bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2023–01–08
47 papers selected by
Fawaz Alzaïd, Sorbonne Université
  1. The mitochondrial Hsp70 controls the assembly of the F1FO-ATP synthase.
  2. Metabolic regulation of species-specific developmental rates.
  3. Human mitochondria require mtRF1 for translation termination at non-canonical stop codons.
  4. Increased adipose catecholamine levels and protection from obesity with loss of Allograft Inflammatory Factor-1.
  5. Insights into Alzheimer's disease from single-cell genomic approaches.
  6. TH17 cell heterogeneity and its role in tissue inflammation.
  7. Top Reads.
  8. An antisteatosis response regulated by oleic acid through lipid droplet-mediated ERAD enhancement.
  9. Antagonizing cholecystokinin A receptor in the lung attenuates obesity-induced airway hyperresponsiveness.
  10. CD8+ T cell-intrinsic IL-6 signaling promotes resistance to anti-PD-L1 immunotherapy.
  11. Illuminating lactate in cells, mice, and patient samples.
  12. STAT5 facts.
  13. Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis.
  14. Regulatory T cells suppress CD4+ effector T cell activation by controlling protein synthesis.
  15. Long non-coding RNAs: definitions, functions, challenges and recommendations.
  16. Phenotypic signatures of immune selection in HIV-1 reservoir cells.
  17. STAT3 and autoimmunity.
  18. Diet modulates genetic effects on longevity.
  19. T cells drive aging of the brain.
  20. Engineering human stem cell-derived islets to evade immune rejection and promote localized immune tolerance.
  21. mascRNA alleviates STING-TBK1 signaling-mediated immune response through promoting ubiquitination of STING.
  22. NIAID workshop on T cell technologies.
  23. De novo genes with an lncRNA origin encode unique human brain developmental functionality.
  24. DNA methylation provides molecular links underlying complex traits.
  25. Microbiota contributions.
  26. An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis.
  27. PD-1highCXCR5-CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infection.
  28. Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
  29. Targeting Epsins to Inhibit Fibroblast Growth Factor Signaling While Potentiating Transforming Growth Factor-β Signaling Constrains Endothelial-to-Mesenchymal Transition in Atherosclerosis.
  30. Structural basis of regulated m7G tRNA modification by METTL1-WDR4.
  31. Early immune pressure makes tumors metabolically stronger.
  32. β-adrenoreceptor-triggered PKA activation negatively regulates the innate antiviral response.
  33. Single-cell recording of cellular RNAs in bacteria.
  34. Sec22b is a critical and nonredundant regulator of plasma cell maintenance.
  35. Identification of astrocyte regulators by nucleic acid cytometry.
  36. The COVID-19 immunology masterclass enters its third year.
  37. Check(point) yourself before you wreck yourself in tumors.
  38. Tired of persevering.
  39. Lactate metabolism is essential in early-onset mitochondrial myopathy.
  40. Liver-resident CD8+ T cells in viral hepatitis: not always good guys.
  41. Longitudinal liver sampling in patients with chronic hepatitis B starting antiviral therapy reveals hepatotoxic CD8+ T cells.
  42. Intestinal epithelial HDAC3 and MHC class II coordinate microbiota-specific immunity.
  43. Solid-phase capture and profiling of open chromatin by spatial ATAC.
  44. Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins.
  45. The neuropeptide CGRP enters the macrophage cytosol to suppress the NLRP3 inflammasome during pulmonary infection.
  46. Profilin 1 deficiency drives mitotic defects and reduces genome stability.
  47. STAT proteins in cancer: orchestration of metabolism.
  1. Nat Commun. 2023 Jan 03. 14(1): 39
    The mitochondrial Hsp70 controls the assembly of the F1FO-ATP synthase.
    Jiyao Song, Liesa Steidle, Isabelle Steymans, Jasjot Singh, Anne Sanner, Lena Böttinger, Dominic Winter, Thomas Becker.
