bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2023–04–02
sixty-two papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. Finding my way home.
  2. Age-dependent Pdgfrβ signaling drives adipocyte progenitor dysfunction to alter the beige adipogenic niche in male mice.
  3. The neuronal pentraxin Nptx2 regulates complement activity and restrains microglia-mediated synapse loss in neurodegeneration.
  4. Monocytes can proliferate in vacant niches before differentiation into macrophages.
  5. Structural insights into the mechanism of leptin receptor activation.
  6. VMP1 prevents Ca2+ overload in endoplasmic reticulum and maintains naive T cell survival.
  7. An aging, pathology burden, and glial senescence build-up hypothesis for late onset Alzheimer's disease.
  8. A neutrophil response linked to tumor control in immunotherapy.
  9. Hypothalamic melanin-concentrating hormone neurons integrate food-motivated appetitive and consummatory processes in rats.
  10. Primitive haematopoiesis in the human placenta gives rise to macrophages with epigenetically silenced HLA-DR.
  11. Human inherited complete STAT2 deficiency underlies inflammatory viral diseases.
  12. Enhanced Ca2+-channeling complex formation at the ER-mitochondria interface underlies the pathogenesis of alcohol-associated liver disease.
  13. NAMPT-dependent NAD+ biosynthesis controls circadian metabolism in a tissue-specific manner.
  14. Single-molecule localization microscopy reveals the ultrastructural constitution of distal appendages in expanded mammalian centrioles.
  15. 'Astonishing' molecular syringe ferries proteins into human cells.
  16. Imaging the biological microcosmos with a tiny telescope.
  17. Functional comparison of metabolic networks across species.
  18. Negative allosteric modulation of the glucagon receptor by RAMP2.
  19. Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.
  20. A gene drive is a gene drive: the debate over lumping or splitting definitions.
  21. The orphan receptor Nur77 binds cytoplasmic LPS to activate the non-canonical NLRP3 inflammasome.
  22. SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data.
  23. Lipid nanoparticle-enabled gene editing in the lung via inhalation.
  24. TAK1 deficiency promotes liver injury and tumorigenesis via ferroptosis and macrophage cGAS-STING signalling.
  25. Smad3 is essential for polarization of tumor-associated neutrophils in non-small cell lung carcinoma.
  26. Targeting G-CSF to treat autoinflammation.
  27. Fibroblastic reticular cells provide a supportive niche for lymph node-resident macrophages.
  28. Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis.
  29. Bacterial 'syringes' could inject drugs directly into human cells.
  30. Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution.
  31. Lack of Herpes Virus Entry Mediator Signals in Thymocytes Impairs Conventional CD8 T Cell Selection and Promotes Memory-like CD8 T Cell Development.
  32. The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
  33. TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks.
  34. Resting natural killer cell homeostasis relies on tryptophan/NAD+ metabolism and HIF-1α.
  35. A boost in learning by removing nuclear phosphodiesterases and enhancing nuclear cAMP signaling.
  36. Unselfish traits and social decision-making patterns characterize six populations of real-world extraordinary altruists.
  37. Single-cell analysis of peripheral blood from high-altitude pulmonary hypertension patients identifies a distinct monocyte phenotype.
  38. The RNA-binding protein hnRNP F is required for the germinal center B cell response.
  39. ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology.
  40. Nucleotide metabolism regulates human telomere length via telomerase activation.
  41. Quantitative profiling of pseudouridylation landscape in the human transcriptome.
  42. UT(se)X differences during immune responses.
  43. microRNA-449a reduces growth hormone-stimulated senescent cell burden through PI3K-mTOR signaling.
  44. Structural and functional analysis of human pannexin 2 channel.
  45. Perturbations in beta-cell heterogeneity in the pathogenesis of type 2 diabetes.
  46. Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance.
  47. Reflective multi-immersion microscope objectives inspired by the Schmidt telescope.
  48. NK-like CD8+ γδ T cells are expanded in persistent Mycobacterium tuberculosis infection.
  49. CERT1 mutations perturb human development by disrupting sphingolipid homeostasis.
  50. A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics.
  51. IEC-intrinsic IL-1R signaling holds dual roles in regulating intestinal homeostasis and inflammation.
  52. An affinity tool for the isolation of endogenous active mTORC1 from various cellular sources.
  53. Productive HIV-1 infection of tissue macrophages by fusion with infected CD4+ T cells.
  54. Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells.
  55. Site-1 protease inhibits mitochondrial respiration by controlling the TGF-β target gene Mss51.
  56. Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions.
  57. G-CSF drives autoinflammation in APLAID.
  58. Mitochondrial ATP synthase as a direct molecular target of chromium(III) to ameliorate hyperglycaemia stress.
  59. Protect newborn screening programs.
  60. The ubiquitin E3 ligase TRIM10 promotes STING aggregation and activation in the Golgi apparatus.
  61. Adaptive meets innate: CD8+ T cells kill MHC-I-negative tumour cells.
  62. Mitochondria-derived H2O2 triggers liver regeneration via FoxO3a signaling pathway after partial hepatectomy in mice.
  1. Science. 2023 Mar 31. 379(6639): 1370
    Finding my way home.
    Andrea Del Valle.
      
    DOI:  https://doi.org/10.1126/science.adh9605
  2. Nat Commun. 2023 Mar 31. 14(1): 1806
    Age-dependent Pdgfrβ signaling drives adipocyte progenitor dysfunction to alter the beige adipogenic niche in male mice.
    Abigail M Benvie, Derek Lee, Benjamin M Steiner, Siwen Xue, Yuwei Jiang, Daniel C Berry.
      Perivascular adipocyte progenitor cells (APCs) can generate cold temperature-induced thermogenic beige adipocytes within white adipose tissue (WAT), an effect that could counteract excess fat mass and metabolic pathologies. Yet, the ability to generate beige adipocytes declines with age, creating a key challenge for their therapeutic potential. Here we show that ageing beige APCs overexpress platelet derived growth factor receptor beta (Pdgfrβ) to prevent beige adipogenesis. We show that genetically deleting Pdgfrβ, in adult male mice, restores beige adipocyte generation whereas activating Pdgfrβ in juvenile mice blocks beige fat formation. Mechanistically, we find that Stat1 phosphorylation mediates Pdgfrβ beige APC signaling to suppress IL-33 induction, which dampens immunological genes such as IL-13 and IL-5. Moreover, pharmacologically targeting Pdgfrβ signaling restores beige adipocyte development by rejuvenating the immunological niche. Thus, targeting Pdgfrβ signaling could be a strategy to restore WAT immune cell function to stimulate beige fat in adult mammals.
    DOI:  https://doi.org/10.1038/s41467-023-37386-z
  3. Sci Transl Med. 2023 Mar 29. 15(689): eadf0141
    The neuronal pentraxin Nptx2 regulates complement activity and restrains microglia-mediated synapse loss in neurodegeneration.
    Jiechao Zhou, Sarah D Wade, David Graykowski, Mei-Fang Xiao, Binhui Zhao, Lucia A A Giannini, Jesse E Hanson, John C van Swieten, Morgan Sheng, Paul F Worley, Borislav Dejanovic.
      Complement overactivation mediates microglial synapse elimination in neurological diseases such as Alzheimer's disease (AD) and frontotemporal dementia (FTD), but how complement activity is regulated in the brain remains largely unknown. We identified that the secreted neuronal pentraxin Nptx2 binds complement C1q and thereby regulates its activity in the brain. Nptx2-deficient mice show increased complement activity, C1q-dependent microglial synapse engulfment, and loss of excitatory synapses. In a neuroinflammation culture model and in aged TauP301S mice, adeno-associated virus (AAV)-mediated neuronal overexpression of Nptx2 was sufficient to restrain complement activity and ameliorate microglia-mediated synapse loss. Analysis of human cerebrospinal fluid (CSF) samples from a genetic FTD cohort revealed reduced concentrations of Nptx2 and Nptx2-C1q protein complexes in symptomatic patients, which correlated with elevated C1q and activated C3. Together, these results show that Nptx2 regulates complement activity and microglial synapse elimination in the brain and that diminished Nptx2 concentrations might exacerbate complement-mediated neurodegeneration in patients with FTD.
    DOI:  https://doi.org/10.1126/scitranslmed.adf0141
  4. Nat Immunol. 2023 Mar 30.
    Monocytes can proliferate in vacant niches before differentiation into macrophages.
      
    DOI:  https://doi.org/10.1038/s41590-023-01480-7
  5. Nat Commun. 2023 Mar 31. 14(1): 1797
    Structural insights into the mechanism of leptin receptor activation.
    Robert A Saxton, Nathanael A Caveney, Maria Dolores Moya-Garzon, Karsten D Householder, Grayson E Rodriguez, Kylie A Burdsall, Jonathan Z Long, K Christopher Garcia.
      Leptin is an adipocyte-derived protein hormone that promotes satiety and energy homeostasis by activating the leptin receptor (LepR)-STAT3 signaling axis in a subset of hypothalamic neurons. Leptin signaling is dysregulated in obesity, however, where appetite remains elevated despite high levels of circulating leptin. To gain insight into the mechanism of leptin receptor activation, here we determine the structure of a stabilized leptin-bound LepR signaling complex using single particle cryo-EM. The structure reveals an asymmetric architecture in which a single leptin induces LepR dimerization via two distinct receptor-binding sites. Analysis of the leptin-LepR binding interfaces reveals the molecular basis for human obesity-associated mutations. Structure-based design of leptin variants that destabilize the asymmetric LepR dimer yield both partial and biased agonists that partially suppress STAT3 activation in the presence of wild-type leptin and decouple activation of STAT3 from LepR negative regulators. Together, these results reveal the structural basis for LepR activation and provide insights into the differential plasticity of signaling pathways downstream of LepR.
    DOI:  https://doi.org/10.1038/s41467-023-37169-6
  6. J Exp Med. 2023 Jun 05. pii: e20221068. [Epub ahead of print]220(6):
    VMP1 prevents Ca2+ overload in endoplasmic reticulum and maintains naive T cell survival.
    Ying Liu, Yuying Ma, Jing Xu, Guangyue Zhang, Xiaocui Zhao, Zihao He, Lixia Wang, Na Yin, Min Peng.
      Ca2+ in endoplasmic reticulum (ER) dictates T cell activation, proliferation, and function via store-operated Ca2+ entry. How naive T cells maintain an appropriate level of Ca2+ in ER remains poorly understood. Here, we show that the ER transmembrane protein VMP1 is essential for maintaining ER Ca2+ homeostasis in naive T cells. VMP1 promotes Ca2+ release from ER under steady state, and its deficiency leads to ER Ca2+ overload, ER stress, and secondary Ca2+ overload in mitochondria, resulting in massive apoptosis of naive T cells and defective T cell response. Aspartic acid 272 (D272) of VMP1 is critical for its ER Ca2+ releasing activity, and a knockin mouse strain with D272 mutated to asparagine (D272N) demonstrates all functions of VMP1 in T cells in vivo depend on its regulation of ER Ca2+. These data uncover an indispensable role of VMP1 in preventing ER Ca2+ overload and maintaining naive T cell survival.
    DOI:  https://doi.org/10.1084/jem.20221068
  7. Nat Commun. 2023 Mar 25. 14(1): 1670
    An aging, pathology burden, and glial senescence build-up hypothesis for late onset Alzheimer's disease.
    Victor Lau, Leanne Ramer, Marie-Ève Tremblay.
