bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2023–09–24
48 papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. My failure comeback.
  2. People.
  3. Human regulatory T cells turn into cytotoxic 'exTreg' cells in atherosclerosis.
  4. γδ stress detectors.
  5. Acetylation discriminates disease-specific tau deposition.
  6. Ser14 phosphorylation of Bcl-xL mediates compensatory cardiac hypertrophy in male mice.
  7. Glycerol contributes to tuberculosis susceptibility in male mice with type 2 diabetes.
  8. Structural insights into FSP1 catalysis and ferroptosis inhibition.
  9. Functional characterization of Alzheimer's disease genetic variants in microglia.
  10. Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping.
  11. Ultrasound trapping and navigation of microrobots in the mouse brain vasculature.
  12. Top Reads.
  13. Metabolic Reprogramming via ACOD1 depletion enhances function of human induced pluripotent stem cell-derived CAR-macrophages in solid tumors.
  14. Reductive carboxylation epigenetically instructs T cell differentiation.
  15. Catching proteins at play: the method revealing the cell's inner mysteries.
  16. Temporal landscape of mitochondrial proteostasis governed by the UPRmt.
  17. FedEx for your cells: this biological delivery service could treat disease.
  18. Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on Kupffer cell epigenomes and transcriptomes.
  19. Metabolic control of antitumor immunity.
  20. Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex.
  21. Post-COVID-19 epigenetic signatures.
  22. CREB1-driven CXCR4hi neutrophils promote skin inflammation in mouse models and human patients.
  23. Mitochondria-ER contact mediated by MFN2-SERCA2 interaction supports CD8+ T cell metabolic fitness and function in tumors.
  24. Defining E3 ligase-substrate relationships through multiplex CRISPR screening.
  25. Loss of Grin2a causes a transient delay in the electrophysiological maturation of hippocampal parvalbumin interneurons.
  26. NLRP3 selectively drives IL-1β secretion by Pseudomonas aeruginosa infected neutrophils and regulates corneal disease severity.
  27. Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease.
  28. CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms.
  29. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas.
  30. The VCAM1-ApoE pathway directs microglial chemotaxis and alleviates Alzheimer's disease pathology.
  31. ABCC1 and glutathione metabolism limit the efficacy of BCL-2 inhibitors in acute myeloid leukemia.
  32. Endothelial Sp1/Sp3 are essential to the effect of captopril on blood pressure in male mice.
  33. Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition.
  34. Single-cell genotypic and phenotypic analysis of measurable residual disease in acute myeloid leukemia.
  35. Light-enhanced molecular polarity enabling multispectral color-cognitive memristor for neuromorphic visual system.
  36. Circadian clock disruption promotes the degeneration of dopaminergic neurons in male Drosophila.
  37. A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps.
  38. C9orf72-ALS human iPSC microglia are pro-inflammatory and toxic to co-cultured motor neurons via MMP9.
  39. The β1-adrenergic receptor links sympathetic nerves to T cell exhaustion.
  40. Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.
  41. MAD2-dependent insulin receptor endocytosis regulates metabolic homeostasis.
  42. Supervised discovery of interpretable gene programs from single-cell data.
  43. A revolution in obesity treatment.
  44. Molecular basis for maternal inheritance of human mitochondrial DNA.
  45. For Health Equity, Location Matters.
  46. Epithelial plasticity and innate immune activation promote lung tissue remodeling following respiratory viral infection.
  47. Nucleolar condensates: A cellular machinery necessary for T cell activation.
  48. Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks.
  1. Science. 2023 Sep 22. 381(6664): 1366
    My failure comeback.
    Lan Nguyen Chaplin.
      
    DOI:  https://doi.org/10.1126/science.adk8817
  2. Nat Biotechnol. 2023 Sep;41(9): 1356
    People.
      
    DOI:  https://doi.org/10.1038/s41587-023-01941-2
  3. Nat Immunol. 2023 Sep 21.
    Human regulatory T cells turn into cytotoxic 'exTreg' cells in atherosclerosis.
      
    DOI:  https://doi.org/10.1038/s41590-023-01629-4
  4. Nat Immunol. 2023 Sep 21.
    γδ stress detectors.
    Nicholas J Bernard.
      
    DOI:  https://doi.org/10.1038/s41590-023-01638-3
  5. Nat Commun. 2023 Sep 22. 14(1): 5919
    Acetylation discriminates disease-specific tau deposition.
    Pijush Chakraborty, Gwladys Rivière, Alina Hebestreit, Alain Ibáñez de Opakua, Ina M Vorberg, Loren B Andreas, Markus Zweckstetter.
      Pathogenic aggregation of the protein tau is a hallmark of Alzheimer's disease and several other tauopathies. Tauopathies are characterized by the deposition of specific tau isoforms as disease-related tau filament structures. The molecular processes that determine isoform-specific deposition of tau are however enigmatic. Here we show that acetylation of tau discriminates its isoform-specific aggregation. We reveal that acetylation strongly attenuates aggregation of four-repeat tau protein, but promotes amyloid formation of three-repeat tau. We further identify acetylation of lysine 298 as a hot spot for isoform-specific tau aggregation. Solid-state NMR spectroscopy demonstrates that amyloid fibrils formed by unmodified and acetylated three-repeat tau differ in structure indicating that site-specific acetylation modulates tau structure. The results implicate acetylation as a critical regulator that guides the selective aggregation of three-repeat tau and the development of tau isoform-specific neurodegenerative diseases.
    DOI:  https://doi.org/10.1038/s41467-023-41672-1
  6. Nat Commun. 2023 09 19. 14(1): 5805
    Ser14 phosphorylation of Bcl-xL mediates compensatory cardiac hypertrophy in male mice.
    Michinari Nakamura, Mariko Aoyagi Keller, Nadezhda Fefelova, Peiyong Zhai, Tong Liu, Yimin Tian, Shohei Ikeda, Dominic P Del Re, Hong Li, Lai-Hua Xie, Junichi Sadoshima.
      The anti-apoptotic function of Bcl-xL in the heart during ischemia/reperfusion is diminished by K-Ras-Mst1-mediated phosphorylation of Ser14, which allows dissociation of Bcl-xL from Bax and promotes cardiomyocyte death. Here we show that Ser14 phosphorylation of Bcl-xL is also promoted by hemodynamic stress in the heart, through the H-Ras-ERK pathway. Bcl-xL Ser14 phosphorylation-resistant knock-in male mice develop less cardiac hypertrophy and exhibit contractile dysfunction and increased mortality during acute pressure overload. Bcl-xL Ser14 phosphorylation enhances the Ca2+ transient by blocking the inhibitory interaction between Bcl-xL and IP3Rs, thereby promoting Ca2+ release and activation of the calcineurin-NFAT pathway, a Ca2+-dependent mechanism that promotes cardiac hypertrophy. These results suggest that phosphorylation of Bcl-xL at Ser14 in response to acute pressure overload plays an essential role in mediating compensatory hypertrophy by inducing the release of Bcl-xL from IP3Rs, alleviating the negative constraint of Bcl-xL upon the IP3R-NFAT pathway.
    DOI:  https://doi.org/10.1038/s41467-023-41595-x
  7. Nat Commun. 2023 09 20. 14(1): 5840
    Glycerol contributes to tuberculosis susceptibility in male mice with type 2 diabetes.
    Nuria Martinez, Lorissa J Smulan, Michael L Jameson, Clare M Smith, Kelly Cavallo, Michelle Bellerose, John Williams, Kim West, Christopher M Sassetti, Amit Singhal, Hardy Kornfeld.
