bims-nimamd 2022-09-04 papers

bims-nimamd

Biomed News

on Neuroimmunity and neuroinflammation in ageing and metabolic disease

Issue of 2022–09–04
forty-two papers selected by
Fawaz Alzaïd, Sorbonne Université

Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells.
Biliary NIK promotes ductular reaction and liver injury and fibrosis in mice.
Heterogeneity and transcriptome changes of human CD8+ T cells across nine decades of life.
PD-L2 controls peripherally induced regulatory T cells by maintaining metabolic activity and Foxp3 stability.
Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data.
Adipocytes control food intake and weight regain via Vacuolar-type H+ ATPase.
Cell type-specific inference of differential expression in spatial transcriptomics.
Characterization of sequence determinants of enhancer function using natural genetic variation.
Limited impact of fingolimod treatment during the initial weeks of ART in SIV-infected rhesus macaques.
A brainstem map for visceral sensations.
Alterations in high-dimensional T-cell profile and gene signature of immune aging in HIV-infected older adults without viremia.
Identification of two pathways mediating protein targeting from ER to lipid droplets.
Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling.
Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome.
Endophenotype effect sizes support variant pathogenicity in monogenic disease susceptibility genes.
Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways.
IgD+ age-associated B cells are the progenitors of the main T-independent B cell response to infection that generates protective Ab and can be induced by an inactivated vaccine in the aged.
A brainstem monosynaptic excitatory pathway that drives locomotor activities and sympathetic cardiovascular responses.
Somatic mutations in single human cardiomyocytes reveal age-associated DNA damage and widespread oxidative genotoxicity.
A lysosomal regulatory circuit essential for the development and function of microglia.
A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility.
Development of RAG2 -/- IL2Rγ -/Y immune deficient FAH-knockout miniature pig.
Proton-driven alternating access in a spinster lipid transporter.
Ventromedial hypothalamic OGT drives adipose tissue lipolysis and curbs obesity.
BACH2 in TRegs Limits the Number of Adipose Tissue Regulatory T Cells and Restrains Type 2 Immunity to Fungal Allergens.
Forced Fox-P3 expression can improve the safety and antigen-specific function of engineered regulatory T cells.
JAG1-NOTCH4 mechanosensing drives atherosclerosis.
VAMP4 regulates insulin levels by targeting secretory granules to lysosomes.
Orosomucoid 2 maintains hepatic lipid homeostasis through suppression of de novo lipogenesis.
Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation.
Protein import motor complex reacts to mitochondrial misfolding by reducing protein import and activating mitophagy.
The human mitochondrial genome contains a second light strand promoter.
Embryonic and neonatal waves generate distinct populations of hepatic ILC1s.
NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis.
Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection.
Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin.
Retromer deficiency in Tauopathy models enhances the truncation and toxicity of Tau.
Tracking Regulatory T Cell Development in the Thymus Using scRNA-Seq/TCR-Seq.
Production of MHCII-expressing classical monocytes increases during aging in mice and humans.
Early macrophage response to obesity encompasses Interferon Regulatory Factor 5 regulated mitochondrial architecture remodelling.
Pathological structural conversion of α-synuclein at the mitochondria induces neuronal toxicity.
Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy.

Nat Commun. 2022 Sep 02. 13(1): 5184

Distinct metabolic states guide maturation of inflammatory and tolerogenic dendritic cells.

Juraj Adamik, Paul V Munson, Felix J Hartmann, Alexis J Combes, Philippe Pierre, Matthew F Krummel, Sean C Bendall, Rafael J Argüello, Lisa H Butterfield.

Cellular metabolism underpins immune cell functionality, yet our understanding of metabolic influences in human dendritic cell biology and their ability to orchestrate immune responses is poorly developed. Here, we map single-cell metabolic states and immune profiles of inflammatory and tolerogenic monocytic dendritic cells using recently developed multiparametric approaches. Single-cell metabolic pathway activation scores reveal simultaneous engagement of multiple metabolic pathways in distinct monocytic dendritic cell differentiation stages. GM-CSF/IL4-induce rapid reprogramming of glycolytic monocytes and transient co-activation of mitochondrial pathways followed by TLR4-dependent maturation of dendritic cells. Skewing of the mTOR:AMPK phosphorylation balance and upregulation of OXPHOS, glycolytic and fatty acid oxidation metabolism underpin metabolic hyperactivity and an immunosuppressive phenotype of tolerogenic dendritic cells, which exhibit maturation-resistance and a de-differentiated immune phenotype marked by unique immunoregulatory receptor signatures. This single-cell dataset provides important insights into metabolic pathways impacting the immune profiles of human dendritic cells.

DOI: https://doi.org/10.1038/s41467-022-32849-1
Nat Commun. 2022 Aug 30. 13(1): 5111

Biliary NIK promotes ductular reaction and liver injury and fibrosis in mice.

Zhiguo Zhang, Xiao Zhong, Hong Shen, Liang Sheng, Suthat Liangpunsakul, Anna S Lok, M Bishr Omary, Shaomeng Wang, Liangyou Rui.

Excessive cholangiocyte expansion (ductular reaction) promotes liver disease progression, but the underlying mechanism is poorly understood. Here we identify biliary NF-κB-inducing kinase (NIK) as a pivotal regulator of ductular reaction. NIK is known to activate the noncanonical IKKα/NF-κB2 pathway and regulate lymphoid tissue development. We find that cholangiocyte NIK is upregulated in mice with cholestasis induced by bile duct ligation (BDL), 5-diethoxycarbonyl-1,4-dihydrocollidine (DDC), or α-naphtyl-isothiocyanate (ANIT). DDC, ANIT, or BDL induces ductular reaction, liver injury, inflammation, and fibrosis in mice. Cholangiocyte-specific deletion of NIK, but not IKKα, blunts these pathological alterations. NIK inhibitor treatment similarly ameliorates DDC-induced ductular reaction, liver injury, and fibrosis. Biliary NIK directly increases cholangiocyte proliferation while suppressing cholangiocyte death, and it also promotes secretion of cholangiokines from cholangiocytes. Cholangiokines stimulate liver macrophages and hepatic stellate cells, augmenting liver inflammation and fibrosis. These results unveil a NIK/ductular reaction axis and a NIK/cholangiokine axis that promote liver disease progression.

DOI: https://doi.org/10.1038/s41467-022-32575-8
Nat Commun. 2022 Sep 01. 13(1): 5128

Heterogeneity and transcriptome changes of human CD8+ T cells across nine decades of life.

Jian Lu, Raheel Ahmad, Thomas Nguyen, Jeffrey Cifello, Humza Hemani, Jiangyuan Li, Jinguo Chen, Siyi Li, Jing Wang, Achouak Achour, Joseph Chen, Meagan Colie, Ana Lustig, Christopher Dunn, Linda Zukley, Chee W Chia, Irina Burd, Jun Zhu, Luigi Ferrucci, Nan-Ping Weng.

The decline of CD8+ T cell functions contributes to deteriorating health with aging, but the mechanisms that underlie this phenomenon are not well understood. We use single-cell RNA sequencing with both cross-sectional and longitudinal samples to assess how human CD8+ T cell heterogeneity and transcriptomes change over nine decades of life. Eleven subpopulations of CD8+ T cells and their dynamic changes with age are identified. Age-related changes in gene expression result from changes in the percentage of cells expressing a given transcript, quantitative changes in the transcript level, or a combination of these two. We develop a machine learning model capable of predicting the age of individual cells based on their transcriptomic features, which are closely associated with their differentiation and mutation burden. Finally, we validate this model in two separate contexts of CD8+ T cell aging: HIV infection and CAR T cell expansion in vivo.

DOI: https://doi.org/10.1038/s41467-022-32869-x
Nat Commun. 2022 Aug 31. 13(1): 5118

PD-L2 controls peripherally induced regulatory T cells by maintaining metabolic activity and Foxp3 stability.

Benjamin P Hurrell, Doumet Georges Helou, Emily Howard, Jacob D Painter, Pedram Shafiei-Jahani, Arlene H Sharpe, Omid Akbari.

Regulatory T (Treg) cells are central to limit immune responses to allergens. Here we show that PD-L2 deficiency prevents the induction of tolerance to ovalbumin and control of airway hyperreactivity, in particular by limiting pTreg numbers and function. In vitro, PD-1/PD-L2 interactions increase iTreg numbers and stability. In mice lacking PD-L2 we find lower numbers of splenic pTregs at steady state, producing less IL-10 upon activation and with reduced suppressive activity. Remarkably, the numbers of splenic pTregs are restored by adoptively transferring PD-L2high dendritic cells to PD-L2KO mice. Functionally, activated pTregs lacking PD-L2 show lower Foxp3 expression, higher methylation of the Treg-Specific Demethylation Region (TSDR) and a decreased Tricarboxylic Acid (TCA) cycle associated with a defect in mitochondrial function and ATP production. Consequently, pyruvate treatment of PD-L2KO mice partially restores IL-10 production and airway tolerance. Together, our study highlights the importance of the PD-1/PD-L2 axis in the control of metabolic pathways regulating pTreg Foxp3 stability and suppressive functions, opening up avenues to further improve mucosal immunotherapy.