      The mitochondrial F1FO-ATP synthase produces the bulk of cellular ATP. The soluble F1 domain contains the catalytic head that is linked via the central stalk and the peripheral stalk to the membrane embedded rotor of the FO domain. The assembly of the F1 domain and its linkage to the peripheral stalk is poorly understood. Here we show a dual function of the mitochondrial Hsp70 (mtHsp70) in the formation of the ATP synthase. First, it cooperates with the assembly factors Atp11 and Atp12 to form the F1 domain of the ATP synthase. Second, the chaperone transfers Atp5 into the assembly line to link the catalytic head with the peripheral stalk. Inactivation of mtHsp70 leads to integration of assembly-defective Atp5 variants into the mature complex, reflecting a quality control function of the chaperone. Thus, mtHsp70 acts as an assembly and quality control factor in the biogenesis of the F1FO-ATP synthase.
    DOI:  https://doi.org/10.1038/s41467-022-35720-5
  2. Nature. 2023 Jan 04.
    Metabolic regulation of species-specific developmental rates.
    Margarete Diaz-Cuadros, Teemu P Miettinen, Owen S Skinner, Dylan Sheedy, Carlos Manlio Díaz-García, Svetlana Gapon, Alexis Hubaud, Gary Yellen, Scott R Manalis, William M Oldham, Olivier Pourquié.
      Animals display substantial inter-species variation in the rate of embryonic development despite a broad conservation of the overall sequence of developmental events. Differences in biochemical reaction rates, including the rates of protein production and degradation, are thought to be responsible for species-specific rates of development1-3. However, the cause of differential biochemical reaction rates between species remains unknown. Here, using pluripotent stem cells, we have established an in vitro system that recapitulates the twofold difference in developmental rate between mouse and human embryos. This system provides a quantitative measure of developmental speed as revealed by the period of the segmentation clock, a molecular oscillator associated with the rhythmic production of vertebral precursors. Using this system, we show that mass-specific metabolic rates scale with the developmental rate and are therefore higher in mouse cells than in human cells. Reducing these metabolic rates by inhibiting the electron transport chain slowed down the segmentation clock by impairing the cellular NAD+/NADH redox balance and, further downstream, lowering the global rate of protein synthesis. Conversely, increasing the NAD+/NADH ratio in human cells by overexpression of the Lactobacillus brevis NADH oxidase LbNOX increased the translation rate and accelerated the segmentation clock. These findings represent a starting point for the manipulation of developmental rate, with multiple translational applications including accelerating the differentiation of human pluripotent stem cells for disease modelling and cell-based therapies.
    DOI:  https://doi.org/10.1038/s41586-022-05574-4
  3. Nat Commun. 2023 Jan 03. 14(1): 30
    Human mitochondria require mtRF1 for translation termination at non-canonical stop codons.
    Annika Krüger, Cristina Remes, Dmitrii Igorevich Shiriaev, Yong Liu, Henrik Spåhr, Rolf Wibom, Ilian Atanassov, Minh Duc Nguyen, Barry S Cooperman, Joanna Rorbach.
      The mitochondrial translation machinery highly diverged from its bacterial counterpart. This includes deviation from the universal genetic code, with AGA and AGG codons lacking cognate tRNAs in human mitochondria. The locations of these codons at the end of COX1 and ND6 open reading frames, respectively, suggest they might function as stop codons. However, while the canonical stop codons UAA and UAG are known to be recognized by mtRF1a, the release mechanism at AGA and AGG codons remains a debated issue. Here, we show that upon the loss of another member of the mitochondrial release factor family, mtRF1, mitoribosomes accumulate specifically at AGA and AGG codons. Stalling of mitoribosomes alters COX1 transcript and protein levels, but not ND6 synthesis. In addition, using an in vitro reconstituted mitochondrial translation system, we demonstrate the specific peptide release activity of mtRF1 at the AGA and AGG codons. Together, our results reveal the role of mtRF1 in translation termination at non-canonical stop codons in mitochondria.
    DOI:  https://doi.org/10.1038/s41467-022-35684-6
  4. Nat Commun. 2023 Jan 03. 14(1): 38
    Increased adipose catecholamine levels and protection from obesity with loss of Allograft Inflammatory Factor-1.