      Diabetes mellitus increases risk for tuberculosis disease and adverse outcomes. Most people with both conditions have type 2 diabetes, but it is unknown if type 1 and type 2 diabetes have identical effects on tuberculosis susceptibility. Here we show that male mice receiving a high-fat diet and streptozotocin to model type 2 diabetes, have higher mortality, more lung pathology, and higher bacterial burden following Mycobacterium tuberculosis infection compared to mice treated with streptozotocin or high-fat diet alone. Type 2 diabetes model mice have elevated plasma glycerol, which is a preferred carbon source for M. tuberculosis. Infection studies with glycerol kinase mutant M. tuberculosis reveal that glycerol utilization contributes to the susceptibility of the type 2 diabetes mice. Hyperglycemia impairs protective immunity against M. tuberculosis in both forms of diabetes, but our data show that elevated glycerol contributes to an additional adverse effect uniquely relevant to type 2 diabetes.
    DOI:  https://doi.org/10.1038/s41467-023-41519-9
  8. Nat Commun. 2023 Sep 22. 14(1): 5933
    Structural insights into FSP1 catalysis and ferroptosis inhibition.
    Yun Lv, Chunhui Liang, Qichao Sun, Jing Zhu, Haiyan Xu, Xiaoqing Li, Yao-Yao Li, Qihai Wang, Huiqing Yuan, Bo Chu, Deyu Zhu.
      Ferroptosis suppressor protein 1 (FSP1, also known as AIMF2, AMID or PRG3) is a recently identified glutathione-independent ferroptosis suppressor1-3, but its underlying structural mechanism remains unknown. Here we report the crystal structures of Gallus gallus FSP1 in its substrate-free and ubiquinone-bound forms. The structures reveal a FAD-binding domain and a NAD(P)H-binding domain, both of which are shared with AIF and NADH oxidoreductases4-9, and a characteristic carboxy-terminal domain as well. We demonstrate that the carboxy-terminal domain is crucial for the catalytic activity and ferroptosis inhibition of FSP1 by mediating the functional dimerization of FSP1, and the formation of two active sites located on two sides of FAD, which are responsible for ubiquinone reduction and a unique FAD hydroxylation respectively. We also identify that FSP1 can catalyze the production of H2O2 and the conversion of FAD to 6-hydroxy-FAD in the presence of oxygen and NAD(P)H in vitro, and 6-hydroxy-FAD directly inhibits ferroptosis in cells. Together, these findings further our understanding on the catalytic and ferroptosis suppression mechanisms of FSP1 and establish 6-hydroxy-FAD as an active cofactor in FSP1 and a potent radical-trapping antioxidant in ferroptosis inhibition.
    DOI:  https://doi.org/10.1038/s41467-023-41626-7
  9. Nat Genet. 2023 Sep 21.
    Functional characterization of Alzheimer's disease genetic variants in microglia.
    Xiaoyu Yang, Jia Wen, Han Yang, Ian R Jones, Xiaodong Zhu, Weifang Liu, Bingkun Li, Claire D Clelland, Wenjie Luo, Man Ying Wong, Xingjie Ren, Xiekui Cui, Michael Song, Hongjiang Liu, Cady Chen, Nicolas Eng, Mirunalini Ravichandran, Yang Sun, David Lee, Eric Van Buren, Min-Zhi Jiang, Candace S Y Chan, Chun Jimmie Ye, Rushika M Perera, Li Gan, Yun Li, Yin Shen.
      Candidate cis-regulatory elements (cCREs) in microglia demonstrate the most substantial enrichment for Alzheimer's disease (AD) heritability compared to other brain cell types. However, whether and how these genome-wide association studies (GWAS) variants contribute to AD remain elusive. Here we prioritize 308 previously unreported AD risk variants at 181 cCREs by integrating genetic information with microglia-specific 3D epigenome annotation. We further establish the link between functional variants and target genes by single-cell CRISPRi screening in microglia. In addition, we show that AD variants exhibit allelic imbalance on target gene expression. In particular, rs7922621 is the effective variant in controlling TSPAN14 expression among other nominated variants in the same cCRE and exerts multiple physiological effects including reduced cell surface ADAM10 and altered soluble TREM2 (sTREM2) shedding. Our work represents a systematic approach to prioritize and characterize AD-associated variants and provides a roadmap for advancing genetic association to experimentally validated cell-type-specific phenotypes and mechanisms.
    DOI:  https://doi.org/10.1038/s41588-023-01506-8
  10. Mol Cell. 2023 Sep 21. pii: S1097-2765(23)00658-5. [Epub ahead of print]83(18): 3377-3392.e6
    Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping.
    Zhiqian Zhang, Brandon Sie, Aiquan Chang, Yumei Leng, Christopher Nardone, Richard T Timms, Stephen J Elledge.
      The ubiquitin-proteasome system plays a critical role in biology by regulating protein degradation. Despite their importance, precise recognition specificity is known for a few of the 600 E3s. Here, we establish a two-pronged strategy for identifying and mapping critical residues of internal degrons on a proteome-scale in HEK-293T cells. We employ global protein stability profiling combined with machine learning to identify 15,800 peptides likely to contain sequence-dependent degrons. We combine this with scanning mutagenesis to define critical residues for over 5,000 predicted degrons. Focusing on Cullin-RING ligase degrons, we generated mutational fingerprints for 219 degrons and developed DegronID, a computational algorithm enabling the clustering of degron peptides with similar motifs. CRISPR analysis enabled the discovery of E3-degron pairs, of which we uncovered 16 pairs that revealed extensive degron variability and structural determinants. We provide the visualization of these data on the public DegronID data browser as a resource for future exploration.
    Keywords:  Alphafold2; CRL; Cullin-RING ligase; DegronID; E3 ubiquitin ligase; GPS; degron; global protein stability; protein degradation; ubiquitination
    DOI:  https://doi.org/10.1016/j.molcel.2023.08.022
  11. Nat Commun. 2023 Sep 21. 14(1): 5889
    Ultrasound trapping and navigation of microrobots in the mouse brain vasculature.
    Alexia Del Campo Fonseca, Chaim Glück, Jeanne Droux, Yann Ferry, Carole Frei, Susanne Wegener, Bruno Weber, Mohamad El Amki, Daniel Ahmed.
      The intricate and delicate anatomy of the brain poses significant challenges for the treatment of cerebrovascular and neurodegenerative diseases. Thus, precise local drug delivery in hard-to-reach brain regions remains an urgent medical need. Microrobots offer potential solutions; however, their functionality in the brain remains restricted by limited imaging capabilities and complications within blood vessels, such as high blood flows, osmotic pressures, and cellular responses. Here, we introduce ultrasound-activated microrobots for in vivo navigation in brain vasculature. Our microrobots consist of lipid-shelled microbubbles that autonomously aggregate and propel under ultrasound irradiation. We investigate their capacities in vitro within microfluidic-based vasculatures and in vivo within vessels of a living mouse brain. These microrobots self-assemble and execute upstream motion in brain vasculature, achieving velocities up to 1.5 µm/s and moving against blood flows of ~10 mm/s. This work represents a substantial advance towards the therapeutic application of microrobots within the complex brain vasculature.
    DOI:  https://doi.org/10.1038/s41467-023-41557-3
  12. J Immunol. 2023 Oct 01. 211(7): 1063
    Top Reads.
      
    DOI:  https://doi.org/10.4049/jimmunol.2390016
  13. Nat Commun. 2023 09 18. 14(1): 5778
    Metabolic Reprogramming via ACOD1 depletion enhances function of human induced pluripotent stem cell-derived CAR-macrophages in solid tumors.
    Xudong Wang, Siyu Su, Yuqing Zhu, Xiaolong Cheng, Chen Cheng, Leilei Chen, Anhua Lei, Li Zhang, Yuyan Xu, Dan Ye, Yi Zhang, Wei Li, Jin Zhang.