DOI: https://doi.org/10.1038/s41467-022-32899-5
Nat Genet. 2022 Sep 01.

Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data.

Martin Jinye Zhang, Kangcheng Hou, Kushal K Dey, Saori Sakaue, Karthik A Jagadeesh, Kathryn Weinand, Aris Taychameekiatchai, Poorvi Rao, Angela Oliveira Pisco, James Zou, Bruce Wang, Michael Gandal, Soumya Raychaudhuri, Bogdan Pasaniuc, Alkes L Price.

Single-cell RNA sequencing (scRNA-seq) provides unique insights into the pathology and cellular origin of disease. We introduce single-cell disease relevance score (scDRS), an approach that links scRNA-seq with polygenic disease risk at single-cell resolution, independent of annotated cell types. scDRS identifies cells exhibiting excess expression across disease-associated genes implicated by genome-wide association studies (GWASs). We applied scDRS to 74 diseases/traits and 1.3 million single-cell gene-expression profiles across 31 tissues/organs. Cell-type-level results broadly recapitulated known cell-type-disease associations. Individual-cell-level results identified subpopulations of disease-associated cells not captured by existing cell-type labels, including T cell subpopulations associated with inflammatory bowel disease, partially characterized by their effector-like states; neuron subpopulations associated with schizophrenia, partially characterized by their spatial locations; and hepatocyte subpopulations associated with triglyceride levels, partially characterized by their higher ploidy levels. Genes whose expression was correlated with the scDRS score across cells (reflecting coexpression with GWAS disease-associated genes) were strongly enriched for gold-standard drug target and Mendelian disease genes.

DOI: https://doi.org/10.1038/s41588-022-01167-z
Nat Commun. 2022 Aug 30. 13(1): 5092

Adipocytes control food intake and weight regain via Vacuolar-type H+ ATPase.

Rizaldy C Zapata, Maria Carretero, Felipe Castellani Gomes Reis, Besma S Chaudry, Jachelle Ofrecio, Dinghong Zhang, Roman Sasik, Theodore Ciaraldi, Michael Petrascheck, Olivia Osborn.

Energy metabolism becomes dysregulated in individuals with obesity and many of these changes persist after weight loss and likely play a role in weight regain. In these studies, we use a mouse model of diet-induced obesity and weight loss to study the transcriptional memory of obesity. We found that the 'metabolic memory' of obesity is predominantly localized in adipocytes. Utilizing a C. elegans-based food intake assay, we identify 'metabolic memory' genes that play a role in food intake regulation. We show that expression of ATP6v0a1, a subunit of V-ATPase, is significantly induced in both obese mouse and human adipocytes that persists after weight loss. C. elegans mutants deficient in Atp6v0A1/unc32 eat less than WT controls. Adipocyte-specific Atp6v0a1 knockout mice have reduced food intake and gain less weight in response to HFD. Pharmacological disruption of V-ATPase assembly leads to decreased food intake and less weight re-gain. In summary, using a series of genetic tools from invertebrates to vertebrates, we identify ATP6v0a1 as a regulator of peripheral metabolic memory, providing a potential target for regulation of food intake, weight loss maintenance and the treatment of obesity.

DOI: https://doi.org/10.1038/s41467-022-32764-5
Nat Methods. 2022 Sep 01.

Cell type-specific inference of differential expression in spatial transcriptomics.

Dylan M Cable, Evan Murray, Vignesh Shanmugam, Simon Zhang, Luli S Zou, Michael Diao, Haiqi Chen, Evan Z Macosko, Rafael A Irizarry, Fei Chen.

A central problem in spatial transcriptomics is detecting differentially expressed (DE) genes within cell types across tissue context. Challenges to learning DE include changing cell type composition across space and measurement pixels detecting transcripts from multiple cell types. Here, we introduce a statistical method, cell type-specific inference of differential expression (C-SIDE), that identifies cell type-specific DE in spatial transcriptomics, accounting for localization of other cell types. We model gene expression as an additive mixture across cell types of log-linear cell type-specific expression functions. C-SIDE's framework applies to many contexts: DE due to pathology, anatomical regions, cell-to-cell interactions and cellular microenvironment. Furthermore, C-SIDE enables statistical inference across multiple/replicates. Simulations and validation experiments on Slide-seq, MERFISH and Visium datasets demonstrate that C-SIDE accurately identifies DE with valid uncertainty quantification. Last, we apply C-SIDE to identify plaque-dependent immune activity in Alzheimer's disease and cellular interactions between tumor and immune cells. We distribute C-SIDE within the R package https://github.com/dmcable/spacexr .

DOI: https://doi.org/10.1038/s41592-022-01575-3
Elife. 2022 Aug 31. pii: e76500. [Epub ahead of print]11

Characterization of sequence determinants of enhancer function using natural genetic variation.

Marty G Yang, Emi Ling, Christopher J Cowley, Michael E Greenberg, Thomas Vierbuchen.

  Sequence variation in enhancers that control cell type-specific gene transcription contributes significantly to phenotypic variation within human populations. However, it remains difficult to predict precisely the effect of any given sequence variant on enhancer function due to the complexity of DNA sequence motifs that determine transcription factor (TF) binding to enhancers in their native genomic context. Using F1-hybrid cells derived from crosses between distantly related inbred strains of mice, we identified thousands of enhancers with allele-specific TF binding and/or activity. We find that genetic variants located within the central region of enhancers are most likely to alter TF binding and enhancer activity. We observe that the AP-1 family of TFs (Fos/Jun) are frequently required for binding of TEAD TFs and for enhancer function. However, many sequence variants outside of core motifs for AP-1 and TEAD also impact enhancer function, including sequences flanking core TF motifs and AP-1 half sites. Taken together, these data represent one of the most comprehensive assessments of allele-specific TF binding and enhancer function to date and reveal how sequence changes at enhancers alter their function across evolutionary timescales.

Keywords:  chromosomes; gene expression; genetics; genomics; mouse

DOI:  https://doi.org/10.7554/eLife.76500
Nat Commun. 2022 Aug 27. 13(1): 5055

Limited impact of fingolimod treatment during the initial weeks of ART in SIV-infected rhesus macaques.

Maria Pino, Amélie Pagliuzza, M Betina Pampena, Claire Deleage, Elise G Viox, Kevin Nguyen, Inbo Shim, Adam Zhang, Justin L Harper, Sadia Samer, Colin T King, Barbara Cervasi, Kiran P Gill, Stephanie Ehnert, Sherrie M Jean, Michael L Freeman, Jeffrey D Lifson, Deanna Kulpa, Michael R Betts, Nicolas Chomont, Michael M Lederman, Mirko Paiardini.

Antiretroviral therapy (ART) is not curative due to the persistence of a reservoir of HIV-infected cells, particularly in tissues such as lymph nodes, with the potential to cause viral rebound after treatment cessation. In this study, fingolimod (FTY720), a lysophospholipid sphingosine-1-phosphate receptor modulator is administered to SIV-infected rhesus macaques at initiation of ART to block the egress from lymphoid tissues of natural killer and T-cells, thereby promoting proximity between cytolytic cells and infected CD4+ T-cells. When compared with the ART-only controls, FTY720 treatment during the initial weeks of ART induces a profound lymphopenia and increases frequencies of CD8+ T-cells expressing perforin in lymph nodes, but not their killing capacity; FTY720 also increases frequencies of cytolytic NK cells in lymph nodes. This increase of cytolytic cells, however, does not limit measures of viral persistence during ART, including intact proviral genomes. After ART interruption, a subset of animals that initially receives FTY720 displays a modest delay in viral rebound, with reduced plasma viremia and frequencies of infected T follicular helper cells. Further research is needed to optimize the potential utility of FTY720 when coupled with strategies that boost the antiviral function of T-cells in lymphoid tissues.

DOI: https://doi.org/10.1038/s41467-022-32698-y
Nature. 2022 Aug 31.

A brainstem map for visceral sensations.

Chen Ran, Jack C Boettcher, Judith A Kaye, Catherine E Gallori, Stephen D Liberles.

The nervous system uses various coding strategies to process sensory inputs. For example, the olfactory system uses large receptor repertoires and is wired to recognize diverse odours, whereas the visual system provides high acuity of object position, form and movement1-5. Compared to external sensory systems, principles that underlie sensory processing by the interoceptive nervous system remain poorly defined. Here we developed a two-photon calcium imaging preparation to understand internal organ representations in the nucleus of the solitary tract (NTS), a sensory gateway in the brainstem that receives vagal and other inputs from the body. Focusing on gut and upper airway stimuli, we observed that individual NTS neurons are tuned to detect signals from particular organs and are topographically organized on the basis of body position. Moreover, some mechanosensory and chemosensory inputs from the same organ converge centrally. Sensory inputs engage specific NTS domains with defined locations, each containing heterogeneous cell types. Spatial representations of different organs are further sharpened in the NTS beyond what is achieved by vagal axon sorting alone, as blockade of brainstem inhibition broadens neural tuning and disorganizes visceral representations. These findings reveal basic organizational features used by the brain to process interoceptive inputs.

