https://doi.org/10.1038/s41593-022-01128-z
  9. Science. 2022 Aug 05. 377(6606): 621-629
    Mitochondrial remodeling and ischemic protection by G protein-coupled receptor 35 agonists.
    Gregory A Wyant, Wenyu Yu, IIias P Doulamis, Rio S Nomoto, Mossab Y Saeed, Thomas Duignan, James D McCully, William G Kaelin.
      Kynurenic acid (KynA) is tissue protective in cardiac, cerebral, renal, and retinal ischemia models, but the mechanism is unknown. KynA can bind to multiple receptors, including the aryl hydrocarbon receptor, the a7 nicotinic acetylcholine receptor (a7nAChR), multiple ionotropic glutamate receptors, and the orphan G protein-coupled receptor GPR35. Here, we show that GPR35 activation was necessary and sufficient for ischemic protection by KynA. When bound by KynA, GPR35 activated Gi- and G12/13-coupled signaling and trafficked to the outer mitochondria membrane, where it bound, apparantly indirectly, to ATP synthase inhibitory factor subunit 1 (ATPIF1). Activated GPR35, in an ATPIF1-dependent and pertussis toxin-sensitive manner, induced ATP synthase dimerization, which prevented ATP loss upon ischemia. These findings provide a rationale for the development of specific GPR35 agonists for the treatment of ischemic diseases.
    DOI:  https://doi.org/10.1126/science.abm1638
  10. Nat Commun. 2022 Aug 03. 13(1): 4503
    An intranasal ASO therapeutic targeting SARS-CoV-2.
    Chi Zhu, Justin Y Lee, Jia Z Woo, Lei Xu, Xammy Nguyenla, Livia H Yamashiro, Fei Ji, Scott B Biering, Erik Van Dis, Federico Gonzalez, Douglas Fox, Eddie Wehri, Arjun Rustagi, Benjamin A Pinsky, Julia Schaletzky, Catherine A Blish, Charles Chiu, Eva Harris, Ruslan I Sadreyev, Sarah Stanley, Sakari Kauppinen, Silvi Rouskin, Anders M Näär.
      The COVID-19 pandemic is exacting an increasing toll worldwide, with new SARS-CoV-2 variants emerging that exhibit higher infectivity rates and that may partially evade vaccine and antibody immunity. Rapid deployment of non-invasive therapeutic avenues capable of preventing infection by all SARS-CoV-2 variants could complement current vaccination efforts and help turn the tide on the COVID-19 pandemic. Here, we describe a novel therapeutic strategy targeting the SARS-CoV-2 RNA using locked nucleic acid antisense oligonucleotides (LNA ASOs). We identify an LNA ASO binding to the 5' leader sequence of SARS-CoV-2 that disrupts a highly conserved stem-loop structure with nanomolar efficacy in preventing viral replication in human cells. Daily intranasal administration of this LNA ASO in the COVID-19 mouse model potently suppresses viral replication (>80-fold) in the lungs of infected mice. We find that the LNA ASO is efficacious in countering all SARS-CoV-2 "variants of concern" tested both in vitro and in vivo. Hence, inhaled LNA ASOs targeting SARS-CoV-2 represents a promising therapeutic approach to reduce or prevent transmission and decrease severity of COVID-19 in infected individuals. LNA ASOs are chemically stable and can be flexibly modified to target different viral RNA sequences and could be stockpiled for future coronavirus pandemics.
    DOI:  https://doi.org/10.1038/s41467-022-32216-0
  11. Nat Med. 2022 Aug 01.
    Large-scale genome-wide association study of coronary artery disease in genetically diverse populations.
    Regeneron Genetics Center
      We report a genome-wide association study (GWAS) of coronary artery disease (CAD) incorporating nearly a quarter of a million cases, in which existing studies are integrated with data from cohorts of white, Black and Hispanic individuals from the Million Veteran Program. We document near equivalent heritability of CAD across multiple ancestral groups, identify 95 novel loci, including nine on the X chromosome, detect eight loci of genome-wide significance in Black and Hispanic individuals, and demonstrate that two common haplotypes at the 9p21 locus are responsible for risk stratification in all populations except those of African origin, in which these haplotypes are virtually absent. Moreover, in the largest GWAS for angiographically derived coronary atherosclerosis performed to date, we find 15 loci of genome-wide significance that robustly overlap with established loci for clinical CAD. Phenome-wide association analyses of novel loci and polygenic risk scores (PRSs) augment signals related to insulin resistance, extend pleiotropic associations of these loci to include smoking and family history, and precisely document the markedly reduced transferability of existing PRSs to Black individuals. Downstream integrative analyses reinforce the critical roles of vascular endothelial, fibroblast, and smooth muscle cells in CAD susceptibility, but also point to a shared biology between atherosclerosis and oncogenesis. This study highlights the value of diverse populations in further characterizing the genetic architecture of CAD.