      The pro-inflammatory state of macrophages, underpinned by their metabolic condition, is essentially affecting their capacity of combating tumor cells. Here we find, via a pooled metabolic gene knockout CRISPR screen that KEAP1 and ACOD1 are strong regulators of the pro-inflammatory state in macrophages. We show that ACOD1 knockout macrophages, generated in our induced pluripotent stem cell-derived CAR-macrophage (CAR-iMAC) platform, are strongly and persistently polarized toward the pro-inflammatory state, which manifests in increased reactive oxygen species (ROS) production, more potent phagocytosis and enhanced cytotoxic functions against cancer cells in vitro. In ovarian or pancreatic cancer mouse models, ACOD1-depleted CAR-iMACs exhibit enhanced capacity in repressing tumors, leading to increased survival. In addition, combining ACOD1-depleted CAR-iMACs with immune checkpoint inhibitors (ICI), such as anti-CD47 or anti-PD1 antibodies, result in even stronger tumor suppressing effect. Mechanistically, the depletion of ACOD1 reduces levels of the immuno-metabolite itaconate, allowing KEAP1 to prevent NRF2 from entering the nucleus to activate an anti-inflammatory program. This study thus lays down the proof of principle for targeting ACOD1 in myeloid cells for cancer immunotherapy and introduces metabolically engineered human iPSC-derived CAR-iMACs cells with enhanced polarization and anti-tumor functions in adoptive cell transfer therapies.
    DOI:  https://doi.org/10.1038/s41467-023-41470-9
  14. Nature. 2023 Sep 20.
    Reductive carboxylation epigenetically instructs T cell differentiation.
    Alison Jaccard, Tania Wyss, Noelia Maldonado-Pérez, Jan A Rath, Alessio Bevilacqua, Jhan-Jie Peng, Anouk Lepez, Christine Von Gunten, Fabien Franco, Kung-Chi Kao, Nicolas Camviel, Francisco Martín, Bart Ghesquière, Denis Migliorini, Caroline Arber, Pedro Romero, Ping-Chih Ho, Mathias Wenes.
      Protective immunity against pathogens or cancer is mediated by the activation and clonal expansion of antigen-specific naive T cells into effector T cells. To sustain their rapid proliferation and effector functions, naive T cells switch their quiescent metabolism to an anabolic metabolism through increased levels of aerobic glycolysis, but also through mitochondrial metabolism and oxidative phosphorylation, generating energy and signalling molecules1-3. However, how that metabolic rewiring drives and defines the differentiation of T cells remains unclear. Here we show that proliferating effector CD8+ T cells reductively carboxylate glutamine through the mitochondrial enzyme isocitrate dehydrogenase 2 (IDH2). Notably, deletion of the gene encoding IDH2 does not impair the proliferation of T cells nor their effector function, but promotes the differentiation of memory CD8+ T cells. Accordingly, inhibiting IDH2 during ex vivo manufacturing of chimeric antigen receptor (CAR) T cells induces features of memory T cells and enhances antitumour activity in melanoma, leukaemia and multiple myeloma. Mechanistically, inhibition of IDH2 activates compensating metabolic pathways that cause a disequilibrium in metabolites regulating histone-modifying enzymes, and this maintains chromatin accessibility at genes that are required for the differentiation of memory T cells. These findings show that reductive carboxylation in CD8+ T cells is dispensable for their effector response and proliferation, but that it mainly produces a pattern of metabolites that epigenetically locks CD8+ T cells into a terminal effector differentiation program. Blocking this metabolic route allows the increased formation of memory T cells, which could be exploited to optimize the therapeutic efficacy of CAR T cells.
    DOI:  https://doi.org/10.1038/s41586-023-06546-y
  15. Nature. 2023 Sep;621(7979): 646-648
    Catching proteins at play: the method revealing the cell's inner mysteries.
    Michael Eisenstein.
      
    Keywords:  Biological techniques; Cell biology; Microscopy; Structural biology
    DOI:  https://doi.org/10.1038/d41586-023-02909-7
  16. Sci Adv. 2023 Sep 22. 9(38): eadh8228
    Temporal landscape of mitochondrial proteostasis governed by the UPRmt.
    Louise Uoselis, Runa Lindblom, Wai Kit Lam, Catharina J Küng, Marvin Skulsuppaisarn, Grace Khuu, Thanh N Nguyen, Danielle L Rudler, Aleksandra Filipovska, Ralf B Schittenhelm, Michael Lazarou.
      Breakdown of mitochondrial proteostasis activates quality control pathways including the mitochondrial unfolded protein response (UPRmt) and PINK1/Parkin mitophagy. However, beyond the up-regulation of chaperones and proteases, we have a limited understanding of how the UPRmt remodels and restores damaged mitochondrial proteomes. Here, we have developed a functional proteomics framework, termed MitoPQ (Mitochondrial Proteostasis Quantification), to dissect the UPRmt's role in maintaining proteostasis during stress. We find essential roles for the UPRmt in both protecting and repairing proteostasis, with oxidative phosphorylation metabolism being a central target of the UPRmt. Transcriptome analyses together with MitoPQ reveal that UPRmt transcription factors drive independent signaling arms that act in concert to maintain proteostasis. Unidirectional interplay between the UPRmt and PINK1/Parkin mitophagy was found to promote oxidative phosphorylation recovery when the UPRmt failed. Collectively, this study defines the network of proteostasis mediated by the UPRmt and highlights the value of functional proteomics in decoding stressed proteomes.
    DOI:  https://doi.org/10.1126/sciadv.adh8228
  17. Nature. 2023 Sep;621(7979): 462-464
    FedEx for your cells: this biological delivery service could treat disease.
    Alison Abbott.
      
    Keywords:  Cell biology; Molecular biology; Therapeutics
    DOI:  https://doi.org/10.1038/d41586-023-02906-w
  18. Nat Immunol. 2023 Sep 21.
    Discrimination of cell-intrinsic and environment-dependent effects of natural genetic variation on Kupffer cell epigenomes and transcriptomes.
    Hunter Bennett, Ty D Troutman, Enchen Zhou, Nathanael J Spann, Verena M Link, Jason S Seidman, Christian K Nickl, Yohei Abe, Mashito Sakai, Martina P Pasillas, Justin M Marlman, Carlos Guzman, Mojgan Hosseini, Bernd Schnabl, Christopher K Glass.
      Noncoding genetic variation drives phenotypic diversity, but underlying mechanisms and affected cell types are incompletely understood. Here, investigation of effects of natural genetic variation on the epigenomes and transcriptomes of Kupffer cells derived from inbred mouse strains identified strain-specific environmental factors influencing Kupffer cell phenotypes, including leptin signaling in Kupffer cells from a steatohepatitis-resistant strain. Cell-autonomous and non-cell-autonomous effects of genetic variation were resolved by analysis of F1 hybrid mice and cells engrafted into an immunodeficient host. During homeostasis, non-cell-autonomous trans effects of genetic variation dominated control of Kupffer cells, while strain-specific responses to acute lipopolysaccharide injection were dominated by actions of cis-acting effects modifying response elements for lineage-determining and signal-dependent transcription factors. These findings demonstrate that epigenetic landscapes report on trans effects of genetic variation and serve as a resource for deeper analyses into genetic control of transcription in Kupffer cells and macrophages in vitro.
    DOI:  https://doi.org/10.1038/s41590-023-01631-w
  19. Science. 2023 Sep 22. 381(6664): 1287-1288
    Metabolic control of antitumor immunity.
    Andromachi Pouikli, Christian Frezza.
      Mitochondrial metabolite reduces melanoma growth by boosting antigen presentation.