DOI: https://doi.org/10.1038/s41586-022-05139-5
Aging Cell. 2022 Aug 29. e13702

Alterations in high-dimensional T-cell profile and gene signature of immune aging in HIV-infected older adults without viremia.

Min Sun Shin, Hong-Jai Park, Syim Salahuddin, Ruth R Montgomery, Brinda Emu, Albert C Shaw, Insoo Kang.

  Alterations in the components of the immune system occur with aging. The introduction of combination antiretroviral therapy (ART) has dramatically improved life expectancy in human immunodeficiency virus (HIV) infected individuals by suppressing viral replication and increasing CD4+ T-cell counts. Immunosenescence-like changes, including the expansion of memory CD8+ T cells with senescent features, are reported in young HIV-infected individuals who do not have clinically detectable viremia on ART. However, it is less known whether HIV infection affects the immunosenescent status in older HIV-infected individuals. Here, we addressed this question in older HIV-infected, HIV-uninfected, and frail individuals (all groups age ≥65 years) by examining a set of aging-associated genes in peripheral blood mononuclear cells (PBMCs) as well as by analyzing subsets of CD4+ and CD8+ T cells in depth using high-dimensional CyTOF analysis. Older HIV-infected individuals had increased expression of aging-associated genes such as CX3CR1 in PBMCs which are related to IL-7 receptor low effector memory (IL-7Rαlow EM) CD8+ T cells, a cell population known to expand with age. The subsets of IL-7Rαlow EM CD8+ T cells expressing senescent, cytotoxic, and inflammatory molecules, including CD57, perforin, and CX3CR1, as well as memory CD4+ T cells expressing CD161 and CXCR3, molecules associated with replication-competent HIV-1 harboring cells, were increased in older HIV-infected individuals. Overall, older HIV-infected individuals without detectable viremia on ART had augmented levels of age-associated immune alterations in PBMCs, suggesting that HIV infection has a persistent impact on senescence in older HIV-infected individuals despite the clinically controlled viremia.

Keywords:  T cells; age; gene expression; human; human immunodeficiency virus (HIV)

DOI:  https://doi.org/10.1111/acel.13702
Nat Cell Biol. 2022 Sep 01.

Identification of two pathways mediating protein targeting from ER to lipid droplets.

Jiunn Song, Arda Mizrak, Chia-Wei Lee, Marcelo Cicconet, Zon Weng Lai, Wei-Chun Tang, Chieh-Han Lu, Stephanie E Mohr, Robert V Farese, Tobias C Walther.

Pathways localizing proteins to their sites of action are essential for eukaryotic cell organization and function. Although mechanisms of protein targeting to many organelles have been defined, how proteins, such as metabolic enzymes, target from the endoplasmic reticulum (ER) to cellular lipid droplets (LDs) is poorly understood. Here we identify two distinct pathways for ER-to-LD protein targeting: early targeting at LD formation sites during formation, and late targeting to mature LDs after their formation. Using systematic, unbiased approaches in Drosophila cells, we identified specific membrane-fusion machinery, including regulators, a tether and SNARE proteins, that are required for the late targeting pathway. Components of this fusion machinery localize to LD-ER interfaces and organize at ER exit sites. We identified multiple cargoes for early and late ER-to-LD targeting pathways. Our findings provide a model for how proteins target to LDs from the ER either during LD formation or by protein-catalysed formation of membrane bridges.

DOI: https://doi.org/10.1038/s41556-022-00974-0
Nat Commun. 2022 Aug 29. 13(1): 5075

Structure of a nucleosome-bound MuvB transcription factor complex reveals DNA remodelling.

Marios G Koliopoulos, Reyhan Muhammad, Theodoros I Roumeliotis, Fabienne Beuron, Jyoti S Choudhary, Claudio Alfieri.

Genes encoding the core cell cycle machinery are transcriptionally regulated by the MuvB family of protein complexes in a cell cycle-specific manner. Complexes of MuvB with the transcription factors B-MYB and FOXM1 activate mitotic genes during cell proliferation. The mechanisms of transcriptional regulation by these complexes are still poorly characterised. Here, we combine biochemical analysis and in vitro reconstitution, with structural analysis by cryo-electron microscopy and cross-linking mass spectrometry, to functionally examine these complexes. We find that the MuvB:B-MYB complex binds and remodels nucleosomes, thereby exposing nucleosomal DNA. This remodelling activity is supported by B-MYB which directly binds the remodelled DNA. Given the remodelling activity on the nucleosome, we propose that the MuvB:B-MYB complex functions as a pioneer transcription factor complex. In this work, we rationalise prior biochemical and cellular studies and provide a molecular framework of interactions on a protein complex that is key for cell cycle regulation.

DOI: https://doi.org/10.1038/s41467-022-32798-9
Cell. 2022 Aug 24. pii: S0092-8674(22)00992-8. [Epub ahead of print]

Microbiota imbalance induced by dietary sugar disrupts immune-mediated protection from metabolic syndrome.

Yoshinaga Kawano, Madeline Edwards, Yiming Huang, Angelina M Bilate, Leandro P Araujo, Takeshi Tanoue, Koji Atarashi, Mark S Ladinsky, Steven L Reiner, Harris H Wang, Daniel Mucida, Kenya Honda, Ivaylo I Ivanov.

  How intestinal microbes regulate metabolic syndrome is incompletely understood. We show that intestinal microbiota protects against development of obesity, metabolic syndrome, and pre-diabetic phenotypes by inducing commensal-specific Th17 cells. High-fat, high-sugar diet promoted metabolic disease by depleting Th17-inducing microbes, and recovery of commensal Th17 cells restored protection. Microbiota-induced Th17 cells afforded protection by regulating lipid absorption across intestinal epithelium in an IL-17-dependent manner. Diet-induced loss of protective Th17 cells was mediated by the presence of sugar. Eliminating sugar from high-fat diets protected mice from obesity and metabolic syndrome in a manner dependent on commensal-specific Th17 cells. Sugar and ILC3 promoted outgrowth of Faecalibaculum rodentium that displaced Th17-inducing microbiota. These results define dietary and microbiota factors posing risk for metabolic syndrome. They also define a microbiota-dependent mechanism for immuno-pathogenicity of dietary sugar and highlight an elaborate interaction between diet, microbiota, and intestinal immunity in regulation of metabolic disorders.

Keywords:  CD36; IL-17; Th17 cells; lipid absoprtion; metabolic syndrome; micobiota; mucosal immunity; obesity; segmented filamentous bacteria; sugar

DOI:  https://doi.org/10.1016/j.cell.2022.08.005
Nat Commun. 2022 Aug 30. 13(1): 5106

Endophenotype effect sizes support variant pathogenicity in monogenic disease susceptibility genes.

NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium

Accurate and efficient classification of variant pathogenicity is critical for research and clinical care. Using data from three large studies, we demonstrate that population-based associations between rare variants and quantitative endophenotypes for three monogenic diseases (low-density-lipoprotein cholesterol for familial hypercholesterolemia, electrocardiographic QTc interval for long QT syndrome, and glycosylated hemoglobin for maturity-onset diabetes of the young) provide evidence for variant pathogenicity. Effect sizes are associated with pathogenic ClinVar assertions (P < 0.001 for each trait) and discriminate pathogenic from non-pathogenic variants (area under the curve 0.82-0.84 across endophenotypes). An effect size threshold of ≥ 0.5 times the endophenotype standard deviation nominates up to 35% of rare variants of uncertain significance or not in ClinVar in disease susceptibility genes with pathogenic potential. We propose that variant associations with quantitative endophenotypes for monogenic diseases can provide evidence supporting pathogenicity.

DOI: https://doi.org/10.1038/s41467-022-32009-5
Nat Commun. 2022 Sep 01. 13(1): 5144

Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways.

