bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022–08–14
27 papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. Pyramidal neuron subtype diversity governs microglia states in the neocortex.
  2. IFN-γ stimulated murine and human neurons mount anti-parasitic defenses against the intracellular parasite Toxoplasma gondii.
  3. Prokaryotic innate immunity through pattern recognition of conserved viral proteins.
  4. Blocking ActRIIB and restoring appetite reverses cachexia and improves survival in mice with lung cancer.
  5. Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish.
  6. Competition between hematopoietic stem and progenitor cells controls hematopoietic stem cell compartment size.
  7. Loss of heat shock factor 1 promotes hepatic stellate cell activation and drives liver fibrosis.
  8. Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells.
  9. Microbe capture by splenic macrophages triggers sepsis via T cell-death-dependent neutrophil lifespan shortening.
  10. A Bcl6 Intronic Element Regulates T Follicular Helper Cell Differentiation.
  11. Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes.
  12. Generation of T-cell-receptor-negative CD8αβ-positive CAR T cells from T-cell-derived induced pluripotent stem cells.
  13. The MARCHF6 E3 ubiquitin ligase acts as an NADPH sensor for the regulation of ferroptosis.
  14. A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states.
  15. MYC sensitises cells to apoptosis by driving energetic demand.
  16. High-throughput sequencing analysis of nuclear-encoded mitochondrial genes reveals a genetic signature of human longevity.
  17. The Mitochondrial NAD Kinase Functions as a Major Metabolic Regulator Upon Increased Energy Demand.
  18. SEMA7AR148W mutation promotes lipid accumulation and NAFLD progression via increased localization on the hepatocyte surface.
  19. Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.
  20. A single-cell atlas of the multicellular ecosystem of primary and metastatic hepatocellular carcinoma.
  21. Lipid droplets promote efficient mitophagy.
  22. Neutrophils restrain sepsis associated coagulopathy via extracellular vesicles carrying superoxide dismutase 2 in a murine model of lipopolysaccharide induced sepsis.
  23. Neuroinflammation inhibition by small-molecule targeting USP7 noncatalytic domain for neurodegenerative disease therapy.
  24. The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCRβ and TCRα Genes and Influences Development of αβ T Cell Lineages.
  25. The psychiatric risk gene BRD1 modulates mitochondrial bioenergetics by transcriptional regulation.
  26. Cyclic nucleotide-induced helical structure activates a TIR immune effector.
  27. PD-1 blockade following ART interruption enhances control of pathogenic SIV in rhesus macaques.
  1. Nature. 2022 Aug 10.
    Pyramidal neuron subtype diversity governs microglia states in the neocortex.
    Jeffrey A Stogsdill, Kwanho Kim, Loïc Binan, Samouil L Farhi, Joshua Z Levin, Paola Arlotta.
      Microglia are specialized macrophages in the brain parenchyma that exist in multiple transcriptional states and reside within a wide range of neuronal environments1-4. However, how and where these states are generated remains poorly understood. Here, using the mouse somatosensory cortex, we demonstrate that microglia density and molecular state acquisition are determined by the local composition of pyramidal neuron classes. Using single-cell and spatial transcriptomic profiling, we unveil the molecular signatures and spatial distributions of diverse microglia populations and show that certain states are enriched in specific cortical layers, whereas others are broadly distributed throughout the cortex. Notably, conversion of deep-layer pyramidal neurons to an alternate class identity reconfigures the distribution of local, layer-enriched homeostatic microglia to match the new neuronal niche. Leveraging the transcriptional diversity of pyramidal neurons in the neocortex, we construct a ligand-receptor atlas describing interactions between individual pyramidal neuron subtypes and microglia states, revealing rules of neuron-microglia communication. Our findings uncover a fundamental role for neuronal diversity in instructing the acquisition of microglia states as a potential mechanism for fine-tuning neuroimmune interactions within the cortical local circuitry.
    DOI:  https://doi.org/10.1038/s41586-022-05056-7
  2. Nat Commun. 2022 Aug 08. 13(1): 4605
    IFN-γ stimulated murine and human neurons mount anti-parasitic defenses against the intracellular parasite Toxoplasma gondii.
    Sambamurthy Chandrasekaran, Joshua A Kochanowsky, Emily F Merritt, Joseph S Lagas, Ayesha Swannigan, Anita A Koshy.
      Dogma holds that Toxoplasma gondii persists in neurons because neurons cannot clear intracellular parasites, even with IFN-γ stimulation. As several recent studies questioned this idea, here we use primary murine neuronal cultures from wild type and transgenic mice in combination with IFN-γ stimulation and parental and transgenic parasites to reassess IFN-γ dependent neuronal clearance of intracellular parasites. We find that neurons respond to IFN-γ and that a subset of neurons clear intracellular parasites via immunity regulated GTPases. Whole neuron reconstructions from mice infected with parasites that trigger neuron GFP expression only after full invasion reveal that ~50% of these T. gondii-invaded neurons no longer harbor parasites. Finally, IFN-γ stimulated human pluripotent stem cell derived neurons show an ~50% decrease in parasite infection rate when compared to unstimulated cultures. This work highlights the capability of human and murine neurons to mount cytokine-dependent anti-T. gondii defense mechanisms in vitro and in vivo.
    DOI:  https://doi.org/10.1038/s41467-022-32225-z
  3. Science. 2022 Aug 12. 377(6607): eabm4096
    Prokaryotic innate immunity through pattern recognition of conserved viral proteins.
    Linyi Alex Gao, Max E Wilkinson, Jonathan Strecker, Kira S Makarova, Rhiannon K Macrae, Eugene V Koonin, Feng Zhang.
      Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain-like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo-electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.