    DOI:  https://doi.org/10.1126/science.adk1785
  20. Nat Commun. 2023 Sep 22. 14(1): 5907
    Determining subunit-subunit interaction from statistics of cryo-EM images: observation of nearest-neighbor coupling in a circadian clock protein complex.
    Xu Han, Dongliang Zhang, Lu Hong, Daqi Yu, Zhaolong Wu, Tian Yang, Michael Rust, Yuhai Tu, Qi Ouyang.
      Biological processes are typically actuated by dynamic multi-subunit molecular complexes. However, interactions between subunits, which govern the functions of these complexes, are hard to measure directly. Here, we develop a general approach combining cryo-EM imaging technology and statistical modeling and apply it to study the hexameric clock protein KaiC in Cyanobacteria. By clustering millions of KaiC monomer images, we identify two major conformational states of KaiC monomers. We then classify the conformational states of (>160,000) KaiC hexamers by the thirteen distinct spatial arrangements of these two subunit states in the hexamer ring. We find that distributions of the thirteen hexamer conformational patterns for two KaiC phosphorylation mutants can be fitted quantitatively by an Ising model, which reveals a significant cooperativity between neighboring subunits with phosphorylation shifting the probability of subunit conformation. Our results show that a KaiC hexamer can respond in a switch-like manner to changes in its phosphorylation level.
    DOI:  https://doi.org/10.1038/s41467-023-41575-1
  21. Nat Immunol. 2023 Sep 21.
    Post-COVID-19 epigenetic signatures.
    Laurie A Dempsey.
      
    DOI:  https://doi.org/10.1038/s41590-023-01639-2
  22. Nat Commun. 2023 Sep 22. 14(1): 5894
    CREB1-driven CXCR4hi neutrophils promote skin inflammation in mouse models and human patients.
    Jiaoling Chen, Yaxing Bai, Ke Xue, Zhiguo Li, Zhenlai Zhu, Qingyang Li, Chen Yu, Bing Li, Shengxian Shen, Pei Qiao, Caixia Li, Yixin Luo, Hongjiang Qiao, Erle Dang, Wen Yin, Johann E Gudjonsson, Gang Wang, Shuai Shao.
      Neutrophils have a pathogenic function in inflammation via releasing pro-inflammatory mediators or neutrophil extracellular traps (NETs). However, their heterogeneity and pro-inflammatory mechanisms remain unclear. Here, we demonstrate that CXCR4hi neutrophils accumulate in the blood and inflamed skin in human psoriasis, and correlate with disease severity. Compared to CXCR4lo neutrophils, CXCR4hi neutrophils have enhanced NETs formation, phagocytic function, neutrophil degranulation, and overexpression of pro-inflammatory cytokines and chemokines in vitro. This is accompanied by a metabolic shift in CXCR4hi neutrophils toward glycolysis and lactate release, thereby promoting vascular permeability and remodeling. CXCR4 expression in neutrophils is dependent on CREB1, a transcription factor activated by TNF and CXCL12, and regulated by de novo synthesis. In vivo, CXCR4hi neutrophil infiltration amplifies skin inflammation, whereas blockade of CXCR4hi neutrophils through CXCR4 or CXCL12 inhibition leads to suppression of immune responses. In this work, our study identifies CREB1 as a critical regulator of CXCR4hi neutrophil development and characterizes the contribution of CXCR4hi neutrophils to vascular remodeling and inflammatory responses in skin.
    DOI:  https://doi.org/10.1038/s41467-023-41484-3
  23. Sci Immunol. 2023 Sep 29. 8(87): eabq2424
    Mitochondria-ER contact mediated by MFN2-SERCA2 interaction supports CD8+ T cell metabolic fitness and function in tumors.
    Jie-Feng Yang, Xudong Xing, Li Luo, Xin-Wei Zhou, Jian-Xiong Feng, Kang-Bo Huang, Huashan Liu, Shanzhao Jin, Yi-Na Liu, Shi-Hui Zhang, Yi-Hui Pan, Bing Yu, Jin-Yu Yang, Yu-Lu Cao, Yun Cao, Cliff Y Yang, Yuan Wang, Yuxia Zhang, Jiang Li, Xiaojun Xia, Tiebang Kang, Rui-Hua Xu, Ping Lan, Jun-Hang Luo, Hui Han, Fan Bai, Song Gao.
      Metabolic fitness of T cells is essential for their vitality, which is largely dependent on the behavior of the mitochondria. The nature of mitochondrial behavior in tumor-infiltrating T cells remains poorly understood. In this study, we show that mitofusin-2 (MFN2) expression is positively correlated with the prognosis of multiple cancers. Genetic ablation of Mfn2 in CD8+ T cells dampens mitochondrial metabolism and function and promotes tumor progression. In tumor-infiltrating CD8+ T cells, MFN2 enhances mitochondria-endoplasmic reticulum (ER) contact by interacting with ER-embedded Ca2+-ATPase SERCA2, facilitating the mitochondrial Ca2+ influx required for efficient mitochondrial metabolism. MFN2 stimulates the ER Ca2+ retrieval activity of SERCA2, thereby preventing excessive mitochondrial Ca2+ accumulation and apoptosis. Elevating mitochondria-ER contact by increasing MFN2 in CD8+ T cells improves the efficacy of cancer immunotherapy. Thus, we reveal a tethering-and-buffering mechanism of organelle cross-talk that regulates the metabolic fitness of tumor-infiltrating CD8+ T cells and highlights the therapeutic potential of enhancing MFN2 expression to optimize T cell function.
    DOI:  https://doi.org/10.1126/sciimmunol.abq2424
  24. Nat Cell Biol. 2023 Sep 21.
    Defining E3 ligase-substrate relationships through multiplex CRISPR screening.
    Richard T Timms, Elijah L Mena, Yumei Leng, Mamie Z Li, Iva A Tchasovnikarova, Itay Koren, Stephen J Elledge.
      Specificity within the ubiquitin-proteasome system is primarily achieved through E3 ubiquitin ligases, but for many E3s their substrates-and in particular the molecular features (degrons) that they recognize-remain largely unknown. Current approaches for assigning E3s to their cognate substrates are tedious and low throughput. Here we developed a multiplex CRISPR screening platform to assign E3 ligases to their cognate substrates at scale. A proof-of-principle multiplex screen successfully performed ~100 CRISPR screens in a single experiment, refining known C-degron pathways and identifying an additional pathway through which Cul2FEM1B targets C-terminal proline. Further, by identifying substrates for Cul1FBXO38, Cul2APPBP2, Cul3GAN, Cul3KLHL8, Cul3KLHL9/13 and Cul3KLHL15, we demonstrate that the approach is compatible with pools of full-length protein substrates of varying stabilities and, when combined with site-saturation mutagenesis, can assign E3 ligases to their cognate degron motifs. Thus, multiplex CRISPR screening will accelerate our understanding of how specificity is achieved within the ubiquitin-proteasome system.
    DOI:  https://doi.org/10.1038/s41556-023-01229-2
  25. Commun Biol. 2023 09 19. 6(1): 952
    Loss of Grin2a causes a transient delay in the electrophysiological maturation of hippocampal parvalbumin interneurons.
    Chad R Camp, Anna Vlachos, Chiara Klöckner, Ilona Krey, Tue G Banke, Nima Shariatzadeh, Sarah M Ruggiero, Peter Galer, Kristen L Park, Adam Caccavano, Sarah Kimmel, Xiaoqing Yuan, Hongjie Yuan, Ingo Helbig, Tim A Benke, Johannes R Lemke, Kenneth A Pelkey, Chris J McBain, Stephen F Traynelis.