    Prameladevi Chinnasamy, Isabel Casimiro, Dario F Riascos-Bernal, Shreeganesh Venkatesh, Dippal Parikh, Alishba Maira, Aparna Srinivasan, Wei Zheng, Elena Tarabra, Haihong Zong, Smitha Jayakumar, Venkatesh Jeganathan, Kith Pradan, Jose O Aleman, Rajat Singh, Sayan Nandi, Jeffrey E Pessin, Nicholas E S Sibinga.
      Recent studies implicate macrophages in regulation of thermogenic, sympathetic neuron-mediated norepinephrine (NE) signaling in adipose tissues, but understanding of such non-classical macrophage activities is incomplete. Here we show that male mice lacking the allograft inflammatory factor-1 (AIF1) protein resist high fat diet (HFD)-induced obesity and hyperglycemia. We link this phenotype to higher adipose NE levels that stem from decreased monoamine oxidase A (MAOA) expression and NE clearance by AIF1-deficient macrophages, and find through reciprocal bone marrow transplantation that donor Aif1-/- vs WT genotype confers the obesity phenotype in mice. Interestingly, human sequence variants near the AIF1 locus associate with obesity and diabetes; in adipose samples from participants with obesity, we observe direct correlation of AIF1 and MAOA transcript levels. These findings identify AIF1 as a regulator of MAOA expression in macrophages and catecholamine activity in adipose tissues - limiting energy expenditure and promoting energy storage - and suggest how it might contribute to human obesity.
    DOI:  https://doi.org/10.1038/s41467-022-35683-7
  5. Nat Neurosci. 2023 Jan 02.
    Insights into Alzheimer's disease from single-cell genomic approaches.
    Mitchell H Murdock, Li-Huei Tsai.
      Alzheimer's disease (AD) is an age-related disease pathologically defined by the deposition of amyloid plaques and neurofibrillary tangles in the brain parenchyma. Single-cell profiling has shown that Alzheimer's dementia involves the complex interplay of virtually every major brain cell type. Here, we highlight cell-type-specific molecular perturbations in AD. We discuss how genomic information from single cells expands existing paradigms of AD pathogenesis and highlight new opportunities for therapeutic interventions.
    DOI:  https://doi.org/10.1038/s41593-022-01222-2
  6. Nat Immunol. 2023 Jan;24(1): 19-29
    TH17 cell heterogeneity and its role in tissue inflammation.
    Alexandra Schnell, Dan R Littman, Vijay K Kuchroo.
      Since their discovery almost two decades ago, interleukin-17-producing CD4+ T cells (TH17 cells) have been implicated in the pathogenesis of multiple autoimmune and inflammatory disorders. In addition, TH17 cells have been found to play an important role in tissue homeostasis, especially in the intestinal mucosa. Recently, the use of single-cell technologies, along with fate mapping and various mutant mouse models, has led to substantial progress in the understanding of TH17 cell heterogeneity in tissues and of TH17 cell plasticity leading to alternative T cell states and differing functions. In this Review, we discuss the heterogeneity of TH17 cells and the role of this heterogeneity in diverse functions of TH17 cells from homeostasis to tissue inflammation. In addition, we discuss TH17 cell plasticity and its incorporation into the current understanding of T cell subsets and alternative views on the role of TH17 cells in autoimmune and inflammatory diseases.
    DOI:  https://doi.org/10.1038/s41590-022-01387-9
  7. J Immunol. 2023 Jan 15. 210(2): 117
    Top Reads.
      
    DOI:  https://doi.org/10.4049/jimmunol.2290026
  8. Sci Adv. 2023 Jan 04. 9(1): eadc8917
    An antisteatosis response regulated by oleic acid through lipid droplet-mediated ERAD enhancement.
    Jorge Iván Castillo-Quan, Michael J Steinbaugh, Laura Paulette Fernández-Cárdenas, Nancy K Pohl, Ziyun Wu, Feimei Zhu, Natalie Moroz, Veronica Teixeira, Monet S Bland, Nicolas J Lehrbach, Lorenza Moronetti, Magdalena Teufl, T Keith Blackwell.
