bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022–03–13
38 papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.
  2. Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function.
  3. Gut microbiota-derived short-chain fatty acids regulates group 3 innate lymphoid cells in hepatocellular carcinoma.
  4. A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts.
  5. Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain.
  6. Homotypic fibrillization of TMEM106B across diverse neurodegenerative diseases.
  7. T Cell-Specific Deletion of TRAIL Receptor Reveals Its Critical Role for Regulating Pathologic T Cell Activation and Disease Induction in Experimental Autoimmune Encephalomyelitis.
  8. Motor cortical output for skilled forelimb movement is selectively distributed across projection neuron classes.
  9. Emerging enterococcus pore-forming toxins with MHC/HLA-I as receptors.
  10. Lymph node CXCR5+ NK cells associate with control of chronic SHIV infection.
  11. OpenCell: Endogenous tagging for the cartography of human cellular organization.
  12. KLF15 cistromes reveal a hepatocyte pathway governing plasma corticosteroid transport and systemic inflammation.
  13. A non-canonical tricarboxylic acid cycle underlies cellular identity.
  14. End COVID-19 in low- and middle-income countries.
  15. Ageing induces tissue-specific transcriptomic changes in Caenorhabditis elegans.
  16. The YΦ motif defines the structure-activity relationships of human 20S proteasome activators.
  17. First-in-human immunoPET imaging of HIV-1 infection using 89Zr-labeled VRC01 broadly neutralizing antibody.
  18. MITI minimum information guidelines for highly multiplexed tissue images.
  19. Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers.
  20. The Extracellular ATP Receptor P2RX7 Imprints a Promemory Transcriptional Signature in Effector CD8+ T Cells.
  21. Competition for refueling rather than cyclic reentry initiation evident in germinal centers.
  22. CRISPR/Cas9-Mediated Insertion of HIV Long Terminal Repeat within BACH2 Promotes Expansion of T Regulatory-like Cells.
  23. Eosinophils are an essential element of a type 2 immune axis that controls thymus regeneration.
  24. Elucidating mechanisms of genetic cross-disease associations at the PROCR vascular disease locus.
  25. Restoring nuclear entry of Sirtuin 2 in oligodendrocyte progenitor cells promotes remyelination during ageing.
  26. A high-resolution view of intra-tumoral B cell immunity.
  27. A hierarchical regulatory network ensures stable albumin transcription under various pathophysiological conditions.
  28. DNA replication fork speed underlies cell fate changes and promotes reprogramming.
  29. A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.
  30. Coincidence of cholinergic pauses, dopaminergic activation and depolarisation of spiny projection neurons drives synaptic plasticity in the striatum.
  31. Structure of a Janus kinase cytokine receptor complex reveals the basis for dimeric activation.
  32. Uptake of N2O5 by aqueous aerosol unveiled using chemically accurate many-body potentials.
  33. Nascent transcription as a predictor and driver of histone modifications.
  34. The evolution, evolvability and engineering of gene regulatory DNA.
  35. Neurons detect cognitive boundaries to structure episodic memories in humans.
  36. Hepatic glucocorticoid-induced transcriptional regulation is androgen-dependent after chronic but not acute glucocorticoid exposure.
  37. CTLA4Ig/VISTAIg combination therapy selectively induces CD4+ T cell-mediated immune tolerance by targeting the SOCS1 signaling pathway in porcine islet xenotransplantation.
  38. A partial form of inherited human USP18 deficiency underlies infection and inflammation.
  1. Science. 2022 Mar 08. eabi9591
    KIR+CD8+ T cells suppress pathogenic T cells and are active in autoimmune diseases and COVID-19.
    Jing Li, Maxim Zaslavsky, Yapeng Su, Jing Guo, Michael J Sikora, Vincent van Unen, Asbjørn Christophersen, Shin-Heng Chiou, Liang Chen, Jiefu Li, Xuhuai Ji, Julie Wilhelmy, Alana M McSween, Brad A Palanski, Venkata Vamsee Aditya Mallajosyula, Nathan A Bracey, Gopal Krishna R Dhondalay, Kartik Bhamidipati, Joy Pai, Lucas B Kipp, Jeffrey E Dunn, Stephen L Hauser, Jorge R Oksenberg, Ansuman T Satpathy, William H Robinson, Cornelia L Dekker, Lars M Steinmetz, Chaitan Khosla, Paul J Utz, Ludvig M Sollid, Yueh-Hsiu Chien, James R Heath, Nielsen Q Fernandez-Becker, Kari C Nadeau, Naresha Saligrama, Mark M Davis.
      Here we find that CD8+ T cells expressing inhibitory killer cell immunoglobulin-like receptors (KIRs) are the human equivalent of Ly49+CD8+ regulatory T cells in mice and are increased in the blood and inflamed tissues of patients with a variety of autoimmune diseases. Moreover, these CD8+ T cells efficiently eliminated pathogenic gliadin-specific CD4+ T cells from celiac disease patients' leukocytes in vitro. We also find elevated levels of KIR+CD8+ T cells, but not CD4+ regulatory T cells, in COVID-19 patients, which correlated with disease severity and vasculitis. Selective ablation of Ly49+CD8+ T cells in virus-infected mice led to autoimmunity post infection. Our results indicate that in both species, these regulatory CD8+ T cells act uniquely to suppress pathogenic T cells in autoimmune and infectious diseases.
    DOI:  https://doi.org/10.1126/science.abi9591
  2. Sci Immunol. 2022 Mar 11. 7(69): eabm0631
    Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function.
    Ruihan Tang, Nandini Acharya, Ayshwarya Subramanian, Vinee Purohit, Marcin Tabaka, Yu Hou, Danyang He, Karen O Dixon, Connor Lambden, Junrong Xia, Orit Rozenblatt-Rosen, Raymond A Sobel, Chao Wang, Aviv Regev, Ana C Anderson, Vijay K Kuchroo.
      Dendritic cells (DCs) sense environmental cues and adopt either an immune-stimulatory or regulatory phenotype, thereby fine-tuning immune responses. Identifying endogenous regulators that determine DC function can thus inform the development of therapeutic strategies for modulating the immune response in different disease contexts. Tim-3 plays an important role in regulating immune responses by inhibiting the activation status and the T cell priming ability of DC in the setting of cancer. Bat3 is an adaptor protein that binds to the tail of Tim-3; therefore, we studied its role in regulating the functional status of DCs. In murine models of autoimmunity (experimental autoimmune encephalomyelitis) and cancer (MC38-OVA-implanted tumor), lack of Bat3 expression in DCs alters the T cell compartment-it decreases TH1, TH17 and cytotoxic effector cells, increases regulatory T cells, and exhausted CD8+ tumor-infiltrating lymphocytes, resulting in the attenuation of autoimmunity and acceleration of tumor growth. We found that Bat3 expression levels were differentially regulated by activating versus inhibitory stimuli in DCs, indicating a role for Bat3 in the functional calibration of DC phenotypes. Mechanistically, loss of Bat3 in DCs led to hyperactive unfolded protein response and redirected acetyl-coenzyme A to increase cell intrinsic steroidogenesis. The enhanced steroidogenesis in Bat3-deficient DC suppressed T cell response in a paracrine manner. Our findings identified Bat3 as an endogenous regulator of DC function, which has implications for DC-based immunotherapies.
    DOI:  https://doi.org/10.1126/sciimmunol.abm0631
  3. Hepatology. 2022 Mar 09.
    Gut microbiota-derived short-chain fatty acids regulates group 3 innate lymphoid cells in hepatocellular carcinoma.
    Chupeng Hu, Bingqing Xu, Xiaodong Wang, Wen-Hua Wan, Jinying Lu, Deyuan Kong, Yu Jin, Wenhua You, Hua Sun, Xiaoxin Mu, Dongju Feng, Yun Chen.
       BACKGROUND AND AIMS: Type 3 innate lymphoid cells (ILC3s) are essential for host defense against infection and tissue homeostasis. However, its role in the development of hepatocellular carcinoma (HCC) has not been adequately confirmed. In this study, we investigated the immunomodulatory role of short-chain fatty acids (SCFAs) derived from intestinal microbiota in ILC3 regulation.