    DOI:  https://doi.org/10.1126/science.abm4096
  4. Nat Commun. 2022 Aug 08. 13(1): 4633
    Blocking ActRIIB and restoring appetite reverses cachexia and improves survival in mice with lung cancer.
    Andre Lima Queiroz, Ezequiel Dantas, Shakti Ramsamooj, Anirudh Murthy, Mujmmail Ahmed, Elizabeth R M Zunica, Roger J Liang, Jessica Murphy, Corey D Holman, Curtis J Bare, Gregory Ghahramani, Zhidan Wu, David E Cohen, John P Kirwan, Lewis C Cantley, Christopher L Axelrod, Marcus D Goncalves.
      Cancer cachexia is a common, debilitating condition with limited therapeutic options. Using an established mouse model of lung cancer, we find that cachexia is characterized by reduced food intake, spontaneous activity, and energy expenditure accompanied by muscle metabolic dysfunction and atrophy. We identify Activin A as a purported driver of cachexia and treat with ActRIIB-Fc, a decoy ligand for TGF-β/activin family members, together with anamorelin (Ana), a ghrelin receptor agonist, to reverse muscle dysfunction and anorexia, respectively. Ana effectively increases food intake but only the combination of drugs increases lean mass, restores spontaneous activity, and improves overall survival. These beneficial effects are limited to female mice and are dependent on ovarian function. In agreement, high expression of Activin A in human lung adenocarcinoma correlates with unfavorable prognosis only in female patients, despite similar expression levels in both sexes. This study suggests that multimodal, sex-specific, therapies are needed to reverse cachexia.
    DOI:  https://doi.org/10.1038/s41467-022-32135-0
  5. J Exp Med. 2022 Sep 05. pii: e20220038. [Epub ahead of print]219(9):
    Single-cell analyses reveal early thymic progenitors and pre-B cells in zebrafish.
    Sara A Rubin, Chloé S Baron, Cecilia Pessoa Rodrigues, Madeleine Duran, Alexandra F Corbin, Song P Yang, Cole Trapnell, Leonard I Zon.
      The zebrafish has proven to be a valuable model organism for studying hematopoiesis, but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single-cell RNA sequencing on ∼70,000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus, elucidated B- and T-cell developmental trajectories, and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic-like cell populations and provided evidence in support of the existence of a pre-B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies.
    DOI:  https://doi.org/10.1084/jem.20220038
  6. Nat Commun. 2022 Aug 08. 13(1): 4611
    Competition between hematopoietic stem and progenitor cells controls hematopoietic stem cell compartment size.
    Runfeng Miao, Harim Chun, Xing Feng, Ana Cordeiro Gomes, Jungmin Choi, João P Pereira.
      Cellular competition for limiting hematopoietic factors is a physiologically regulated but poorly understood process. Here, we studied this phenomenon by hampering hematopoietic progenitor access to Leptin receptor+ mesenchymal stem/progenitor cells (MSPCs) and endothelial cells (ECs). We show that HSC numbers increase by 2-fold when multipotent and lineage-restricted progenitors fail to respond to CXCL12 produced by MSPCs and ECs. HSCs are qualitatively normal, and HSC expansion only occurs when early hematopoietic progenitors but not differentiated hematopoietic cells lack CXCR4. Furthermore, the MSPC and EC transcriptomic heterogeneity is stable, suggesting that it is impervious to major changes in hematopoietic progenitor interactions. Instead, HSC expansion correlates with increased availability of membrane-bound stem cell factor (mSCF) on MSPCs and ECs presumably due to reduced consumption by cKit-expressing hematopoietic progenitors. These studies suggest that an intricate homeostatic balance between HSCs and proximal hematopoietic progenitors is regulated by cell competition for limited amounts of mSCF.
    DOI:  https://doi.org/10.1038/s41467-022-32228-w
  7. Hepatol Commun. 2022 Aug 09.
    Loss of heat shock factor 1 promotes hepatic stellate cell activation and drives liver fibrosis.
    Asmita Choudhury, Anuradha Ratna, Arlene Lim, Rebecca M Sebastian, Christopher L Moore, Aveline A Filliol, Jacob Bledsoe, Chengkai Dai, Robert F Schwabe, Matthew D Shoulders, Pranoti Mandrekar.
      Liver fibrosis is an aberrant wound healing response that results from chronic injury and is mediated by hepatocellular death and activation of hepatic stellate cells (HSCs). While induction of oxidative stress is well established in fibrotic livers, there is limited information on stress-mediated mechanisms of HSC activation. Cellular stress triggers an adaptive defense mechanism via master protein homeostasis regulator, heat shock factor 1 (HSF1), which induces heat shock proteins to respond to proteotoxic stress. Although the importance of HSF1 in restoring cellular homeostasis is well-established, its potential role in liver fibrosis is unknown. Here, we show that HSF1 messenger RNA is induced in human cirrhotic and murine fibrotic livers. Hepatocytes exhibit nuclear HSF1, whereas stellate cells expressing alpha smooth muscle actin do not express nuclear HSF1 in human cirrhosis. Interestingly, despite nuclear HSF1, murine fibrotic livers did not show induction of HSF1 DNA binding activity compared with controls. HSF1-deficient mice exhibit augmented HSC activation and fibrosis despite limited pro-inflammatory cytokine response and display delayed fibrosis resolution. Stellate cell and hepatocyte-specific HSF1 knockout mice exhibit higher induction of profibrogenic response, suggesting an important role for HSF1 in HSC activation and fibrosis. Stable expression of dominant negative HSF1 promotes fibrogenic activation of HSCs. Overactivation of HSF1 decreased phosphorylation of JNK and prevented HSC activation, supporting a protective role for HSF1. Our findings identify an unconventional role for HSF1 in liver fibrosis. Conclusion: Our results show that deficiency of HSF1 is associated with exacerbated HSC activation promoting liver fibrosis, whereas activation of HSF1 prevents profibrogenic HSC activation.