      Although excessive lipid accumulation is a hallmark of obesity-related pathologies, some lipids are beneficial. Oleic acid (OA), the most abundant monounsaturated fatty acid (FA), promotes health and longevity. Here, we show that OA benefits Caenorhabditis elegans by activating the endoplasmic reticulum (ER)-resident transcription factor SKN-1A (Nrf1/NFE2L1) in a lipid homeostasis response. SKN-1A/Nrf1 is cleared from the ER by the ER-associated degradation (ERAD) machinery and stabilized when proteasome activity is low and canonically maintains proteasome homeostasis. Unexpectedly, OA increases nuclear SKN-1A levels independently of proteasome activity, through lipid droplet-dependent enhancement of ERAD. In turn, SKN-1A reduces steatosis by reshaping the lipid metabolism transcriptome and mediates longevity from OA provided through endogenous accumulation, reduced H3K4 trimethylation, or dietary supplementation. Our findings reveal an unexpected mechanism of FA signal transduction, as well as a lipid homeostasis pathway that provides strategies for opposing steatosis and aging, and may mediate some benefits of the OA-rich Mediterranean diet.
    DOI:  https://doi.org/10.1126/sciadv.adc8917
  9. Nat Commun. 2023 Jan 04. 14(1): 47
    Antagonizing cholecystokinin A receptor in the lung attenuates obesity-induced airway hyperresponsiveness.
    Ronald Allan M Panganiban, Zhiping Yang, Maoyun Sun, Chan Young Park, David I Kasahara, Niccole Schaible, Ramaswamy Krishnan, Alvin T Kho, Elliot Israel, Marc B Hershenson, Scott T Weiss, Blanca E Himes, Jeffrey J Fredberg, Kelan G Tantisira, Stephanie A Shore, Quan Lu.
      Obesity increases asthma prevalence and severity. However, the underlying mechanisms are poorly understood, and consequently, therapeutic options for asthma patients with obesity remain limited. Here we report that cholecystokinin-a metabolic hormone best known for its role in signaling satiation and fat metabolism-is increased in the lungs of obese mice and that pharmacological blockade of cholecystokinin A receptor signaling reduces obesity-associated airway hyperresponsiveness. Activation of cholecystokinin A receptor by the hormone induces contraction of airway smooth muscle cells. In vivo, cholecystokinin level is elevated in the lungs of both genetically and diet-induced obese mice. Importantly, intranasal administration of cholecystokinin A receptor antagonists (proglumide and devazepide) suppresses the airway hyperresponsiveness in the obese mice. Together, our results reveal an unexpected role for cholecystokinin in the lung and support the repurposing of cholecystokinin A receptor antagonists as a potential therapy for asthma patients with obesity.
    DOI:  https://doi.org/10.1038/s41467-022-35739-8
  10. Cell Rep Med. 2022 Dec 22. pii: S2666-3791(22)00442-6. [Epub ahead of print] 100878
    CD8+ T cell-intrinsic IL-6 signaling promotes resistance to anti-PD-L1 immunotherapy.
    Mahrukh A Huseni, Lifen Wang, Joanna E Klementowicz, Kobe Yuen, Beatrice Breart, Christine Orr, Li-Fen Liu, Yijin Li, Vinita Gupta, Congfen Li, Deepali Rishipathak, Jing Peng, Yasin Şenbabaoǧlu, Zora Modrusan, Shilpa Keerthivasan, Shravan Madireddi, Ying-Jiun Chen, Eleanor J Fraser, Ning Leng, Habib Hamidi, Hartmut Koeppen, James Ziai, Kenji Hashimoto, Marcella Fassò, Patrick Williams, David F McDermott, Jonathan E Rosenberg, Thomas Powles, Leisha A Emens, Priti S Hegde, Ira Mellman, Shannon J Turley, Mark S Wilson, Sanjeev Mariathasan, Luciana Molinero, Mark Merchant, Nathaniel R West.