      Alzheimer's disease (AD) predominantly occurs as a late onset (LOAD) form involving neurodegeneration and cognitive decline with progressive memory loss. Risk factors that include aging promote accumulation of AD pathologies, such as amyloid-beta and tau aggregates, as well as inflammation and oxidative stress. Homeostatic glial states regulate and suppress pathology buildup; inflammatory states exacerbate pathology by releasing pro-inflammatory cytokines. Multiple stresses likely induce glial senescence, which could decrease supportive functions and reinforce inflammation. In this perspective, we hypothesize that aging first drives AD pathology burden, whereafter AD pathology putatively induces glial senescence in LOAD. We hypothesize that increasing glial senescence, particularly local senescent microglia accumulation, sustains and drives perpetuating buildup and spread of AD pathologies, glial aging, and further senescence. We predict that increasing glial senescence, particularly local senescent microglia accumulation, also transitions individuals from healthy cognition into mild cognitive impairment and LOAD diagnosis. These pathophysiological underpinnings may centrally contribute to LOAD onset, but require further mechanistic investigation.
    DOI:  https://doi.org/10.1038/s41467-023-37304-3
  8. Cell. 2023 Mar 30. pii: S0092-8674(23)00210-6. [Epub ahead of print]186(7): 1448-1464.e20
    A neutrophil response linked to tumor control in immunotherapy.
    Jeremy Gungabeesoon, Nicolas A Gort-Freitas, Máté Kiss, Evangelia Bolli, Marius Messemaker, Marie Siwicki, Mehdi Hicham, Ruben Bill, Peter Koch, Chiara Cianciaruso, Florent Duval, Christina Pfirschke, Michael Mazzola, Solange Peters, Krisztian Homicsko, Christopher Garris, Ralph Weissleder, Allon M Klein, Mikael J Pittet.
      Neutrophils accumulate in solid tumors, and their abundance correlates with poor prognosis. Neutrophils are not homogeneous, however, and could play different roles in cancer therapy. Here, we investigate the role of neutrophils in immunotherapy, leading to tumor control. We show that successful therapies acutely expanded tumor neutrophil numbers. This expansion could be attributed to a Sellhi state rather than to other neutrophils that accelerate tumor progression. Therapy-elicited neutrophils acquired an interferon gene signature, also seen in human patients, and appeared essential for successful therapy, as loss of the interferon-responsive transcription factor IRF1 in neutrophils led to failure of immunotherapy. The neutrophil response depended on key components of anti-tumor immunity, including BATF3-dependent DCs, IL-12, and IFNγ. In addition, we found that a therapy-elicited systemic neutrophil response positively correlated with disease outcome in lung cancer patients. Thus, we establish a crucial role of a neutrophil state in mediating effective cancer therapy.
    Keywords:  IRF1; SiglecF; anti-CD40; anti-PD-1; cancer; immunotherapy; interferon; lung cancer; neutrophil; single-cell RNA-seq
    DOI:  https://doi.org/10.1016/j.cell.2023.02.032
  9. Nat Commun. 2023 Mar 29. 14(1): 1755
    Hypothalamic melanin-concentrating hormone neurons integrate food-motivated appetitive and consummatory processes in rats.
    Keshav S Subramanian, Logan Tierno Lauer, Anna M R Hayes, Léa Décarie-Spain, Kara McBurnett, Anna C Nourbash, Kristen N Donohue, Alicia E Kao, Alexander G Bashaw, Denis Burdakov, Emily E Noble, Lindsey A Schier, Scott E Kanoski.
      The lateral hypothalamic area (LHA) integrates homeostatic processes and reward-motivated behaviors. Here we show that LHA neurons that produce melanin-concentrating hormone (MCH) are dynamically responsive to both food-directed appetitive and consummatory processes in male rats. Specifically, results reveal that MCH neuron Ca2+ activity increases in response to both discrete and contextual food-predictive cues and is correlated with food-motivated responses. MCH neuron activity also increases during eating, and this response is highly predictive of caloric consumption and declines throughout a meal, thus supporting a role for MCH neurons in the positive feedback consummatory process known as appetition. These physiological MCH neural responses are functionally relevant as chemogenetic MCH neuron activation promotes appetitive behavioral responses to food-predictive cues and increases meal size. Finally, MCH neuron activation enhances preference for a noncaloric flavor paired with intragastric glucose. Collectively, these data identify a hypothalamic neural population that orchestrates both food-motivated appetitive and intake-promoting consummatory processes.
    DOI:  https://doi.org/10.1038/s41467-023-37344-9
  10. Nat Commun. 2023 Mar 30. 14(1): 1764
    Primitive haematopoiesis in the human placenta gives rise to macrophages with epigenetically silenced HLA-DR.
    Jake R Thomas, Anna Appios, Emily F Calderbank, Nagisa Yoshida, Xiaohui Zhao, Russell S Hamilton, Ashley Moffett, Andrew Sharkey, Elisa Laurenti, Courtney W Hanna, Naomi McGovern.
      The earliest macrophages are generated during embryonic development from erythro-myeloid progenitors (EMPs) via primitive haematopoiesis. Although this process is thought to be spatially restricted to the yolk sac in the mouse, in humans, it remains poorly understood. Human foetal placental macrophages, or Hofbauer cells (HBC), arise during the primitive haematopoietic wave ~18 days post conception and lack expression of human leukocyte antigen (HLA) class II. Here, we identify a population of placental erythro-myeloid progenitors (PEMPs) in the early human placenta that have conserved features of primitive yolk sac EMPs, including the lack of HLF expression. Using in vitro culture experiments we demonstrate that PEMP generate HBC-like cells lacking HLA-DR expression. We find the absence of HLA-DR in primitive macrophages is mediated via epigenetic silencing of class II transactivator, CIITA, the master regulator of HLA class II gene expression. These findings establish the human placenta as an additional site of primitive haematopoiesis.
    DOI:  https://doi.org/10.1038/s41467-023-37383-2
  11. J Clin Invest. 2023 Mar 28. pii: e168321. [Epub ahead of print]
    Human inherited complete STAT2 deficiency underlies inflammatory viral diseases.
    Giorgia Bucciol, Leen Moens, Masato Ogishi, Darawan Rinchai, Daniela Matuozzo, Mana Momenilandi, Nacim Kerrouche, Catherine M Cale, Elsa R Treffeisen, Mohammad Al Salamah, Bandar K Al-Saud, Alain Lachaux, Remi Duclaux-Loras, Marie Meignien, Aziz Bousfiha, Ibtihal Benhsaien, Anna Shcherbina, Anna Roppelt, Florian Gothe, Nadhira Houhou-Fidouh, Scott J Hackett, Lisa M Bartnikas, Michelle C Maciag, Mohammed F Alosaimi, Janet Chou, Reem W Mohammed, Bishara J Freij, Emmanuelle Jouanguy, Shen-Ying Zhang, Stephanie Boisson-Dupuis, Vivien Béziat, Qian Zhang, Christopher Ja Duncan, Sophie Hambleton, Jean-Laurent Casanova, Isabelle Meyts.
      STAT2 is a transcription factor activated by type I and III interferons. We report 23 patients with loss of function variants causing autosomal recessive (AR), complete STAT2 deficiency. Both cells transfected with mutant STAT2 alleles and the patients' cells display impaired expression of interferon stimulated genes and impaired control of in-vitro viral infections. Clinical manifestations from early childhood onward include severe adverse reaction to live attenuated viral vaccines (LAV, 12/17 patients) and severe viral infections (10/23 patients), particularly critical influenza pneumonia (6 patients), critical COVID-19 pneumonia (1 patient), and herpes simplex encephalitis (1 patient). The patients display various types of hyperinflammation, often triggered by viral infection or after LAV administration, which probably attests to unresolved viral infection in the absence of STAT2-dependent type I and III IFN immunity (7 patients). Transcriptomic analysis reveals that circulating monocytes, neutrophils, and CD8 memory T cells contribute to this inflammation. Eight patients died (35%, 2 months-7 years): one of HSV-1 encephalitis, one of fulminant hepatitis, and six of heart failure during a febrile illness with no identified etiology. 15 patients remain alive (5-40 years). AR complete STAT2 deficiency underlies severe viral diseases, with half of the patients surviving into teenage years or adulthood.
    Keywords:  Genetic diseases; Immunology; Influenza; Innate immunity
    DOI:  https://doi.org/10.1172/JCI168321
  12. Nat Commun. 2023 Mar 27. 14(1): 1703
    Enhanced Ca2+-channeling complex formation at the ER-mitochondria interface underlies the pathogenesis of alcohol-associated liver disease.
    Themis Thoudam, Dipanjan Chanda, Jung Yi Lee, Min-Kyo Jung, Ibotombi Singh Sinam, Byung-Gyu Kim, Bo-Yoon Park, Woong Hee Kwon, Hyo-Jeong Kim, Myeongjin Kim, Chae Won Lim, Hoyul Lee, Yang Hoon Huh, Caroline A Miller, Romil Saxena, Nicholas J Skill, Nazmul Huda, Praveen Kusumanchi, Jing Ma, Zhihong Yang, Min-Ji Kim, Ji Young Mun, Robert A Harris, Jae-Han Jeon, Suthat Liangpunsakul, In-Kyu Lee.
      Ca2+ overload-induced mitochondrial dysfunction is considered as a major contributing factor in the pathogenesis of alcohol-associated liver disease (ALD). However, the initiating factors that drive mitochondrial Ca2+ accumulation in ALD remain elusive. Here, we demonstrate that an aberrant increase in hepatic GRP75-mediated mitochondria-associated ER membrane (MAM) Ca2+-channeling (MCC) complex formation promotes mitochondrial dysfunction in vitro and in male mouse model of ALD. Unbiased transcriptomic analysis reveals PDK4 as a prominently inducible MAM kinase in ALD. Analysis of human ALD cohorts further corroborate these findings. Additional mass spectrometry analysis unveils GRP75 as a downstream phosphorylation target of PDK4. Conversely, non-phosphorylatable GRP75 mutation or genetic ablation of PDK4 prevents alcohol-induced MCC complex formation and subsequent mitochondrial Ca2+ accumulation and dysfunction. Finally, ectopic induction of MAM formation reverses the protective effect of PDK4 deficiency in alcohol-induced liver injury. Together, our study defines a mediatory role of PDK4 in promoting mitochondrial dysfunction in ALD.
    DOI:  https://doi.org/10.1038/s41467-023-37214-4
  13. Proc Natl Acad Sci U S A. 2023 Apr 04. 120(14): e2220102120
    NAMPT-dependent NAD+ biosynthesis controls circadian metabolism in a tissue-specific manner.
    Astrid L Basse, Karen N Nielsen, Iuliia Karavaeva, Lars R Ingerslev, Tao Ma, Jesper F Havelund, Thomas S Nielsen, Mikkel Frost, Julia Peics, Emilie Dalbram, Morten Dall, Juleen R Zierath, Romain Barrès, Nils J Færgeman, Jonas T Treebak, Zachary Gerhart-Hines.