    DOI:  https://doi.org/10.1002/hep4.2058
  8. Nat Commun. 2022 Aug 11. 13(1): 4724
    Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells.
    M Kyle Cromer, Valentin V Barsan, Erich Jaeger, Mengchi Wang, Jessica P Hampton, Feng Chen, Drew Kennedy, Jenny Xiao, Irina Khrebtukova, Ana Granat, Tiffany Truong, Matthew H Porteus.
      As CRISPR-based therapies enter the clinic, evaluation of safety remains a critical and active area of study. Here, we employ a clinical next generation sequencing (NGS) workflow to achieve high sequencing depth and detect ultra-low frequency variants across exons of genes associated with cancer, all exons, and genome wide. In three separate primary human hematopoietic stem and progenitor cell (HSPC) donors assessed in technical triplicates, we electroporated high-fidelity Cas9 protein targeted to three loci (AAVS1, HBB, and ZFPM2) and harvested genomic DNA at days 4 and 10. Our results demonstrate that clinically relevant delivery of high-fidelity Cas9 to primary HSPCs and ex vivo culture up to 10 days does not introduce or enrich for tumorigenic variants and that even a single SNP in a gRNA spacer sequence is sufficient to eliminate Cas9 off-target activity in primary, repair-competent human HSPCs.
    DOI:  https://doi.org/10.1038/s41467-022-32233-z
  9. Nat Commun. 2022 Aug 09. 13(1): 4658
    Microbe capture by splenic macrophages triggers sepsis via T cell-death-dependent neutrophil lifespan shortening.
    Marianna Ioannou, Dennis Hoving, Iker Valle Aramburu, Mia I Temkin, Nathalia M De Vasconcelos, Theodora-Dorita Tsourouktsoglou, Qian Wang, Stefan Boeing, Robert Goldstone, Spyros Vernardis, Vadim Demichev, Markus Ralser, Sascha David, Klaus Stahl, Christian Bode, Venizelos Papayannopoulos.
      The mechanisms linking systemic infection to hyperinflammation and immune dysfunction in sepsis are poorly understood. Extracellular histones promote sepsis pathology, but their source and mechanism of action remain unclear. Here, we show that by controlling fungi and bacteria captured by splenic macrophages, neutrophil-derived myeloperoxidase attenuates sepsis by suppressing histone release. In systemic candidiasis, microbial capture via the phagocytic receptor SIGNR1 neutralizes myeloperoxidase by facilitating marginal zone infiltration and T cell death-dependent histone release. Histones and hyphae induce cytokines in adjacent CD169 macrophages including G-CSF that selectively depletes mature Ly6Ghigh neutrophils by shortening their lifespan in favour of immature Ly6Glow neutrophils with a defective oxidative burst. In sepsis patient plasma, these mediators shorten mature neutrophil lifespan and correlate with neutrophil mortality markers. Consequently, high G-CSF levels and neutrophil lifespan shortening activity are associated with sepsis patient mortality. Hence, by exploiting phagocytic receptors, pathogens degrade innate and adaptive immunity through the detrimental impact of downstream effectors on neutrophil lifespan.
    DOI:  https://doi.org/10.1038/s41467-022-32320-1
  10. J Immunol. 2022 Aug 10. pii: ji2100777. [Epub ahead of print]
    A Bcl6 Intronic Element Regulates T Follicular Helper Cell Differentiation.
    Chen-Yen Lai, Nimi Marcel, Allen W Yaldiko, Arnaud Delpoux, Stephen M Hedrick.
      In response to an intracellular infectious agent, the immune system produces a specific cellular response as well as a T cell-dependent Ab response. Precursor T cells differentiate into effector T cells, including Th1 cells, and T follicular helper (TFH) cells. The latter cooperate with B cells to form germinal centers and induce the formation of Ab-forming plasmacytes. One major focal point for control of T cell differentiation is the transcription factor BCL6. In this study, we demonstrated that the Bcl6 gene is regulated by FOXO1-binding, cis-acting sequences located in a highly conserved region of the first Bcl6 intron. In both mouse and human T cells, deletion of the tandem FOXO1 binding sites increased the expression of BCL6 and enhanced the proportion of TFH cells. These results reveal a fundamental control point for cellular versus humoral immunity.
    DOI:  https://doi.org/10.4049/jimmunol.2100777
  11. Genome Biol. 2022 Aug 09. 23(1): 170
    Balanced mitochondrial and cytosolic translatomes underlie the biogenesis of human respiratory complexes.
    Iliana Soto, Mary Couvillion, Katja G Hansen, Erik McShane, J Conor Moran, Antoni Barrientos, L Stirling Churchman.
       BACKGROUND: Oxidative phosphorylation (OXPHOS) complexes consist of nuclear and mitochondrial DNA-encoded subunits. Their biogenesis requires cross-compartment gene regulation to mitigate the accumulation of disproportionate subunits. To determine how human cells coordinate mitochondrial and nuclear gene expression processes, we tailored ribosome profiling for the unique features of the human mitoribosome.
    RESULTS: We resolve features of mitochondrial translation initiation and identify a small ORF in the 3' UTR of MT-ND5. Analysis of ribosome footprints in five cell types reveals that average mitochondrial synthesis levels correspond precisely to cytosolic levels across OXPHOS complexes, and these average rates reflect the relative abundances of the complexes. Balanced mitochondrial and cytosolic synthesis does not rely on rapid feedback between the two translation systems, and imbalance caused by mitochondrial translation deficiency is associated with the induction of proteotoxicity pathways.