    DOI:  https://doi.org/10.1038/s41591-022-01891-3
  12. Proc Natl Acad Sci U S A. 2022 Aug 09. 119(32): e2205360119
    Microenvironmental sensing by fibroblasts controls macrophage population size.
    Xu Zhou, Ruth A Franklin, Miri Adler, Trevor S Carter, Emily Condiff, Taylor S Adams, Scott D Pope, Naomi H Philip, Matthew L Meizlish, Naftali Kaminski, Ruslan Medzhitov.
      Animal tissues comprise diverse cell types. However, the mechanisms controlling the number of each cell type within tissue compartments remain poorly understood. Here, we report that different cell types utilize distinct strategies to control population numbers. Proliferation of fibroblasts, stromal cells important for tissue integrity, is limited by space availability. In contrast, proliferation of macrophages, innate immune cells involved in defense, repair, and homeostasis, is constrained by growth factor availability. Examination of density-dependent gene expression in fibroblasts revealed that Hippo and TGF-β target genes are both regulated by cell density. We found YAP1, the transcriptional coactivator of the Hippo signaling pathway, directly regulates expression of Csf1, the lineage-specific growth factor for macrophages, through an enhancer of Csf1 that is specifically active in fibroblasts. Activation of YAP1 in fibroblasts elevates Csf1 expression and is sufficient to increase the number of macrophages at steady state. Our data also suggest that expression programs in fibroblasts that change with density may result from sensing of mechanical force through actin-dependent mechanisms. Altogether, we demonstrate that two different modes of population control are connected and coordinated to regulate cell numbers of distinct cell types. Sensing of the tissue environment may serve as a general strategy to control tissue composition.
    Keywords:  fibroblast; growth factor; macrophage
    DOI:  https://doi.org/10.1073/pnas.2205360119
  13. Nat Neurosci. 2022 Aug;25(8): 1049-1058
    Temporally divergent regulatory mechanisms govern neuronal diversification and maturation in the mouse and marmoset neocortex.
    Wen Yuan, Sai Ma, Juliana R Brown, Kwanho Kim, Vanessa Murek, Lucia Trastulla, Alexander Meissner, Simona Lodato, Ashwin S Shetty, Joshua Z Levin, Jason D Buenrostro, Michael J Ziller, Paola Arlotta.
      Mammalian neocortical neurons span one of the most diverse cell type spectra of any tissue. Cortical neurons are born during embryonic development, and their maturation extends into postnatal life. The regulatory strategies underlying progressive neuronal development and maturation remain unclear. Here we present an integrated single-cell epigenomic and transcriptional analysis of individual mouse and marmoset cortical neuron classes, spanning both early postmitotic stages of identity acquisition and later stages of neuronal plasticity and circuit integration. We found that, in both species, the regulatory strategies controlling early and late stages of pan-neuronal development diverge. Early postmitotic neurons use more widely shared and evolutionarily conserved molecular regulatory programs. In contrast, programs active during later neuronal maturation are more brain- and neuron-specific and more evolutionarily divergent. Our work uncovers a temporal shift in regulatory choices during neuronal diversification and maturation in both mice and marmosets, which likely reflects unique evolutionary constraints on distinct events of neuronal development in the neocortex.
    DOI:  https://doi.org/10.1038/s41593-022-01123-4
  14. J Clin Invest. 2022 Aug 01. pii: e161288. [Epub ahead of print]132(15):
    Does immune destruction drive all forms of bone marrow failure?
    Brian M Dulmovits, Timothy S Olson.