    APPROACH AND RESULTS: Here, we reported that the Lactobacillus reuteri was markedly reduced in the gut microbiota of mice with hepatocellular carcinoma (HCC), accompanied by decreased short chain fatty acids (SCFAs) levels, especially acetate. Additionally, transplantation of fecal bacteria from wild type mice or Lactobacillus reuteri could promote an anticancer effect, elevate acetate level and reduce IL17A secretion in mice with HCC. Mechanistically, acetate reduced the production of IL17A in hepatic ILC3s through inhibiting histone deacetylase (HDAC) activity, increasing the acetylation of Sox13 in the site of K30 and decreasing expression of Sox13. Moreover, the combination of acetate with PD-1/PD-L1 blockade significantly enhanced anti-tumor immunity. Consistently, Tumor-infiltrating ILC3s correlated with negative prognosis in patients with HCC, which could be functionally mediated via acetate.
    CONCLUSIONS: These findings suggested that modifying bacteria, changing SCFAs, reducing IL17A-producing ILC3s infiltration and combining with immune checkpoint inhibitors will contribute to the clinical treatment of HCC.
    DOI:  https://doi.org/10.1002/hep.32449
  4. Immunity. 2022 Mar 08. pii: S1074-7613(22)00083-8. [Epub ahead of print]55(3): 494-511.e11
    A nonredundant role for T cell-derived interleukin 22 in antibacterial defense of colonic crypts.
    Carlene L Zindl, Steven J Witte, Vincent A Laufer, Min Gao, Zongliang Yue, Karen M Janowski, Baiyi Cai, Blake F Frey, Daniel J Silberger, Stacey N Harbour, Jeffrey R Singer, Henrietta Turner, Frances E Lund, Bruce A Vallance, Alexander F Rosenberg, Trenton R Schoeb, Jake Y Chen, Robin D Hatton, Casey T Weaver.
      Interleukin (IL)-22 is central to immune defense at barrier sites. We examined the contributions of innate lymphoid cell (ILC) and T cell-derived IL-22 during Citrobacter rodentium (C.r) infection using mice that both report Il22 expression and allow lineage-specific deletion. ILC-derived IL-22 activated STAT3 in C.r-colonized surface intestinal epithelial cells (IECs) but only temporally restrained bacterial growth. T cell-derived IL-22 induced a more robust and extensive activation of STAT3 in IECs, including IECs lining colonic crypts, and T cell-specific deficiency of IL-22 led to pathogen invasion of the crypts and increased mortality. This reflected a requirement for T cell-derived IL-22 for the expression of a host-protective transcriptomic program that included AMPs, neutrophil-recruiting chemokines, and mucin-related molecules, and it restricted IFNγ-induced proinflammatory genes. Our findings demonstrate spatiotemporal differences in the production and action of IL-22 by ILCs and T cells during infection and reveal an indispensable role for IL-22-producing T cells in the protection of the intestinal crypts.
    Keywords:  AMPs; CD4 T cells; Citrobacter rodentium; IFNγ; IL-22; TNF; chemokines; colonic crypt IECs; colonic surface IECs; innate cells; mucins
    DOI:  https://doi.org/10.1016/j.immuni.2022.02.003
  5. Nat Neurosci. 2022 Mar;25(3): 306-316
    Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain.
    Samuel E Marsh, Alec J Walker, Tushar Kamath, Lasse Dissing-Olesen, Timothy R Hammond, T Yvanka de Soysa, Adam M H Young, Sarah Murphy, Abdulraouf Abdulraouf, Naeem Nadaf, Connor Dufort, Alicia C Walker, Liliana E Lucca, Velina Kozareva, Charles Vanderburg, Soyon Hong, Harry Bulstrode, Peter J Hutchinson, Daniel J Gaffney, David A Hafler, Robin J M Franklin, Evan Z Macosko, Beth Stevens.
      A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues into single-cell suspensions. While many protocols have been optimized for optimal cell yield, they have often overlooked the effects that dissociation can have on ex vivo gene expression. Here, we demonstrate that use of enzymatic dissociation on brain tissue induces an aberrant ex vivo gene expression signature, most prominently in microglia, which is prevalent in published literature and can substantially confound downstream analyses. To address this issue, we present a rigorously validated protocol that preserves both in vivo transcriptional profiles and cell-type diversity and yield across tissue types and species. We also identify a similar signature in postmortem human brain single-nucleus RNA-sequencing datasets, and show that this signature is induced in freshly isolated human tissue by exposure to elevated temperatures ex vivo. Together, our results provide a methodological solution for preventing artifactual gene expression changes during fresh tissue digestion and a reference for future deeper analysis of the potential confounding states present in postmortem human samples.
    DOI:  https://doi.org/10.1038/s41593-022-01022-8
  6. Cell. 2022 Mar 01. pii: S0092-8674(22)00259-8. [Epub ahead of print]
    Homotypic fibrillization of TMEM106B across diverse neurodegenerative diseases.
    Andrew Chang, Xinyu Xiang, Jing Wang, Carolyn Lee, Tamta Arakhamia, Marija Simjanoska, Chi Wang, Yari Carlomagno, Guoan Zhang, Shikhar Dhingra, Manon Thierry, Jolien Perneel, Bavo Heeman, Lauren M Forgrave, Michael DeTure, Mari L DeMarco, Casey N Cook, Rosa Rademakers, Dennis W Dickson, Leonard Petrucelli, Michael H B Stowell, Ian R A Mackenzie, Anthony W P Fitzpatrick.
      Misfolding and aggregation of disease-specific proteins, resulting in the formation of filamentous cellular inclusions, is a hallmark of neurodegenerative disease with characteristic filament structures, or conformers, defining each proteinopathy. Here we show that a previously unsolved amyloid fibril composed of a 135 amino acid C-terminal fragment of TMEM106B is a common finding in distinct human neurodegenerative diseases, including cases characterized by abnormal aggregation of TDP-43, tau, or α-synuclein protein. A combination of cryoelectron microscopy and mass spectrometry was used to solve the structures of TMEM106B fibrils at a resolution of 2.7 Å from postmortem human brain tissue afflicted with frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP, n = 8), progressive supranuclear palsy (PSP, n = 2), or dementia with Lewy bodies (DLB, n = 1). The commonality of abundant amyloid fibrils composed of TMEM106B, a lysosomal/endosomal protein, to a broad range of debilitating human disorders indicates a shared fibrillization pathway that may initiate or accelerate neurodegeneration.
    Keywords:  DLB; FTLD-TDP; PSP; TMEM106B; amyloid fibrils; cryo-EM; endosome; lysosome; neurodegeneration; proteolysis
    DOI:  https://doi.org/10.1016/j.cell.2022.02.026
  7. J Immunol. 2022 Mar 09. pii: ji2100788. [Epub ahead of print]
    T Cell-Specific Deletion of TRAIL Receptor Reveals Its Critical Role for Regulating Pathologic T Cell Activation and Disease Induction in Experimental Autoimmune Encephalomyelitis.
    I-Tsu Chyuan, Ching-Liang Chu, Chia-Lang Hsu, Meng-Hsun Pan, Hsiu-Jung Liao, Chien-Sheng Wu, Ping-Ning Hsu.
      Recent evidence from several autoimmune animal models has demonstrated that TRAIL suppresses the activation of T cells and inhibits autoimmune inflammation via an apoptosis-independent pathway. However, it remains unclear whether the immunosuppressive effects of TRAIL are dependent on its direct effects on T cells or on other immune cells to regulate T cells for the induction of disease. Therefore, we generated mice with T cell-specific TRAIL receptor (TRAIL-R) conditional knockout to investigate the impact of TRAIL on autoimmune inflammation and disease induction in experimental autoimmune encephalomyelitis (EAE). T cell-specific TRAIL-R knockout mice were found to completely reverse the TRAIL-mediated suppression of inflammation and disease induction, indicating that TRAIL-R on T cells is essential for TRAIL-mediated suppression of inflammation and disease induction in EAE. Moreover, the immune suppression effects were not due to the induction of cell apoptosis, but to the direct inhibition of T cell activation. In addition, RNA sequencing and transcriptome analysis revealed that TRAIL-R signaling significantly downregulated the genes involved in TCR signaling pathways, T cell differentiation, and proinflammatory cytokines. These results indicate that TRAIL-R on T cells is critical for pathologic T cell activation and induction of inflammation in EAE, suggesting that TRAIL-R serves as a novel immune checkpoint receptor in T cell-mediated autoimmune diseases.