William J Young, Najim Lahrouchi, Aaron Isaacs, ThuyVy Duong, Luisa Foco, Farah Ahmed, Jennifer A Brody, Reem Salman, Raymond Noordam, Jan-Walter Benjamins, Jeffrey Haessler, Leo-Pekka Lyytikäinen, Linda Repetto, Maria Pina Concas, Marten E van den Berg, Stefan Weiss, Antoine R Baldassari, Traci M Bartz, James P Cook, Daniel S Evans, Rebecca Freudling, Oliver Hines, Jonas L Isaksen, Honghuang Lin, Hao Mei, Arden Moscati, Martina Müller-Nurasyid, Casia Nursyifa, Yong Qian, Anne Richmond, Carolina Roselli, Kathleen A Ryan, Eduardo Tarazona-Santos, Sébastien Thériault, Stefan van Duijvenboden, Helen R Warren, Jie Yao, Dania Raza, Stefanie Aeschbacher, Gustav Ahlberg, Alvaro Alonso, Laura Andreasen, Joshua C Bis, Eric Boerwinkle, Archie Campbell, Eulalia Catamo, Massimiliano Cocca, Michael J Cutler, Dawood Darbar, Alessandro De Grandi, Antonio De Luca, Jun Ding, Christina Ellervik, Patrick T Ellinor, Stephan B Felix, Philippe Froguel, Christian Fuchsberger, Martin Gögele, Claus Graff, Mariaelisa Graff, Xiuqing Guo, Torben Hansen, Susan R Heckbert, Paul L Huang, Heikki V Huikuri, Nina Hutri-Kähönen, M Arfan Ikram, Rebecca D Jackson, Juhani Junttila, Maryam Kavousi, Jan A Kors, Thiago P Leal, Rozenn N Lemaitre, Henry J Lin, Lars Lind, Allan Linneberg, Simin Liu, Peter W MacFarlane, Massimo Mangino, Thomas Meitinger, Massimo Mezzavilla, Pashupati P Mishra, Rebecca N Mitchell, Nina Mononen, May E Montasser, Alanna C Morrison, Matthias Nauck, Victor Nauffal, Pau Navarro, Kjell Nikus, Guillaume Pare, Kristen K Patton, Giulia Pelliccione, Alan Pittman, David J Porteous, Peter P Pramstaller, Michael H Preuss, Olli T Raitakari, Alexander P Reiner, Antonio Luiz P Ribeiro, Kenneth M Rice, Lorenz Risch, David Schlessinger, Ulrich Schotten, Claudia Schurmann, Xia Shen, M Benjamin Shoemaker, Gianfranco Sinagra, Moritz F Sinner, Elsayed Z Soliman, Monika Stoll, Konstantin Strauch, Kirill Tarasov, Kent D Taylor, Andrew Tinker, Stella Trompet, André Uitterlinden, Uwe Völker, Henry Völzke, Melanie Waldenberger, Lu-Chen Weng, Eric A Whitsel, James G Wilson, Christy L Avery, David Conen, Adolfo Correa, Francesco Cucca, Marcus Dörr, Sina A Gharib, Giorgia Girotto, Niels Grarup, Caroline Hayward, Yalda Jamshidi, Marjo-Riitta Järvelin, J Wouter Jukema, Stefan Kääb, Mika Kähönen, Jørgen K Kanters, Charles Kooperberg, Terho Lehtimäki, Maria Fernanda Lima-Costa, Yongmei Liu, Ruth J F Loos, Steven A Lubitz, Dennis O Mook-Kanamori, Andrew P Morris, Jeffrey R O'Connell, Morten Salling Olesen, Michele Orini, Sandosh Padmanabhan, Cristian Pattaro, Annette Peters, Bruce M Psaty, Jerome I Rotter, Bruno Stricker, Pim van der Harst, Cornelia M van Duijn, Niek Verweij, James F Wilson, Dan E Arking, Julia Ramirez, Pier D Lambiase, Nona Sotoodehnia, Borbala Mifsud, Christopher Newton-Cheh, Patricia B Munroe.

The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.

DOI: https://doi.org/10.1038/s41467-022-32821-z
Aging Cell. 2022 Sep 02. e13705

IgD+ age-associated B cells are the progenitors of the main T-independent B cell response to infection that generates protective Ab and can be induced by an inactivated vaccine in the aged.

Olivia Kugler-Umana, Wenliang Zhang, Yi Kuang, Jialing Liang, Catherine H Castonguay, Susan L Tonkonogy, Ann Marshak-Rothstein, Priyadharshini Devarajan, Susan L Swain.

  Age-associated B cells (ABC) accumulate with age and are associated with autoimmunity and chronic infection. However, their contributions to acute infection in the aged and their developmental pathways are unclear. We find that the response against influenza A virus infection in aged mice is dominated by a Fas+ GL7- effector B cell population we call infection-induced ABC (iABC). Most iABC express IgM and include antibody-secreting cells in the spleen, lung, and bone marrow. We find that in response to influenza, IgD+ CD21- CD23- ABC are the precursors of iABC and become memory B cells. These IgD+ ABC develop in germ-free mice, so are independent of foreign antigen recognition. The response of ABC to influenza infection, resulting in iABC, is T cell independent and requires both extrinsic TLR7 and TLR9 signals. In response to influenza infection, IgD+ ABC can induce a faster recovery of weight and higher total anti-influenza IgG and IgM titers that can neutralize virus. Immunization with whole inactivated virus also generates iABC in aged mice. Thus, in unimmunized aged mice, whose other B and T cell responses have waned, IgD+ ABC are likely the naive B cells with the potential to become Ab-secreting cells and to provide protection from infection in the aged.

Keywords:  TLR signals; adaptive immunity; age-associated B cells; aging; influenza

DOI:  https://doi.org/10.1111/acel.13705
Nat Commun. 2022 Aug 29. 13(1): 5079

A brainstem monosynaptic excitatory pathway that drives locomotor activities and sympathetic cardiovascular responses.

Satoshi Koba, Nao Kumada, Emi Narai, Naoya Kataoka, Kazuhiro Nakamura, Tatsuo Watanabe.

Exercise including locomotion requires appropriate autonomic cardiovascular adjustments to meet the metabolic demands of contracting muscles, yet the functional brain architecture underlying these adjustments remains unknown. Here, we demonstrate brainstem circuitry that plays an essential role in relaying volitional motor signals, i.e., central command, to drive locomotor activities and sympathetic cardiovascular responses. Mesencephalic locomotor neurons in rats transmit central command-driven excitatory signals onto the rostral ventrolateral medulla at least partially via glutamatergic processes, to activate both somatomotor and sympathetic nervous systems. Optogenetic excitation of this monosynaptic pathway elicits locomotor and cardiovascular responses as seen during running exercise, whereas pathway inhibition suppresses the locomotor activities and blood pressure elevation during voluntary running without affecting basal cardiovascular homeostasis. These results demonstrate an important subcortical pathway that transmits central command signals, providing a key insight into the central circuit mechanism required for the physiological conditioning essential to maximize exercise performance.

DOI: https://doi.org/10.1038/s41467-022-32823-x
Nat Aging. 2022 Aug;2(8): 714-725

Somatic mutations in single human cardiomyocytes reveal age-associated DNA damage and widespread oxidative genotoxicity.

Sangita Choudhury, August Yue Huang, Junho Kim, Zinan Zhou, Katherine Morillo, Eduardo A Maury, Jessica W Tsai, Michael B Miller, Michael A Lodato, Sarah Araten, Nazia Hilal, Eunjung Alice Lee, Ming Hui Chen, Christopher A Walsh.

The accumulation of somatic DNA mutations over time is a hallmark of aging in many dividing and nondividing cells but has not been studied in postmitotic human cardiomyocytes. Using single-cell whole-genome sequencing, we identified and characterized the landscape of somatic single-nucleotide variants (sSNVs) in 56 single cardiomyocytes from 12 individuals (aged from 0.4 to 82 years). Cardiomyocyte sSNVs accumulate with age at rates that are faster than in many dividing cell types and nondividing neurons. Cardiomyocyte sSNVs show distinctive mutational signatures that implicate failed nucleotide excision repair and base excision repair of oxidative DNA damage, and defective mismatch repair. Since age-accumulated sSNVs create many damaging mutations that disrupt gene functions, polyploidization in cardiomyocytes may provide a mechanism of genetic compensation to minimize the complete knockout of essential genes during aging. Age-related accumulation of cardiac mutations provides a paradigm to understand the influence of aging on cardiac dysfunction.

DOI: https://doi.org/10.1038/s43587-022-00261-5
Sci Adv. 2022 Sep 02. 8(35): eabp8321

A lysosomal regulatory circuit essential for the development and function of microglia.

Harini Iyer, Kimberle Shen, Ana M Meireles, William S Talbot.

As the primary phagocytic cells of the central nervous system, microglia exquisitely regulate their lysosomal activity to facilitate brain development and homeostasis. However, mechanisms that coordinate lysosomal activity with microglia development, chemotaxis, and function remain unclear. Here, we show that embryonic macrophages require the lysosomal guanosine triphosphatase (GTPase) RagA and the GTPase-activating protein Folliculin to colonize the brain in zebrafish. We demonstrate that embryonic macrophages in rraga mutants show increased expression of lysosomal genes but display significant down-regulation of immune- and chemotaxis-related genes. Furthermore, we find that RagA and Folliculin repress the key lysosomal transcription factor Tfeb and its homologs Tfe3a and Tfe3b in the macrophage lineage. Using RNA sequencing, we establish that Tfeb and Tfe3 are required for activation of lysosomal target genes under conditions of stress but not for basal expression of lysosomal pathways. Collectively, our data define a lysosomal regulatory circuit essential for macrophage development and function in vivo.