      Current paradigms of bone marrow failure (BMF) pathophysiology suggest that immune-mediated destruction of hematopoietic stem and progenitor cells (HSPCs) drives acquired aplastic anemia. In contrast, loss of HSPCs due to senescence and/or apoptosis causes BMF in inherited BMF syndromes. In this issue of the JCI, Casado and colleagues challenge this dichotomous conception by demonstrating that NK cell-dependent, immune-mediated hematopoietic suppression and HSPC clearance drive BMF in Fanconi anemia (FA). They show that genotoxic stress upregulates natural killer group 2 member D ligands (NKG2D-L) on FA HSPCs leading to NK cell cytotoxicity through NKG2D receptor activation. Inhibition of NKG2D-NKG2D-L interactions enhanced FA HSPC clonogenic potential and improved cytopenias in vivo. These results provide alternative targets for the development of immunosuppressive therapies to reduce HSPC loss and mitigate the risk of hematologic malignancies in FA.
    DOI:  https://doi.org/10.1172/JCI161288
  15. Nat Commun. 2022 Jul 30. 13(1): 4423
    Maladaptive positive feedback production of ChREBPβ underlies glucotoxic β-cell failure.
    Liora S Katz, Gabriel Brill, Pili Zhang, Anil Kumar, Sharon Baumel-Alterzon, Lee B Honig, Nicolás Gómez-Banoy, Esra Karakose, Marius Tanase, Ludivine Doridot, Alexandra Alvarsson, Bennett Davenport, Peng Wang, Luca Lambertini, Sarah A Stanley, Dirk Homann, Andrew F Stewart, James C Lo, Mark A Herman, Adolfo Garcia-Ocaña, Donald K Scott.
      Preservation and expansion of β-cell mass is a therapeutic goal for diabetes. Here we show that the hyperactive isoform of carbohydrate response-element binding protein (ChREBPβ) is a nuclear effector of hyperglycemic stress occurring in β-cells in response to prolonged glucose exposure, high-fat diet, and diabetes. We show that transient positive feedback induction of ChREBPβ is necessary for adaptive β-cell expansion in response to metabolic challenges. Conversely, chronic excessive β-cell-specific overexpression of ChREBPβ results in loss of β-cell identity, apoptosis, loss of β-cell mass, and diabetes. Furthermore, β-cell "glucolipotoxicity" can be prevented by deletion of ChREBPβ. Moreover, ChREBPβ-mediated cell death is mitigated by overexpression of the alternate CHREBP gene product, ChREBPα, or by activation of the antioxidant Nrf2 pathway in rodent and human β-cells. We conclude that ChREBPβ, whether adaptive or maladaptive, is an important determinant of β-cell fate and a potential target for the preservation of β-cell mass in diabetes.
    DOI:  https://doi.org/10.1038/s41467-022-32162-x
  16. Sci Rep. 2022 Aug 05. 12(1): 13484
    Single-cell transcriptome and cell type-specific molecular pathways of human non-alcoholic steatohepatitis.
    Rikard G Fred, Julie Steen Pedersen, Jonatan J Thompson, Julie Lee, Pascal N Timshel, Stefan Stender, Marte Opseth Rygg, Lise Lotte Gluud, Viggo Bjerregaard Kristiansen, Flemming Bendtsen, Torben Hansen, Tune H Pers.
      The aim of this study is to characterize cell type-specific transcriptional signatures in non-alcoholic steatohepatitis (NASH) to improve our understanding of the disease. We performed single-cell RNA sequencing on liver biopsies from 10 patients with NASH. We applied weighted gene co-expression network analysis and validated our findings using a publicly available RNA sequencing data set derived from 160 patients with non-alcoholic fatty liver disease (NAFLD) and 24 controls with normal liver histology. Our study provides a comprehensive single-cell analysis of NASH pathology in humans, describing 19,627 single-cell transcriptomes from biopsy-proven NASH patients. Our data suggest that the previous notion of "NASH-associated macrophages" can be explained by an up-regulation of normally existing subpopulations of liver macrophages. Similarly, we describe two distinct populations of activated hepatic stellate cells, associated with the level of fibrosis. Finally, we find that the expression of several circulating markers of NAFLD are co-regulated in hepatocytes together with predicted effector genes from NAFLD genome-wide association studies (GWAS), coupled to abnormalities in the complement system. In sum, our single-cell transcriptomic data set provides insights into novel cell type-specific and general biological processes associated with inflammation and fibrosis, emphasizing the importance of studying cell type-specific biological processes in human NASH.
    DOI:  https://doi.org/10.1038/s41598-022-16754-7
  17. Curr Opin Virol. 2022 Jul 28. pii: S1879-6257(22)00065-7. [Epub ahead of print]55 101254
    Viral-host interactions during splicing and nuclear export of influenza virus mRNAs.