      Molecular clocks in the periphery coordinate tissue-specific daily biorhythms by integrating input from the hypothalamic master clock and intracellular metabolic signals. One such key metabolic signal is the cellular concentration of NAD+, which oscillates along with its biosynthetic enzyme, nicotinamide phosphoribosyltransferase (NAMPT). NAD+ levels feed back into the clock to influence rhythmicity of biological functions, yet whether this metabolic fine-tuning occurs ubiquitously across cell types and is a core clock feature is unknown. Here, we show that NAMPT-dependent control over the molecular clock varies substantially between tissues. Brown adipose tissue (BAT) requires NAMPT to sustain the amplitude of the core clock, whereas rhythmicity in white adipose tissue (WAT) is only moderately dependent on NAD+ biosynthesis, and the skeletal muscle clock is completely refractory to loss of NAMPT. In BAT and WAT, NAMPT differentially orchestrates oscillation of clock-controlled gene networks and the diurnality of metabolite levels. NAMPT coordinates the rhythmicity of TCA cycle intermediates in BAT, but not in WAT, and loss of NAD+ abolishes these oscillations similarly to high-fat diet-induced circadian disruption. Moreover, adipose NAMPT depletion improved the ability of animals to defend body temperature during cold stress but in a time-of-day-independent manner. Thus, our findings reveal that peripheral molecular clocks and metabolic biorhythms are shaped in a highly tissue-specific manner by NAMPT-dependent NAD+ synthesis.
    Keywords:  Brown adipose tissue; Circadian metabolism; Clock rhythm; NAD; Skeletal muscle
    DOI:  https://doi.org/10.1073/pnas.2220102120
  14. Nat Commun. 2023 Mar 27. 14(1): 1688
    Single-molecule localization microscopy reveals the ultrastructural constitution of distal appendages in expanded mammalian centrioles.
    Ting-Jui Ben Chang, Jimmy Ching-Cheng Hsu, T Tony Yang.
      Distal appendages (DAPs) are vital in cilia formation, mediating vesicular and ciliary docking to the plasma membrane during early ciliogenesis. Although numerous DAP proteins arranging a nine-fold symmetry have been studied using superresolution microscopy analyses, the extensive ultrastructural understanding of the DAP structure developing from the centriole wall remains elusive owing to insufficient resolution. Here, we proposed a pragmatic imaging strategy for two-color single-molecule localization microscopy of expanded mammalian DAP. Importantly, our imaging workflow enables us to push the resolution limit of a light microscope well close to a molecular level, thus achieving an unprecedented mapping resolution inside intact cells. Upon this workflow, we unravel the ultra-resolved higher-order protein complexes of the DAP and its associated proteins. Intriguingly, our images show that C2CD3, microtubule triplet, MNR, CEP90, OFD1, and ODF2 jointly constitute a unique molecular configuration at the DAP base. Moreover, our finding suggests that ODF2 plays an auxiliary role in coordinating and maintaining DAP nine-fold symmetry. Together, we develop an organelle-based drift correction protocol and a two-color solution with minimum crosstalk, allowing a robust localization microscopy imaging of expanded DAP structures deep into the gel-specimen composites.
    DOI:  https://doi.org/10.1038/s41467-023-37342-x
  15. Nature. 2023 Mar 29.
    'Astonishing' molecular syringe ferries proteins into human cells.
    Heidi Ledford.
      
    Keywords:  Gene therapy; Microbiology; Molecular biology
    DOI:  https://doi.org/10.1038/d41586-023-00922-4
  16. Nat Biotechnol. 2023 Mar 31.
    Imaging the biological microcosmos with a tiny telescope.
      
    DOI:  https://doi.org/10.1038/s41587-023-01740-9
  17. Nat Commun. 2023 Mar 27. 14(1): 1699
    Functional comparison of metabolic networks across species.
    Charlotte Ramon, Jörg Stelling.
      Metabolic phenotypes are pivotal for many areas, but disentangling how evolutionary history and environmental adaptation shape these phenotypes is an open problem. Especially for microbes, which are metabolically diverse and often interact in complex communities, few phenotypes can be determined directly. Instead, potential phenotypes are commonly inferred from genomic information, and rarely were model-predicted phenotypes employed beyond the species level. Here, we propose sensitivity correlations to quantify similarity of predicted metabolic network responses to perturbations, and thereby link genotype and environment to phenotype. We show that these correlations provide a consistent functional complement to genomic information by capturing how network context shapes gene function. This enables, for example, phylogenetic inference across all domains of life at the organism level. For 245 bacterial species, we identify conserved and variable metabolic functions, elucidate the quantitative impact of evolutionary history and ecological niche on these functions, and generate hypotheses on associated metabolic phenotypes. We expect our framework for the joint interpretation of metabolic phenotypes, evolution, and environment to help guide future empirical studies.
    DOI:  https://doi.org/10.1038/s41467-023-37429-5
  18. Cell. 2023 Mar 30. pii: S0092-8674(23)00171-X. [Epub ahead of print]186(7): 1465-1477.e18
    Negative allosteric modulation of the glucagon receptor by RAMP2.
    Kaavya Krishna Kumar, Evan S O'Brien, Chris H Habrian, Naomi R Latorraca, Haoqing Wang, Inga Tuneew, Elizabeth Montabana, Susan Marqusee, Daniel Hilger, Ehud Y Isacoff, Jesper Mosolff Mathiesen, Brian K Kobilka.
      Receptor activity-modifying proteins (RAMPs) modulate the activity of many Family B GPCRs. We show that RAMP2 directly interacts with the glucagon receptor (GCGR), a Family B GPCR responsible for blood sugar homeostasis, and broadly inhibits receptor-induced downstream signaling. HDX-MS experiments demonstrate that RAMP2 enhances local flexibility in select locations in and near the receptor extracellular domain (ECD) and in the 6th transmembrane helix, whereas smFRET experiments show that this ECD disorder results in the inhibition of active and intermediate states of the intracellular surface. We determined the cryo-EM structure of the GCGR-Gs complex at 2.9 Å resolution in the presence of RAMP2. RAMP2 apparently does not interact with GCGR in an ordered manner; however, the receptor ECD is indeed largely disordered along with rearrangements of several intracellular hallmarks of activation. Our studies suggest that RAMP2 acts as a negative allosteric modulator of GCGR by enhancing conformational sampling of the ECD.
    Keywords:  G-protein; G-protein coupled receptor; GPCR; HDX-MS; allostery; cell signaling; cryo-EM; cryo-electron microscopy; glucagon receptor; hydrogen-deuterium exchange monitored by mass spectrometry; protein dynamics; receptor activity-modifying protein RAMP; single molecule fluorescence resonance energy transfer; smFRET
    DOI:  https://doi.org/10.1016/j.cell.2023.02.028
  19. Commun Biol. 2023 Mar 28. 6(1): 335
    Genetic variation in cis-regulatory domains suggests cell type-specific regulatory mechanisms in immunity.
    Diana Avalos, Guillaume Rey, Diogo M Ribeiro, Anna Ramisch, Emmanouil T Dermitzakis, Olivier Delaneau.
      Studying the interplay between genetic variation, epigenetic changes, and regulation of gene expression is crucial to understand the modification of cellular states in various conditions, including immune diseases. In this study, we characterize the cell-specificity in three key cells of the human immune system by building cis maps of regulatory regions with coordinated activity (CRDs) from ChIP-seq peaks and methylation data. We find that only 33% of CRD-gene associations are shared between cell types, revealing how similarly located regulatory regions provide cell-specific modulation of gene activity. We emphasize important biological mechanisms, as most of our associations are enriched in cell-specific transcription factor binding sites, blood-traits, and immune disease-associated loci. Notably, we show that CRD-QTLs aid in interpreting GWAS findings and help prioritize variants for testing functional hypotheses within human complex diseases. Additionally, we map trans CRD regulatory associations, and among 207 trans-eQTLs discovered, 46 overlap with the QTLGen Consortium meta-analysis in whole blood, showing that mapping functional regulatory units using population genomics allows discovering important mechanisms in the regulation of gene expression in immune cells. Finally, we constitute a comprehensive resource describing multi-omics changes to gain a greater understanding of cell-type specific regulatory mechanisms of immunity.
    DOI:  https://doi.org/10.1038/s42003-023-04688-3
  20. Nat Commun. 2023 Mar 29. 14(1): 1749
    A gene drive is a gene drive: the debate over lumping or splitting definitions.
    Stephanie L James, David A O'Brochta, Filippo Randazzo, Omar S Akbari.
      
    DOI:  https://doi.org/10.1038/s41467-023-37483-z
  21. Immunity. 2023 Mar 24. pii: S1074-7613(23)00123-1. [Epub ahead of print]
    The orphan receptor Nur77 binds cytoplasmic LPS to activate the non-canonical NLRP3 inflammasome.
    Fangrui Zhu, Juan Ma, Weitao Li, Qiannv Liu, Xiwen Qin, Yan Qian, Chunlei Wang, Yan Zhang, Yi Li, Dong Jiang, Shuo Wang, Pengyan Xia.
      Intracellular sensing of lipopolysaccharide (LPS) by murine caspase-11 or human caspase-4 initiates a protease cascade, termed the non-canonical inflammasome, that results in gasdermin D (GSDMD) processing and subsequent NLRP3 inflammasome activation. In an effort aimed at identifying additional sensors for intracellular LPS by biochemical screening, we identified the nuclear orphan receptor Nur77 as an LPS-binding protein in macrophage lysates. Nr4a1-/- macrophages exhibited impaired activation of the NLRP3 inflammasome, but not caspase-11, in response to LPS. Biochemical mapping revealed that Nur77 bound LPS directly through a domain in its C terminus. Yeast two-hybrid assays identified NLRP3 as a binding partner for Nur77. The association between Nur77 and NLRP3 required the presence of LPS and dsDNA. The source of dsDNA was the mitochondria, requiring the formation of gasdermin-D pores. In vivo, Nur77 deficiency ameliorated host response to endotoxins. Thus, Nur77 functions as an intracellular LPS sensor, binding mitochondrial DNA and LPS to activate the non-canonical NLRP3 inflammasome.
    Keywords:  LPS; NLRP3; Nur77; caspase-11; non-canonical inflammasome
    DOI:  https://doi.org/10.1016/j.immuni.2023.03.003
  22. Nat Biotechnol. 2023 Mar 27.
    SEACells infers transcriptional and epigenomic cellular states from single-cell genomics data.
    Sitara Persad, Zi-Ning Choo, Christine Dien, Noor Sohail, Ignas Masilionis, Ronan Chaligné, Tal Nawy, Chrysothemis C Brown, Roshan Sharma, Itsik Pe'er, Manu Setty, Dana Pe'er.
      Metacells are cell groupings derived from single-cell sequencing data that represent highly granular, distinct cell states. Here we present single-cell aggregation of cell states (SEACells), an algorithm for identifying metacells that overcome the sparsity of single-cell data while retaining heterogeneity obscured by traditional cell clustering. SEACells outperforms existing algorithms in identifying comprehensive, compact and well-separated metacells in both RNA and assay for transposase-accessible chromatin (ATAC) modalities across datasets with discrete cell types and continuous trajectories. We demonstrate the use of SEACells to improve gene-peak associations, compute ATAC gene scores and infer the activities of critical regulators during differentiation. Metacell-level analysis scales to large datasets and is particularly well suited for patient cohorts, where per-patient aggregation provides more robust units for data integration. We use our metacells to reveal expression dynamics and gradual reconfiguration of the chromatin landscape during hematopoietic differentiation and to uniquely identify CD4 T cell differentiation and activation states associated with disease onset and severity in a Coronavirus Disease 2019 (COVID-19) patient cohort.