      N-methyl-D-aspartate receptors (NMDARs) are ligand-gated ionotropic glutamate receptors that mediate a calcium-permeable component to fast excitatory neurotransmission. NMDARs are heterotetrameric assemblies of two obligate GluN1 subunits (GRIN1) and two GluN2 subunits (GRIN2A-GRIN2D). Sequencing data shows that 43% (297/679) of all currently known NMDAR disease-associated genetic variants are within the GRIN2A gene, which encodes the GluN2A subunit. Here, we show that unlike missense GRIN2A variants, individuals affected with disease-associated null GRIN2A variants demonstrate a transient period of seizure susceptibility that begins during infancy and diminishes near adolescence. We show increased circuit excitability and CA1 pyramidal cell output in juvenile mice of both Grin2a+/- and Grin2a-/- mice. These alterations in somatic spiking are not due to global upregulation of most Grin genes (including Grin2b). Deeper evaluation of the developing CA1 circuit led us to uncover age- and Grin2a gene dosing-dependent transient delays in the electrophysiological maturation programs of parvalbumin (PV) interneurons. We report that Grin2a+/+ mice reach PV cell electrophysiological maturation between the neonatal and juvenile neurodevelopmental timepoints, with Grin2a+/- mice not reaching PV cell electrophysiological maturation until preadolescence, and Grin2a-/- mice not reaching PV cell electrophysiological maturation until adulthood. Overall, these data may represent a molecular mechanism describing the transient nature of seizure susceptibility in disease-associated null GRIN2A patients.
    DOI:  https://doi.org/10.1038/s42003-023-05298-9
  26. Nat Commun. 2023 09 20. 14(1): 5832
    NLRP3 selectively drives IL-1β secretion by Pseudomonas aeruginosa infected neutrophils and regulates corneal disease severity.
    Martin S Minns, Karl Liboro, Tatiane S Lima, Serena Abbondante, Brandon A Miller, Michaela E Marshall, Jolynn Tran Chau, Alicia Roistacher, Arne Rietsch, George R Dubyak, Eric Pearlman.
      Macrophages infected with Gram-negative bacteria expressing Type III secretion system (T3SS) activate the NLRC4 inflammasome, resulting in Gasdermin D (GSDMD)-dependent, but GSDME independent IL-1β secretion and pyroptosis. Here we examine inflammasome signaling in neutrophils infected with Pseudomonas aeruginosa strain PAO1 that expresses the T3SS effectors ExoS and ExoT. IL-1β secretion by neutrophils requires the T3SS needle and translocon proteins and GSDMD. In macrophages, PAO1 and mutants lacking ExoS and ExoT (ΔexoST) require NLRC4 for IL-1β secretion. While IL-1β release from ΔexoST infected neutrophils is also NLRC4-dependent, infection with PAO1 is instead NLRP3-dependent and driven by the ADP ribosyl transferase activity of ExoS. Genetic and pharmacologic approaches using MCC950 reveal that NLRP3 is also essential for bacterial killing and disease severity in a murine model of P. aeruginosa corneal infection (keratitis). Overall, these findings reveal a function for ExoS ADPRT in regulating inflammasome subtype usage in neutrophils versus macrophages and an unexpected role for NLRP3 in P. aeruginosa keratitis.
    DOI:  https://doi.org/10.1038/s41467-023-41391-7
  27. Nat Commun. 2023 09 18. 14(1): 5327
    Circular RNAs in the human brain are tailored to neuron identity and neuropsychiatric disease.
    Xianjun Dong, Yunfei Bai, Zhixiang Liao, David Gritsch, Xiaoli Liu, Tao Wang, Rebeca Borges-Monroy, Alyssa Ehrlich, Geidy E Serrano, Mel B Feany, Thomas G Beach, Clemens R Scherzer.
      Little is known about circular RNAs (circRNAs) in specific brain cells and human neuropsychiatric disease. Here, we systematically identify over 11,039 circRNAs expressed in vulnerable dopamine and pyramidal neurons laser-captured from 190 human brains and non-neuronal cells using ultra-deep, total RNA sequencing. 1526 and 3308 circRNAs are custom-tailored to the cell identity of dopamine and pyramidal neurons and enriched in synapse pathways. 29% of Parkinson's and 12% of Alzheimer's disease-associated genes produced validated circRNAs. circDNAJC6, which is transcribed from a juvenile-onset Parkinson's gene, is already dysregulated during prodromal, onset stages of common Parkinson's disease neuropathology. Globally, addiction-associated genes preferentially produce circRNAs in dopamine neurons, autism-associated genes in pyramidal neurons, and cancers in non-neuronal cells. This study shows that circular RNAs in the human brain are tailored to neuron identity and implicate circRNA-regulated synaptic specialization in neuropsychiatric diseases.
    DOI:  https://doi.org/10.1038/s41467-023-40348-0
  28. Cell. 2023 Sep 12. pii: S0092-8674(23)00912-1. [Epub ahead of print]
    CD1 lipidomes reveal lipid-binding motifs and size-based antigen-display mechanisms.
    Shouxiong Huang, Adam Shahine, Tan-Yun Cheng, Yi-Ling Chen, Soo Weei Ng, Gautham R Balaji, Rachel Farquhar, Stephanie Gras, Clare S Hardman, John D Altman, Nabil Tahiri, Adriaan J Minnaard, Graham S Ogg, Jacob A Mayfield, Jamie Rossjohn, D Branch Moody.
      The CD1 system binds lipid antigens for display to T cells. Here, we solved lipidomes for the four human CD1 antigen-presenting molecules, providing a map of self-lipid display. Answering a basic question, the detection of >2,000 CD1-lipid complexes demonstrates broad presentation of self-sphingolipids and phospholipids. Whereas peptide antigens are chemically processed, many lipids are presented in an unaltered form. However, each type of CD1 protein differentially edits the self-lipidome to show distinct capture motifs based on lipid length and chemical composition, suggesting general antigen display mechanisms. For CD1a and CD1d, lipid size matches the CD1 cleft volume. CD1c cleft size is more variable, and CD1b is the outlier, where ligands and clefts show an extreme size mismatch that is explained by uniformly seating two small lipids in one cleft. Furthermore, the list of compounds that comprise the integrated CD1 lipidome supports the ongoing discovery of lipid blockers and antigens for T cells.
    Keywords:  CD1; T cell receptor; T cells; antigen presentation; antigen processing; dendritic cells; lipidomics; major histocompatibility complex; sphingolipids
    DOI:  https://doi.org/10.1016/j.cell.2023.08.022
  29. Nat Commun. 2023 Sep 21. 14(1): 5884
    DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas.
    Harry Carey, Michael Pegios, Lewis Martin, Chris Saleeba, Anita J Turner, Nicholas A Everett, Ingvild E Bjerke, Maja A Puchades, Jan G Bjaalie, Simon McMullan.
      Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analyzed, yet accurate registration remains expertise-dependent and slow. In order to address this limitation, we have trained a neural network, DeepSlice, to register mouse brain histological images to the Allen Brain Common Coordinate Framework, retaining registration accuracy while improving speed by >1000 fold.
    DOI:  https://doi.org/10.1038/s41467-023-41645-4
  30. Nat Aging. 2023 Sep 21.
    The VCAM1-ApoE pathway directs microglial chemotaxis and alleviates Alzheimer's disease pathology.
    Shun-Fat Lau, Wei Wu, Hiu Yi Wong, Li Ouyang, Yi Qiao, Jiahui Xu, Jessica Hiu-Yan Lau, Carlton Wong, Yuanbing Jiang, David M Holtzman, Amy K Y Fu, Nancy Y Ip.