    Matthew Esparza, Prasanna Bhat, Beatriz Ma Fontoura.
      As influenza-A viruses (IAV) replicate in the host cell nucleus, intranuclear pathways are usurped for viral gene expression. The eight genomic viral ribonucleoproteins (vRNPs) segments of IAV are transcribed and two generate viral mRNAs (M and NS) that undergo alternative splicing followed by export from the nucleus. The focus of this review is on viral RNA splicing and nuclear export. Recent mechanistic advances on M and NS splicing show differential regulation by RNA-binding proteins as well as distinct intranuclear localization. After a review of IAV splicing, we will discuss the nuclear export of viral mRNAs, which occur by interacting with specific constituents of the host mRNA export machinery that translocate viral mRNAs through the nuclear pore complex for translation in the cytoplasm.
    DOI:  https://doi.org/10.1016/j.coviro.2022.101254
  18. Nat Commun. 2022 Jul 30. 13(1): 4429
    Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data with SpaTalk.
    Xin Shao, Chengyu Li, Haihong Yang, Xiaoyan Lu, Jie Liao, Jingyang Qian, Kai Wang, Junyun Cheng, Penghui Yang, Huajun Chen, Xiao Xu, Xiaohui Fan.
      Spatially resolved transcriptomics provides genetic information in space toward elucidation of the spatial architecture in intact organs and the spatially resolved cell-cell communications mediating tissue homeostasis, development, and disease. To facilitate inference of spatially resolved cell-cell communications, we here present SpaTalk, which relies on a graph network and knowledge graph to model and score the ligand-receptor-target signaling network between spatially proximal cells by dissecting cell-type composition through a non-negative linear model and spatial mapping between single-cell transcriptomic and spatially resolved transcriptomic data. The benchmarked performance of SpaTalk on public single-cell spatial transcriptomic datasets is superior to that of existing inference methods. Then we apply SpaTalk to STARmap, Slide-seq, and 10X Visium data, revealing the in-depth communicative mechanisms underlying normal and disease tissues with spatial structure. SpaTalk can uncover spatially resolved cell-cell communications for single-cell and spot-based spatially resolved transcriptomic data universally, providing valuable insights into spatial inter-cellular tissue dynamics.
    DOI:  https://doi.org/10.1038/s41467-022-32111-8
  19. Am J Hum Genet. 2022 Aug 04. pii: S0002-9297(22)00265-8. [Epub ahead of print]109(8): 1366-1387
    A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids.
    Million Veterans Program
      A major challenge of genome-wide association studies (GWASs) is to translate phenotypic associations into biological insights. Here, we integrate a large GWAS on blood lipids involving 1.6 million individuals from five ancestries with a wide array of functional genomic datasets to discover regulatory mechanisms underlying lipid associations. We first prioritize lipid-associated genes with expression quantitative trait locus (eQTL) colocalizations and then add chromatin interaction data to narrow the search for functional genes. Polygenic enrichment analysis across 697 annotations from a host of tissues and cell types confirms the central role of the liver in lipid levels and highlights the selective enrichment of adipose-specific chromatin marks in high-density lipoprotein cholesterol and triglycerides. Overlapping transcription factor (TF) binding sites with lipid-associated loci identifies TFs relevant in lipid biology. In addition, we present an integrative framework to prioritize causal variants at GWAS loci, producing a comprehensive list of candidate causal genes and variants with multiple layers of functional evidence. We highlight two of the prioritized genes, CREBRF and RRBP1, which show convergent evidence across functional datasets supporting their roles in lipid biology.
    Keywords:  complex traits; fine-mapping; functional genomics; lipid biology; post-GWAS; regulatory mechanism; variant prioritization
    DOI:  https://doi.org/10.1016/j.ajhg.2022.06.012
  20. Science. 2022 Aug 05. 377(6606): eabn5800
    The continuum of Drosophila embryonic development at single-cell resolution.
    Diego Calderon, Ronnie Blecher-Gonen, Xingfan Huang, Stefano Secchia, James Kentro, Riza M Daza, Beth Martin, Alessandro Dulja, Christoph Schaub, Cole Trapnell, Erica Larschan, Kate M O'Connor-Giles, Eileen E M Furlong, Jay Shendure.