    DOI:  https://doi.org/10.1038/s41587-023-01716-9
  23. Nat Biotechnol. 2023 Mar 30.
    Lipid nanoparticle-enabled gene editing in the lung via inhalation.
      
    DOI:  https://doi.org/10.1038/s41587-023-01689-9
  24. JHEP Rep. 2023 May;5(5): 100695
    TAK1 deficiency promotes liver injury and tumorigenesis via ferroptosis and macrophage cGAS-STING signalling.
    Wantong Su, Weicheng Gao, Rui Zhang, Qi Wang, Lei Li, Qingfa Bu, Zibo Xu, Zheng Liu, Mingming Wang, Yaqing Zhu, Guoping Wu, Haoming Zhou, Xun Wang, Ling Lu.
       Background & Aims: Oxidative stress-mediated ferroptosis and macrophage-related inflammation play an important role in various liver diseases. Here, we explored if and how hepatocyte ferroptosis regulates macrophage stimulator of interferon genes (STING) activation in the development of spontaneous liver damage, fibrosis, and tumorigenesis.
    Methods: We used a transforming growth factor-beta-activated kinase 1 (TAK1) deficiency-induced model of spontaneous liver damage, fibrosis, and tumorigenesis to investigate hepatocyte ferroptosis and its impact on macrophage STING signalling. Primary hepatocytes and macrophages were used for in vitro experiments.
    Results: Significant liver injury and increased numbers of intrahepatic M1 macrophages were found in hepatocyte-specific TAK1-deficient (TAK1ΔHEP) mice, peaking at 4 weeks and gradually decreasing at 8 and 12 weeks. Meanwhile, activation of STING signalling was observed in livers from TAK1ΔHEP mice at 4 weeks and had decreased at 8 and 12 weeks. Treatment with a STING inhibitor promoted macrophage M2 polarisation and alleviated liver injury, fibrosis, and tumour burden. TAK1 deficiency exacerbated liver iron metabolism in mice with a high-iron diet. Moreover, consistent with the results from single-cell RNA-Seq dataset, TAK1ΔHEP mice demonstrated an increased oxidative response and hepatocellular ferroptosis, which could be inhibited by reactive oxygen species scavenging. Suppression of ferroptosis by ferrostatin-1 inhibited the activation of macrophage STING signalling, leading to attenuated liver injury and fibrosis and a reduced tumour burden. Mechanistically, increased intrahepatic and serum levels of 8-hydroxydeoxyguanosine were detected in TAK1ΔHEP mice, which was suppressed by ferroptosis inhibition. Treatment with 8-hydroxydeoxyguanosine antibody inhibited macrophage STING activation in TAK1ΔHEP mice.
    Conclusions: Hepatocellular ferroptosis-derived oxidative DNA damage promotes macrophage STING activation to facilitate the development of liver injury, fibrosis, and tumorigenesis. Inhibition of macrophage STING may represent a novel therapeutic approach for the prevention of chronic liver disease.
    Impact and implications: The precise mechanism by which hepatocyte ferroptosis regulates macrophage STING activation in the progression of liver damage, fibrosis, and tumorigenesis remains unclear. Herein, we show that deletion of TAK1 in hepatocytes caused oxidative stress-mediated ferroptosis and macrophage-related inflammation in the development of spontaneous liver injury, fibrosis, and hepatocellular carcinoma.
    Keywords:  Ferroptosis; Oxidative stress; STING; TAK1; Tumorigenesis
    DOI:  https://doi.org/10.1016/j.jhepr.2023.100695
  25. Nat Commun. 2023 Mar 31. 14(1): 1794
    Smad3 is essential for polarization of tumor-associated neutrophils in non-small cell lung carcinoma.
    Jeff Yat-Fai Chung, Philip Chiu-Tsun Tang, Max Kam-Kwan Chan, Vivian Weiwen Xue, Xiao-Ru Huang, Calvin Sze-Hang Ng, Dongmei Zhang, Kam-Tong Leung, Chun-Kwok Wong, Tin-Lap Lee, Eric W-F Lam, David J Nikolic-Paterson, Ka-Fai To, Hui-Yao Lan, Patrick Ming-Kuen Tang.
      Neutrophils are dynamic with their phenotype and function shaped by the microenvironment, such as the N1 antitumor and N2 pro-tumor states within the tumor microenvironment (TME), but its regulation remains undefined. Here we examine TGF-β1/Smad3 signaling in tumor-associated neutrophils (TANs) in non-small cell lung carcinoma (NSCLC) patients. Smad3 activation in N2 TANs is negatively correlate with the N1 population and patient survival. In experimental lung carcinoma, TANs switch from a predominant N2 state in wild-type mice to an N1 state in Smad3-KO mice which associate with enhanced neutrophil infiltration and tumor regression. Neutrophil depletion abrogates the N1 anticancer phenotype in Smad3-KO mice, while adoptive transfer of Smad3-KO neutrophils reproduces this protective effect in wild-type mice. Single-cell analysis uncovers a TAN subset showing a mature N1 phenotype in Smad3-KO TME, whereas wild-type TANs mainly retain an immature N2 state due to Smad3. Mechanistically, TME-induced Smad3 target genes related to cell fate determination to preserve the N2 state of TAN. Importantly, genetic deletion and pharmaceutical inhibition of Smad3 enhance the anticancer capacity of neutrophils against NSCLC via promoting their N1 maturation. Thus, our work suggests that Smad3 signaling in neutrophils may represent a therapeutic target for cancer immunotherapy.
    DOI:  https://doi.org/10.1038/s41467-023-37515-8
  26. Nat Immunol. 2023 Mar 30.
    Targeting G-CSF to treat autoinflammation.
    Tom D Bunney, Matilda Katan.
      
    DOI:  https://doi.org/10.1038/s41590-023-01474-5
  27. Eur J Immunol. 2023 Mar 29. e2250355
    Fibroblastic reticular cells provide a supportive niche for lymph node-resident macrophages.
    Joshua D'Rozario, Konstantin Knoblich, Mechthild Lütge, Christian Pérez Shibayama, Hung-Wei Cheng, Yannick O Alexandre, David Roberts, Joana Campos, Emma Dutton, Muath Suliman, Alice E Denton, Shannon J Turley, Richard L Boyd, Scott N Mueller, Burkhard Ludewig, Tracy S P Heng, Anne L Fletcher.
      The lymph node (LN) is home to resident macrophage populations that are essential for immune function and homeostasis, but key factors controlling this niche are undefined. Here we show that fibroblastic reticular cells (FRCs) are an essential component of the LN macrophage niche. Genetic ablation of FRCs caused rapid loss of macrophages and monocytes from LNs across two in vivo models. Macrophages co-localised with FRCs in human LNs, and murine single-cell RNA-sequencing revealed that FRC subsets broadly expressed master macrophage regulator CSF1. Functional assays containing purified FRCs and monocytes showed that CSF1R signalling was sufficient to support macrophage development. These effects were conserved between mouse and human systems. These data indicate an important role for FRCs in maintaining the lymph node parenchymal macrophage niche. This article is protected by copyright. All rights reserved.
    Keywords:  CSF1; fibroblastic reticular cells; human lymph nodes; lymph node stromal cells; macrophages
    DOI:  https://doi.org/10.1002/eji.202250355
  28. J Hepatol. 2023 Mar 25. pii: S0168-8278(23)00190-3. [Epub ahead of print]
    Single-cell atlas of the liver myeloid compartment before and after cure of chronic viral hepatitis.
    Ang Cui, Bo Li, Michael S Wallace, Anna L K Gonye, Christopher Oetheimer, Hailey Patel, Pierre Tonnerre, Jacinta A Holmes, David Lieb, Brianna S Yao, Aileen Ma, Kela Roberts, Marcos Damasio, Jonathan H Chen, Daphnee Piou, Charles Carlton-Smith, Joelle Brown, Ravi Mylvaganam, Jeremy Man Hon Fung, Moshe Sade-Feldman, Jasneet Aneja, Jenna Gustafson, Eliana T Epstein, Shadi Salloum, Cynthia Brisac, Ashraf Thabet, Arthur Y Kim, Georg M Lauer, Nir Hacohen, Raymond T Chung, Nadia Alatrakchi.
       BACKGROUND & AIMS: Chronic viral infections present serious public health challenges; however, direct-acting antivirals (DAAs) are now able to cure nearly all patients infected with the hepatitis C virus (HCV), representing the only cure of a human chronic viral infection to date. DAAs provide a valuable opportunity to study immune pathways in the reversal of chronic immune failures in an in vivo human system.
    METHODS: To leverage this opportunity, we used plate-based single-cell RNA-seq (scRNA-seq) to deeply profile myeloid cells from liver fine needle aspirates (FNAs) in HCV patients before and after DAA treatment. We comprehensively characterized liver neutrophils, eosinophils, mast cells, conventional dendritic cells (cDCs), plasmacytoid dendritic cells (pDCs), classical monocytes, non-classical monocytes, and macrophages, and defined fine-grained subpopulations of several cell types.
    RESULTS: We discovered cell-type-specific changes post-cure, including an increase in MCM7+STMN1+ proliferating CD1C+ cDCs, which may support restoration from chronic exhaustion. We observed an expected downregulation of interferon stimulated genes (ISGs) post-cure as well as an unexpected inverse relationship between pre-treatment viral load and post-cure ISG expression in each cell type, revealing a link between viral loads and sustained modifications of the host's immune system. We found an upregulation of PD-L1/L2 expression in ISG-high neutrophils and IDO1 expression in eosinophils, pinpointing cell subpopulations crucial for immune regulation. We identified three recurring gene programs shared by multiple cell types, distilling core functions of the myeloid compartment.
    CONCLUSION: This comprehensive scRNA-seq atlas of human liver myeloid cells in response to a cure of chronic viral infections reveals principles of liver immunity and provides immunotherapeutic insights.
    IMPACT AND IMPLICATIONS: Chronic viral liver infections continue to be a major public health problem. Single-cell characterization of liver immune cells in hepatitis C and post-cure provides unique insights into the architecture of liver immunity contributing to the resolution of the first curable chronic viral infection of humans. Multiple layers of innate immune regulation during chronic infections and persistent immune modifications after cure are revealed. Researchers and clinicians may leverage these findings to develop methods to optimize the post-cure environment for HCV and develop novel therapeutic approaches.
    CLINICAL TRIAL NUMBER: NCT02476617.
    Keywords:  chronic infections; direct-acting antiviral; fine needle aspiration; hepatitis C virus; immune cells; innate immunity; liver; myeloid cells; single-cell RNA-sequencing; viral infections
    DOI:  https://doi.org/10.1016/j.jhep.2023.02.040
  29. Nature. 2023 Mar 29.
    Bacterial 'syringes' could inject drugs directly into human cells.
    Benjamin Thompson, Nick Petrić Howe.
      
    Keywords:  Health care; Microbiology; Molecular biology
    DOI:  https://doi.org/10.1038/d41586-023-00926-0
  30. medRxiv. 2023 Mar 20. pii: 2023.03.14.23287257. [Epub ahead of print]
    Mapping the dynamic genetic regulatory architecture of HLA genes at single-cell resolution.
    Accelerating Medicines Partnership Program: Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Network
      The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning autoimmune and infectious diseases, transplantation, and cancer. While coding variation in HLA genes has been extensively documented, regulatory genetic variation modulating HLA expression levels has not been comprehensively investigated. Here, we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues, using personalized reference genomes to mitigate technical confounding. We identified cell-type-specific cis- eQTLs for every classical HLA gene. Modeling eQTLs at single-cell resolution revealed that many eQTL effects are dynamic across cell states even within a cell type. HLA-DQ genes exhibit particularly cell-state-dependent effects within myeloid, B, and T cells. Dynamic HLA regulation may underlie important interindividual variability in immune responses.