      Although immune checkpoint inhibitors (ICIs) are established as effective cancer therapies, overcoming therapeutic resistance remains a critical challenge. Here we identify interleukin 6 (IL-6) as a correlate of poor response to atezolizumab (anti-PD-L1) in large clinical trials of advanced kidney, breast, and bladder cancers. In pre-clinical models, combined blockade of PD-L1 and the IL-6 receptor (IL6R) causes synergistic regression of large established tumors and substantially improves anti-tumor CD8+ cytotoxic T lymphocyte (CTL) responses compared with anti-PD-L1 alone. Circulating CTLs from cancer patients with high plasma IL-6 display a repressed functional profile based on single-cell RNA sequencing, and IL-6-STAT3 signaling inhibits classical cytotoxic differentiation of CTLs in vitro. In tumor-bearing mice, CTL-specific IL6R deficiency is sufficient to improve anti-PD-L1 activity. Thus, based on both clinical and experimental evidence, agents targeting IL-6 signaling are plausible partners for combination with ICIs in cancer patients.
    Keywords:  CD8 T cell; IL-6; PD-L1; atezolizumab; cancer; checkpoint blockade immunotherapy; clinical trial; interleukin 6
    DOI:  https://doi.org/10.1016/j.xcrm.2022.100878
  11. Cell Metab. 2023 Jan 03. pii: S1550-4131(22)00544-7. [Epub ahead of print]35(1): 5-7
    Illuminating lactate in cells, mice, and patient samples.
    Zefan Li, Hui-Wang Ai.
      Lactate has emerged as a central metabolic fuel and an important signaling molecule. In this issue of Cell Metabolism, Li et al. develop a high-quality lactate sensor, allowing them to monitor lactate levels in cells, subcellular organelles, live mice, and human body fluids.
    DOI:  https://doi.org/10.1016/j.cmet.2022.12.007
  12. Nat Immunol. 2023 Jan;24(1): 1
    STAT5 facts.
    Laurie A Dempsey.
      
    DOI:  https://doi.org/10.1038/s41590-022-01406-9
  13. Nat Commun. 2023 Jan 04. 14(1): 57
    Unique ligand and kinase-independent roles of the insulin receptor in regulation of cell cycle, senescence and apoptosis.
    Hirofumi Nagao, Ashok Kumar Jayavelu, Weikang Cai, Hui Pan, Jonathan M Dreyfuss, Thiago M Batista, Bruna B Brandão, Matthias Mann, C Ronald Kahn.
      Insulin acts through the insulin receptor (IR) tyrosine kinase to exert its classical metabolic and mitogenic actions. Here, using receptors with either short or long deletion of the β-subunit or mutation of the kinase active site (K1030R), we have uncovered a second, previously unrecognized IR signaling pathway that is intracellular domain-dependent, but ligand and tyrosine kinase-independent (LYK-I). These LYK-I actions of the IR are linked to changes in phosphorylation of a network of proteins involved in the regulation of extracellular matrix organization, cell cycle, ATM signaling and cellular senescence; and result in upregulation of expression of multiple extracellular matrix-related genes and proteins, down-regulation of immune/interferon-related genes and proteins, and increased sensitivity to apoptosis. Thus, in addition to classical ligand and tyrosine kinase-dependent (LYK-D) signaling, the IR regulates a second, ligand and tyrosine kinase-independent (LYK-I) pathway, which regulates the cellular machinery involved in senescence, matrix interaction and response to extrinsic challenges.
    DOI:  https://doi.org/10.1038/s41467-022-35693-5
  14. J Exp Med. 2023 Mar 06. pii: e20221676. [Epub ahead of print]220(3):
    Regulatory T cells suppress CD4+ effector T cell activation by controlling protein synthesis.
    Lomon So, Kazushige Obata-Ninomiya, Alex Hu, Virginia S Muir, Ayako Takamori, Jing Song, Jane H Buckner, Ram Savan, Steven F Ziegler.
      Regulatory T cells (Tregs) suppress the activation and subsequent effector functions of CD4 effector T cells (Teffs). However, molecular mechanisms that enforce Treg-mediated suppression in CD4 Teff are unclear. We found that Tregs suppressed activation-induced global protein synthesis in CD4 Teffs prior to cell division. We analyzed genome-wide changes in the transcriptome and translatome of activated CD4 Teffs. We show that mRNAs encoding for the protein synthesis machinery are regulated at the level of translation in activated CD4 Teffs by Tregs. Tregs suppressed global protein synthesis of CD4 Teffs by specifically inhibiting mRNAs of the translation machinery at the level of mTORC1-mediated translation control through concerted action of immunosuppressive cytokines IL-10 and TGFβ. Lastly, we found that the therapeutic targeting of protein synthesis with the RNA helicase eIF4A inhibitor rocaglamide A can alleviate inflammatory CD4 Teff activation caused by acute Treg depletion in vivo. These data show that peripheral tolerance is enforced by Tregs through mRNA translational control in CD4 Teffs.