      In Alzheimer's disease (AD), sensome receptor dysfunction impairs microglial danger-associated molecular pattern (DAMP) clearance and exacerbates disease pathology. Although extrinsic signals, including interleukin-33 (IL-33), can restore microglial DAMP clearance, it remains largely unclear how the sensome receptor is regulated and interacts with DAMP during phagocytic clearance. Here, we show that IL-33 induces VCAM1 in microglia, which promotes microglial chemotaxis toward amyloid-beta (Aβ) plaque-associated ApoE, and leads to Aβ clearance. We show that IL-33 stimulates a chemotactic state in microglia, characterized by Aβ-directed migration. Functional screening identified that VCAM1 directs microglial Aβ chemotaxis by sensing Aβ plaque-associated ApoE. Moreover, we found that disrupting VCAM1-ApoE interaction abolishes microglial Aβ chemotaxis, resulting in decreased microglial clearance of Aβ. In patients with AD, higher cerebrospinal fluid levels of soluble VCAM1 were correlated with impaired microglial Aβ chemotaxis. Together, our findings demonstrate that promoting VCAM1-ApoE-dependent microglial functions ameliorates AD pathology.
    DOI:  https://doi.org/10.1038/s43587-023-00491-1
  31. Nat Commun. 2023 09 19. 14(1): 5709
    ABCC1 and glutathione metabolism limit the efficacy of BCL-2 inhibitors in acute myeloid leukemia.
    Jessica Ebner, Johannes Schmoellerl, Martin Piontek, Gabriele Manhart, Selina Troester, Bing Z Carter, Heidi Neubauer, Richard Moriggl, Gergely Szakács, Johannes Zuber, Thomas Köcher, Michael Andreeff, Wolfgang R Sperr, Peter Valent, Florian Grebien.
      The BCL-2 inhibitor Venetoclax is a promising agent for the treatment of acute myeloid leukemia (AML). However, many patients are refractory to Venetoclax, and resistance develops quickly. ATP-binding cassette (ABC) transporters mediate chemotherapy resistance but their role in modulating the activity of targeted small-molecule inhibitors is unclear. Using CRISPR/Cas9 screening, we find that loss of ABCC1 strongly increases the sensitivity of AML cells to Venetoclax. Genetic and pharmacologic ABCC1 inactivation potentiates the anti-leukemic effects of BCL-2 inhibitors and efficiently re-sensitizes Venetoclax-resistant leukemia cells. Conversely, ABCC1 overexpression induces resistance to BCL-2 inhibitors by reducing intracellular drug levels, and high ABCC1 levels predicts poor response to Venetoclax therapy in patients. Consistent with ABCC1-specific export of glutathionylated substrates, inhibition of glutathione metabolism increases the potency of BCL-2 inhibitors. These results identify ABCC1 and glutathione metabolism as mechanisms limiting efficacy of BCL-2 inhibitors, which may pave the way to development of more effective therapies.
    DOI:  https://doi.org/10.1038/s41467-023-41229-2
  32. Nat Commun. 2023 Sep 21. 14(1): 5891
    Endothelial Sp1/Sp3 are essential to the effect of captopril on blood pressure in male mice.
    Hanlin Lu, Xiuxin Jiang, Lifan He, Xuyang Ji, Xinyun Li, Shaozhuang Liu, Yuanyuan Sun, Xiaoteng Qin, Xiwen Xiong, Sjaak Philipsen, Bo Xi, Meng Zhang, Jianmin Yang, Cheng Zhang, Yun Zhang, Wencheng Zhang.
      Endothelial dysfunction represents a major cardiovascular risk factor for hypertension. Sp1 and Sp3 belong to the specificity protein and Krüppel-like transcription factor families. They are ubiquitously expressed and closely associated with cardiovascular development. We investigate the role of Sp1 and Sp3 in endothelial cells in vivo and evaluate whether captopril, an angiotensin-converting enzyme inhibitor (ACEI), targets Sp1/Sp3 to exert its effects. Inducible endothelial-specific Sp1/Sp3 knockout mice are generated to elucidate their role in endothelial cells. Tamoxifen-induced deletion of endothelial Sp1 and Sp3 in male mice decreases the serum nitrite/nitrate level, impairs endothelium-dependent vasodilation, and causes hypertension and cardiac remodeling. The beneficial actions of captopril are abolished by endothelial-specific deletion of Sp1/Sp3, indicating that they may be targets for ACEIs. Captopril increases Sp1/Sp3 protein levels by recruiting histone deacetylase 1, which elevates deacetylation and suppressed degradation of Sp1/Sp3. Sp1/Sp3 represents innovative therapeutic target for captopril to prevent cardiovascular diseases.
    DOI:  https://doi.org/10.1038/s41467-023-41567-1
  33. Nat Commun. 2023 Sep 22. 14(1): 5910
    Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition.
    Valdemaras Petrosius, Pedro Aragon-Fernandez, Nil Üresin, Gergo Kovacs, Teeradon Phlairaharn, Benjamin Furtwängler, Jeff Op De Beeck, Sarah L Skovbakke, Steffen Goletz, Simon Francis Thomsen, Ulrich Auf dem Keller, Kedar N Natarajan, Bo T Porse, Erwin M Schoof.
      Single-cell resolution analysis of complex biological tissues is fundamental to capture cell-state heterogeneity and distinct cellular signaling patterns that remain obscured with population-based techniques. The limited amount of material encapsulated in a single cell however, raises significant technical challenges to molecular profiling. Due to extensive optimization efforts, single-cell proteomics by Mass Spectrometry (scp-MS) has emerged as a powerful tool to facilitate proteome profiling from ultra-low amounts of input, although further development is needed to realize its full potential. To this end, we carry out comprehensive analysis of orbitrap-based data-independent acquisition (DIA) for limited material proteomics. Notably, we find a fundamental difference between optimal DIA methods for high- and low-load samples. We further improve our low-input DIA method by relying on high-resolution MS1 quantification, thus enhancing sensitivity by more efficiently utilizing available mass analyzer time. With our ultra-low input tailored DIA method, we are able to accommodate long injection times and high resolution, while keeping the scan cycle time low enough to ensure robust quantification. Finally, we demonstrate the capability of our approach by profiling mouse embryonic stem cell culture conditions, showcasing heterogeneity in global proteomes and highlighting distinct differences in key metabolic enzyme expression in distinct cell subclusters.
    DOI:  https://doi.org/10.1038/s41467-023-41602-1
  34. Sci Adv. 2023 Sep 22. 9(38): eadg0488
    Single-cell genotypic and phenotypic analysis of measurable residual disease in acute myeloid leukemia.
    Troy M Robinson, Robert L Bowman, Sonali Persaud, Ying Liu, Rosemary Neigenfind, Qi Gao, Jingping Zhang, Xiaotian Sun, Linde A Miles, Sheng F Cai, Adam Sciambi, Aaron Llanso, Christopher Famulare, Aaron Goldberg, Ahmet Dogan, Mikhail Roshal, Ross L Levine, Wenbin Xiao.
      Measurable residual disease (MRD), defined as the population of cancer cells that persist following therapy, serves as the critical reservoir for disease relapse in acute myeloid leukemia and other malignancies. Understanding the biology enabling MRD clones to resist therapy is necessary to guide the development of more effective curative treatments. Discriminating between residual leukemic clones, preleukemic clones, and normal precursors remains a challenge with current MRD tools. Here, we developed a single-cell MRD (scMRD) assay by combining flow cytometric enrichment of the targeted precursor/blast population with integrated single-cell DNA sequencing and immunophenotyping. Our scMRD assay shows high sensitivity of approximately 0.01%, deconvolutes clonal architecture, and provides clone-specific immunophenotypic data. In summary, our scMRD assay enhances MRD detection and simultaneously illuminates the clonal architecture of clonal hematopoiesis/preleukemic and leukemic cells surviving acute myeloid leukemia therapy.