    DOI:  https://doi.org/10.1101/2023.03.14.23287257
  31. J Immunol. 2023 Mar 31. pii: ji2200748. [Epub ahead of print]
    Lack of Herpes Virus Entry Mediator Signals in Thymocytes Impairs Conventional CD8 T Cell Selection and Promotes Memory-like CD8 T Cell Development.
    Yuki Kugii, Yui Kuroki, Yasushi Hara, Ryo Goitsuka, Naoko Nakano.
      Thymocytes having diverse Ag specificities are selected in response to self-MHC-peptide expressed in thymic epithelial cells, which contributes to the formation of a T cell repertoire. However, it is not well understood whether additional signals from epithelial cells are required to drive positive selection. In this study, we found that one of the TNFR superfamily members, herpes virus entry mediator (HVEM), when expressed on thymocytes provides signals for positive selection. HVEM deficiency in double-positive (DP) thymocytes impaired positive selection of CD8 thymocytes. HVEM-deficient thymocytes in OT-1 TCR transgenic mice exhibited significant defects in positive selection and impaired CD69 upregulation of selected thymocytes. HVEM ligands (lymphotoxin-like, exhibits inducible expression, and competes with HSV glycoprotein D for HVEM, a receptor expressed by T lymphocytes, and B and T lymphocyte attenuator) were expressed in cortical thymic epithelial cells. Weak TCR ligation combined with HVEM signals enhanced ERK activation in DP thymocytes developed in vitro. Insufficient signals for positive selection in HVEM-deficient DP thymocytes led to the development of innate memory-like CD8 T cells expressing high levels of CD122, along with the increased development of PLZF+ NKT cells. These results suggest that thymocytes receive activation signals through HVEM during positive selection. Thus, our findings provide evidence that the threshold of thymocyte positive selection is set by signals from TCR in association with HVEM.
    DOI:  https://doi.org/10.4049/jimmunol.2200748
  32. Cell Rep. 2023 Mar 31. pii: S2211-1247(23)00343-1. [Epub ahead of print]42(4): 112332
    The mitochondrial protease OMA1 acts as a metabolic safeguard upon nuclear DNA damage.
    Pablo Rivera-Mejías, Álvaro Jesús Narbona-Pérez, Lidwina Hasberg, Lara Kroczek, Amir Bahat, Steffen Lawo, Kat Folz-Donahue, Anna-Lena Schumacher, Sofia Ahola, Fiona Carola Mayer, Patrick Giavalisco, Hendrik Nolte, Sergio Lavandero, Thomas Langer.
      The metabolic plasticity of mitochondria ensures cell development, differentiation, and survival. The peptidase OMA1 regulates mitochondrial morphology via OPA1 and stress signaling via DELE1 and orchestrates tumorigenesis and cell survival in a cell- and tissue-specific manner. Here, we use unbiased systems-based approaches to show that OMA1-dependent cell survival depends on metabolic cues. A metabolism-focused CRISPR screen combined with an integrated analysis of human gene expression data found that OMA1 protects against DNA damage. Nucleotide deficiencies induced by chemotherapeutic agents promote p53-dependent apoptosis of cells lacking OMA1. The protective effect of OMA1 does not depend on OMA1 activation or OMA1-mediated OPA1 and DELE1 processing. OMA1-deficient cells show reduced glycolysis and accumulate oxidative phosphorylation (OXPHOS) proteins upon DNA damage. OXPHOS inhibition restores glycolysis and confers resistance against DNA damage. Thus, OMA1 dictates the balance between cell death and survival through the control of glucose metabolism, shedding light on its role in cancerogenesis.
    Keywords:  CP: Metabolism; DNA damage; OMA1; OXPHOS; glucose metabolism; mitochondria; nucleotides; p53
    DOI:  https://doi.org/10.1016/j.celrep.2023.112332
  33. Nat Commun. 2023 Mar 31. 14(1): 1810
    TRABID overexpression enables synthetic lethality to PARP inhibitor via prolonging 53BP1 retention at double-strand breaks.
    Jian Ma, Yingke Zhou, Penglin Pan, Haixin Yu, Zixi Wang, Lei Lily Li, Bing Wang, Yuqian Yan, Yunqian Pan, Qi Ye, Tianjie Liu, Xiaoyu Feng, Shan Xu, Ke Wang, Xinyang Wang, Yanlin Jian, Bohan Ma, Yizeng Fan, Yang Gao, Haojie Huang, Lei Li.
      53BP1 promotes nonhomologous end joining (NHEJ) over homologous recombination (HR) repair by mediating inactivation of DNA end resection. Ubiquitination plays an important role in regulating dissociation of 53BP1 from DNA double-strand breaks (DSBs). However, how this process is regulated remains poorly understood. Here, we demonstrate that TRABID deubiquitinase binds to 53BP1 at endogenous level and regulates 53BP1 retention at DSB sites. TRABID deubiquitinates K29-linked polyubiquitination of 53BP1 mediated by E3 ubiquitin ligase SPOP and prevents 53BP1 dissociation from DSBs, consequently inducing HR defects and chromosomal instability. Prostate cancer cells with TRABID overexpression exhibit a high sensitivity to poly (ADP-ribose) polymerase (PARP) inhibitors. Our work shows that TRABID facilitates NHEJ repair over HR during DNA repair by inducing prolonged 53BP1 retention at DSB sites, suggesting that TRABID overexpression may predict HR deficiency and the potential therapeutic use of PARP inhibitors in prostate cancer.
    DOI:  https://doi.org/10.1038/s41467-023-37499-5
  34. EMBO Rep. 2023 Mar 29. e56156
    Resting natural killer cell homeostasis relies on tryptophan/NAD+ metabolism and HIF-1α.
    Abigaelle Pelletier, Eric Nelius, Zheng Fan, Ekaterina Khatchatourova, Abdiel Alvarado-Diaz, Jingyi He, Ewelina Krzywinska, Michal Sobecki, Shunmugam Nagarajan, Yann Kerdiles, Joachim Fandrey, Dagmar Gotthardt, Veronika Sexl, Katrien de Bock, Christian Stockmann.
      Natural killer (NK) cells are forced to cope with different oxygen environments even under resting conditions. The adaptation to low oxygen is regulated by oxygen-sensitive transcription factors, the hypoxia-inducible factors (HIFs). The function of HIFs for NK cell activation and metabolic rewiring remains controversial. Activated NK cells are predominantly glycolytic, but the metabolic programs that ensure the maintenance of resting NK cells are enigmatic. By combining in situ metabolomic and transcriptomic analyses in resting murine NK cells, our study defines HIF-1α as a regulator of tryptophan metabolism and cellular nicotinamide adenine dinucleotide (NAD+ ) levels. The HIF-1α/NAD+ axis prevents ROS production during oxidative phosphorylation (OxPhos) and thereby blocks DNA damage and NK cell apoptosis under steady-state conditions. In contrast, in activated NK cells under hypoxia, HIF-1α is required for glycolysis, and forced HIF-1α expression boosts glycolysis and NK cell performance in vitro and in vivo. Our data highlight two distinct pathways by which HIF-1α interferes with NK cell metabolism. While HIF-1α-driven glycolysis is essential for NK cell activation, resting NK cell homeostasis relies on HIF-1α-dependent tryptophan/NAD+ metabolism.
    Keywords:  HIF; immunometabolism; natural killer cells; nicotinamide adenine dinucleotide; tryptophan
    DOI:  https://doi.org/10.15252/embr.202256156
  35. Sci Signal. 2023 Mar 28. 16(778): eadg9504
    A boost in learning by removing nuclear phosphodiesterases and enhancing nuclear cAMP signaling.
    Vsevolod V Gurevich, Eugenia V Gurevich.
      cAMP signaling in the nucleus leads to the expression of immediate early genes in neurons and learning and memory. In this issue of Science Signaling, Martinez et al. found that activation of the β2-adrenergic receptor enhances nuclear cAMP signaling that supports learning and memory in mice by removing the phosphodiesterase PDE4D5 from the nucleus through arrestin3 bound to the internalized receptor.
    DOI:  https://doi.org/10.1126/scisignal.adg9504
  36. Nat Commun. 2023 Mar 31. 14(1): 1807
    Unselfish traits and social decision-making patterns characterize six populations of real-world extraordinary altruists.
    Shawn A Rhoads, Kruti M Vekaria, Katherine O'Connell, Hannah S Elizabeth, David G Rand, Megan N Kozak Williams, Abigail A Marsh.
      Acts of extraordinary, costly altruism, in which significant risks or costs are assumed to benefit strangers, have long represented a motivational puzzle. But the features that consistently distinguish individuals who engage in such acts have not been identified. We assess six groups of real-world extraordinary altruists who had performed costly or risky and normatively rare (<0.00005% per capita) altruistic acts: heroic rescues, non-directed and directed kidney donations, liver donations, marrow or hematopoietic stem cell donations, and humanitarian aid work. Here, we show that the features that best distinguish altruists from controls are traits and decision-making patterns indicating unusually high valuation of others' outcomes: high Honesty-Humility, reduced Social Discounting, and reduced Personal Distress. Two independent samples of adults who were asked what traits would characterize altruists failed to predict this pattern. These findings suggest that theories regarding self-focused motivations for altruism (e.g., self-enhancing reciprocity, reputation enhancement) alone are insufficient explanations for acts of real-world self-sacrifice.
    DOI:  https://doi.org/10.1038/s41467-023-37283-5
  37. Nat Commun. 2023 Mar 31. 14(1): 1820
    Single-cell analysis of peripheral blood from high-altitude pulmonary hypertension patients identifies a distinct monocyte phenotype.
    Xin-Hua Wu, Yang-Yang He, Zhang-Rong Chen, Ze-Yuan He, Yi Yan, Yangzhige He, Guang-Ming Wang, Yu Dong, Ying Yang, Yi-Min Sun, Yong-Hong Ren, Qiu-Yan Zhao, Xiao-Dan Yang, Li-Ying Wang, Cai-Jun Fu, Miao He, Si-Jin Zhang, Ji-Fen Fu, Hong Liu, Zhi-Cheng Jing.
      Immune and inflammatory responses have an important function in the pathophysiology of pulmonary hypertension (PH). However, little is known about the immune landscape in peripheral circulation in patients with high-altitude pulmonary hypertension (HAPH). We apply single-cell transcriptomics to characterize the monocytes that are significantly enriched in the peripheral blood mononuclear cells (PBMC) of HAPH patients. We discover an increase in C1 (non-classical) and C2 (intermediate) monocytes in PBMCs and a decrease in hypoxia-inducible transcription factor-1α (HIF-1α) in all monocyte subsets associated with HAPH. In addition, we demonstrate that similar immune adaptations may exist in HAPH and PH. Overall, we characterize an immune cell atlas of the peripheral blood in HAPH patients. Our data provide evidence that specific monocyte subsets and HIF-1α downregulation might be implicated in the pathogenesis of HAPH.
    DOI:  https://doi.org/10.1038/s41467-023-37527-4
  38. Nat Commun. 2023 Mar 30. 14(1): 1731
    The RNA-binding protein hnRNP F is required for the germinal center B cell response.