DOI: https://doi.org/10.1126/sciadv.abp8321
Cell. 2022 Sep 01. pii: S0092-8674(22)00979-5. [Epub ahead of print]185(18): 3390-3407.e18

A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility.

Shu-Hsien Sheu, Srigokul Upadhyayula, Vincent Dupuy, Song Pang, Fei Deng, Jinxia Wan, Deepika Walpita, H Amalia Pasolli, Justin Houser, Silvia Sanchez-Martinez, Sebastian E Brauchi, Sambashiva Banala, Melanie Freeman, C Shan Xu, Tom Kirchhausen, Harald F Hess, Luke Lavis, Yulong Li, Séverine Chaumont-Dubel, David E Clapham.

  Chemical synapses between axons and dendrites mediate neuronal intercellular communication. Here, we describe a synapse between axons and primary cilia: the axo-ciliary synapse. Using enhanced focused ion beam-scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between brainstem serotonergic axons and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, the 5-hydroxytryptamine receptor 6 (5-HTR6). Using a cilia-targeted serotonin sensor, we show that opto- and chemogenetic stimulation of serotonergic axons releases serotonin onto cilia. Ciliary 5-HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway, which modulates nuclear actin and increases histone acetylation and chromatin accessibility. Ablation of this pathway reduces chromatin accessibility in CA1 pyramidal neurons. As a signaling apparatus with proximity to the nucleus, axo-ciliary synapses short circuit neurotransmission to alter the postsynaptic neuron's epigenetic state.

Keywords:  FIB-SEM; GPCR signaling; chromatin accessibility; fluorescence lifetime imaging; histone modification; nuclear actin; primary cilia; pyramidal neurons; serotonin

DOI:  https://doi.org/10.1016/j.cell.2022.07.026
Front Immunol. 2022 ;13 950194

Development of RAG2 -/- IL2Rγ -/Y immune deficient FAH-knockout miniature pig.

Heng Zhao, Weijian Ye, Jianxiong Guo, Jiaoxiang Wang, Deling Jiao, Kaixiang Xu, Chang Yang, Shuhan Chen, Muhammad Ameen Jamal, Zhongbin Bai, Taiyun Wei, Jie Cai, Tien Dat Nguyen, Yubo Qing, Wenmin Cheng, Baoyu Jia, Honghui Li, Hong-Ye Zhao, Qingfeng Chen, Hong-Jiang Wei.

  Human hepatocyte transplantation for liver disease treatment have been hampered by the lack of quality human hepatocytes. Pigs with their large body size, longevity and physiological similarities with human are appropriate animal models for the in vivo expansion of human hepatocytes. Here we report on the generation of RAG2-/-IL2Rγ-/YFAH-/- (RGFKO) pigs via CRISPR/Cas9 system and somatic cell nuclear transfer. We showed that thymic and splenic development in RGFKO pigs was impaired. V(D)J recombination processes were also inactivated. Consequently, RGFKO pigs had significantly reduced numbers of porcine T, B and NK cells. Moreover, due to the loss of FAH, porcine hepatocytes continuously undergo apoptosis and consequently suffer hepatic damage. Thus, RGFKO pigs are both immune deficient and constantly suffer liver injury in the absence of NTBC supplementation. These results suggest that RGFKO pigs have the potential to be engrafted with human hepatocytes without immune rejection, thereby allowing for large scale expansion of human hepatocytes.

Keywords:  FAH; IL2Rγ; RAG2; immunodeficient; liver damage; pig

DOI:  https://doi.org/10.3389/fimmu.2022.950194
Nat Commun. 2022 Sep 02. 13(1): 5161

Proton-driven alternating access in a spinster lipid transporter.

Reza Dastvan, Ali Rasouli, Sepehr Dehghani-Ghahnaviyeh, Samantha Gies, Emad Tajkhorshid.

Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P transporter in endothelial cells, making it a potential drug target for modulating S1P signaling. Here, we employed an integrated approach in lipid membranes to identify unknown conformational states of a bacterial Spns from Hyphomonas neptunium (HnSpns) and to define its proton- and substrate-coupled conformational dynamics. Our systematic study reveals conserved residues critical for protonation steps and their regulation, and how sequential protonation of these proton switches coordinates the conformational transitions in the context of a noncanonical ligand-dependent alternating access. A conserved periplasmic salt bridge (Asp60TM2:Arg289TM7) keeps the transporter in a closed conformation, while proton-dependent conformational dynamics are significantly enhanced on the periplasmic side, providing a pathway for ligand exchange.

DOI: https://doi.org/10.1038/s41467-022-32759-2
Sci Adv. 2022 Sep 02. 8(35): eabn8092

Ventromedial hypothalamic OGT drives adipose tissue lipolysis and curbs obesity.

Qi Wang, Bichen Zhang, Bernardo Stutz, Zhong-Wu Liu, Tamas L Horvath, Xiaoyong Yang.

The ventromedial hypothalamus (VMH) is known to regulate body weight and counterregulatory response. However, how VMH neurons regulate lipid metabolism and energy balance remains unknown. O-linked β-d-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation), catalyzed by O-GlcNAc transferase (OGT), is considered a cellular sensor of nutrients and hormones. Here, we report that genetic ablation of OGT in VMH neurons inhibits neuronal excitability. Mice with VMH neuron-specific OGT deletion show rapid weight gain, increased adiposity, and reduced energy expenditure, without significant changes in food intake or physical activity. The obesity phenotype is associated with adipocyte hypertrophy and reduced lipolysis of white adipose tissues. In addition, OGT deletion in VMH neurons down-regulates the sympathetic activity and impairs the sympathetic innervation of white adipose tissues. These findings identify OGT in the VMH as a homeostatic set point that controls body weight and underscore the importance of the VMH in regulating lipid metabolism through white adipose tissue-specific innervation.

DOI: https://doi.org/10.1126/sciadv.abn8092
J Immunol Res. 2022 ;2022 6789055

BACH2 in TRegs Limits the Number of Adipose Tissue Regulatory T Cells and Restrains Type 2 Immunity to Fungal Allergens.

Amanda Contreras, Darin L Wiesner, Brock Kingstad-Bakke, Woojong Lee, John P Svaren, Bruce S Klein, M Suresh.

FoxP3+ regulatory T cells (Tregs) are essential for self-tolerance and moderating tissue-damaging inflammation. Tregs that develop and mature in the thymus are classified as central Tregs or effector Tregs based on whether Tregs predominately inhabit secondary lymphoid organs (central Tregs) or tissues (effector Tregs). By generating mice that are conditionally deficient for Bach2 in peripheral Tregs, we have examined the role of Bach2 in regulating Treg homeostasis and effector functions. Unlike global and T cell-specific Bach2-deficient mice, Treg-specific Bach2 ablation did not result in unprovoked TH2 inflammation in the lungs. However, Bach2 deficiency in Tregs led to augmented expressions of IRF4, BATF, and GATA3 and a significant increase in the accumulation of ST2 (IL-33R)+ve effector Tregs in the spleen and visceral adipose tissue (VAT) but not in the lungs. Enhanced Bach2-deficient Treg numbers in VAT was not linked to hyperresponsiveness to exogenous IL-33 in vivo. Most strikingly, Treg-specific Bach2 deficiency resulted in enhanced fungal protease-induced Type 2 allergic inflammation in the lungs, with no detectable effects on Type 1 responses to systemic or respiratory viral infections. In summary, we ascribe vital roles for Bach2 in peripheral Tregs: as a transcriptional checkpoint to limit precocious differentiation into effector Tregs in lymphoid tissues and as a regulator of the functional program that restrains Type 2 but not Type 1 inflammation in lungs. Results presented in this manuscript implicate dysregulated Tregs in the pathogenesis of airway hypersensitivities, asthma, and other allergic disorders.

DOI: https://doi.org/10.1155/2022/6789055
J Autoimmun. 2022 Aug 29. pii: S0896-8411(22)00096-8. [Epub ahead of print]132 102888

Forced Fox-P3 expression can improve the safety and antigen-specific function of engineered regulatory T cells.

Jenny McGovern, Angelika Holler, Sharyn Thomas, Hans J Stauss.