    DOI:  https://doi.org/10.4049/jimmunol.2100788
  8. Sci Adv. 2022 Mar 11. 8(10): eabj5167
    Motor cortical output for skilled forelimb movement is selectively distributed across projection neuron classes.
    Junchol Park, James W Phillips, Jian-Zhong Guo, Kathleen A Martin, Adam W Hantman, Joshua T Dudman.
      The interaction of descending neocortical outputs and subcortical premotor circuits is critical for shaping skilled movements. Two broad classes of motor cortical output projection neurons provide input to many subcortical motor areas: pyramidal tract (PT) neurons, which project throughout the neuraxis, and intratelencephalic (IT) neurons, which project within the cortex and subcortical striatum. It is unclear whether these classes are functionally in series or whether each class carries distinct components of descending motor control signals. Here, we combine large-scale neural recordings across all layers of motor cortex with cell type-specific perturbations to study cortically dependent mouse motor behaviors: kinematically variable manipulation of a joystick and a kinematically precise reach-to-grasp. We find that striatum-projecting IT neuron activity preferentially represents amplitude, whereas pons-projecting PT neurons preferentially represent the variable direction of forelimb movements. Thus, separable components of descending motor cortical commands are distributed across motor cortical projection cell classes.
    DOI:  https://doi.org/10.1126/sciadv.abj5167
  9. Cell. 2022 Mar 02. pii: S0092-8674(22)00142-8. [Epub ahead of print]
    Emerging enterococcus pore-forming toxins with MHC/HLA-I as receptors.
    Xiaozhe Xiong, Songhai Tian, Pan Yang, Francois Lebreton, Huan Bao, Kuanwei Sheng, Linxiang Yin, Pengsheng Chen, Jie Zhang, Wanshu Qi, Jianbin Ruan, Hao Wu, Hong Chen, David T Breault, Hao Wu, Ashlee M Earl, Michael S Gilmore, Jonathan Abraham, Min Dong.
      Enterococci are a part of human microbiota and a leading cause of multidrug resistant infections. Here, we identify a family of Enterococcus pore-forming toxins (Epxs) in E. faecalis, E. faecium, and E. hirae strains isolated across the globe. Structural studies reveal that Epxs form a branch of β-barrel pore-forming toxins with a β-barrel protrusion (designated the top domain) sitting atop the cap domain. Through a genome-wide CRISPR-Cas9 screen, we identify human leukocyte antigen class I (HLA-I) complex as a receptor for two members (Epx2 and Epx3), which preferentially recognize human HLA-I and homologous MHC-I of equine, bovine, and porcine, but not murine, origin. Interferon exposure, which stimulates MHC-I expression, sensitizes human cells and intestinal organoids to Epx2 and Epx3 toxicity. Co-culture with Epx2-harboring E. faecium damages human peripheral blood mononuclear cells and intestinal organoids, and this toxicity is neutralized by an Epx2 antibody, demonstrating the toxin-mediated virulence of Epx-carrying Enterococcus.
    Keywords:  CRISPR screen; E. faecalis; E. faecium; E. hirae; Enterococcus; HLA-I; MHC-I; bacterial toxin; interferon; pore-forming toxin
    DOI:  https://doi.org/10.1016/j.cell.2022.02.002
  10. JCI Insight. 2022 Mar 10. pii: e155601. [Epub ahead of print]
    Lymph node CXCR5+ NK cells associate with control of chronic SHIV infection.
    Sheikh Abdul Rahman, James Billinglsley, Ashish Arunkumar Sharma, Tiffany M Styles, Sakthivel Govindaraj, Uma Shanmugasundaram, Hemalatha Babu, Susan Pereira Ribeiro, Syed A Ali, Gregory K Tharp, Chris Ibegbu, Stephen Waggoner, R Paul Johnson, Rafick-Pierre Sékaly, Francois Villinger, Steven E Bosinger, Rama Rao Amara, Vijayakumar Velu.
      The persistence of virally infected cells as reservoirs despite effective antiretroviral therapy is a major barrier to HIV/simian immunodeficiency virus (SIV) cure. These reservoirs are predominately contained within cells present in the B cell follicles (BCF) of secondary lymphoid tissues, a site that is characteristically difficult for most cytolytic antiviral effector cells to penetrate. Here, we identified a population of natural killer (NK) cells in macaque lymph nodes that expressed BCF-homing receptor C-X-C chemokine receptor 5 (CXCR5) and accumulated within BCF during chronic SHIV infection. These CXCR5+ follicular NK cells exhibited an activated phenotype coupled with heightened effector functions and a unique transcriptome characterized by elevated expression of cytolytic mediators (e.g. perforin and granzymes, LAMP-1). CXCR5+ NK cells exhibited high expression of FcγRIIa and FcγRIIIa, suggesting a potential for elevated antibody-dependent effector functionality. Consistently, accumulation of CXCR5+ NK cells showed a strong inverse association with plasma viral load and the frequency of germinal center follicular helper T cells that comprises a significant fraction of the viral reservoir. Moreover, CXCR5+ NK cells showed increased expression of transcripts associated with IL-12 and IL-15 signaling compared to the CXCR5- subset. Indeed, in vitro treatment with IL-12 and IL-15 enhanced the proliferation of CXCR5+ granzyme-B+ NK cells. Our findings suggest that follicular homing NK cells might be important in immune control of chronic SHIV infection, which may have important implications for HIV cure strategies.
    Keywords:  AIDS/HIV; Immunology; Innate immunity; NK cells
    DOI:  https://doi.org/10.1172/jci.insight.155601
  11. Science. 2022 Mar 11. 375(6585): eabi6983
    OpenCell: Endogenous tagging for the cartography of human cellular organization.
    Nathan H Cho, Keith C Cheveralls, Andreas-David Brunner, Kibeom Kim, André C Michaelis, Preethi Raghavan, Hirofumi Kobayashi, Laura Savy, Jason Y Li, Hera Canaj, James Y S Kim, Edna M Stewart, Christian Gnann, Frank McCarthy, Joana P Cabrera, Rachel M Brunetti, Bryant B Chhun, Greg Dingle, Marco Y Hein, Bo Huang, Shalin B Mehta, Jonathan S Weissman, Rafael Gómez-Sjöberg, Daniel N Itzhak, Loïc A Royer, Matthias Mann, Manuel D Leonetti.
      Elucidating the wiring diagram of the human cell is a central goal of the postgenomic era. We combined genome engineering, confocal live-cell imaging, mass spectrometry, and data science to systematically map the localization and interactions of human proteins. Our approach provides a data-driven description of the molecular and spatial networks that organize the proteome. Unsupervised clustering of these networks delineates functional communities that facilitate biological discovery. We found that remarkably precise functional information can be derived from protein localization patterns, which often contain enough information to identify molecular interactions, and that RNA binding proteins form a specific subgroup defined by unique interaction and localization properties. Paired with a fully interactive website (opencell.czbiohub.org), our work constitutes a resource for the quantitative cartography of human cellular organization.
    DOI:  https://doi.org/10.1126/science.abi6983
  12. Sci Adv. 2022 Mar 11. 8(10): eabj2917
    KLF15 cistromes reveal a hepatocyte pathway governing plasma corticosteroid transport and systemic inflammation.
    Zhen Jiang, Selma Z Elsarrag, Qiming Duan, Edward L LaGory, Zhe Wang, Michael Alexanian, Sarah McMahon, Ingrid C Rulifson, Sarah Winchester, Yi Wang, Christian Vaisse, Jonathan D Brown, Mattia Quattrocelli, Charles Y Lin, Saptarsi M Haldar.