    DOI:  https://doi.org/10.1126/sciadv.adg0488
  35. Nat Commun. 2023 Sep 18. 14(1): 5775
    Light-enhanced molecular polarity enabling multispectral color-cognitive memristor for neuromorphic visual system.
    Jongmin Lee, Bum Ho Jeong, Eswaran Kamaraj, Dohyung Kim, Hakjun Kim, Sanghyuk Park, Hui Joon Park.
      An optoelectronic synapse having a multispectral color-discriminating ability is an essential prerequisite to emulate the human retina for realizing a neuromorphic visual system. Several studies based on the three-terminal transistor architecture have shown its feasibility; however, its implementation with a two-terminal memristor architecture, advantageous to achieving high integration density as a simple crossbar array for an ultra-high-resolution vision chip, remains a challenge. Furthermore, regardless of the architecture, it requires specific material combinations to exhibit the photo-synaptic functionalities, and thus its integration into various systems is limited. Here, we suggest an approach that can universally introduce a color-discriminating synaptic functionality into a two-terminal memristor irrespective of the kinds of switching medium. This is possible by simply introducing the molecular interlayer with long-lasting photo-enhanced dipoles that can adjust the resistance of the memristor at the light-irradiation. We also propose the molecular design principle that can afford this feature. The optoelectronic synapse array having a color-discriminating functionality is confirmed to improve the inference accuracy of the convolutional neural network for the colorful image recognition tasks through a visual pre-processing. Additionally, the wavelength-dependent optoelectronic synapse can also be leveraged in the design of a light-programmable reservoir computing system.
    DOI:  https://doi.org/10.1038/s41467-023-41419-y
  36. Nat Commun. 2023 Sep 22. 14(1): 5908
    Circadian clock disruption promotes the degeneration of dopaminergic neurons in male Drosophila.
    Michaëla Majcin Dorcikova, Lou C Duret, Emma Pottié, Emi Nagoshi.
      Sleep and circadian rhythm disruptions are frequent comorbidities of Parkinson's disease (PD), a disorder characterized by the progressive loss of dopaminergic (DA) neurons in the substantia nigra. However, the causal role of circadian clocks in the degenerative process remains uncertain. We demonstrated here that circadian clocks regulate the rhythmicity and magnitude of the vulnerability of DA neurons to oxidative stress in male Drosophila. Circadian pacemaker neurons are presynaptic to a subset of DA neurons and rhythmically modulate their susceptibility to degeneration. The arrhythmic period (per) gene null mutation exacerbates the age-dependent loss of DA neurons and, in combination with brief oxidative stress, causes premature animal death. These findings suggest that circadian clock disruption promotes dopaminergic neurodegeneration.
    DOI:  https://doi.org/10.1038/s41467-023-41540-y
  37. Nat Commun. 2023 09 19. 14(1): 5802
    A robust normalized local filter to estimate compositional heterogeneity directly from cryo-EM maps.
    Björn O Forsberg, Pranav N M Shah, Alister Burt.
      Cryo electron microscopy (cryo-EM) is used by biological research to visualize biomolecular complexes in 3D, but the heterogeneity of cryo-EM reconstructions is not easily estimated. Current processing paradigms nevertheless exert great effort to reduce flexibility and heterogeneity to improve the quality of the reconstruction. Clustering algorithms are typically employed to identify populations of data with reduced variability, but lack assessment of remaining heterogeneity. Here we develope a fast and simple algorithm based on spatial filtering to estimate the heterogeneity of a reconstruction. In the absence of flexibility, this estimate approximates macromolecular component occupancy. We show that our implementation can derive reasonable input parameters, that composition heterogeneity can be estimated based on contrast loss, and that the reconstruction can be modified accordingly to emulate altered constituent occupancy. This stands to benefit conventionally employed maximum-likelihood classification methods, whereas we here limit considerations to cryo-EM map interpretation, quantification, and particle-image signal subtraction.
    DOI:  https://doi.org/10.1038/s41467-023-41478-1
  38. Nat Commun. 2023 Sep 22. 14(1): 5898
    C9orf72-ALS human iPSC microglia are pro-inflammatory and toxic to co-cultured motor neurons via MMP9.
    Björn F Vahsen, Sumedha Nalluru, Georgia R Morgan, Lucy Farrimond, Emily Carroll, Yinyan Xu, Kaitlyn M L Cramb, Benazir Amein, Jakub Scaber, Antigoni Katsikoudi, Ana Candalija, Mireia Carcolé, Ruxandra Dafinca, Adrian M Isaacs, Richard Wade-Martins, Elizabeth Gray, Martin R Turner, Sally A Cowley, Kevin Talbot.
      Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease characterized by progressive motor neuron loss, with additional pathophysiological involvement of non-neuronal cells such as microglia. The commonest ALS-associated genetic variant is a hexanucleotide repeat expansion (HRE) mutation in C9orf72. Here, we study its consequences for microglial function using human iPSC-derived microglia. By RNA-sequencing, we identify enrichment of pathways associated with immune cell activation and cyto-/chemokines in C9orf72 HRE mutant microglia versus healthy controls, most prominently after LPS priming. Specifically, LPS-primed C9orf72 HRE mutant microglia show consistently increased expression and release of matrix metalloproteinase-9 (MMP9). LPS-primed C9orf72 HRE mutant microglia are toxic to co-cultured healthy motor neurons, which is ameliorated by concomitant application of an MMP9 inhibitor. Finally, we identify release of dipeptidyl peptidase-4 (DPP4) as a marker for MMP9-dependent microglial dysregulation in co-culture. These results demonstrate cellular dysfunction of C9orf72 HRE mutant microglia, and a non-cell-autonomous role in driving C9orf72-ALS pathophysiology in motor neurons through MMP9 signaling.
    DOI:  https://doi.org/10.1038/s41467-023-41603-0
  39. Nature. 2023 Sep 20.
    The β1-adrenergic receptor links sympathetic nerves to T cell exhaustion.
    Anna-Maria Globig, Steven Zhao, Jessica Roginsky, Vivien I Maltez, Juan Guiza, Natalia Avina-Ochoa, Maximilian Heeg, Filipe Araujo Hoffmann, Omkar Chaudhary, Jiawei Wang, Gokhan Senturk, Dan Chen, Carolyn O'Connor, Samuel Pfaff, Ronald N Germain, Kurt A Schalper, Brinda Emu, Susan M Kaech.
      CD8+ T cells are essential components of the immune response against viral infections and tumours, and are capable of eliminating infected and cancerous cells. However, when the antigen cannot be cleared, T cells enter a state known as exhaustion1. Although it is clear that chronic antigen contributes to CD8+ T cell exhaustion, less is known about how stress responses in tissues regulate T cell function. Here we show a new link between the stress-associated catecholamines and the progression of T cell exhaustion through the β1-adrenergic receptor ADRB1. We identify that exhausted CD8+ T cells increase ADRB1 expression and that exposure of ADRB1+ T cells to catecholamines suppresses their cytokine production and proliferation. Exhausted CD8+ T cells cluster around sympathetic nerves in an ADRB1-dependent manner. Ablation of β1-adrenergic signalling limits the progression of T cells towards the exhausted state in chronic infection and improves effector functions when combined with immune checkpoint blockade (ICB) in melanoma. In a pancreatic cancer model resistant to ICB, β-blockers and ICB synergize to boost CD8+ T cell responses and induce the development of tissue-resident memory-like T cells. Malignant disease is associated with increased catecholamine levels in patients2,3, and our results establish a connection between the sympathetic stress response, tissue innervation and T cell exhaustion. Here, we uncover a new mechanism by which blocking β-adrenergic signalling in CD8+ T cells rejuvenates anti-tumour functions.