Regulatory T cells (Treg) are potent inhibitors of autoreactive T cells. The intracellular transcription factor FoxP3 controls the expression levels of a diverse set of genes and plays a critical role in programming functional Tregs. Although, antigen-specific Tregs are more potent than polyclonal Tregs in treating ongoing autoimmunity, phenotype plasticity associated with loss of FoxP3 expression in Tregs can lead to the conversion into antigen-specific effector T cells which might exacerbate autoimmune pathology. In this study, we designed a retroviral vector driving the expression of FoxP3 and a human HLA-DR-restricted TCR from the same promoter. Transduction of purified human Tregs revealed that all TCR-positive cells had elevated levels of FoxP3 expression, increased CD25 and CTLA4 expression and potent suppressive function. Elevated FoxP3 expression did not impair the in vitro expansion of engineered Tregs. Adoptive transfer into HLA-DR transgenic mice revealed that FoxP3+TCR engineered Tregs showed long-term persistence with stable FoxP3 and TCR expression. In contrast, adoptive transfer of Tregs engineered with TCR only resulted in the accumulation of TCR-positive, FoxP3-negative T cells which displayed antigen-specific effector function when stimulated with the TCR-recognised peptides. Our data indicate that forced expression of FoxP3 can prevent accumulation of antigen-specific effector T cells without impairing the engraftment and persistence of engineered Tregs.

DOI: https://doi.org/10.1016/j.jaut.2022.102888
Sci Adv. 2022 Sep 02. 8(35): eabo7958

JAG1-NOTCH4 mechanosensing drives atherosclerosis.

Celine Souilhol, Blanca Tardajos Ayllon, Xiuying Li, Mannekomba R Diagbouga, Ziqi Zhou, Lindsay Canham, Hannah Roddie, Daniela Pirri, Emily V Chambers, Mark J Dunning, Mark Ariaans, Jin Li, Yun Fang, Helle F Jørgensen, Michael Simons, Rob Krams, Johannes Waltenberger, Maria Fragiadaki, Victoria Ridger, Sarah De Val, Sheila E Francis, Timothy Ja Chico, Jovana Serbanovic-Canic, Paul C Evans.

Endothelial cell (EC) sensing of disturbed blood flow triggers atherosclerosis, a disease of arteries that causes heart attack and stroke, through poorly defined mechanisms. The Notch pathway plays a central role in blood vessel growth and homeostasis, but its potential role in sensing of disturbed flow has not been previously studied. Here, we show using porcine and murine arteries and cultured human coronary artery EC that disturbed flow activates the JAG1-NOTCH4 signaling pathway. Light-sheet imaging revealed enrichment of JAG1 and NOTCH4 in EC of atherosclerotic plaques, and EC-specific genetic deletion of Jag1 (Jag1ECKO) demonstrated that Jag1 promotes atherosclerosis at sites of disturbed flow. Mechanistically, single-cell RNA sequencing in Jag1ECKO mice demonstrated that Jag1 suppresses subsets of ECs that proliferate and migrate. We conclude that JAG1-NOTCH4 sensing of disturbed flow enhances atherosclerosis susceptibility by regulating EC heterogeneity and that therapeutic targeting of this pathway may treat atherosclerosis.

DOI: https://doi.org/10.1126/sciadv.abo7958
J Cell Biol. 2022 Oct 03. pii: e202110164. [Epub ahead of print]221(10):

VAMP4 regulates insulin levels by targeting secretory granules to lysosomes.

Min Li, Fengping Feng, Han Feng, Pengkai Hu, Yanhong Xue, Tao Xu, Eli Song.

Insulin levels are essential for the maintenance of glucose homeostasis, and deviations lead to pathoglycemia or diabetes. However, the metabolic mechanism controlling insulin quantity and quality is poorly understood. In pancreatic β cells, insulin homeostasis and release are tightly governed by insulin secretory granule (ISG) trafficking, but the required regulators and mechanisms are largely unknown. Here, we identified that VAMP4 controlled the insulin levels in response to glucose challenge. VAMP4 deficiency led to increased blood insulin levels and hyperresponsiveness to glucose. In β cells, VAMP4 is packaged into immature ISGs (iISGs) at trans-Golgi networks and subsequently resorted to clathrin-coated vesicles during granule maturation. VAMP4-positive iISGs and resorted vesicles then fuse with lysosomes facilitated by a SNARE complex consisting of VAMP4, STX7, STX8, and VTI1B, which ensures the breakdown of excess (pro)insulin and obsolete materials and thus maintenance of intracellular insulin homeostasis. Thus, VAMP4 is a key factor regulating the insulin levels and a potential target for the treatment of diabetes.

DOI: https://doi.org/10.1083/jcb.202110164
Nat Metab. 2022 Sep 01.

Orosomucoid 2 maintains hepatic lipid homeostasis through suppression of de novo lipogenesis.

Bing Zhou, Yunchen Luo, Nana Ji, Cheng Hu, Yan Lu.

Non-alcoholic fatty liver disease (NAFLD) is caused by imbalance in lipid metabolism. In this study, we show that the hepatokine orosomucoid (ORM) 2 is a key regulator of de novo lipogenesis in the liver. Hepatic and plasma ORM2 levels are markedly decreased in obese murine models and patients with NAFLD. Through multiple loss- and gain-of function studies, we demonstrate that ORM2 is essential to maintain hepatic and systemic lipid homeostasis. At the mechanistic level, ORM2 binds to inositol 1, 4, 5-trisphosphate receptor type 2 to activate AMP-activated protein kinase signaling, thereby inhibiting sterol regulatory element binding protein 1c-mediated lipogenic gene program. Notably, intraperitoneal injections of recombinant ORM2 protein or stabilized ORM2-FC fusion protein markedly improved liver steatosis, steatohepatitis and atherosclerosis in preclinical mouse models, without adverse effects on body weight or food intake. Thus, these findings suggest that ORM2 may serve as a potential target for therapeutic intervention in NAFLD, non-alcoholic steatohepatitis and related lipid disorders.

DOI: https://doi.org/10.1038/s42255-022-00627-4
Nat Commun. 2022 Aug 30. 13(1): 5114

Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation.

Wenqi Hu, Haitao Zeng, Yanan Shi, Chuanchuan Zhou, Jiana Huang, Lei Jia, Siqi Xu, Xiaoyu Feng, Yanyan Zeng, Tuanlin Xiong, Wenze Huang, Peng Sun, Yajie Chang, Tingting Li, Cong Fang, Keliang Wu, Lingbo Cai, Wuhua Ni, Yan Li, Zhiyong Yang, Qiangfeng Cliff Zhang, RiCheng Chian, Zijiang Chen, Xiaoyan Liang, Kehkooi Kee.

The combined use of transcriptome and translatome as indicators of gene expression profiles is usually more accurate than the use of transcriptomes alone, especially in cell types governed by translational regulation, such as mammalian oocytes. Here, we developed a dual-omics methodology that includes both transcriptome and translatome sequencing (T&T-seq) of single-cell oocyte samples, and we used it to characterize the transcriptomes and translatomes during mouse and human oocyte maturation. T&T-seq analysis revealed distinct translational expression patterns between mouse and human oocytes and delineated a sequential gene expression regulation from the cytoplasm to the nucleus during human oocyte maturation. By these means, we also identified a functional role of OOSP2 inducing factor in human oocyte maturation, as human recombinant OOSP2 induced in vitro maturation of human oocytes, which was blocked by anti-OOSP2. Single-oocyte T&T-seq analyses further elucidated that OOSP2 induces specific signaling pathways, including small GTPases, through translational regulation.

DOI: https://doi.org/10.1038/s41467-022-32791-2
Nat Commun. 2022 Sep 02. 13(1): 5164

Protein import motor complex reacts to mitochondrial misfolding by reducing protein import and activating mitophagy.

Jonas Benjamin Michaelis, Melinda Elaine Brunstein, Süleyman Bozkurt, Ludovico Alves, Martin Wegner, Manuel Kaulich, Christian Pohl, Christian Münch.

Mitophagy is essential to maintain mitochondrial function and prevent diseases. It activates upon mitochondria depolarization, which causes PINK1 stabilization on the mitochondrial outer membrane. Strikingly, a number of conditions, including mitochondrial protein misfolding, can induce mitophagy without a loss in membrane potential. The underlying molecular details remain unclear. Here, we report that a loss of mitochondrial protein import, mediated by the pre-sequence translocase-associated motor complex PAM, is sufficient to induce mitophagy in polarized mitochondria. A genome-wide CRISPR/Cas9 screen for mitophagy inducers identifies components of the PAM complex. Protein import defects are able to induce mitophagy without a need for depolarization. Upon mitochondrial protein misfolding, PAM dissociates from the import machinery resulting in decreased protein import and mitophagy induction. Our findings extend the current mitophagy model to explain mitophagy induction upon conditions that do not affect membrane polarization, such as mitochondrial protein misfolding.

DOI: https://doi.org/10.1038/s41467-022-32564-x
Mol Cell. 2022 Aug 23. pii: S1097-2765(22)00764-X. [Epub ahead of print]

The human mitochondrial genome contains a second light strand promoter.

Benedict G Tan, Christian D Mutti, Yonghong Shi, Xie Xie, Xuefeng Zhu, Pedro Silva-Pinheiro, Katja E Menger, Héctor Díaz-Maldonado, Wei Wei, Thomas J Nicholls, Patrick F Chinnery, Michal Minczuk, Maria Falkenberg, Claes M Gustafsson.