      Circulating corticosteroids orchestrate stress adaptation, including inhibition of inflammation. While pathways governing corticosteroid biosynthesis and intracellular signaling are well understood, less is known about mechanisms controlling plasma corticosteroid transport. Here, we show that hepatocyte KLF15 (Kruppel-like factor 15) controls plasma corticosteroid transport and inflammatory responses through direct transcriptional activation of Serpina6, which encodes corticosteroid-binding globulin (CBG). Klf15-deficient mice have profoundly low CBG, reduced plasma corticosteroid binding capacity, and heightened mortality during inflammatory stress. These defects are completely rescued by reconstituting CBG, supporting that KLF15 works primarily through CBG to control plasma corticosterone homeostasis. To understand transcriptional mechanisms, we generated the first KLF15 cistromes using newly engineered Klf153xFLAG mice. Unexpectedly, liver KLF15 is predominantly promoter enriched, including Serpina6, where it binds a palindromic GC-rich motif, opens chromatin, and transactivates genes with minimal associated direct gene repression. Overall, we provide critical mechanistic insight into KLF15 function and identify a hepatocyte-intrinsic transcriptional module that potently regulates systemic corticosteroid transport and inflammation.
    DOI:  https://doi.org/10.1126/sciadv.abj2917
  13. Nature. 2022 Mar 09.
    A non-canonical tricarboxylic acid cycle underlies cellular identity.
    Paige K Arnold, Benjamin T Jackson, Katrina I Paras, Julia S Brunner, Madeleine L Hart, Oliver J Newsom, Sydney P Alibeckoff, Jennifer Endress, Esther Drill, Lucas B Sullivan, Lydia W S Finley.
      The tricarboxylic acid (TCA) cycle is a central hub of cellular metabolism, oxidizing nutrients to generate reducing equivalents for energy production and critical metabolites for biosynthetic reactions. Despite the importance of the products of the TCA cycle for cell viability and proliferation, mammalian cells display diversity in TCA-cycle activity1,2. How this diversity is achieved, and whether it is critical for establishing cell fate, remains poorly understood. Here we identify a non-canonical TCA cycle that is required for changes in cell state. Genetic co-essentiality mapping revealed a cluster of genes that is sufficient to compose a biochemical alternative to the canonical TCA cycle, wherein mitochondrially derived citrate exported to the cytoplasm is metabolized by ATP citrate lyase, ultimately regenerating mitochondrial oxaloacetate to complete this non-canonical TCA cycle. Manipulating the expression of ATP citrate lyase or the canonical TCA-cycle enzyme aconitase 2 in mouse myoblasts and embryonic stem cells revealed that changes in the configuration of the TCA cycle accompany cell fate transitions. During exit from pluripotency, embryonic stem cells switch from canonical to non-canonical TCA-cycle metabolism. Accordingly, blocking the non-canonical TCA cycle prevents cells from exiting pluripotency. These results establish a context-dependent alternative to the traditional TCA cycle and reveal that appropriate TCA-cycle engagement is required for changes in cell state.
    DOI:  https://doi.org/10.1038/s41586-022-04475-w
  14. Science. 2022 Mar 11. 375(6585): 1105-1110
    End COVID-19 in low- and middle-income countries.
    Ahmed Mushfiq Mobarak, Edward Miguel, Jason Abaluck, Amrita Ahuja, Marcella Alsan, Abhijit Banerjee, Emily Breza, Arun G Chandrasekhar, Esther Duflo, James Dzansi, Denise Garrett, Paul Goldsmith-Pinkham, Gregg S Gonsalves, Muhammad Maqsud Hossain, Aleksandra Jakubowski, Gagandeep Kang, Arjun Kharel, Michael Kremer, Niccolo Meriggi, Carol Nekesa, Benjamin A Olken, Saad B Omer, Firdausi Qadri, Helen Rees, Babatunde Salako, Maarten Voors, Shana Warren, Witold Więcek.
      
    DOI:  https://doi.org/10.1126/science.abo4089
  15. EMBO J. 2022 Mar 07. e109633
    Ageing induces tissue-specific transcriptomic changes in Caenorhabditis elegans.
    Xueqing Wang, Quanlong Jiang, Yuanyuan Song, Zhidong He, Hongdao Zhang, Mengjiao Song, Xiaona Zhang, Yumin Dai, Oezlem Karalay, Christoph Dieterich, Adam Antebi, Ligang Wu, Jing-Dong J Han, Yidong Shen.
      Ageing is a complex process with common and distinct features across tissues. Unveiling the underlying processes driving ageing in individual tissues is indispensable to decipher the mechanisms of organismal longevity. Caenorhabditis elegans is a well-established model organism that has spearheaded ageing research with the discovery of numerous genetic pathways controlling its lifespan. However, it remains challenging to dissect the ageing of worm tissues due to the limited description of tissue pathology and access to tissue-specific molecular changes during ageing. In this study, we isolated cells from five major tissues in young and old worms and profiled the age-induced transcriptomic changes within these tissues. We observed a striking diversity of ageing across tissues and identified different sets of longevity regulators therein. In addition, we found novel tissue-specific factors, including irx-1 and myrf-2, which control the integrity of the intestinal barrier and sarcomere structure during ageing respectively. This study demonstrates the complexity of ageing across worm tissues and highlights the power of tissue-specific transcriptomic profiling during ageing, which can serve as a resource to the field.
    Keywords:   Caenorhabditis elegans ; ageing; tissue; transcription factor; transcriptomic change
    DOI:  https://doi.org/10.15252/embj.2021109633
  16. Nat Commun. 2022 Mar 09. 13(1): 1226
    The YΦ motif defines the structure-activity relationships of human 20S proteasome activators.
    Kwadwo A Opoku-Nsiah, Andres H de la Pena, Sarah K Williams, Nikita Chopra, Andrej Sali, Gabriel C Lander, Jason E Gestwicki.
      The 20S proteasome (20S) facilitates turnover of most eukaryotic proteins. Substrate entry into the 20S first requires opening of gating loops through binding of HbYX motifs that are present at the C-termini of certain proteasome activators (PAs). The HbYX motif has been predominantly characterized in the archaeal 20S, whereas little is known about the sequence preferences of the human 20S (h20S). Here, we synthesize and screen ~120 HbYX-like peptides, revealing unexpected differences from the archaeal system and defining the h20S recognition sequence as the Y-F/Y (YФ) motif. To gain further insight, we create a functional chimera of the optimized sequence, NLSYYT, fused to the model activator, PA26E102A. A cryo-EM structure of PA26E102A-h20S is used to identify key interactions, including non-canonical contacts and gate-opening mechanisms. Finally, we demonstrate that the YФ sequence preferences are tuned by valency, allowing multivalent PAs to sample greater sequence space. These results expand the model for termini-mediated gating and provide a template for the design of h20S activators.
    DOI:  https://doi.org/10.1038/s41467-022-28864-x
  17. Nat Commun. 2022 Mar 09. 13(1): 1219
    First-in-human immunoPET imaging of HIV-1 infection using 89Zr-labeled VRC01 broadly neutralizing antibody.
    Denis R Beckford-Vera, Robert R Flavell, Youngho Seo, Enrique Martinez-Ortiz, Maya Aslam, Cassandra Thanh, Emily Fehrman, Marion Pardons, Shreya Kumar, Amelia N Deitchman, Vahid Ravanfar, Brailee Schulte, I-Wei Katherine Wu, Tony Pan, Jacqueline D Reeves, Christopher C Nixon, Nikita S Iyer, Leonel Torres, Sadie E Munter, Tony Hyunh, Christos J Petropoulos, Rebecca Hoh, Benjamin L Franc, Lucio Gama, Richard A Koup, John R Mascola, Nicolas Chomont, Steven G Deeks, Henry F VanBrocklin, Timothy J Henrich.