    CONCLUSIONS: Based on our findings, we propose that human OXPHOS complexes are synthesized proportionally to each other, with mitonuclear balance relying on the regulation of OXPHOS subunit translation across cellular compartments, which may represent a proteostasis vulnerability.
    DOI:  https://doi.org/10.1186/s13059-022-02732-9
  12. Nat Biomed Eng. 2022 Aug 08.
    Generation of T-cell-receptor-negative CD8αβ-positive CAR T cells from T-cell-derived induced pluripotent stem cells.
    Sjoukje J C van der Stegen, Pieter L Lindenbergh, Roseanna M Petrovic, Hongyao Xie, Mame P Diop, Vera Alexeeva, Yuzhe Shi, Jorge Mansilla-Soto, Mohamad Hamieh, Justin Eyquem, Annalisa Cabriolu, Xiuyan Wang, Ramzey Abujarour, Tom Lee, Raedun Clarke, Bahram Valamehr, Maria Themeli, Isabelle Riviere, Michel Sadelain.
      The production of autologous T cells expressing a chimaeric antigen receptor (CAR) is time-consuming, costly and occasionally unsuccessful. T-cell-derived induced pluripotent stem cells (TiPS) are a promising source for the generation of 'off-the-shelf' CAR T cells, but the in vitro differentiation of TiPS often yields T cells with suboptimal features. Here we show that the premature expression of the T-cell receptor (TCR) or a constitutively expressed CAR in TiPS promotes the acquisition of an innate phenotype, which can be averted by disabling the TCR and relying on the CAR to drive differentiation. Delaying CAR expression and calibrating its signalling strength in TiPS enabled the generation of human TCR- CD8αβ+ CAR T cells that perform similarly to CD8αβ+ CAR T cells from peripheral blood, achieving effective tumour control on systemic administration in a mouse model of leukaemia and without causing graft-versus-host disease. Driving T-cell maturation in TiPS in the absence of a TCR by taking advantage of a CAR may facilitate the large-scale development of potent allogeneic CD8αβ+ T cells for a broad range of immunotherapies.
    DOI:  https://doi.org/10.1038/s41551-022-00915-0
  13. Nat Cell Biol. 2022 Aug;24(8): 1239-1251
    The MARCHF6 E3 ubiquitin ligase acts as an NADPH sensor for the regulation of ferroptosis.
    Kha The Nguyen, Sang-Hyeon Mun, Jihye Yang, Jongeun Lee, Ok-Hee Seok, Eunjeong Kim, Dasom Kim, So Young An, Dong-Young Seo, Jeong-Yong Suh, Yoontae Lee, Cheol-Sang Hwang.
      Ferroptosis is a unique form of cell death caused by excessive iron-dependent lipid peroxidation. The level of the anabolic reductant NADPH is a biomarker of ferroptosis sensitivity. However, specific regulators that detect cellular NADPH levels, thereby modulating downstream ferroptosis cascades, are largely unknown. We show here that the transmembrane endoplasmic reticulum MARCHF6 E3 ubiquitin ligase recognizes NADPH through its C-terminal regulatory region. This interaction upregulates the E3 ligase activity of MARCHF6, thus downregulating ferroptosis. We also found that MARCHF6 mediates the degradation of the key ferroptosis effectors ACSL4 and p53. Furthermore, inhibiting ferroptosis rescued the growth of MARCHF6-deficient tumours and peri-natal lethality of Marchf6-/- mice. Together, these findings identify MARCHF6 as a previously unknown NADPH sensor in the ubiquitin system and a crucial regulator of ferroptosis.
    DOI:  https://doi.org/10.1038/s41556-022-00973-1
  14. Nat Neurosci. 2022 Aug 11.
    A CRISPRi/a platform in human iPSC-derived microglia uncovers regulators of disease states.
    Nina M Dräger, Sydney M Sattler, Cindy Tzu-Ling Huang, Olivia M Teter, Kun Leng, Sayed Hadi Hashemi, Jason Hong, Giovanni Aviles, Claire D Clelland, Lihong Zhan, Joe C Udeochu, Lay Kodama, Andrew B Singleton, Mike A Nalls, Justin Ichida, Michael E Ward, Faraz Faghri, Li Gan, Martin Kampmann.
      Microglia are emerging as key drivers of neurological diseases. However, we lack a systematic understanding of the underlying mechanisms. Here, we present a screening platform to systematically elucidate functional consequences of genetic perturbations in human induced pluripotent stem cell-derived microglia. We developed an efficient 8-day protocol for the generation of microglia-like cells based on the inducible expression of six transcription factors. We established inducible CRISPR interference and activation in this system and conducted three screens targeting the 'druggable genome'. These screens uncovered genes controlling microglia survival, activation and phagocytosis, including neurodegeneration-associated genes. A screen with single-cell RNA sequencing as the readout revealed that these microglia adopt a spectrum of states mirroring those observed in human brains and identified regulators of these states. A disease-associated state characterized by osteopontin (SPP1) expression was selectively depleted by colony-stimulating factor-1 (CSF1R) inhibition. Thus, our platform can systematically uncover regulators of microglial states, enabling their functional characterization and therapeutic targeting.
    DOI:  https://doi.org/10.1038/s41593-022-01131-4
  15. Nat Commun. 2022 Aug 09. 13(1): 4674
    MYC sensitises cells to apoptosis by driving energetic demand.