    DOI:  https://doi.org/10.1084/jem.20221676
  15. Nat Rev Mol Cell Biol. 2023 Jan 03.
    Long non-coding RNAs: definitions, functions, challenges and recommendations.
    John S Mattick, Paulo P Amaral, Piero Carninci, Susan Carpenter, Howard Y Chang, Ling-Ling Chen, Runsheng Chen, Caroline Dean, Marcel E Dinger, Katherine A Fitzgerald, Thomas R Gingeras, Mitchell Guttman, Tetsuro Hirose, Maite Huarte, Rory Johnson, Chandrasekhar Kanduri, Philipp Kapranov, Jeanne B Lawrence, Jeannie T Lee, Joshua T Mendell, Timothy R Mercer, Kathryn J Moore, Shinichi Nakagawa, John L Rinn, David L Spector, Igor Ulitsky, Yue Wan, Jeremy E Wilusz, Mian Wu.
      Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.
    DOI:  https://doi.org/10.1038/s41580-022-00566-8
  16. Nature. 2023 Jan 04.
    Phenotypic signatures of immune selection in HIV-1 reservoir cells.
    Weiwei Sun, Ce Gao, Ciputra Adijaya Hartana, Matthew R Osborn, Kevin B Einkauf, Xiaodong Lian, Benjamin Bone, Nathalie Bonheur, Tae-Wook Chun, Eric S Rosenberg, Bruce D Walker, Xu G Yu, Mathias Lichterfeld.
      Human immunodeficiency virus 1 (HIV-1) reservoir cells persist lifelong despite antiretroviral treatment1,2 but may be vulnerable to host immune responses that could be exploited in strategies to cure HIV-1. Here we used a single-cell, next-generation sequencing approach for the direct ex vivo phenotypic profiling of individual HIV-1-infected memory CD4+ T cells from peripheral blood and lymph nodes of people living with HIV-1 and receiving antiretroviral treatment for approximately 10 years. We demonstrate that in peripheral blood, cells harbouring genome-intact proviruses and large clones of virally infected cells frequently express ensemble signatures of surface markers conferring increased resistance to immune-mediated killing by cytotoxic T and natural killer cells, paired with elevated levels of expression of immune checkpoint markers likely to limit proviral gene transcription; this phenotypic profile might reduce HIV-1 reservoir cell exposure to and killing by cellular host immune responses. Viral reservoir cells harbouring intact HIV-1 from lymph nodes exhibited a phenotypic signature primarily characterized by upregulation of surface markers promoting cell survival, including CD44, CD28, CD127 and the IL-21 receptor. Together, these results suggest compartmentalized phenotypic signatures of immune selection in HIV-1 reservoir cells, implying that only small subsets of infected cells with optimal adaptation to their anatomical immune microenvironment are able to survive during long-term antiretroviral treatment. The identification of phenotypic markers distinguishing viral reservoir cells may inform future approaches for strategies to cure and eradicate HIV-1.
    DOI:  https://doi.org/10.1038/s41586-022-05538-8
  17. Nat Immunol. 2023 Jan;24(1): 1
    STAT3 and autoimmunity.
    Stephanie Houston.
      
    DOI:  https://doi.org/10.1038/s41590-022-01404-x
  18. Nat Genet. 2023 Jan 05.
    Diet modulates genetic effects on longevity.
      
    DOI:  https://doi.org/10.1038/s41588-022-01247-0
  19. Nat Immunol. 2023 Jan;24(1): 12-13
    T cells drive aging of the brain.
    Adrian Liston, Lidia Yshii.
      
    DOI:  https://doi.org/10.1038/s41590-022-01390-0
  20. Cell Rep Med. 2022 Dec 22. pii: S2666-3791(22)00443-8. [Epub ahead of print] 100879
    Engineering human stem cell-derived islets to evade immune rejection and promote localized immune tolerance.