      A major obstacle to achieving long-term antiretroviral (ART) free remission or functional cure of HIV infection is the presence of persistently infected cells that establish a long-lived viral reservoir. HIV largely resides in anatomical regions that are inaccessible to routine sampling, however, and non-invasive methods to understand the longitudinal tissue-wide burden of HIV persistence are urgently needed. Positron emission tomography (PET) imaging is a promising strategy to identify and characterize the tissue-wide burden of HIV. Here, we assess the efficacy of using immunoPET imaging to characterize HIV reservoirs and identify anatomical foci of persistent viral transcriptional activity using a radiolabeled HIV Env-specific broadly neutralizing antibody, 89Zr-VRC01, in HIV-infected individuals with detectable viremia and on suppressive ART compared to uninfected controls (NCT03729752). We also assess the relationship between PET tracer uptake in tissues and timing of ART initiation and direct HIV protein expression in CD4 T cells obtained from lymph node biopsies. We observe significant increases in 89Zr-VRC01 uptake in various tissues (including lymph nodes and gut) in HIV-infected individuals with detectable viremia (N = 5) and on suppressive ART (N = 5) compared to uninfected controls (N = 5). Importantly, PET tracer uptake in inguinal lymph nodes in viremic and ART-suppressed participants significantly and positively correlates with HIV protein expression measured directly in tissue. Our strategy may allow non-invasive longitudinal characterization of residual HIV infection and lays the framework for the development of immunoPET imaging in a variety of other infectious diseases.
    DOI:  https://doi.org/10.1038/s41467-022-28727-5
  18. Nat Methods. 2022 Mar;19(3): 262-267
    MITI minimum information guidelines for highly multiplexed tissue images.
    Human Tumor Atlas Network
      
    DOI:  https://doi.org/10.1038/s41592-022-01415-4
  19. Immunity. 2022 Mar 08. pii: S1074-7613(22)00084-X. [Epub ahead of print]55(3): 557-574.e7
    Human epigenetic and transcriptional T cell differentiation atlas for identifying functional T cell-specific enhancers.
    Josephine R Giles, Sasikanth Manne, Elizabeth Freilich, Derek A Oldridge, Amy E Baxter, Sangeeth George, Zeyu Chen, Hua Huang, Lakshmi Chilukuri, Mary Carberry, Lydia Giles, Nan-Ping P Weng, Regina M Young, Carl H June, Lynn M Schuchter, Ravi K Amaravadi, Xiaowei Xu, Giorgos C Karakousis, Tara C Mitchell, Alexander C Huang, Junwei Shi, E John Wherry.
      The clinical benefit of T cell immunotherapies remains limited by incomplete understanding of T cell differentiation and dysfunction. We generated an epigenetic and transcriptional atlas of T cell differentiation from healthy humans that included exhausted CD8 T cells and applied this resource in three ways. First, we identified modules of gene expression and chromatin accessibility, revealing molecular coordination of differentiation after activation and between central memory and effector memory. Second, we applied this healthy molecular framework to three settings-a neoadjuvant anti-PD1 melanoma trial, a basal cell carcinoma scATAC-seq dataset, and autoimmune disease-associated SNPs-yielding insights into disease-specific biology. Third, we predicted genome-wide cis-regulatory elements and validated this approach for key effector genes using CRISPR interference, providing functional annotation and demonstrating the ability to identify targets for non-coding cellular engineering. These studies define epigenetic and transcriptional regulation of human T cells and illustrate the utility of interrogating disease in the context of a healthy T cell atlas.
    Keywords:  CD8 T cell differentiation; CRISPR; epigenetic regulation; epigenome engineering
    DOI:  https://doi.org/10.1016/j.immuni.2022.02.004
  20. J Immunol. 2022 Mar 09. pii: ji2100555. [Epub ahead of print]
    The Extracellular ATP Receptor P2RX7 Imprints a Promemory Transcriptional Signature in Effector CD8+ T Cells.
    Trupti Vardam-Kaur, Sarah van Dijk, Changwei Peng, Kelsey M Wanhainen, Stephen C Jameson, Henrique Borges da Silva.
      Development of CD8+ central memory T (Tcm) and resident memory T (Trm) cells, which promote immunity in the circulation and in barrier tissues, respectively, is not completely understood. Tcm and Trm cells may arise from common precursors; however, their fate-inducing signals are elusive. We found that virus-specific effector CD8+ T cells display heterogeneous expression of the extracellular ATP sensor P2RX7. P2RX7-high expression is confined, at peak effector phase, to CD62L+ memory precursors, which preferentially form Tcm cells. Among early effector CD8+ T cells, asymmetrical P2RX7 distribution correlated with distinct transcriptional signatures, with P2RX7-high cells enriched for memory and tissue residency sets. P2RX7-high early effectors preferentially form both Tcm and Trm cells. Defective Tcm and Trm cell formation in P2RX7 deficiency is significantly reverted when the transcriptional repressor Zeb2 is ablated. Mechanistically, P2RX7 negatively regulates Zeb2 expression, at least partially through TGF-β sensing in early effector CD8+ T cells. Our study indicates that unequal P2RX7 upregulation in effector CD8+ T cells is a foundational element of the early Tcm/Trm fate.
    DOI:  https://doi.org/10.4049/jimmunol.2100555
  21. Sci Immunol. 2022 Mar 11. 7(69): eabm0775
    Competition for refueling rather than cyclic reentry initiation evident in germinal centers.
    Ziqi Long, Bethan Phillips, Daniel Radtke, Michael Meyer-Hermann, Oliver Bannard.
      Antibody affinity maturation occurs in germinal centers (GCs) through iterative rounds of somatic hypermutation and proliferation in dark zones (DZs) and selection in light zones (LZs). GC B cells exit cell cycle a number of hours before entering LZs; therefore, continued participation in responses requires that they subsequently reenter cell cycle and move back to DZs, a process known as cyclic reentry. Affinity enhancements are thought to arise by B cells having to compete to initiate cyclic reentry each time they enter LZs, with T cell help being a major determinant; however, direct proof is lacking. Using Fucci2 mice, we confirmed an association between B cell receptor affinity and the first step of cyclic reentry, S phase initiation from a resting LZ state. However, neither T cell ablation nor MHCII deletion prevented resting LZ cells from reentering cell cycle, and this late G1-S transition was also not detectably restricted by competition. In contrast, using BATF induction as exemplar, we found that T cells "refueled" LZ cells in an affinity-dependent manner that was limited by both competition and cells' intrinsic antigen-acquiring abilities. Therefore, cyclic reentry initiation and B cell refueling are independently regulated in GCs, which may contribute to permitting cells of different competencies to be sustained alongside each other and allow T cell support to be provided across a dynamic range commensurate with affinity. We speculate that this less binary selection mechanism could help GCs nurture complex antibody maturation pathways and support the clonal diversity required for countering fast-evolving pathogens.
    DOI:  https://doi.org/10.1126/sciimmunol.abm0775
  22. J Immunol. 2022 Mar 09. pii: ji2100491. [Epub ahead of print]
    CRISPR/Cas9-Mediated Insertion of HIV Long Terminal Repeat within BACH2 Promotes Expansion of T Regulatory-like Cells.
    Michelle L Christian, Michael J Dapp, Samuel C Scharffenberger, Hank Jones, Chaozhong Song, Lisa M Frenkel, Anthony Krumm, James I Mullins, David J Rawlings.
      One key barrier to curative therapies for HIV is the limited understanding of HIV persistence. HIV provirus integration sites (ISs) within BACH2 are common, and almost all sites mapped to date are located upstream of the start codon in the same transcriptional orientation as the gene. These unique features suggest the possibility of insertional mutagenesis at this location. Using CRISPR/Cas9-based homology-directed repair in primary human CD4+ T cells, we directly modeled the effects of HIV integration within BACH2 Integration of the HIV long terminal repeat (LTR) and major splice donor increased BACH2 mRNA and protein levels, altered gene expression, and promoted selective outgrowth of an activated, proliferative, and T regulatory-like cell population. In contrast, introduction of the HIV-LTR alone or an HIV-LTR-major splice donor construct into STAT5B, a second common HIV IS, had no functional impact. Thus, HIV LTR-driven BACH2 expression modulates T cell programming and leads to cellular outgrowth and unique phenotypic changes, findings that support a direct role for IS-dependent HIV-1 persistence.