    Joy Edwards-Hicks, Huizhong Su, Maurizio Mangolini, Kubra K Yoneten, Jimi Wills, Giovanny Rodriguez-Blanco, Christine Young, Kevin Cho, Heather Barker, Morwenna Muir, Ania Naila Guerrieri, Xue-Feng Li, Rachel White, Piotr Manasterski, Elena Mandrou, Karen Wills, Jingyu Chen, Emily Abraham, Kianoosh Sateri, Bin-Zhi Qian, Peter Bankhead, Mark Arends, Noor Gammoh, Alex von Kriegsheim, Gary J Patti, Andrew H Sims, Juan Carlos Acosta, Valerie Brunton, Kamil R Kranc, Maria Christophorou, Erika L Pearce, Ingo Ringshausen, Andrew J Finch.
      The MYC oncogene is a potent driver of growth and proliferation but also sensitises cells to apoptosis, which limits its oncogenic potential. MYC induces several biosynthetic programmes and primary cells overexpressing MYC are highly sensitive to glutamine withdrawal suggesting that MYC-induced sensitisation to apoptosis may be due to imbalance of metabolic/energetic supply and demand. Here we show that MYC elevates global transcription and translation, even in the absence of glutamine, revealing metabolic demand without corresponding supply. Glutamine withdrawal from MRC-5 fibroblasts depletes key tricarboxylic acid (TCA) cycle metabolites and, in combination with MYC activation, leads to AMP accumulation and nucleotide catabolism indicative of energetic stress. Further analyses reveal that glutamine supports viability through TCA cycle energetics rather than asparagine biosynthesis and that TCA cycle inhibition confers tumour suppression on MYC-driven lymphoma in vivo. In summary, glutamine supports the viability of MYC-overexpressing cells through an energetic rather than a biosynthetic mechanism.
    DOI:  https://doi.org/10.1038/s41467-022-32368-z
  16. Geroscience. 2022 Aug 10.
    High-throughput sequencing analysis of nuclear-encoded mitochondrial genes reveals a genetic signature of human longevity.
    Brenda Gonzalez, Archana Tare, Seungjin Ryu, Simon C Johnson, Gil Atzmon, Nir Barzilai, Matt Kaeberlein, Yousin Suh.
      Mitochondrial dysfunction is a well-known contributor to aging and age-related diseases. The precise mechanisms through which mitochondria impact human lifespan, however, remain unclear. We hypothesize that humans with exceptional longevity harbor rare variants in nuclear-encoded mitochondrial genes (mitonuclear genes) that confer resistance against age-related mitochondrial dysfunction. Here we report an integrated functional genomics study to identify rare functional variants in ~ 660 mitonuclear candidate genes discovered by target capture sequencing analysis of 496 centenarians and 572 controls of Ashkenazi Jewish descent. We identify and prioritize longevity-associated variants, genes, and mitochondrial pathways that are enriched with rare variants. We provide functional gene variants such as those in MTOR (Y2396Lfs*29), CPS1 (T1406N), and MFN2 (G548*) as well as LRPPRC (S1378G) that is predicted to affect mitochondrial translation. Taken together, our results suggest a functional role for specific mitonuclear genes and pathways in human longevity.
    Keywords:  Aging; Centenarian; Genetic variant; Longevity; Mitochondria
    DOI:  https://doi.org/10.1007/s11357-022-00634-z
  17. Mol Metab. 2022 Aug 06. pii: S2212-8778(22)00131-4. [Epub ahead of print] 101562
    The Mitochondrial NAD Kinase Functions as a Major Metabolic Regulator Upon Increased Energy Demand.
    Hyunbae Kim, Zhiyao Fu, Zhao Yang, Zhenfeng Song, El Hussain Shamsa, Thangal Yumnamcha, Shengyi Sun, Wanqing Liu, Ahmed S Ibrahim, Nathan R Qi, Ren Zhang, Kezhong Zhang.
      The mitochondrial nicotinamide adenine dinucleotide (NAD) kinase (MNADK) mediates de novo mitochondrial NADP biosynthesis by catalyzing the phosphorylation of NAD to yield NADP. In this study, we investigated the function and mechanistic basis by which MNADK regulates metabolic homeostasis. Generalized gene-set analysis by aggregating human patient genomic databases indicated that human MNADK common gene variants or decreased expression of the gene are significantly associated with the occurrence of type-2 diabetes, non-alcoholic fatty liver disease (NAFLD), or hepatocellular carcinoma (HCC). Ablation of the MNADK gene in mice led to decreased fat oxidation, coincident with increased respiratory exchange ratio (RER) and decreased energy expenditure upon energy demand triggered by endurance exercise or fasting. On an atherogenic high-fat diet (HFD), MNADK-null mice exhibited hepatic insulin resistance and glucose intolerance, indicating a type-2 diabetes-like phenotype in the absence of MNADK. Further investigation revealed that MNADK deficiency led to a decrease in mitochondrial NADP(H) but an increase in cellular reactive oxygen species (ROS) in mouse livers. Consistently, protein levels of the major metabolic regulators or enzymes were decreased, while their acetylation modifications were increased in the livers of MNADK-null mice. Further, feeding mice with a HFD caused S-nitrosylation (SNO) modification, a posttranslational modification that represses protein activities, on MNADK protein in the liver. Reconstitution of an SNO-resistant MNADK variant, MNADK-S193, into MNADK-null mice mitigated hepatic steatosis induced by HFD. In summary, our studies define that MNADK, the only known mammalian mitochondrial NAD kinase, plays important roles in preserving energy homeostasis to mitigate the risk of metabolic disorders.
    DOI:  https://doi.org/10.1016/j.molmet.2022.101562
  18. JCI Insight. 2022 Aug 08. pii: e154113. [Epub ahead of print]7(15):
    SEMA7AR148W mutation promotes lipid accumulation and NAFLD progression via increased localization on the hepatocyte surface.