    Hengjun Huang, Yuxing Li, Gaopu Zhang, Gui-Xin Ruan, Zhijian Zhu, Wenjing Chen, Jia Zou, Rui Zhang, Jing Wang, Yu Ouyang, Shengli Xu, Xijun Ou.
      The T cell-dependent (TD) antibody response involves the generation of high affinity, immunoglobulin heavy chain class-switched antibodies that are generated through germinal center (GC) response. This process is controlled by coordinated transcriptional and post-transcriptional gene regulatory mechanisms. RNA-binding proteins (RBPs) have emerged as critical players in post-transcriptional gene regulation. Here we demonstrate that B cell-specific deletion of RBP hnRNP F leads to diminished production of class-switched antibodies with high affinities in response to a TD antigen challenge. B cells deficient in hnRNP F are characterized by defective proliferation and c-Myc upregulation upon antigenic stimulation. Mechanistically, hnRNP F directly binds to the G-tracts of Cd40 pre-mRNA to promote the inclusion of Cd40 exon 6 that encodes its transmembrane domain, thus enabling appropriate CD40 cell surface expression. Furthermore, we find that hnRNP A1 and A2B1 can bind to the same region of Cd40 pre-mRNA but suppress exon 6 inclusion, suggesting that these hnRNPs and hnRNP F might antagonize each-other's effects on Cd40 splicing. In summary, our study uncovers an important posttranscriptional mechanism regulating the GC response.
    DOI:  https://doi.org/10.1038/s41467-023-37308-z
  39. Nat Methods. 2023 Mar 30.
    ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology.
    Meng Lu, Charles N Christensen, Jana M Weber, Tasuku Konno, Nino F Läubli, Katharina M Scherer, Edward Avezov, Pietro Lio, Alexei A Lapkin, Gabriele S Kaminski Schierle, Clemens F Kaminski.
      The ability to quantify structural changes of the endoplasmic reticulum (ER) is crucial for understanding the structure and function of this organelle. However, the rapid movement and complex topology of ER networks make this challenging. Here, we construct a state-of-the-art semantic segmentation method that we call ERnet for the automatic classification of sheet and tubular ER domains inside individual cells. Data are skeletonized and represented by connectivity graphs, enabling precise and efficient quantification of network connectivity. ERnet generates metrics on topology and integrity of ER structures and quantifies structural change in response to genetic or metabolic manipulation. We validate ERnet using data obtained by various ER-imaging methods from different cell types as well as ground truth images of synthetic ER structures. ERnet can be deployed in an automatic high-throughput and unbiased fashion and identifies subtle changes in ER phenotypes that may inform on disease progression and response to therapy.
    DOI:  https://doi.org/10.1038/s41592-023-01815-0
  40. Nat Genet. 2023 Mar 30.
    Nucleotide metabolism regulates human telomere length via telomerase activation.
    Tracy M Bryan.
      
    DOI:  https://doi.org/10.1038/s41588-023-01359-1
  41. Nat Chem Biol. 2023 Mar 30.
    Quantitative profiling of pseudouridylation landscape in the human transcriptome.
    Meiling Zhang, Zhe Jiang, Yichen Ma, Wenqing Liu, Yuan Zhuang, Bo Lu, Kai Li, Jinying Peng, Chengqi Yi.
      Pseudouridine (Ψ) is an abundant post-transcriptional RNA modification in ncRNA and mRNA. However, stoichiometric measurement of individual Ψ sites in human transcriptome remains unaddressed. Here we develop 'PRAISE', via selective chemical labeling of Ψ by bisulfite to induce nucleotide deletion signature during reverse transcription, to realize quantitative assessment of the Ψ landscape in the human transcriptome. Unlike traditional bisulfite treatment, our approach is based on quaternary base mapping and revealed an ~10% median modification level for 2,209 confident Ψ sites in HEK293T cells. By perturbing pseudouridine synthases, we obtained differential mRNA targets of PUS1, PUS7, TRUB1 and DKC1, with TRUB1 targets showing the highest modification stoichiometry. In addition, we quantified known and new Ψ sites in mitochondrial mRNA catalyzed by PUS1. Collectively, we provide a sensitive and convenient method to measure transcriptome-wide Ψ; we envision this quantitative approach would facilitate emerging efforts to elucidate the function and mechanism of mRNA pseudouridylation.
    DOI:  https://doi.org/10.1038/s41589-023-01304-7
  42. Nat Immunol. 2023 Mar 30.
    UT(se)X differences during immune responses.
    Alexandros Galaras, Mihalis Verykokakis.
      
    DOI:  https://doi.org/10.1038/s41590-023-01481-6
  43. Proc Natl Acad Sci U S A. 2023 Apr 04. 120(14): e2213207120
    microRNA-449a reduces growth hormone-stimulated senescent cell burden through PI3K-mTOR signaling.
    Sarah Noureddine, Jia Nie, Augusto Schneider, Vinal Menon, Zoubeida Fliesen, Joseph Dhahbi, Berta Victoria, Jeremiah Oyer, Liza Robles-Carrillo, Allancer Divino De Carvalho Nunes, Sarah Ashiqueali, Artur Janusz, Alicja Copik, Paul D Robbins, Nicolas Musi, Michal M Masternak.
      Cellular senescence, a hallmark of aging, has been implicated in the pathogenesis of many major age-related disorders, including neurodegeneration, atherosclerosis, and metabolic disease. Therefore, investigating novel methods to reduce or delay the accumulation of senescent cells during aging may attenuate age-related pathologies. microRNA-449a-5p (miR-449a) is a small, noncoding RNA down-regulated with age in normal mice but maintained in long-living growth hormone (GH)-deficient Ames Dwarf (df/df) mice. We found increased fibroadipogenic precursor cells, adipose-derived stem cells, and miR-449a levels in visceral adipose tissue of long-living df/df mice. Gene target analysis and our functional study with miR-449a-5p have revealed its potential as a serotherapeutic. Here, we test the hypothesis that miR-449a reduces cellular senescence by targeting senescence-associated genes induced in response to strong mitogenic signals and other damaging stimuli. We demonstrated that GH downregulates miR-449a expression and accelerates senescence while miR-449a upregulation using mimetics reduces senescence, primarily through targeted reduction of p16Ink4a, p21Cip1, and the PI3K-mTOR signaling pathway. Our results demonstrate that miR-449a is important in modulating key signaling pathways that control cellular senescence and the progression of age-related pathologies.
    Keywords:  adipose; growth hormone; longevity; miR-449a; senescence
    DOI:  https://doi.org/10.1073/pnas.2213207120
  44. Nat Commun. 2023 Mar 27. 14(1): 1712
    Structural and functional analysis of human pannexin 2 channel.
    Zhihui He, Yonghui Zhao, Michael J Rau, James A J Fitzpatrick, Rajan Sah, Hongzhen Hu, Peng Yuan.
      The pannexin 2 channel (PANX2) participates in multiple physiological processes including skin homeostasis, neuronal development, and ischemia-induced brain injury. However, the molecular basis of PANX2 channel function remains largely unknown. Here, we present a cryo-electron microscopy structure of human PANX2, which reveals pore properties contrasting with those of the intensely studied paralog PANX1. The extracellular selectivity filter, defined by a ring of basic residues, more closely resembles that of the distantly related volume-regulated anion channel (VRAC) LRRC8A, rather than PANX1. Furthermore, we show that PANX2 displays a similar anion permeability sequence as VRAC, and that PANX2 channel activity is inhibited by a commonly used VRAC inhibitor, DCPIB. Thus, the shared channel properties between PANX2 and VRAC may complicate dissection of their cellular functions through pharmacological manipulation. Collectively, our structural and functional analysis provides a framework for development of PANX2-specific reagents that are needed for better understanding of channel physiology and pathophysiology.
    DOI:  https://doi.org/10.1038/s41467-023-37413-z
  45. Nat Cell Biol. 2023 Mar 27.
    Perturbations in beta-cell heterogeneity in the pathogenesis of type 2 diabetes.
      
    DOI:  https://doi.org/10.1038/s41556-023-01105-z
  46. Nat Commun. 2023 Mar 29. 14(1): 1756
    Histone demethylase KDM2A is a selective vulnerability of cancers relying on alternative telomere maintenance.
    Fei Li, Yizhe Wang, Inah Hwang, Ja-Young Jang, Libo Xu, Zhong Deng, Eun Young Yu, Yiming Cai, Caizhi Wu, Zhenbo Han, Yu-Han Huang, Xiangao Huang, Ling Zhang, Jun Yao, Neal F Lue, Paul M Lieberman, Haoqiang Ying, Jihye Paik, Hongwu Zheng.
      Telomere length maintenance is essential for cellular immortalization and tumorigenesis. 5% - 10% of human cancers rely on a recombination-based mechanism termed alternative lengthening of telomeres (ALT) to sustain their replicative immortality, yet there are currently no targeted therapies. Through CRISPR/Cas9-based genetic screens in an ALT-immortalized isogenic cellular model, here we identify histone lysine demethylase KDM2A as a molecular vulnerability selectively for cells contingent on ALT-dependent telomere maintenance. Mechanistically, we demonstrate that KDM2A is required for dissolution of the ALT-specific telomere clusters following recombination-directed telomere DNA synthesis. We show that KDM2A promotes de-clustering of ALT multitelomeres through facilitating isopeptidase SENP6-mediated SUMO deconjugation at telomeres. Inactivation of KDM2A or SENP6 impairs post-recombination telomere de-SUMOylation and thus dissolution of ALT telomere clusters, leading to gross chromosome missegregation and mitotic cell death. These findings together establish KDM2A as a selective molecular vulnerability and a promising drug target for ALT-dependent cancers.
    DOI:  https://doi.org/10.1038/s41467-023-37480-2
  47. Nat Biotechnol. 2023 Mar 30.
    Reflective multi-immersion microscope objectives inspired by the Schmidt telescope.
    Fabian F Voigt, Anna Maria Reuss, Thomas Naert, Sven Hildebrand, Martina Schaettin, Adriana L Hotz, Lachlan Whitehead, Armin Bahl, Stephan C F Neuhauss, Alard Roebroeck, Esther T Stoeckli, Soeren S Lienkamp, Adriano Aguzzi, Fritjof Helmchen.
      Imaging large, cleared samples requires microscope objectives that combine a large field of view (FOV) with a long working distance (WD) and a high numerical aperture (NA). Ideally, such objectives should be compatible with a wide range of immersion media, which is challenging to achieve with conventional lens-based objective designs. Here we introduce the multi-immersion 'Schmidt objective' consisting of a spherical mirror and an aspherical correction plate as a solution to this problem. We demonstrate that a multi-photon variant of the Schmidt objective is compatible with all homogeneous immersion media and achieves an NA of 1.08 at a refractive index of 1.56, 1.1-mm FOV and 11-mm WD. We highlight its versatility by imaging cleared samples in various media ranging from air and water to benzyl alcohol/benzyl benzoate, dibenzyl ether and ethyl cinnamate and by imaging of neuronal activity in larval zebrafish in vivo. In principle, the concept can be extended to any imaging modality, including wide-field, confocal and light-sheet microscopy.
    DOI:  https://doi.org/10.1038/s41587-023-01717-8
  48. Sci Immunol. 2023 Mar 31. 8(81): eade3525
    NK-like CD8+ γδ T cells are expanded in persistent Mycobacterium tuberculosis infection.