    DOI:  https://doi.org/10.4049/jimmunol.2100491
  23. Sci Immunol. 2022 Mar 11. 7(69): eabn3286
    Eosinophils are an essential element of a type 2 immune axis that controls thymus regeneration.
    Emilie J Cosway, Andrea J White, Sonia M Parnell, Edina Schweighoffer, Helen E Jolin, Andrea Bacon, Hans-Reimer Rodewald, Victor Tybulewicz, Andrew N J McKenzie, William E Jenkinson, Graham Anderson.
      Therapeutic interventions used for cancer treatment provoke thymus damage and limit the recovery of protective immunity. Here, we show that eosinophils are an essential part of an intrathymic type 2 immune network that enables thymus recovery after ablative therapy. Within hours of damage, the thymus undergoes CCR3-dependent colonization by peripheral eosinophils, which reestablishes the epithelial microenvironments that control thymopoiesis. Eosinophil regulation of thymus regeneration occurs via the concerted action of NKT cells that trigger CCL11 production via IL4 receptor signaling in thymic stroma, and ILC2 that represent an intrathymic source of IL5, a cytokine that therapeutically boosts thymus regeneration after damage. Collectively, our findings identify an intrathymic network composed of multiple innate immune cells that restores thymus function during reestablishment of the adaptive immune system.
    DOI:  https://doi.org/10.1126/sciimmunol.abn3286
  24. Nat Commun. 2022 Mar 09. 13(1): 1222
    Elucidating mechanisms of genetic cross-disease associations at the PROCR vascular disease locus.
    CHARGE Hemostasis Working Group
      Many individual genetic risk loci have been associated with multiple common human diseases. However, the molecular basis of this pleiotropy often remains unclear. We present an integrative approach to reveal the molecular mechanism underlying the PROCR locus, associated with lower coronary artery disease (CAD) risk but higher venous thromboembolism (VTE) risk. We identify PROCR-p.Ser219Gly as the likely causal variant at the locus and protein C as a causal factor. Using genetic analyses, human recall-by-genotype and in vitro experimentation, we demonstrate that PROCR-219Gly increases plasma levels of (activated) protein C through endothelial protein C receptor (EPCR) ectodomain shedding in endothelial cells, attenuating leukocyte-endothelial cell adhesion and vascular inflammation. We also associate PROCR-219Gly with an increased pro-thrombotic state via coagulation factor VII, a ligand of EPCR. Our study, which links PROCR-219Gly to CAD through anti-inflammatory mechanisms and to VTE through pro-thrombotic mechanisms, provides a framework to reveal the mechanisms underlying similar cross-phenotype associations.
    DOI:  https://doi.org/10.1038/s41467-022-28729-3
  25. Nat Commun. 2022 Mar 09. 13(1): 1225
    Restoring nuclear entry of Sirtuin 2 in oligodendrocyte progenitor cells promotes remyelination during ageing.
    Xiao-Ru Ma, Xudong Zhu, Yujie Xiao, Hui-Min Gu, Shuang-Shuang Zheng, Liang Li, Fan Wang, Zhao-Jun Dong, Di-Xian Wang, Yang Wu, Chenyu Yang, Wenhong Jiang, Ke Yao, Yue Yin, Yang Zhang, Chao Peng, Lixia Gao, Zhuoxian Meng, Zeping Hu, Chong Liu, Li Li, Hou-Zao Chen, Yousheng Shu, Zhenyu Ju, Jing-Wei Zhao.
      The age-dependent decline in remyelination potential of the central nervous system during ageing is associated with a declined differentiation capacity of oligodendrocyte progenitor cells (OPCs). The molecular players that can enhance OPC differentiation or rejuvenate OPCs are unclear. Here we show that, in mouse OPCs, nuclear entry of SIRT2 is impaired and NAD+ levels are reduced during ageing. When we supplement β-nicotinamide mononucleotide (β-NMN), an NAD+ precursor, nuclear entry of SIRT2 in OPCs, OPC differentiation, and remyelination were rescued in aged animals. We show that the effects on myelination are mediated via the NAD+-SIRT2-H3K18Ac-ID4 axis, and SIRT2 is required for rejuvenating OPCs. Our results show that SIRT2 and NAD+ levels rescue the aged OPC differentiation potential to levels comparable to young age, providing potential targets to enhance remyelination during ageing.
    DOI:  https://doi.org/10.1038/s41467-022-28844-1
  26. Immunity. 2022 Mar 08. pii: S1074-7613(22)00089-9. [Epub ahead of print]55(3): 387-389
    A high-resolution view of intra-tumoral B cell immunity.
    Xihao Hu, X Shirley Liu.
      In this issue of Immunity, Meylan et al. (2022) uses spatial transcriptomics to examine B cell immunity within intratumoral tertiary lymphoid structures (TLSs). They find that B cells expand and mature into plasma cells (PCs) within the TLS, migrate along fibroblastic tracks to tumor beds, and produce IgG antibodies that target cancer cells.
    DOI:  https://doi.org/10.1016/j.immuni.2022.02.009
  27. Hepatology. 2022 Feb 19.
    A hierarchical regulatory network ensures stable albumin transcription under various pathophysiological conditions.
    Rilu Feng, Kejia Kan, Carsten Sticht, Yujia Li, Shanshan Wang, Hui Liu, Chen Shao, Stefan Munker, Hanno Niess, Sai Wang, Christoph Meyer, Roman Liebe, Matthias P Ebert, Steven Dooley, Huiguo Ding, Honglei Weng.
       BACKGROUND AND AIMS: It remains unknown how patients with liver failure maintain essential albumin levels. Here, we delineate a hierarchical transcription regulatory network that ensures albumin expression under different disease conditions.
    APPROACH AND RESULTS: We examined albumin levels in liver tissues and serum in 157 patients, including 84 with HCC, 38 decompensated cirrhosis, and 35 acute liver failure. Even in patients with liver failure, the average serum albumin concentrations were 30.55 g/L. In healthy subjects and patients with chronic liver diseases, albumin was expressed in hepatocytes. In patients with massive hepatocyte loss, albumin was expressed in liver progenitor cells (LPCs). The albumin gene (ALB) core promoter possesses a TATA box and nucleosome-free area, which allows constitutive RNA polymerase II binding and transcription initiation. Chromatin immunoprecipitation assays revealed that hepatocyte nuclear factor 4 alpha (HNF4α), CCAAT/enhancer-binding protein alpha (C/EBPα), and forkhead box A2 (FOXA2) bound to the ALB enhancer. Knockdown of either of these factors reduced albumin expression in hepatocytes. FOXA2 acts as a pioneer factor to support HNF4α and C/EBPα. In hepatocytes lacking HNF4α and C/EBPα expression, FOXA2 synergized with retinoic acid receptor (RAR) to maintain albumin transcription. RAR nuclear translocation was induced by retinoic acids released by activated HSCs. In patients with massive hepatocyte loss, LPCs expressed HNF4α and FOXA2. RNA sequencing and quantitative PCR analyses revealed that lack of HNF4α and C/EBPα in hepatocytes increased hedgehog ligand biosynthesis. Hedgehog up-regulates FOXA2 expression through glioblastoma family zinc finger 2 binding to the FOXA2 promoter in both hepatocytes and LPCs.
    CONCLUSIONS: A hierarchical regulatory network formed by master and pioneer transcription factors ensures essential albumin expression in various pathophysiological conditions.
    DOI:  https://doi.org/10.1002/hep.32414
  28. Nat Genet. 2022 Mar 07.
    DNA replication fork speed underlies cell fate changes and promotes reprogramming.
    Tsunetoshi Nakatani, Jiangwei Lin, Fei Ji, Andreas Ettinger, Julien Pontabry, Mikiko Tokoro, Luis Altamirano-Pacheco, Jonathan Fiorentino, Elmir Mahammadov, Yu Hatano, Capucine Van Rechem, Damayanti Chakraborty, Elias R Ruiz-Morales, Paola Y Arguello Pascualli, Antonio Scialdone, Kazuo Yamagata, Johnathan R Whetstine, Ruslan I Sadreyev, Maria-Elena Torres-Padilla.