    Nan Zhao, Xiaoxun Zhang, Jingjing Ding, Qiong Pan, Ming-Hua Zheng, Wen-Yue Liu, Gang Luo, Jiaquan Qu, Mingqiao Li, Ling Li, Ying Cheng, Ying Peng, Qiaoling Xie, Qinglin Wei, Qiao Li, Lingyun Zou, Xinshou Ouyang, Shi-Ying Cai, James L Boyer, Jin Chai.
      Genetic polymorphisms are associated with the development of nonalcoholic fatty liver disease (NAFLD). Semaphorin7a (Sema7a) deficiency in mouse peritoneal macrophages reduces fatty acid (FA) oxidation. Here, we identified 17 individuals with SEMA7A heterozygous mutations in 470 patients with biopsy-proven NAFLD. SEMA7A heterozygous mutations increased susceptibility to NAFLD, steatosis severity, and NAFLD activity scores in humans and mice. The Sema7aR145W mutation (equivalent to human SEMA7AR148W) significantly induced small lipid droplet accumulation in mouse livers compared with WT mouse livers. Mechanistically, the Sema7aR145W mutation increased N-glycosylated Sema7a and its receptor integrin β1 proteins in the cell membranes of hepatocytes. Furthermore, Sema7aR145W mutation enhanced its protein interaction with integrin β1 and PKC-α and increased PKC-α phosphorylation, which were both abrogated by integrin β1 silencing. Induction of PKCα_WT, but not PKCα_dominant negative, overexpression induced transcriptional factors Srebp1, Chrebp, and Lxr expression and their downstream Acc1, Fasn, and Cd36 expression in primary mouse hepatocytes. Collectively, our findings demonstrate that the SEMA7AR148W mutation is a potentially new strong genetic determinant of NAFLD and promotes intrahepatic lipid accumulation and NAFLD in mice by enhancing PKC-α-stimulated FA and triglyceride synthesis and FA uptake. The inhibition of hepatic PKC-α signaling may lead to novel NAFLD therapies.
    Keywords:  Genetic variation; Hepatology; Metabolism; Molecular biology; Mouse models
    DOI:  https://doi.org/10.1172/jci.insight.154113
  19. Nat Commun. 2022 Aug 11. 13(1): 4521
    Transcription-coupled and epigenome-encoded mechanisms direct H3K4 methylation.
    Satoyo Oya, Mayumi Takahashi, Kazuya Takashima, Tetsuji Kakutani, Soichi Inagaki.
      Mono-, di-, and trimethylation of histone H3 lysine 4 (H3K4me1/2/3) are associated with transcription, yet it remains controversial whether H3K4me1/2/3 promote or result from transcription. Our previous characterizations of Arabidopsis H3K4 demethylases suggest roles for H3K4me1 in transcription. However, the control of H3K4me1 remains unexplored in Arabidopsis, in which no methyltransferase for H3K4me1 has been identified. Here, we identify three Arabidopsis methyltransferases that direct H3K4me1. Analyses of their genome-wide localization using ChIP-seq and machine learning reveal that one of the enzymes cooperates with the transcription machinery, while the other two are associated with specific histone modifications and DNA sequences. Importantly, these two types of localization patterns are also found for the other H3K4 methyltransferases in Arabidopsis and mice. These results suggest that H3K4me1/2/3 are established and maintained via interplay with transcription as well as inputs from other chromatin features, presumably enabling elaborate gene control.
    DOI:  https://doi.org/10.1038/s41467-022-32165-8
  20. Nat Commun. 2022 Aug 06. 13(1): 4594
    A single-cell atlas of the multicellular ecosystem of primary and metastatic hepatocellular carcinoma.
    Yiming Lu, Aiqing Yang, Cheng Quan, Yingwei Pan, Haoyun Zhang, Yuanfeng Li, Chengming Gao, Hao Lu, Xueting Wang, Pengbo Cao, Hongxia Chen, Shichun Lu, Gangqiao Zhou.
      Hepatocellular carcinoma (HCC) represents a paradigm of the relation between tumor microenvironment (TME) and tumor development. Here, we generate a single-cell atlas of the multicellular ecosystem of HCC from four tissue sites. We show the enrichment of central memory T cells (TCM) in the early tertiary lymphoid structures (E-TLSs) in HCC and assess the relationships between chronic HBV/HCV infection and T cell infiltration and exhaustion. We find the MMP9+ macrophages to be terminally differentiated tumor-associated macrophages (TAMs) and PPARγ to be the pivotal transcription factor driving their differentiation. We also characterize the heterogeneous subpopulations of malignant hepatocytes and their multifaceted functions in shaping the immune microenvironment of HCC. Finally, we identify seven microenvironment-based subtypes that can predict prognosis of HCC patients. Collectively, this large-scale atlas deepens our understanding of the HCC microenvironment, which might facilitate the development of new immune therapy strategies for this malignancy.
    DOI:  https://doi.org/10.1038/s41467-022-32283-3
  21. Autophagy. 2022 Aug 08. 1-2
    Lipid droplets promote efficient mitophagy.
    Maeve Long, Thomas G McWilliams.
      Mitophagy neutralizes defective mitochondria via lysosomal elimination. Increased levels of mitophagy hallmark metabolic transitions and are induced by iron depletion, yet its metabolic basis has not been studied in-depth. How mitophagy integrates with different homeostatic mechanisms to support metabolic integrity is incompletely understood. We examined metabolic adaptations in cells treated with deferiprone (DFP), a therapeutic iron chelator known to induce PINK1-PRKN-independent mitophagy. We found that iron depletion profoundly rewired the cellular metabolome, remodeling lipid metabolism within minutes of treatment. DGAT1-dependent lipid droplet biosynthesis occurs upstream of mitochondrial turnover, with many LDs bordering mitochondria upon iron chelation. Surprisingly, DGAT1 inhibition restricts mitophagy in vitro by lysosomal dysfunction. Genetic depletion of mdy/DGAT1 in vivo impairs neuronal mitophagy and locomotor function in Drosophila, demonstrating the physiological relevance of our findings.