    DOI:  https://doi.org/10.1038/s41586-023-06568-6
  40. Nat Commun. 2023 Sep 22. 14(1): 5930
    Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag.
    Steven Henikoff, Jorja G Henikoff, Kami Ahmad, Ronald M Paranal, Derek H Janssens, Zachary R Russell, Frank Szulzewsky, Sita Kugel, Eric C Holland.
      For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
    DOI:  https://doi.org/10.1038/s41467-023-41666-z
  41. Diabetes. 2023 Sep 19. pii: db230314. [Epub ahead of print]
    MAD2-dependent insulin receptor endocytosis regulates metabolic homeostasis.
    Junhee Park, Catherine Hall, Brandon Hubbard, Traci LaMoia, Rafael Gaspar, Ali Nasiri, Fang Li, Hanrui Zhang, Jiyeon Kim, Rebecca A Haeusler, Domenico Accili, Gerald I Shulman, Hongtao Yu, Eunhee Choi.
      Insulin activates insulin receptor (IR) signaling and subsequently triggers IR endocytosis to attenuate signaling. Cell division regulators MAD2, BUBR1, and p31comet promote IR endocytosis upon insulin stimulation. Here, we show that genetic ablation of the IR-MAD2 interaction in mice delays IR endocytosis, increases IR levels, and prolongs insulin action at the cell surface. This in turn causes a defect in insulin clearance and increases circulating insulin levels, unexpectedly increasing glucagon levels, which alters glucose metabolism modestly. Disruption of the IR-MAD2 interaction increases serum fatty acid concentrations and hepatic fat accumulation in fasted male mice. Furthermore, disruption of the IR-MAD2 interaction distinctly changes metabolic and transcriptomic profiles in the liver and adipose tissues. Our findings establish the function of cell division regulators in insulin signaling and provide insights into the metabolic functions of IR endocytosis.
    DOI:  https://doi.org/10.2337/db23-0314
  42. Nat Biotechnol. 2023 Sep 21.
    Supervised discovery of interpretable gene programs from single-cell data.
    Russell Z Kunes, Thomas Walle, Max Land, Tal Nawy, Dana Pe'er.
      Factor analysis decomposes single-cell gene expression data into a minimal set of gene programs that correspond to processes executed by cells in a sample. However, matrix factorization methods are prone to technical artifacts and poor factor interpretability. We address these concerns with Spectra, an algorithm that combines user-provided gene programs with the detection of novel programs that together best explain expression covariation. Spectra incorporates existing gene sets and cell-type labels as prior biological information, explicitly models cell type and represents input gene sets as a gene-gene knowledge graph using a penalty function to guide factorization toward the input graph. We show that Spectra outperforms existing approaches in challenging tumor immune contexts, as it finds factors that change under immune checkpoint therapy, disentangles the highly correlated features of CD8+ T cell tumor reactivity and exhaustion, finds a program that explains continuous macrophage state changes under therapy and identifies cell-type-specific immune metabolic programs.
    DOI:  https://doi.org/10.1038/s41587-023-01940-3
  43. Nat Med. 2023 Sep 21.
    A revolution in obesity treatment.
    Ildiko Lingvay, Shubham Agarwal.
      
    DOI:  https://doi.org/10.1038/s41591-023-02538-7
  44. Nat Genet. 2023 Sep 18.
    Molecular basis for maternal inheritance of human mitochondrial DNA.
    William Lee, Angelica Zamudio-Ochoa, Gina Buchel, Petar Podlesniy, Nuria Marti Gutierrez, Margalida Puigròs, Anna Calderon, Hsin-Yao Tang, Li Li, Aleksei Mikhalchenko, Amy Koski, Ramon Trullas, Shoukhrat Mitalipov, Dmitry Temiakov.
      Uniparental inheritance of mitochondrial DNA (mtDNA) is an evolutionary trait found in nearly all eukaryotes. In many species, including humans, the sperm mitochondria are introduced to the oocyte during fertilization1,2. The mechanisms hypothesized to prevent paternal mtDNA transmission include ubiquitination of the sperm mitochondria and mitophagy3,4. However, the causative mechanisms of paternal mtDNA elimination have not been defined5,6. We found that mitochondria in human spermatozoa are devoid of intact mtDNA and lack mitochondrial transcription factor A (TFAM)-the major nucleoid protein required to protect, maintain and transcribe mtDNA. During spermatogenesis, sperm cells express an isoform of TFAM, which retains the mitochondrial presequence, ordinarily removed upon mitochondrial import. Phosphorylation of this presequence prevents mitochondrial import and directs TFAM to the spermatozoon nucleus. TFAM relocalization from the mitochondria of spermatogonia to the spermatozoa nucleus directly correlates with the elimination of mtDNA, thereby explaining maternal inheritance in this species.
    DOI:  https://doi.org/10.1038/s41588-023-01505-9
  45. Nature. 2023 Sep;621(7979): S24
    For Health Equity, Location Matters.
    Lauren Gravitz.
      
    Keywords:  Health care; Public health; Society
    DOI:  https://doi.org/10.1038/d41586-023-02612-7
  46. Nat Commun. 2023 09 19. 14(1): 5814
    Epithelial plasticity and innate immune activation promote lung tissue remodeling following respiratory viral infection.
    Andrew K Beppu, Juanjuan Zhao, Changfu Yao, Gianni Carraro, Edo Israely, Anna Lucia Coelho, Katherine Drake, Cory M Hogaboam, William C Parks, Jay K Kolls, Barry R Stripp.
      Epithelial plasticity has been suggested in lungs of mice following genetic depletion of stem cells but is of unknown physiological relevance. Viral infection and chronic lung disease share similar pathological features of stem cell loss in alveoli, basal cell (BC) hyperplasia in small airways, and innate immune activation, that contribute to epithelial remodeling and loss of lung function. We show that a subset of distal airway secretory cells, intralobar serous (IS) cells, are activated to assume BC fates following influenza virus infection. Injury-induced hyperplastic BC (hBC) differ from pre-existing BC by high expression of IL-22Ra1 and undergo IL-22-dependent expansion for colonization of injured alveoli. Resolution of virus-elicited inflammation results in BC to IS re-differentiation in repopulated alveoli, and increased local expression of protective antimicrobial factors, but fails to restore normal alveolar epithelium responsible for gas exchange.
    DOI:  https://doi.org/10.1038/s41467-023-41387-3
  47. J Cell Biol. 2023 10 02. pii: e202309067. [Epub ahead of print]222(10):
    Nucleolar condensates: A cellular machinery necessary for T cell activation.
    Monica Sharma, Andrey S Shaw.
      Naive T cells must shift from a state of quiescence to an active metabolic state. To do this, T cells must ramp up their production of ribosomes. In this issue, Zhou et al. (2023. J. Cell Biol.https://doi.org/10.1083/jcb.202201096) identify DDB1 and Cul4-associated factor 13 (DCAF13) as a T cell activation-induced nucleolar protein that functions to enhance ribosome biosynthesis. DCAF13 binds to nucleophosmin 1 (NPM1) to form a biomolecular condensate that functions, in part, by recruiting the endonuclease UTP23 into the nucleolus.
    DOI:  https://doi.org/10.1083/jcb.202309067
  48. Nat Commun. 2023 Sep 21. 14(1): 5878
    Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks.
    Mehmet Can Uçar, Edouard Hannezo, Emmi Tiilikainen, Inam Liaqat, Emma Jakobsson, Harri Nurmi, Kari Vaahtomeri.
      Branching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization.
    DOI:  https://doi.org/10.1038/s41467-023-41456-7
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