      Totipotency emerges in early embryogenesis, but its molecular underpinnings remain poorly characterized. In the present study, we employed DNA fiber analysis to investigate how pluripotent stem cells are reprogrammed into totipotent-like 2-cell-like cells (2CLCs). We show that totipotent cells of the early mouse embryo have slow DNA replication fork speed and that 2CLCs recapitulate this feature, suggesting that fork speed underlies the transition to a totipotent-like state. 2CLCs emerge concomitant with DNA replication and display changes in replication timing (RT), particularly during the early S-phase. RT changes occur prior to 2CLC emergence, suggesting that RT may predispose to gene expression changes and consequent reprogramming of cell fate. Slowing down replication fork speed experimentally induces 2CLCs. In vivo, slowing fork speed improves the reprogramming efficiency of somatic cell nuclear transfer. Our data suggest that fork speed regulates cellular plasticity and that remodeling of replication features leads to changes in cell fate and reprogramming.
    DOI:  https://doi.org/10.1038/s41588-022-01023-0
  29. Nat Methods. 2022 Mar;19(3): 296-306
    A pan-tissue DNA methylation atlas enables in silico decomposition of human tissue methylomes at cell-type resolution.
    Tianyu Zhu, Jacklyn Liu, Stephan Beck, Sun Pan, David Capper, Matt Lechner, Chrissie Thirlwell, Charles E Breeze, Andrew E Teschendorff.
      Bulk-tissue DNA methylomes represent an average over many different cell types, hampering our understanding of cell-type-specific contributions to disease development. As single-cell methylomics is not scalable to large cohorts of individuals, cost-effective computational solutions are needed, yet current methods are limited to tissues such as blood. Here we leverage the high-resolution nature of tissue-specific single-cell RNA-sequencing datasets to construct a DNA methylation atlas defined for 13 solid tissue types and 40 cell types. We comprehensively validate this atlas in independent bulk and single-nucleus DNA methylation datasets. We demonstrate that it correctly predicts the cell of origin of diverse cancer types and discovers new prognostic associations in olfactory neuroblastoma and stage 2 melanoma. In brain, the atlas predicts a neuronal origin for schizophrenia, with neuron-specific differential DNA methylation enriched for corresponding genome-wide association study risk loci. In summary, the DNA methylation atlas enables the decomposition of 13 different human tissue types at a high cellular resolution, paving the way for an improved interpretation of epigenetic data.
    DOI:  https://doi.org/10.1038/s41592-022-01412-7
  30. Nat Commun. 2022 Mar 11. 13(1): 1296
    Coincidence of cholinergic pauses, dopaminergic activation and depolarisation of spiny projection neurons drives synaptic plasticity in the striatum.
    John N J Reynolds, Riccardo Avvisati, Paul D Dodson, Simon D Fisher, Manfred J Oswald, Jeffery R Wickens, Yan-Feng Zhang.
      Dopamine-dependent long-term plasticity is believed to be a cellular mechanism underlying reinforcement learning. In response to reward and reward-predicting cues, phasic dopamine activity potentiates the efficacy of corticostriatal synapses on spiny projection neurons (SPNs). Since phasic dopamine activity also encodes other behavioural variables, it is unclear how postsynaptic neurons identify which dopamine event is to induce long-term plasticity. Additionally, it is unknown how phasic dopamine released from arborised axons can potentiate targeted striatal synapses through volume transmission. To examine these questions we manipulated striatal cholinergic interneurons (ChIs) and dopamine neurons independently in two distinct in vivo paradigms. We report that long-term potentiation (LTP) at corticostriatal synapses with SPNs is dependent on the coincidence of pauses in ChIs and phasic dopamine activation, critically accompanied by SPN depolarisation. Thus, the ChI pause defines the time window for phasic dopamine to induce plasticity, while depolarisation of SPNs constrains the synapses eligible for plasticity.
    DOI:  https://doi.org/10.1038/s41467-022-28950-0
  31. Science. 2022 Mar 10. eabn8933
    Structure of a Janus kinase cytokine receptor complex reveals the basis for dimeric activation.
    Caleb R Glassman, Naotaka Tsutsumi, Robert A Saxton, Patrick J Lupardus, Kevin M Jude, K Christopher Garcia.
      Cytokines signal through cell surface receptor dimers to initiate activation of intracellular Janus Kinases (JAKs). We report the 3.6-Å resolution cryo-EM structure of full-length JAK1 complexed with a cytokine receptor intracellular Box1/Box2 domain, captured as an activated homodimer bearing the Val→Phe (VF) mutation prevalent in myeloproliferative neoplasms. The seven domains of JAK1 form an extended structural unit whose dimerization is mediated by close-packed pseudokinase (PK) domains. The oncogenic VF mutation lies within the core of the JAK1 PK dimer interface, enhancing packing complementarity to facilitate ligand-independent activation. The C-terminal tyrosine kinase domains are poised to phosphorylate the receptor STAT-recruiting motifs projecting from the overhanging FERM-SH2 domains. Mapping of constitutively active JAK mutants supports a two-step allosteric activation mechanism and reveals new opportunities for selective therapeutic targeting of oncogenic JAK signaling.
    DOI:  https://doi.org/10.1126/science.abn8933
  32. Nat Commun. 2022 Mar 10. 13(1): 1266
    Uptake of N2O5 by aqueous aerosol unveiled using chemically accurate many-body potentials.
    Vinícius Wilian D Cruzeiro, Mirza Galib, David T Limmer, Andreas W Götz.
      The reactive uptake of N2O5 to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Despite its importance, a quantitative picture of the uptake mechanism is missing. Here we use molecular dynamics simulations with a data-driven many-body model of coupled-cluster accuracy to quantify thermodynamics and kinetics of solvation and adsorption of N2O5 in water. The free energy profile highlights that N2O5 is selectively adsorbed to the liquid-vapor interface and weakly solvated. Accommodation into bulk water occurs slowly, competing with evaporation upon adsorption from gas phase. Leveraging the quantitative accuracy of the model, we parameterize and solve a reaction-diffusion equation to determine hydrolysis rates consistent with experimental observations. We find a short reaction-diffusion length, indicating that the uptake is dominated by interfacial features. The parameters deduced here, including solubility, accommodation coefficient, and hydrolysis rate, afford a foundation for which to consider the reactive loss of N2O5 in more complex solutions.
    DOI:  https://doi.org/10.1038/s41467-022-28697-8
  33. Nat Genet. 2022 Mar 10.
    Nascent transcription as a predictor and driver of histone modifications.
    Karen Adelman.
      
    DOI:  https://doi.org/10.1038/s41588-021-01004-9
  34. Nature. 2022 Mar 09.
    The evolution, evolvability and engineering of gene regulatory DNA.
    Eeshit Dhaval Vaishnav, Carl G de Boer, Jennifer Molinet, Moran Yassour, Lin Fan, Xian Adiconis, Dawn A Thompson, Joshua Z Levin, Francisco A Cubillos, Aviv Regev.
      Mutations in non-coding regulatory DNA sequences can alter gene expression, organismal phenotype and fitness1-3. Constructing complete fitness landscapes, in which DNA sequences are mapped to fitness, is a long-standing goal in biology, but has remained elusive because it is challenging to generalize reliably to vast sequence spaces4-6. Here we build sequence-to-expression models that capture fitness landscapes and use them to decipher principles of regulatory evolution. Using millions of randomly sampled promoter DNA sequences and their measured expression levels in the yeast Saccharomyces cerevisiae, we learn deep neural network models that generalize with excellent prediction performance, and enable sequence design for expression engineering. Using our models, we study expression divergence under genetic drift and strong-selection weak-mutation regimes to find that regulatory evolution is rapid and subject to diminishing returns epistasis; that conflicting expression objectives in different environments constrain expression adaptation; and that stabilizing selection on gene expression leads to the moderation of regulatory complexity. We present an approach for using such models to detect signatures of selection on expression from natural variation in regulatory sequences and use it to discover an instance of convergent regulatory evolution. We assess mutational robustness, finding that regulatory mutation effect sizes follow a power law, characterize regulatory evolvability, visualize promoter fitness landscapes, discover evolvability archetypes and illustrate the mutational robustness of natural regulatory sequence populations. Our work provides a general framework for designing regulatory sequences and addressing fundamental questions in regulatory evolution.