    Keywords:  DGAT1; iron; lipid droplet; metabolism; mitophagy
    DOI:  https://doi.org/10.1080/15548627.2022.2089956
  22. Nat Commun. 2022 Aug 06. 13(1): 4583
    Neutrophils restrain sepsis associated coagulopathy via extracellular vesicles carrying superoxide dismutase 2 in a murine model of lipopolysaccharide induced sepsis.
    Wenjie Bao, Huayue Xing, Shiwei Cao, Xin Long, Haifeng Liu, Junwei Ma, Fan Guo, Zimu Deng, Xiaolong Liu.
      Disseminated intravascular coagulation (DIC) is a complication of sepsis currently lacking effective therapeutic options. Excessive inflammatory responses are emerging triggers of coagulopathy during sepsis, but the interplay between the immune system and coagulation are not fully understood. Here we utilize a murine model of intraperitoneal lipopolysaccharide stimulation and show neutrophils in the circulation mitigate the occurrence of DIC, preventing subsequent septic death. We show circulating neutrophils release extracellular vesicles containing mitochondria, which contain superoxide dismutase 2 upon exposure to lipopolysaccharide. Extracellular superoxide dismutase 2 is necessary to induce neutrophils' antithrombotic function by preventing endothelial reactive oxygen species accumulation and alleviating endothelial dysfunction. Intervening endothelial reactive oxygen species accumulation by antioxidants significantly ameliorates disseminated intravascular coagulation improving survival in this murine model of lipopolysaccharide challenge. These findings reveal an interaction between neutrophils and vascular endothelium which critically regulate coagulation in a model of sepsis and may have potential implications for the management of disseminated intravascular coagulation.
    DOI:  https://doi.org/10.1038/s41467-022-32325-w
  23. Sci Adv. 2022 Aug 12. 8(32): eabo0789
    Neuroinflammation inhibition by small-molecule targeting USP7 noncatalytic domain for neurodegenerative disease therapy.
    Xiao-Wen Zhang, Na Feng, Yan-Chen Liu, Qiang Guo, Jing-Kang Wang, Yi-Zhen Bai, Xiao-Ming Ye, Zhuo Yang, Heng Yang, Yang Liu, Mi-Mi Yang, Yan-Hang Wang, Xiao-Meng Shi, Dan Liu, Peng-Fei Tu, Ke-Wu Zeng.
      Neuroinflammation is a fundamental contributor to progressive neuronal damage, which arouses a heightened interest in neurodegenerative disease therapy. Ubiquitin-specific protease 7 (USP7) has a crucial role in regulating protein stability in multiple biological processes; however, the potential role of USP7 in neurodegenerative progression is poorly understood. Here, we discover the natural small molecule eupalinolide B (EB), which targets USP7 to inhibit microglia activation. Cocrystal structure reveals a previously undisclosed covalent allosteric site, Cys576, in a unique noncatalytic HUBL domain. By selectively modifying Cys576, EB allosterically inhibits USP7 to cause a ubiquitination-dependent degradation of Keap1. Keap1 function loss further results in an Nrf2-dependent transcription activation of anti-neuroinflammation genes in microglia. In vivo, pharmacological USP7 inhibition attenuates microglia activation and resultant neuron injury, thereby notably improving behavioral deficits in dementia and Parkinson's disease mouse models. Collectively, our findings provide an attractive future direction for neurodegenerative disease therapy by inhibiting microglia-mediated neuroinflammation by targeting USP7.
    DOI:  https://doi.org/10.1126/sciadv.abo0789
  24. J Immunol. 2022 Aug 10. pii: ji2001441. [Epub ahead of print]
    The RAG1 Ubiquitin Ligase Domain Stimulates Recombination of TCRβ and TCRα Genes and Influences Development of αβ T Cell Lineages.
    Thomas N Burn, Charline Miot, Scott M Gordon, Erica J Culberson, Tamir Diamond, Portia A Kreiger, Katharina E Hayer, Anamika Bhattacharyya, Jessica M Jones, Craig H Bassing, Edward M Behrens.
      RAG1/RAG2 (RAG) endonuclease-mediated assembly of diverse lymphocyte Ag receptor genes by V(D)J recombination is critical for the development and immune function of T and B cells. The RAG1 protein contains a ubiquitin ligase domain that stabilizes RAG1 and stimulates RAG endonuclease activity in vitro. We report in this study that mice with a mutation that inactivates the Rag1 ubiquitin ligase in vitro exhibit decreased rearrangements and altered repertoires of TCRβ and TCRα genes in thymocytes and impaired thymocyte developmental transitions that require the assembly and selection of functional TCRβ and/or TCRα genes. These Rag1 mutant mice present diminished positive selection and superantigen-mediated negative selection of conventional αβ T cells, decreased genesis of invariant NK T lineage αβ T cells, and mature CD4+ αβ T cells with elevated autoimmune potential. Our findings reveal that the Rag1 ubiquitin ligase domain functions in vivo to stimulate TCRβ and TCRα gene recombination and influence differentiation of αβ T lineage cells, thereby establishing replete diversity of αβ TCRs and populations of αβ T cells while restraining generation of potentially autoreactive conventional αβ T cells.