  The human mitochondrial genome must be replicated and expressed in a timely manner to maintain energy metabolism and supply cells with adequate levels of adenosine triphosphate. Central to this process is the idea that replication primers and gene products both arise via transcription from a single light strand promoter (LSP) such that primer formation can influence gene expression, with no consensus as to how this is regulated. Here, we report the discovery of a second light strand promoter (LSP2) in humans, with features characteristic of a bona fide mitochondrial promoter. We propose that the position of LSP2 on the mitochondrial genome allows replication and gene expression to be orchestrated from two distinct sites, which expands our long-held understanding of mitochondrial gene expression in humans.

Keywords:  DdCBE; LSP2; POLRMT; light strand promoter; mitochondria; mitochondrial DNA; mitochondrial gene expression; mitochondrial promoter; mtDNA; transcription

DOI:  https://doi.org/10.1016/j.molcel.2022.08.011
Sci Immunol. 2022 Sep 02. 7(75): eabo6641

Embryonic and neonatal waves generate distinct populations of hepatic ILC1s.

Colin Sparano, Darío Solís-Sayago, Anjali Vijaykumar, Chiara Rickenbach, Marijne Vermeer, Florian Ingelfinger, Gioana Litscher, André Fonseca, Caroline Mussak, Maud Mayoux, Christin Friedrich, César Nombela-Arrieta, Georg Gasteiger, Burkhard Becher, Sonia Tugues.

Group 1 innate lymphoid cells (ILCs) comprising circulating natural killer (cNK) cells and tissue-resident ILC1s are critical for host defense against pathogens and tumors. Despite a growing understanding of their role in homeostasis and disease, the ontogeny of group 1 ILCs remains largely unknown. Here, we used fate mapping and single-cell transcriptomics to comprehensively investigate the origin and turnover of murine group 1 ILCs. Whereas cNK cells are continuously replaced throughout life, we uncovered tissue-dependent development and turnover of ILC1s. A first wave of ILC1s emerges during embryogenesis in the liver and transiently colonizes fetal tissues. After birth, a second wave quickly replaces ILC1s in most tissues apart from the liver, where they layer with embryonic ILC1s, persist until adulthood, and undergo a specific developmental program. Whereas embryonically derived ILC1s give rise to a cytotoxic subset, the neonatal wave establishes the full spectrum of ILC1s. Our findings uncover key ontogenic features of murine group 1 ILCs and their association with cellular identities and functions.

DOI: https://doi.org/10.1126/sciimmunol.abo6641
Nat Commun. 2022 Aug 27. 13(1): 5058

NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis.

Zsolt Karányi, Ágnes Mosolygó-L, Orsolya Feró, Adrienn Horváth, Beáta Boros-Oláh, Éva Nagy, Szabolcs Hetey, Imre Holb, Henrik Mihály Szaker, Márton Miskei, Tibor Csorba, Lóránt Székvölgyi.

Arabidopsis NODULIN HOMEOBOX (NDX) is a nuclear protein described as a regulator of specific euchromatic genes within transcriptionally active chromosome arms. Here we show that NDX is primarily a heterochromatin regulator that functions in pericentromeric regions to control siRNA production and non-CG methylation. Most NDX binding sites coincide with pericentromeric het-siRNA loci that mediate transposon silencing, and are antagonistic with R-loop structures that are prevalent in euchromatic chromosomal arms. Inactivation of NDX leads to differential siRNA accumulation and DNA methylation, of which CHH/CHG hypomethylation colocalizes with NDX binding sites. Hi-C analysis shows significant chromatin structural changes in the ndx mutant, with decreased intrachromosomal interactions at pericentromeres where NDX is enriched in wild-type plants, and increased interchromosomal contacts between KNOT-forming regions, similar to those observed in DNA methylation mutants. We conclude that NDX is a key regulator of heterochromatin that is functionally coupled to het-siRNA loci and non-CG DNA methylation pathways.

DOI: https://doi.org/10.1038/s41467-022-32709-y
Cell Rep. 2022 Aug 30. pii: S2211-1247(22)01106-8. [Epub ahead of print]40(9): 111286

Time-resolved transcriptomes reveal diverse B cell fate trajectories in the early response to Epstein-Barr virus infection.

Elliott D SoRelle, Joanne Dai, Nicolás M Reinoso-Vizcaino, Ashley P Barry, Cliburn Chan, Micah A Luftig.

  Epstein-Barr virus infection of B lymphocytes elicits diverse host responses via well-adapted transcriptional control dynamics. Consequently, this host-pathogen interaction provides a powerful system to explore fundamental processes leading to consensus fate decisions. Here, we use single-cell transcriptomics to construct a genome-wide multistate model of B cell fates upon EBV infection. Additional single-cell data from human tonsils reveal correspondence of model states to analogous in vivo phenotypes within secondary lymphoid tissue, including an EBV+ analog of multipotent activated precursors that can yield early memory B cells. These resources yield exquisitely detailed perspectives of the transforming cellular landscape during an oncogenic viral infection that simulates antigen-induced B cell activation and differentiation. Thus, they support investigations of state-specific EBV-host dynamics, effector B cell fates, and lymphomagenesis. To demonstrate this potential, we identify EBV infection dynamics in FCRL4+/TBX21+ atypical memory B cells that are pathogenically associated with numerous immune disorders.

Keywords:  B cells; B-cell differentiation; CP: Immunology; Epstein-Barr virus; atypical memory B cells; cell fate; cell reprogramming; early memory B cells; germinal center; scRNA-seq; viral oncology

DOI:  https://doi.org/10.1016/j.celrep.2022.111286
Nat Commun. 2022 Sep 01. 13(1): 5133

Crosstalk between SUMOylation and ubiquitylation controls DNA end resection by maintaining MRE11 homeostasis on chromatin.

Tao Zhang, Han Yang, Zenan Zhou, Yongtai Bai, Jiadong Wang, Weibin Wang.

DNA end resection is delicately regulated through various types of post-translational modifications to initiate homologous recombination, but the involvement of SUMOylation in this process remains incompletely understood. Here, we show that MRE11 requires SUMOylation to shield it from ubiquitin-mediated degradation when resecting damaged chromatin. Upon DSB induction, PIAS1 promotes MRE11 SUMOylation on chromatin to initiate DNA end resection. Then, MRE11 is deSUMOylated by SENP3 mainly after it has moved away from DSB sites. SENP3 deficiency results in MRE11 degradation failure and accumulation on chromatin, causing genome instability. We further show that cancer-related MRE11 mutants with impaired SUMOylation exhibit compromised DNA repair ability. Thus, we demonstrate that MRE11 SUMOylation in coordination with ubiquitylation is dynamically controlled by PIAS1 and SENP3 to facilitate DNA end resection and maintain genome stability.

DOI: https://doi.org/10.1038/s41467-022-32920-x
Nat Commun. 2022 Aug 27. 13(1): 5049

Retromer deficiency in Tauopathy models enhances the truncation and toxicity of Tau.

Jamshid Asadzadeh, Evelyne Ruchti, Wei Jiao, Greta Limoni, Catherine MacLachlan, Scott A Small, Graham Knott, Ismael Santa-Maria, Brian D McCabe.

Alteration of the levels, localization or post-translational processing of the microtubule associated protein Tau is associated with many neurodegenerative disorders. Here we develop adult-onset models for human Tau (hTau) toxicity in Drosophila that enable age-dependent quantitative measurement of central nervous system synapse loss and axonal degeneration, in addition to effects upon lifespan, to facilitate evaluation of factors that may contribute to Tau-dependent neurodegeneration. Using these models, we interrogate the interaction of hTau with the retromer complex, an evolutionarily conserved cargo-sorting protein assembly, whose reduced activity has been associated with both Parkinson's and late onset Alzheimer's disease. We reveal that reduction of retromer activity induces a potent enhancement of hTau toxicity upon synapse loss, axon retraction and lifespan through a specific increase in the production of a C-terminal truncated isoform of hTau. Our data establish a molecular and subcellular mechanism necessary and sufficient for the depletion of retromer activity to exacerbate Tau-dependent neurodegeneration.

DOI: https://doi.org/10.1038/s41467-022-32683-5
J Immunol. 2022 Aug 29. pii: ji2200089. [Epub ahead of print]

Tracking Regulatory T Cell Development in the Thymus Using scRNA-Seq/TCR-Seq.

David L Owen, Rebecca S La Rue, Sarah A Munro, Michael A Farrar.