    DOI:  https://doi.org/10.1038/s41586-022-04506-6
  35. Nat Neurosci. 2022 Mar;25(3): 358-368
    Neurons detect cognitive boundaries to structure episodic memories in humans.
    Jie Zheng, Andrea G P Schjetnan, Mar Yebra, Bernard A Gomes, Clayton P Mosher, Suneil K Kalia, Taufik A Valiante, Adam N Mamelak, Gabriel Kreiman, Ueli Rutishauser.
      While experience is continuous, memories are organized as discrete events. Cognitive boundaries are thought to segment experience and structure memory, but how this process is implemented remains unclear. We recorded the activity of single neurons in the human medial temporal lobe (MTL) during the formation and retrieval of memories with complex narratives. Here, we show that neurons responded to abstract cognitive boundaries between different episodes. Boundary-induced neural state changes during encoding predicted subsequent recognition accuracy but impaired event order memory, mirroring a fundamental behavioral tradeoff between content and time memory. Furthermore, the neural state following boundaries was reinstated during both successful retrieval and false memories. These findings reveal a neuronal substrate for detecting cognitive boundaries that transform experience into mnemonic episodes and structure mental time travel during retrieval.
    DOI:  https://doi.org/10.1038/s41593-022-01020-w
  36. FASEB J. 2022 Apr;36(4): e22251
    Hepatic glucocorticoid-induced transcriptional regulation is androgen-dependent after chronic but not acute glucocorticoid exposure.
    Jacobus C Buurstede, Susana N Paul, Karolien De Bosscher, Onno C Meijer, Jan Kroon.
      Glucocorticoids exert their pleiotropic effects by activating the glucocorticoid receptor (GR), which is expressed throughout the body. GR-mediated transcription is regulated by a multitude of tissue- and cell type-specific mechanisms, including interactions with other transcription factors such as the androgen receptor (AR). We previously showed that the transcription of canonical glucocorticoid-responsive genes is dependent on active androgen signaling, but the extent of this glucocorticoid-androgen crosstalk warrants further investigation. In this study, we investigated the overall glucocorticoid-androgen crosstalk in the hepatic transcriptome. Male mice were exposed to GR agonist corticosterone and AR antagonist enzalutamide in order to determine the extent of androgen-dependency after acute and chronic exposure. We found that a substantial proportion of the hepatic transcriptome is androgen-dependent after chronic exposure, while after acute exposure the transcriptomic effects of glucocorticoids are largely androgen-independent. We propose that prolonged glucocorticoid exposure triggers a gradual upregulation of AR expression, instating a situation of androgen dependence which is likely not driven by direct AR-GR interactions. This indirect mode of glucocorticoid-androgen interaction is in accordance with the absence of enriched AR DNA-binding near AR-dependent corticosterone-regulated genes after chronic exposure. In conclusion, we demonstrate that glucocorticoid effects and their interaction with androgen signaling are dependent on the duration of exposure and believe that our findings contribute to a better understanding of hepatic glucocorticoid biology in health and disease.
    Keywords:  androgen receptor; androgens; glucocorticoid receptor; glucocorticoids; liver
    DOI:  https://doi.org/10.1096/fj.202101313R
  37. Immunology. 2022 Mar 09.
    CTLA4Ig/VISTAIg combination therapy selectively induces CD4+ T cell-mediated immune tolerance by targeting the SOCS1 signaling pathway in porcine islet xenotransplantation.
    Dan Wang, Xue Bai, Bin Wang, Qiying Yi, Weihua Yu, Xinying Zhang, Ruoyuan Tian, Xiao Zhang, Caihua Li, Yi Chen, Yang Liu, Yao Cheng, Sirong He.
      T cell inhibitory receptors can regulate the proliferation or function of T cells by binding to their ligands and present a unique opportunity to manage destructive immune responses during porcine islet xenotransplantation. We applied ex vivo porcine islet xenotransplantation and in vitro mixed lymphocyte-islet reaction models to assess immune checkpoint receptor expression profiles in recipient T cells, investigate whether CTLA4 or VISTA immunoglobulin (Ig) combination therapy alone could suppress porcine islet xenograft rejection and further analyze its potential immune tolerance mechanism. Recipient T cells expressed moderate to high levels of CTLA4, PD-1, TIGIT, and VISTA, and the frequency of CTLA4+ CD4+ , TIGIT+ CD4+ , VISTA+ CD4+ and VISTA+ CD8+ T cells was positively correlated with porcine islet xenograft survival time in xenotransplant recipients. Combined treatment with CTLA4Ig and VISTAIg selectively inhibited recipient CD4+ T cell hyperresponsiveness and proinflammatory cytokine production and significantly delayed xenograft rejection. SOCS1 deficiency in CD4+ T cells stimulated by xenogeneic islets facilitated hyperresponsiveness and abolished the suppressive effect of combination therapy on recipient T cell-mediated porcine islet damage in vivo and in vitro. Further mechanistic studies revealed that combined treatment significantly induced SOCS1 expression and inhibited the Jak-STAT signaling pathway in wild-type recipient CD4+ T cells stimulated by xenogeneic islets, whereas SOCS1 deficiency resulted in Jak-STAT signaling pathway activation in recipient CD4+ T cells. We demonstrated a major role for CTLA4 and VISTA as key targets in CD4+ T cell hyperresponsiveness and porcine islet xenograft rejection. The selective inhibition of CD4+ T cell immunity by CTLA4Ig/VISTAIg is based on SOCS1-dependent signaling.
    Keywords:  Combination therapy; Immune checkpoint; Immune tolerance; Porcine islet xenotransplantation
    DOI:  https://doi.org/10.1111/imm.13463
  38. J Exp Med. 2022 Apr 04. pii: e20211273. [Epub ahead of print]219(4):
    A partial form of inherited human USP18 deficiency underlies infection and inflammation.
    Marta Martin-Fernandez, Sofija Buta, Tom Le Voyer, Zhi Li, Lasse Toftdal Dynesen, Françoise Vuillier, Lina Franklin, Fatima Ailal, Alice Muglia Amancio, Louise Malle, Conor Gruber, Ibtihal Benhsaien, Jennie Altman, Justin Taft, Caroline Deswarte, Manon Roynard, Alejandro Nieto-Patlan, Kunihiko Moriya, Jérémie Rosain, Nathalie Boddaert, Aziz Bousfiha, Yanick J Crow, Dragana Jankovic, Alan Sher, Jean-Laurent Casanova, Sandra Pellegrini, Jacinta Bustamante, Dusan Bogunovic.
      Human USP18 is an interferon (IFN)-stimulated gene product and a negative regulator of type I IFN (IFN-I) signaling. It also removes covalently linked ISG15 from proteins, in a process called deISGylation. In turn, ISG15 prevents USP18 from being degraded by the proteasome. Autosomal recessive complete USP18 deficiency is life-threatening in infancy owing to uncontrolled IFN-I-mediated autoinflammation. We report three Moroccan siblings with autoinflammation and mycobacterial disease who are homozygous for a new USP18 variant. We demonstrate that the mutant USP18 (p.I60N) is normally stabilized by ISG15 and efficient for deISGylation but interacts poorly with the receptor-anchoring STAT2 and is impaired in negative regulation of IFN-I signaling. We also show that IFN-γ-dependent induction of IL-12 and IL-23 is reduced owing to IFN-I-mediated impairment of myeloid cells to produce both cytokines. Thus, insufficient negative regulation of IFN-I signaling by USP18-I60N underlies a specific type I interferonopathy, which impairs IL-12 and IL-23 production by myeloid cells, thereby explaining predisposition to mycobacterial disease.
    DOI:  https://doi.org/10.1084/jem.20211273
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