    Roshni Roy Chowdhury, John R Valainis, Megha Dubey, Lotta von Boehmer, Elsa Sola, Julie Wilhelmy, Jing Guo, Oliver Kask, Mane Ohanyan, Meng Sun, Huang Huang, Xianxi Huang, Patricia K Nguyen, Thomas J Scriba, Mark M Davis, Sean C Bendall, Yueh-Hsiu Chien.
      The response of gamma delta (γδ) T cells in the acute versus chronic phases of the same infection is unclear. How γδ T cells function in acute Mycobacterium tuberculosis (Mtb) infection is well characterized, but their response during persistent Mtb infection is not well understood, even though most infections with Mtb manifest as a chronic, clinically asymptomatic state. Here, we analyze peripheral blood γδ T cells from a South African adolescent cohort and show that a unique CD8+ γδ T cell subset with features of "memory inflation" expands in chronic Mtb infection. These cells are hyporesponsive to T cell receptor (TCR)-mediated signaling but, like NK cells, can mount robust CD16-mediated cytotoxic responses. These CD8+ γδ T cells comprise a highly focused TCR repertoire, with clonotypes that are Mycobacterium specific but not phosphoantigen reactive. Using multiparametric single-cell pseudo-time trajectory analysis, we identified the differentiation paths that these CD8+ γδ T cells follow to develop into effectors in this infection state. Last, we found that circulating CD8+ γδ T cells also expand in other chronic inflammatory conditions, including cardiovascular disease and cancer, suggesting that persistent antigenic exposure may drive similar γδ T cell effector programs and differentiation fates.
    DOI:  https://doi.org/10.1126/sciimmunol.ade3525
  49. J Clin Invest. 2023 Mar 28. pii: e165019. [Epub ahead of print]
    CERT1 mutations perturb human development by disrupting sphingolipid homeostasis.
    Charlotte Gehin, Museer A Lone, Winston Lee, Laura Capolupo, Sylvia Ho, Adekemi M Adeyemi, Erica H Gerkes, Alexander Pa Stegmann, Estrella López-Martín, Eva Bermejo-Sánchez, Beatriz Martínez-Delgado, Christiane Zweier, Cornelia Kraus, Bernt Popp, Vincent Strehlow, Daniel Gräfe, Ina Knerr, Eppie R Jones, Stefano Zamuner, Luciano A Abriata, Vidya Kunnathully, Brandon E Moeller, Anthony Vocat, Samuel Rommelaere, Jean-Philippe Bocquete, Evelyne Ruchti, Greta Limoni, Marine Van Campenhoudt, Samuel Bourgeat, Petra Henklein, Christian Gilissen, Bregje W van Bon, Rolph Pfundt, Marjolein H Willemsen, Jolanda H Schieving, Emanuela Leonardi, Fiorenza Soli, Alessandra Murgia, Hui Guo, Qiumeng Zhang, Kun Xia, Christina R Fagerberg, Christoph P Beier, Martin J Larsen, Irene Valenzuela, Paula Fernández-Álvarez, Shiyi Xiong, Robert Śmigiel, Vanesa López-González, Lluís Armengol, Manuela Morleo, Angelo Selicorni, Annalaura Torella, Moira Blyth, Nicola S Cooper, Valerie Wilson, Renske Oegema, Yvan Herenger, Aurore Garde, Ange-Line Bruel, Frederic Tran Mau-Them, Alexis Br Maddocks, Jennifer M Bain, Musadiq A Bhat, Gregory Costain, Peter Kannu, Ashish Marwaha, Neena L Champaigne, Michael J Friez, Ellen B Richardson, Vykuntaraju K Gowda, Varunvenkat M Srinivasan, Yask Gupta, Tze Y Lim, Simone Sanna-Cherchi, Bruno Lemaitre, Toshiyuki Yamaji, Kentaro Hanada, John E Burke, Ana Marija Jakšić, Brian D McCabe, Paolo De Los Rios, Thorsten Hornemann, Giovanni D'Angelo, Vincenzo A Gennarino.
      Neural differentiation, synaptic transmission, and action potential propagation depend on membrane sphingolipids, whose metabolism is tightly regulated. Mutations in the ceramide transporter CERT (CERT1), which is involved in sphingolipid biosynthesis, are associated with intellectual disability, but the pathogenic mechanism remains obscure. Here, we characterize 31 individuals with de novo missense variants in CERT1. Several variants fall into a previously uncharacterized dimeric helical domain that enables CERT homeostatic inactivation, without which sphingolipid production goes unchecked. The clinical severity reflects the degree to which CERT autoregulation is disrupted, and inhibiting CERT pharmacologically corrects morphological and motor abnormalities in a Drosophila model of the disease, which we call CerTra syndrome. These findings uncover a central role for CERT autoregulation in the control of the sphingolipid biosynthetic flux, provide unexpected insight into the structural organisation of CERT, and suggest a possible therapeutic approach for CerTra syndrome patients.
    Keywords:  Cell Biology; Genetics; Lipid rafts; Neurodevelopment
    DOI:  https://doi.org/10.1172/JCI165019
  50. Sci Adv. 2023 Mar 29. 9(13): eadf9717
    A simple, time- and cost-effective, high-throughput depletion strategy for deep plasma proteomics.
    IMPACC Network
      We introduce a cost-effective, robust high-throughput-compatible plasma depletion method enabling in-depth profiling of plasma that detects >1300 proteins per run with a throughput of 60 samples per day. The method has been fully validated by processing >3000 samples with no apparent batch effect at a cost for the depletion step of ~$2.5 per sample.
    DOI:  https://doi.org/10.1126/sciadv.adf9717
  51. J Exp Med. 2023 Jun 05. pii: e20212523. [Epub ahead of print]220(6):
    IEC-intrinsic IL-1R signaling holds dual roles in regulating intestinal homeostasis and inflammation.
    Garrett R Overcast, Hannah E Meibers, Emily M Eshleman, Irene Saha, Lisa Waggoner, Krupaben N Patel, Viral G Jain, David B Haslam, Theresa Alenghat, Kelli L VanDussen, Chandrashekhar Pasare.
      Intestinal epithelial cells (IECs) constitute a critical first line of defense against microbes. While IECs are known to respond to various microbial signals, the precise upstream cues regulating diverse IEC responses are not clear. Here, we discover a dual role for IEC-intrinsic interleukin-1 receptor (IL-1R) signaling in regulating intestinal homeostasis and inflammation. Absence of IL-1R in epithelial cells abrogates a homeostatic antimicrobial program including production of antimicrobial peptides (AMPs). Mice deficient for IEC-intrinsic IL-1R are unable to clear Citrobacter rodentium (C. rodentium) but are protected from DSS-induced colitis. Mechanistically, IL-1R signaling enhances IL-22R-induced signal transducer and activator of transcription 3 (STAT3) phosphorylation in IECs leading to elevated production of AMPs. IL-1R signaling in IECs also directly induces expression of chemokines as well as genes involved in the production of reactive oxygen species. Our findings establish a protective role for IEC-intrinsic IL-1R signaling in combating infections but a detrimental role during colitis induced by epithelial damage.
    DOI:  https://doi.org/10.1084/jem.20212523
  52. J Biol Chem. 2023 Mar 23. pii: S0021-9258(23)00286-7. [Epub ahead of print] 104644
    An affinity tool for the isolation of endogenous active mTORC1 from various cellular sources.
    Yasir H Ibrahim, Spyridon Pantelios, Anders P Mutvei.
      The mechanistic target of rapamycin complex 1 (mTORC1) is a central regulator of mammalian cell growth that is dysregulated in a number of human diseases, including metabolic syndromes, aging and cancer. Structural, biochemical and pharmacological studies that have increased our understanding of how mTORC1 executes growth control often relied upon purified mTORC1 protein. However, current immunoaffinity-based purification methods are expensive, inefficient, and do not necessarily isolate endogenous mTORC1, hampering their overall utility in research. Here we present a simple tool to isolate endogenous mTORC1 from various cellular sources. By recombinantly expressing and isolating mTORC1-binding Rag GTPases from E. Coli and using them as affinity probes, we demonstrate that mTORC1 can be isolated from mouse, bovine and human sources. Our results indicate that mTORC1 isolated by this relatively inexpensive method is catalytically active and amenable to scaling. Collectively, this tool may be utilized to isolate mTORC1 from various cellular sources, organs, and disease contexts, aiding mTORC1-related research.
    DOI:  https://doi.org/10.1016/j.jbc.2023.104644
  53. J Cell Biol. 2023 May 01. pii: e202205103. [Epub ahead of print]222(5):
    Productive HIV-1 infection of tissue macrophages by fusion with infected CD4+ T cells.
    Rémi Mascarau, Marie Woottum, Léa Fromont, Rémi Gence, Vincent Cantaloube-Ferrieu, Zoï Vahlas, Kevin Lévêque, Florent Bertrand, Thomas Beunon, Arnaud Métais, Hicham El Costa, Nabila Jabrane-Ferrat, Yohan Gallois, Nicolas Guibert, Jean-Luc Davignon, Gilles Favre, Isabelle Maridonneau-Parini, Renaud Poincloux, Bernard Lagane, Serge Bénichou, Brigitte Raynaud-Messina, Christel Vérollet.
      Macrophages are essential for HIV-1 pathogenesis and represent major viral reservoirs. Therefore, it is critical to understand macrophage infection, especially in tissue macrophages, which are widely infected in vivo, but poorly permissive to cell-free infection. Although cell-to-cell transmission of HIV-1 is a determinant mode of macrophage infection in vivo, how HIV-1 transfers toward macrophages remains elusive. Here, we demonstrate that fusion of infected CD4+ T lymphocytes with human macrophages leads to their efficient and productive infection. Importantly, several tissue macrophage populations undergo this heterotypic cell fusion, including synovial, placental, lung alveolar, and tonsil macrophages. We also find that this mode of infection is modulated by the macrophage polarization state. This fusion process engages a specific short-lived adhesion structure and is controlled by the CD81 tetraspanin, which activates RhoA/ROCK-dependent actomyosin contractility in macrophages. Our study provides important insights into the mechanisms underlying infection of tissue-resident macrophages, and establishment of persistent cellular reservoirs in patients.
    DOI:  https://doi.org/10.1083/jcb.202205103
  54. Nat Commun. 2023 Mar 27. 14(1): 1709
    Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells.
    Maria A Missinato, Sean Murphy, Michaela Lynott, Michael S Yu, Anaïs Kervadec, Yu-Ling Chang, Suraj Kannan, Mafalda Loreti, Christopher Lee, Prashila Amatya, Hiroshi Tanaka, Chun-Teng Huang, Pier Lorenzo Puri, Chulan Kwon, Peter D Adams, Li Qian, Alessandra Sacco, Peter Andersen, Alexandre R Colas.
      Defining the mechanisms safeguarding cell fate identity in differentiated cells is crucial to improve 1) - our understanding of how differentiation is maintained in healthy tissues or altered in a disease state, and 2) - our ability to use cell fate reprogramming for regenerative purposes. Here, using a genome-wide transcription factor screen followed by validation steps in a variety of reprogramming assays (cardiac, neural and iPSC in fibroblasts and endothelial cells), we identified a set of four transcription factors (ATF7IP, JUNB, SP7, and ZNF207 [AJSZ]) that robustly opposes cell fate reprogramming in both lineage and cell type independent manners. Mechanistically, our integrated multi-omics approach (ChIP, ATAC and RNA-seq) revealed that AJSZ oppose cell fate reprogramming by 1) - maintaining chromatin enriched for reprogramming TF motifs in a closed state and 2) - downregulating genes required for reprogramming. Finally, KD of AJSZ in combination with MGT overexpression, significantly reduced scar size and improved heart function by 50%, as compared to MGT alone post-myocardial infarction. Collectively, our study suggests that inhibition of barrier to reprogramming mechanisms represents a promising therapeutic avenue to improve adult organ function post-injury.