    DOI:  https://doi.org/10.4049/jimmunol.2001441
  25. Transl Psychiatry. 2022 Aug 08. 12(1): 319
    The psychiatric risk gene BRD1 modulates mitochondrial bioenergetics by transcriptional regulation.
    Veerle Paternoster, Cagla Cömert, Louise Sand Kirk, Sanne Hage la Cour, Tue Fryland, Paula Fernandez-Guerra, Magnus Stougaard, Jens Randel Nyengaard, Per Qvist, Peter Bross, Anders Dupont Børglum, Jane Hvarregaard Christensen.
      Bromodomain containing 1 (BRD1) encodes an epigenetic regulator that controls the expression of genetic networks linked to mental illness. BRD1 is essential for normal brain development and its role in psychopathology has been demonstrated in genetic and preclinical studies. However, the neurobiology that bridges its molecular and neuropathological effects remains poorly explored. Here, using publicly available datasets, we find that BRD1 targets nuclear genes encoding mitochondrial proteins in cell lines and that modulation of BRD1 expression, irrespective of whether it is downregulation or upregulation of one or the other existing BRD1 isoforms (BRD1-L and BRD1-S), leads to distinct shifts in the expression profile of these genes. We further show that the expression of nuclear genes encoding mitochondrial proteins is negatively correlated with the expression of BRD1 mRNA during human brain development. In accordance, we identify the key gate-keeper of mitochondrial metabolism, Peroxisome proliferator-activated receptor (PPAR) among BRD1's co-transcription factors and provide evidence that BRD1 acts as a co-repressor of PPAR-mediated transcription. Lastly, when using quantitative PCR, mitochondria-targeted fluorescent probes, and the Seahorse XFe96 Analyzer, we demonstrate that modulation of BRD1 expression in cell lines alters mitochondrial physiology (mtDNA content and mitochondrial mass), metabolism (reducing power), and bioenergetics (among others, basal, maximal, and spare respiration) in an expression level- and isoform-dependent manner. Collectively, our data suggest that BRD1 is a transcriptional regulator of nuclear-encoded mitochondrial proteins and that disruption of BRD1's genomic actions alters mitochondrial functions. This may be the mechanism underlying the cellular and atrophic changes of neurons previously associated with BRD1 deficiency and suggests that mitochondrial dysfunction may be a possible link between genetic variation in BRD1 and psychopathology in humans.
    DOI:  https://doi.org/10.1038/s41398-022-02053-2
  26. Nature. 2022 Aug 10.
    Cyclic nucleotide-induced helical structure activates a TIR immune effector.
    Gaëlle Hogrel, Abbie Guild, Shirley Graham, Hannah Rickman, Sabine Grüschow, Quentin Bertrand, Laura Spagnolo, Malcolm F White.
      Cyclic nucleotide signalling is a key component of antiviral defence in all domains of life. Viral detection activates a nucleotide cyclase to generate a second messenger, resulting in activation of effector proteins. This is exemplified by the metazoan cGAS-STING innate immunity pathway1, which originated in bacteria2. These defence systems require a sensor domain to bind the cyclic nucleotide and are often coupled with an effector domain that, when activated, causes cell death by destroying essential biomolecules3. One example is the Toll/interleukin-1 receptor (TIR) domain, which degrades the essential cofactor NAD+ when activated in response to infection in plants and bacteria2,4,5 or during programmed nerve cell death6. Here we show that a bacterial antiviral defence system generates a cyclic tri-adenylate that binds to a TIR-SAVED effector, acting as the 'glue' to allow assembly of an extended superhelical solenoid structure. Adjacent TIR subunits interact to organize and complete a composite active site, allowing NAD+ degradation. Activation requires extended filament formation, both in vitro and in vivo. Our study highlights an example of large-scale molecular assembly controlled by cyclic nucleotides and reveals key details of the mechanism of TIR enzyme activation.
    DOI:  https://doi.org/10.1038/s41586-022-05070-9
  27. Proc Natl Acad Sci U S A. 2022 Aug 16. 119(33): e2202148119
    PD-1 blockade following ART interruption enhances control of pathogenic SIV in rhesus macaques.
    Vijayakumar Velu, Kehmia Titanji, Hasan Ahmed, Ravi Dyavar Shetty, Lakshmi S Chennareddi, Gordon J Freeman, Rafi Ahmed, Rama Rao Amara.
      Programmed death-1 (PD-1) blockade during chronic Simian immunodeficiency virus (SIV) infection results in restoration of CD8 T-cell function and enhances viral control. Here, we tested the therapeutic benefits of PD-1 blockade administered soon after anti-retrovial therapy (ART) interruption (ATI) by treating SIV-infected and ART-suppressed macaques with either an anti-PD-1 antibody (n = 7) or saline (n = 4) at 4 wk after ATI. Following ATI, the plasma viremia increased rapidly in all animals, and the frequency of SIV-specific CD8 T cells also increased in some animals. PD-1 blockade post ATI resulted in higher proliferation of total memory CD8 and CD4 T cells and natural killer cells. PD-1 blockade also resulted in higher proliferation of SIV-specific CD8 T cells and promoted their differentiation toward better functional quality. Importantly, four out of the seven anti-PD-1 antibody-treated animals showed a rapid decline in plasma viremia by 100- to 2300-fold and this was observed only in animals that showed measurable SIV-specific CD8 T cells post PD-1 blockade. These results demonstrate that PD-1 blockade following ATI can significantly improve the function of anti-viral CD8 T cells and enhance viral control and strongly suggests its potential synergy with other immunotherapies that induce functional CD8 T-cell response under ART. These results have important implications for HIV cure research.
    Keywords:  HIV; HIV cure; PD-1; SIV
    DOI:  https://doi.org/10.1073/pnas.2202148119
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