      Drosophila melanogaster is a powerful, long-standing model for metazoan development and gene regulation. We profiled chromatin accessibility in almost 1 million and gene expression in half a million nuclei from overlapping windows spanning the entirety of embryogenesis. Leveraging developmental asynchronicity within embryo collections, we applied deep neural networks to infer the age of each nucleus, resulting in continuous, multimodal views of molecular and cellular transitions in absolute time. We identify cell lineages; infer their developmental relationships; and link dynamic changes in enhancer usage, transcription factor (TF) expression, and the accessibility of TFs' cognate motifs. With these data, the dynamics of enhancer usage and gene expression can be explored within and across lineages at the scale of minutes, including for precise transitions like zygotic genome activation.
    DOI:  https://doi.org/10.1126/science.abn5800
  21. Nat Commun. 2022 Aug 05. 13(1): 4554
    Metabolic reprogramming from glycolysis to fatty acid uptake and beta-oxidation in platinum-resistant cancer cells.
    Yuying Tan, Junjie Li, Guangyuan Zhao, Kai-Chih Huang, Horacio Cardenas, Yinu Wang, Daniela Matei, Ji-Xin Cheng.
      Increased glycolysis is considered as a hallmark of cancer. Yet, cancer cell metabolic reprograming during therapeutic resistance development is under-studied. Here, through high-throughput stimulated Raman scattering imaging and single cell analysis, we find that cisplatin-resistant cells exhibit increased fatty acids (FA) uptake, accompanied by decreased glucose uptake and lipogenesis, indicating reprogramming from glucose to FA dependent anabolic and energy metabolism. A metabolic index incorporating glucose derived anabolism and FA uptake correlates linearly to the level of cisplatin resistance in ovarian cancer (OC) cell lines and primary cells. The increased FA uptake facilitates cancer cell survival under cisplatin-induced oxidative stress by enhancing beta-oxidation. Consequently, blocking beta-oxidation by a small molecule inhibitor combined with cisplatin or carboplatin synergistically suppresses OC proliferation in vitro and growth of patient-derived xenografts in vivo. Collectively, these findings support a rapid detection method of cisplatin-resistance at single cell level and a strategy for treating cisplatin-resistant tumors.
    DOI:  https://doi.org/10.1038/s41467-022-32101-w
  22. Free Radic Biol Med. 2022 Jul 30. pii: S0891-5849(22)00496-8. [Epub ahead of print]
    Nrf2 as a regulator of mitochondrial function: Energy metabolism and beyond.
    Noemí Esteras, Andrey Y Abramov.
      Mitochondria are unique and essential organelles that mediate many vital cellular processes including energy metabolism and cell death. The transcription factor Nrf2 (NF-E2 p45-related factor 2) has emerged in the last few years as an important modulator of multiple aspects of mitochondrial function. Well-known for controlling cellular redox homeostasis, the cytoprotective effects of Nrf2 extend beyond its ability to regulate a diverse network of antioxidant and detoxification enzymes. Here, we review the role of Nrf2 in the regulation of mitochondrial function and structure. We focus on Nrf2 involvement in promoting mitochondrial quality control and regulation of basic aspects of mitochondrial function, including energy production, reactive oxygen species generation, calcium signalling, and cell death induction. Given the importance of mitochondria in the development of multiple diseases, these findings reinforce the pharmacological activation of Nrf2 as an attractive strategy to counteract mitochondrial dysfunction.
    Keywords:  Calcium; Dynamics; Energy; Fission; Fusion; Mitochondria; Mitochondrial biogenesis; Mitophagy; Nrf2; ROS; mPTP
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2022.07.013
  23. Sci Rep. 2022 Jul 30. 12(1): 13130
    Intravital 3D visualization and segmentation of murine neural networks at micron resolution.
    Ziv Lautman, Yonatan Winetraub, Eran Blacher, Caroline Yu, Itamar Terem, Adelaida Chibukhchyan, James H Marshel, Adam de la Zerda.
      Optical coherence tomography (OCT) allows label-free, micron-scale 3D imaging of biological tissues' fine structures with significant depth and large field-of-view. Here we introduce a novel OCT-based neuroimaging setting, accompanied by a feature segmentation algorithm, which enables rapid, accurate, and high-resolution in vivo imaging of 700 μm depth across the mouse cortex. Using a commercial OCT device, we demonstrate 3D reconstruction of microarchitectural elements through a cortical column. Our system is sensitive to structural and cellular changes at micron-scale resolution in vivo, such as those from injury or disease. Therefore, it can serve as a tool to visualize and quantify spatiotemporal brain elasticity patterns. This highly transformative and versatile platform allows accurate investigation of brain cellular architectural changes by quantifying features such as brain cell bodies' density, volume, and average distance to the nearest cell. Hence, it may assist in longitudinal studies of microstructural tissue alteration in aging, injury, or disease in a living rodent brain.