    DOI:  https://doi.org/10.1038/s41467-023-37256-8
  55. Cell Rep. 2023 Mar 31. pii: S2211-1247(23)00347-9. [Epub ahead of print]42(4): 112336
    Site-1 protease inhibits mitochondrial respiration by controlling the TGF-β target gene Mss51.
    Muhammad G Mousa, Lahari Vuppaladhadiam, Meredith O Kelly, Terri Pietka, Shelby Ek, Karen C Shen, Gretchen A Meyer, Brian N Finck, Rita T Brookheart.
      The mitochondrial response to changes in cellular energy demand is necessary for cellular adaptation and organ function. Many genes are essential in orchestrating this response, including the transforming growth factor (TGF)-β1 target gene Mss51, an inhibitor of skeletal muscle mitochondrial respiration. Although Mss51 is implicated in the pathophysiology of obesity and musculoskeletal disease, how Mss51 is regulated is not entirely understood. Site-1 protease (S1P) is a key activator of several transcription factors required for cellular adaptation. However, the role of S1P in muscle is unknown. Here, we identify S1P as a negative regulator of muscle mass and mitochondrial respiration. S1P disruption in mouse skeletal muscle reduces Mss51 expression and increases muscle mass and mitochondrial respiration. The effects of S1P deficiency on mitochondrial activity are counteracted by overexpressing Mss51, suggesting that one way S1P inhibits respiration is by regulating Mss51. These discoveries expand our understanding of TGF-β signaling and S1P function.
    Keywords:  CP: Metabolism; Mss51; TGF-β; metabolism; mitochondria; muscle mass; respiration; site-1 protease; skeletal muscle
    DOI:  https://doi.org/10.1016/j.celrep.2023.112336
  56. Mol Cell. 2023 Mar 24. pii: S1097-2765(23)00163-6. [Epub ahead of print]
    Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome-depleted regions.
    Benjamin T Donovan, Hengye Chen, Priit Eek, Zhiyuan Meng, Caroline Jipa, Song Tan, Lu Bai, Michael G Poirier.
      Nucleosomes drastically limit transcription factor (TF) occupancy, while pioneer transcription factors (PFs) somehow circumvent this nucleosome barrier. In this study, we compare nucleosome binding of two conserved S. cerevisiae basic helix-loop-helix (bHLH) TFs, Cbf1 and Pho4. A cryo-EM structure of Cbf1 in complex with the nucleosome reveals that the Cbf1 HLH region can electrostatically interact with exposed histone residues within a partially unwrapped nucleosome. Single-molecule fluorescence studies show that the Cbf1 HLH region facilitates efficient nucleosome invasion by slowing its dissociation rate relative to DNA through interactions with histones, whereas the Pho4 HLH region does not. In vivo studies show that this enhanced binding provided by the Cbf1 HLH region enables nucleosome invasion and ensuing repositioning. These structural, single-molecule, and in vivo studies reveal the mechanistic basis of dissociation rate compensation by PFs and how this translates to facilitating chromatin opening inside cells.
    Keywords:  chromatin biology; cryoelectron microscopy single-particle analysis; dissociation rate compensation mechanism; gene regulation; nucleosome-depleted regions; pioneer transcription factors; single-molecule measurement
    DOI:  https://doi.org/10.1016/j.molcel.2023.03.006
  57. Nat Immunol. 2023 Mar 30.
    G-CSF drives autoinflammation in APLAID.
    Elisabeth Mulazzani, Klara Kong, Juan I Aróstegui, Ashley P Ng, Nishika Ranathunga, Waruni Abeysekera, Alexandra L Garnham, Sze-Ling Ng, Paul J Baker, Jacob T Jackson, John D Lich, Margaret L Hibbs, Ian P Wicks, Cynthia Louis, Seth L Masters.
      Missense mutations in PLCG2 can cause autoinflammation with phospholipase C gamma 2-associated antibody deficiency and immune dysregulation (APLAID). Here, we generated a mouse model carrying an APLAID mutation (p.Ser707Tyr) and found that inflammatory infiltrates in the skin and lungs were only partially ameliorated by removing inflammasome function via the deletion of caspase-1. Also, deleting interleukin-6 or tumor necrosis factor did not fully prevent APLAID mutant mice from autoinflammation. Overall, these findings are in accordance with the poor response individuals with APLAID have to treatments that block interleukin-1, JAK1/2 or tumor necrosis factor. Cytokine analysis revealed increased granulocyte colony-stimulating factor (G-CSF) levels as the most distinct feature in mice and individuals with APLAID. Remarkably, treatment with a G-CSF antibody completely reversed established disease in APLAID mice. Furthermore, excessive myelopoiesis was normalized and lymphocyte numbers rebounded. APLAID mice were also fully rescued by bone marrow transplantation from healthy donors, associated with reduced G-CSF production, predominantly from non-hematopoietic cells. In summary, we identify APLAID as a G-CSF-driven autoinflammatory disease, for which targeted therapy is feasible.
    DOI:  https://doi.org/10.1038/s41590-023-01473-6
  58. Nat Commun. 2023 Mar 28. 14(1): 1738
    Mitochondrial ATP synthase as a direct molecular target of chromium(III) to ameliorate hyperglycaemia stress.
    Haibo Wang, Ligang Hu, Hongyan Li, Yau-Tsz Lai, Xueying Wei, Xiaohan Xu, Zhenkun Cao, Huiming Cao, Qianya Wan, Yuen-Yan Chang, Aimin Xu, Qunfang Zhou, Guibin Jiang, Ming-Liang He, Hongzhe Sun.
      Chromium(III) is extensively used as a supplement for muscle development and the treatment of diabetes mellitus. However, its mode of action, essentiality, and physiological/pharmacological effects have been a subject of scientific debate for over half a century owing to the failure in identifying the molecular targets of Cr(III). Herein, by integrating fluorescence imaging with a proteomic approach, we visualized the Cr(III) proteome being mainly localized in the mitochondria, and subsequently identified and validated eight Cr(III)-binding proteins, which are predominately associated with ATP synthesis. We show that Cr(III) binds to ATP synthase at its beta subunit via the catalytic residues of Thr213/Glu242 and the nucleotide in the active site. Such a binding suppresses ATP synthase activity, leading to the activation of AMPK, improving glucose metabolism, and rescuing mitochondria from hyperglycaemia-induced fragmentation. The mode of action of Cr(III) in cells also holds true in type II diabetic male mice. Through this study, we resolve the long-standing question of how Cr(III) ameliorates hyperglycaemia stress at the molecular level, opening a new horizon for further exploration of the pharmacological effects of Cr(III).
    DOI:  https://doi.org/10.1038/s41467-023-37351-w
  59. Science. 2023 Mar 31. 379(6639): 1307-1308
    Protect newborn screening programs.
    Kellie Owens, Carolyn Chapman, Arthur Caplan.
      
    DOI:  https://doi.org/10.1126/science.adh2746
  60. Cell Rep. 2023 Mar 26. pii: S2211-1247(23)00317-0. [Epub ahead of print]42(4): 112306
    The ubiquitin E3 ligase TRIM10 promotes STING aggregation and activation in the Golgi apparatus.
    Lingli Kong, Chao Sui, Tian Chen, Lei Zhang, Wei Zhao, Yi Zheng, Bingyu Liu, Xiaochen Cheng, Chengjiang Gao.
      STING is an endoplasmic reticulum-resident protein regulating innate immunity. After binding with cyclic guanosine monophosphate-AMP (cGAMP), STING translocates from the endoplasmic reticulum (ER) to the Golgi apparatus to stimulate TBK1 and IRF3 activation, leading to expression of type I interferon. However, the exact mechanism concerning STING activation remains largely enigmatic. Here, we identify tripartite motif 10 (TRIM10) as a positive regulator of STING signaling. TRIM10-deficient macrophages exhibit reduced type I interferon production upon double-stranded DNA (dsDNA) or cGAMP stimulation and decreased resistance to herpes simplex virus 1 (HSV-1) infection. Additionally, TRIM10-deficient mice are more susceptible to HSV-1 infection and exhibit faster melanoma growth. Mechanistically, TRIM10 associates with STING and catalyzes K27- and K29-linked polyubiquitination of STING at K289 and K370, which promotes STING trafficking from the ER to the Golgi apparatus, formation of STING aggregates, and recruitment of TBK1 to STING, ultimately enhancing the STING-dependent type I interferon response. Our study defines TRIM10 as a critical activator in cGAS-STING-mediated antiviral and antitumor immunity.
    Keywords:  CP: Cell biology; CP: Immunology; STING; TRIM10; innate immunity; polyubiquitination
    DOI:  https://doi.org/10.1016/j.celrep.2023.112306
  61. Nat Rev Immunol. 2023 Mar 29.
    Adaptive meets innate: CD8+ T cells kill MHC-I-negative tumour cells.
    Bas W A Peeters, Geraldine M Gillespie.
      
    DOI:  https://doi.org/10.1038/s41577-023-00872-y
  62. Cell Death Dis. 2023 Mar 28. 14(3): 216
    Mitochondria-derived H2O2 triggers liver regeneration via FoxO3a signaling pathway after partial hepatectomy in mice.
    Hua Bai, Cong-Wen Fang, Ying Shi, Song Zhai, An Jiang, Ying-Na Li, Lin Wang, Qi-Ling Liu, Geng-Yao Zhou, Jia-Hao Cao, Jia Li, Xue-Kang Yang, Xu-Jun Qin.
      Reactive oxygen species (ROS) can induce oxidative injury and are generally regarded as toxic byproducts, although they are increasingly recognized for their signaling functions. Increased ROS often accompanies liver regeneration (LR) after liver injuries, however, their role in LR and the underlying mechanism remains unclear. Here, by employing a mouse LR model of partial hepatectomy (PHx), we found that PHx induced rapid increases of mitochondrial hydrogen peroxide (H2O2) and intracellular H2O2 at an early stage, using a mitochondria-specific probe. Scavenging mitochondrial H2O2 in mice with liver-specific overexpression of mitochondria-targeted catalase (mCAT) decreased intracellular H2O2 and compromised LR, while NADPH oxidases (NOXs) inhibition did not affect intracellular H2O2 or LR, indicating that mitochondria-derived H2O2 played an essential role in LR after PHx. Furthermore, pharmacological activation of FoxO3a impaired the H2O2-triggered LR, while liver-specific knockdown of FoxO3a by CRISPR-Cas9 technology almost abolished the inhibition of LR by overexpression of mCAT, demonstrating that FoxO3a signaling pathway mediated mitochondria-derived H2O2 triggered LR after PHx. Our findings uncover the beneficial roles of mitochondrial H2O2 and the redox-regulated underlying mechanisms during LR, which shed light on potential therapeutic interventions for LR-related liver injury. Importantly, these findings also indicate that improper antioxidative intervention might impair LR and delay the recovery of LR-related diseases in clinics.
    DOI:  https://doi.org/10.1038/s41419-023-05744-w
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