Recent studies have demonstrated that regulatory T cells (Tregs) develop in the thymus via two pathways involving distinct Treg progenitors (TregP): CD25+FOXP3- (CD25+ TregP) and CD25-FOXP3lo (FOXP3lo TregP) Treg progenitors. To examine this process in more detail, we carried out single-cell RNA sequencing (scRNA-Seq) and TCR-Seq on sorted murine CD4+CD8+ double-positive (DP) thymocytes, CD4+ single-positive (CD4SP) thymocytes, CD25+FOXP3-CD73- TregP, CD25-FOXP3loCD73- TregP, newly generated mature CD25+FOXP3+CD73- Tregs, and FOXP3+CD73+ recirculating/long-term resident Tregs (RT-Tregs). Sorted populations were individually hashtagged and then combined into one scRNA-Seq/TCR-Seq library before sequencing and subsequent analysis. We found that both CD25+ TregP and FOXP3lo TregP arise via an initial agonist-activated state that gives rise to a second transitional stage before differentiating into mature Tregs Using both scRNA-Seq and bulk RNA-Seq on sorted thymocyte subsets, we demonstrate that CD25+ TregP are significantly enriched for Il2 production, suggesting that they are the major source of IL-2 needed to convert TregP into mature Tregs Using TCR-Seq, we found that several TCRs were clearly biased in favor of the conventional or Treg lineages, but that a large fraction of TCRs were found in both these lineages. Finally, we found that RT-Tregs in the thymus are not monomorphic but are composed of multiple distinct subsets and that these RT-Tregs express the most diverse TCR repertoire of all CD4SP thymocytes. Thus, our studies define multiple stages of Treg differentiation within the murine thymus and serve as a resource for future studies on CD4+ thymocyte development and Treg differentiation.

DOI: https://doi.org/10.4049/jimmunol.2200089
Aging Cell. 2022 Aug 30. e13701

Production of MHCII-expressing classical monocytes increases during aging in mice and humans.

Pijus K Barman, Juliana E Shin, Sloan A Lewis, Seokjo Kang, Di Wu, Yizhou Wang, Xiaoming Yang, Prakash S Nagarkatti, Mitzi Nagarkatti, Ilhem Messaoudi, Bérénice A Benayoun, Helen S Goodridge.

  Aging is associated with increased monocyte production and altered monocyte function. Classical monocytes are heterogenous and a shift in their subset composition may underlie some of their apparent functional changes during aging. We have previously shown that mouse granulocyte-monocyte progenitors (GMPs) produce "neutrophil-like" monocytes (NeuMo), whereas monocyte-dendritic cell progenitors (MDPs) produce monocyte-derived dendritic cell (moDC)-producing monocytes (DCMo). Here, we demonstrate that classical monocytes from the bone marrow of old male and female mice have higher expression of DCMo signature genes (H2-Aa, H2-Ab1, H2-Eb1, Cd74), and that more classical monocytes express MHCII and CD74 protein. Moreover, we show that bone marrow MDPs and classical monocytes from old mice yield more moDC. We also demonstrate higher expression of Aw112010 in old monocytes and that Aw112010 lncRNA activity regulates MHCII induction in macrophages, which suggests that elevated Aw112010 levels may underlie increased MHCII expression during monocyte aging. Finally, we show that classical monocyte expression of MHCII is also elevated during healthy aging in humans. Thus, aging-associated changes in monocyte production may underlie altered monocyte function and have implications for aging-associated disorders.

Keywords:  aging; bone marrow progenitors; monocytes

DOI:  https://doi.org/10.1111/acel.13701
Nat Commun. 2022 Aug 30. 13(1): 5089

Early macrophage response to obesity encompasses Interferon Regulatory Factor 5 regulated mitochondrial architecture remodelling.

L Orliaguet, T Ejlalmanesh, A Humbert, R Ballaire, M Diedisheim, J B Julla, D Chokr, J Cuenco, J Michieletto, J Charbit, D Lindén, J Boucher, C Potier, A Hamimi, S Lemoine, C Blugeon, P Legoix, S Lameiras, L G Baudrin, S Baulande, A Soprani, F A Castelli, F Fenaille, J P Riveline, E Dalmas, J Rieusset, J F Gautier, N Venteclef, F Alzaid.

Adipose tissue macrophages (ATM) adapt to changes in their energetic microenvironment. Caloric excess, in a range from transient to diet-induced obesity, could result in the transition of ATMs from highly oxidative and protective to highly inflammatory and metabolically deleterious. Here, we demonstrate that Interferon Regulatory Factor 5 (IRF5) is a key regulator of macrophage oxidative capacity in response to caloric excess. ATMs from mice with genetic-deficiency of Irf5 are characterised by increased oxidative respiration and mitochondrial membrane potential. Transient inhibition of IRF5 activity leads to a similar respiratory phenotype as genomic deletion, and is reversible by reconstitution of IRF5 expression. We find that the highly oxidative nature of Irf5-deficient macrophages results from transcriptional de-repression of the mitochondrial matrix component Growth Hormone Inducible Transmembrane Protein (GHITM) gene. The Irf5-deficiency-associated high oxygen consumption could be alleviated by experimental suppression of Ghitm expression. ATMs and monocytes from patients with obesity or with type-2 diabetes retain the reciprocal regulatory relationship between Irf5 and Ghitm. Thus, our study provides insights into the mechanism of how the inflammatory transcription factor IRF5 controls physiological adaptation to diet-induced obesity via regulating mitochondrial architecture in macrophages.

DOI: https://doi.org/10.1038/s41467-022-32813-z
Nat Neurosci. 2022 Aug 30.

Pathological structural conversion of α-synuclein at the mitochondria induces neuronal toxicity.

Minee L Choi, Alexandre Chappard, Bhanu P Singh, Catherine Maclachlan, Margarida Rodrigues, Evgeniya I Fedotova, Alexey V Berezhnov, Suman De, Christopher J Peddie, Dilan Athauda, Gurvir S Virdi, Weijia Zhang, James R Evans, Anna I Wernick, Zeinab Shadman Zanjani, Plamena R Angelova, Noemi Esteras, Andrey Y Vinokurov, Katie Morris, Kiani Jeacock, Laura Tosatto, Daniel Little, Paul Gissen, David J Clarke, Tilo Kunath, Lucy Collinson, David Klenerman, Andrey Y Abramov, Mathew H Horrocks, Sonia Gandhi.

Aggregation of alpha-synuclein (α-Syn) drives Parkinson's disease (PD), although the initial stages of self-assembly and structural conversion have not been directly observed inside neurons. In this study, we tracked the intracellular conformational states of α-Syn using a single-molecule Förster resonance energy transfer (smFRET) biosensor, and we show here that α-Syn converts from a monomeric state into two distinct oligomeric states in neurons in a concentration-dependent and sequence-specific manner. Three-dimensional FRET-correlative light and electron microscopy (FRET-CLEM) revealed that intracellular seeding events occur preferentially on membrane surfaces, especially at mitochondrial membranes. The mitochondrial lipid cardiolipin triggers rapid oligomerization of A53T α-Syn, and cardiolipin is sequestered within aggregating lipid-protein complexes. Mitochondrial aggregates impair complex I activity and increase mitochondrial reactive oxygen species (ROS) generation, which accelerates the oligomerization of A53T α-Syn and causes permeabilization of mitochondrial membranes and cell death. These processes were also observed in induced pluripotent stem cell (iPSC)-derived neurons harboring A53T mutations from patients with PD. Our study highlights a mechanism of de novo α-Syn oligomerization at mitochondrial membranes and subsequent neuronal toxicity.

DOI: https://doi.org/10.1038/s41593-022-01140-3
Nat Biomed Eng. 2022 Aug 29.

Revealing nanostructures in brain tissue via protein decrowding by iterative expansion microscopy.

Deblina Sarkar, Jinyoung Kang, Asmamaw T Wassie, Margaret E Schroeder, Zhuyu Peng, Tyler B Tarr, Ai-Hui Tang, Emily D Niederst, Jennie Z Young, Hanquan Su, Demian Park, Peng Yin, Li-Huei Tsai, Thomas A Blanpied, Edward S Boyden.

Many crowded biomolecular structures in cells and tissues are inaccessible to labelling antibodies. To understand how proteins within these structures are arranged with nanoscale precision therefore requires that these structures be decrowded before labelling. Here we show that an iterative variant of expansion microscopy (the permeation of cells and tissues by a swellable hydrogel followed by isotropic hydrogel expansion, to allow for enhanced imaging resolution with ordinary microscopes) enables the imaging of nanostructures in expanded yet otherwise intact tissues at a resolution of about 20 nm. The method, which we named 'expansion revealing' and validated with DNA-probe-based super-resolution microscopy, involves gel-anchoring reagents and the embedding, expansion and re-embedding of the sample in homogeneous swellable hydrogels. Expansion revealing enabled us to use confocal microscopy to image the alignment of pre-synaptic calcium channels with post-synaptic scaffolding proteins in intact brain circuits, and to uncover periodic amyloid nanoclusters containing ion-channel proteins in brain tissue from a mouse model of Alzheimer's disease. Expansion revealing will enable the further discovery of previously unseen nanostructures within cells and tissues.

DOI: https://doi.org/10.1038/s41551-022-00912-3