    DOI:  https://doi.org/10.1038/s41598-022-14450-0
  24. Proc Natl Acad Sci U S A. 2022 Aug 09. 119(32): e2114758119
    Targeting acetyl-CoA metabolism attenuates the formation of fear memories through reduced activity-dependent histone acetylation.
    Desi C Alexander, Tanya Corman, Mariel Mendoza, Andrew Glass, Tal Belity, Ranran Wu, Rianne R Campbell, Joseph Han, Ashley A Keiser, Jeffrey Winkler, Marcelo A Wood, Thomas Kim, Benjamin A Garcia, Hagit Cohen, Philipp Mews, Gabor Egervari, Shelley L Berger.
      Histone acetylation is a key component in the consolidation of long-term fear memories. Histone acetylation is fueled by acetyl-coenzyme A (acetyl-CoA), and recently, nuclear-localized metabolic enzymes that produce this metabolite have emerged as direct and local regulators of chromatin. In particular, acetyl-CoA synthetase 2 (ACSS2) mediates histone acetylation in the mouse hippocampus. However, whether ACSS2 regulates long-term fear memory remains to be determined. Here, we show that Acss2 knockout is well tolerated in mice, yet the Acss2-null mouse exhibits reduced acquisition of long-term fear memory. Loss of Acss2 leads to reductions in both histone acetylation and expression of critical learning and memory-related genes in the dorsal hippocampus, specifically following fear conditioning. Furthermore, systemic administration of blood-brain barrier-permeable Acss2 inhibitors during the consolidation window reduces fear-memory formation in mice and rats and reduces anxiety in a predator-scent stress paradigm. Our findings suggest that nuclear acetyl-CoA metabolism via ACSS2 plays a critical, previously unappreciated, role in the formation of fear memories.
    Keywords:  epigenetics; fear conditioning; histone acetylation; learning and memory; mass spectrometry
    DOI:  https://doi.org/10.1073/pnas.2114758119
  25. Cell Metab. 2022 Aug 02. pii: S1550-4131(22)00305-9. [Epub ahead of print]34(8): 1201-1213.e5
    Aberrant iron distribution via hepatocyte-stellate cell axis drives liver lipogenesis and fibrosis.
    Hong Gao, Zhongmou Jin, Gautam Bandyopadhyay, Gaowei Wang, Dinghong Zhang, Karina Cunha E Rocha, Xiao Liu, Huayi Zhao, Tatiana Kisseleva, David A Brenner, Michael Karin, Wei Ying.
      Hepatocytes have important roles in liver iron homeostasis, abnormalities in which are tightly associated with liver steatosis and fibrosis. Here, we show that non-alcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH) are characterized by iron-deficient hepatocytes and iron overload in hepatic stellate cells (HSCs). Iron deficiency enhances hepatocyte lipogenesis and insulin resistance through HIF2α-ATF4 signaling. Elevated secretion of iron-containing hepatocyte extracellular vesicles (EVs), which are normally cleared by Kupffer cells, accounts for hepatocyte iron deficiency and HSC iron overload in NAFLD/NASH livers. Iron accumulation results in overproduction of reactive oxygen species that promote HSC fibrogenic activation. Conversely, blocking hepatocyte EV secretion or depleting EV iron cargo restores liver iron homeostasis, concomitant with mitigation of NAFLD/NASH-associated liver steatosis and fibrosis. Taken together, these studies show that iron distribution disorders contribute to the development of liver metabolic diseases.
    Keywords:  NAFLD; NASH; extracellular vesicle; hepatic stellate cell; hepatocyte; iron; liver fibrosis; liver steatosis
    DOI:  https://doi.org/10.1016/j.cmet.2022.07.006
  26. Hepatol Commun. 2022 Aug 05.
    Cellular communication network factor 1-stimulated liver macrophage efferocytosis drives hepatic stellate cell activation and liver fibrosis.
    Ki-Hyun Kim, Naiyuan Cheng, Lester F Lau.
      Following inflammatory injury in the liver, neutrophils quickly infiltrate the injured tissue to defend against microbes and initiate the repair process; these neutrophils are short lived and rapidly undergo apoptosis. Hepatic stellate cells (HSCs) are the principal precursor cells that transdifferentiate into myofibroblast-like cells, which produce a large amount of extracellular matrix that promotes repair but can also lead to fibrosis if the injury becomes chronic. The matricellular protein cellular communication network factor 1 (CCN1) acts as a bridging molecule by binding phosphatidylserine in apoptotic cells and integrin αv β3 in phagocytes, thereby triggering efferocytosis or phagocytic clearance of the apoptotic cells. Here, we show that CCN1 induces liver macrophage efferocytosis of apoptotic neutrophils in carbon tetrachloride (CCl4 )-induced liver injury, leading to the production of activated transforming growth factor (TGF)-β1, which in turn induces HSC transdifferentiation into myofibroblast-like cells that promote fibrosis development. Consequently, knock-in mice expressing a single amino acid substitution in CCN1 rendering it unable to bind αv β3 or induce efferocytosis are impaired in neutrophil clearance, production of activated TGF-β1, and HSC transdifferentiation, resulting in greatly diminished liver fibrosis following exposure to CCl4 . Conclusion: These results reveal the crucial role of CCN1 in stimulating liver macrophage clearance of apoptotic neutrophils, a process that drives HSC transdifferentiation into myofibroblastic cells and underlies fibrogenesis in chronic liver injury.
    DOI:  https://doi.org/10.1002/hep4.2057
  27. Nat Commun. 2022 Aug 01. 13(1): 4449
    ROR2 regulates self-renewal and maintenance of hair follicle stem cells.
    Anthony Veltri, Christopher M R Lang, Gaia Cangiotti, Chim Kei Chan, Wen-Hui Lien.
      Hair follicles undergo cycles of regeneration fueled by hair follicle stem cells (HFSCs). While β-catenin-dependent canonical Wnt signaling has been extensively studied and implicated in HFSC activation and fate determination, very little is known about the function of β-catenin-independent Wnt signaling in HFSCs. In this study, we investigate the functional role of ROR2, a Wnt receptor, in HFSCs. By analyzing Ror2-depleted HFSCs, we uncover that ROR2 is not only essential to regulate Wnt-activated signaling that is responsible for HFSC activation and self-renewal, but it is also required to maintain proper ATM/ATR-dependent DNA damage response, which is indispensable for the long-term maintenance of HFSCs. In analyzing HFSCs lacking β-catenin, we identify a compensatory role of ROR2-PKC signaling in protecting β-catenin-null HFSCs from the loss of stem cell pool. Collectively, our study unveils a previously unrecognized role of ROR2 in regulation of stem cell self-renewal and maintenance.
    DOI:  https://doi.org/10.1038/s41467-022-32239-7
  28. Nat Cell Biol. 2022 Aug 04.
    Nucleotide imbalance decouples cell growth from cell proliferation.
    Frances F Diehl, Teemu P Miettinen, Ryan Elbashir, Christopher S Nabel, Alicia M Darnell, Brian T Do, Scott R Manalis, Caroline A Lewis, Matthew G Vander Heiden.
      Nucleotide metabolism supports RNA synthesis and DNA replication to enable cell growth and division. Nucleotide depletion can inhibit cell growth and proliferation, but how cells sense and respond to changes in the relative levels of individual nucleotides is unclear. Moreover, the nucleotide requirement for biomass production changes over the course of the cell cycle, and how cells coordinate differential nucleotide demands with cell cycle progression is not well understood. Here we find that excess levels of individual nucleotides can inhibit proliferation by disrupting the relative levels of nucleotide bases needed for DNA replication and impeding DNA replication. The resulting purine and pyrimidine imbalances are not sensed by canonical growth regulatory pathways like mTORC1, Akt and AMPK signalling cascades, causing excessive cell growth despite inhibited proliferation. Instead, cells rely on replication stress signalling to survive during, and recover from, nucleotide imbalance during S phase. We find that ATR-dependent replication stress signalling is activated during unperturbed S phases and promotes nucleotide availability to support DNA replication. Together, these data reveal that imbalanced nucleotide levels are not detected until S phase, rendering cells reliant on replication stress signalling to cope with this metabolic problem and disrupting the coordination of cell growth and division.
    DOI:  https://doi.org/10.1038/s41556-022-00965-1
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