    Dario Gerace, Quan Zhou, Jennifer Hyoje-Ryu Kenty, Adrian Veres, Elad Sintov, Xi Wang, Kyle R Boulanger, Hongfei Li, Douglas A Melton.
      Immunological protection of transplanted stem cell-derived islet (SC-islet) cells is yet to be achieved without chronic immunosuppression or encapsulation. Existing genetic engineering approaches to produce immune-evasive SC-islet cells have so far shown variable results. Here, we show that targeting human leukocyte antigens (HLAs) and PD-L1 alone does not sufficiently protect SC-islet cells from xenograft (xeno)- or allograft (allo)-rejection. As an addition to these approaches, we genetically engineer SC-islet cells to secrete the cytokines interleukin-10 (IL-10), transforming growth factor β (TGF-β), and modified IL-2 such that they promote a tolerogenic local microenvironment by recruiting regulatory T cells (Tregs) to the islet grafts. Cytokine-secreting human SC-β cells resist xeno-rejection and correct diabetes for up to 8 weeks post-transplantation in non-obese diabetic (NOD) mice. Thus, genetically engineering human embryonic SCs (hESCs) to induce a tolerogenic local microenvironment represents a promising approach to provide SC-islet cells as a cell replacement therapy for diabetes without the requirement for encapsulation or immunosuppression.
    Keywords:  cell engineering; cell replacement; diabetes; immune evasion; immune tolerance; stem cells
    DOI:  https://doi.org/10.1016/j.xcrm.2022.100879
  21. Mol Immunol. 2023 Jan 03. pii: S0161-5890(22)00502-8. [Epub ahead of print]154 45-53
    mascRNA alleviates STING-TBK1 signaling-mediated immune response through promoting ubiquitination of STING.
    Yuqing Hu, Xueyi Li, Daoyong Wang, Xiaohua Mao.
      mascRNA (MALAT1-associated small cytoplasmic RNA) is a tRNA-like cytoplasmic small noncoding RNA whose function remains elusive. We previously revealed that this small RNA negatively regulates TLR4/2-triggered proinflammatory response while positively regulates TLR3-induced antiviral response. Here, we investigated whether and how mascRNA influences the stimulator of interferon genes (STING) signaling-triggered immune response. We found that overexpression of mascRNA inhibited the expression of type I interferon (IFN) genes and proinflammatory cytokines in response to cytosolic DNA stimulation; meanwhile, the abundance of STING protein and the level of phosphorylated TBK1 and STAT1 was decreased. By contrast, depletion of mascRNA potentiated the expression of type I IFNs, increased STING protein abundance, and promoted STING-mediated phosphorylation of TBK1 and STAT1 in response to DNA stimulation. In a mouse model of DNA-induced lung injury, exogenous mascRNA mitigated the antiviral response and the severity of lung inflammation. Mechanically, mascRNA was found to promote STING for K48-linked ubiquitination and degradation in macrophages both with and without cytosolic DNA stimulation. Hence, mascRNA suppresses STING-TBK1 signaling-mediated innate immunity through promoting proteasomal degradation of STING, and this tRNA-like small RNA holds promise for the treatment of certain inflammatory diseases such as COVID-19 where aberrant STING signaling drives type I IFN immunopathology.
    Keywords:  Innate immunity; Interferon; Macrophages; STING; mascRNA
    DOI:  https://doi.org/10.1016/j.molimm.2022.12.012
  22. Nat Immunol. 2023 Jan;24(1): 14-18
    NIAID workshop on T cell technologies.
    Timothy A Gondré-Lewis, Chao Jiang, Mandy L Ford, David M Koelle, Alessandro Sette, Alex K Shalek, Paul G Thomas.
      
    DOI:  https://doi.org/10.1038/s41590-022-01377-x
  23. Nat Ecol Evol. 2023 Jan 02.
    De novo genes with an lncRNA origin encode unique human brain developmental functionality.
    Ni A An, Jie Zhang, Fan Mo, Xuke Luan, Lu Tian, Qing Sunny Shen, Xiangshang Li, Chunqiong Li, Fanqi Zhou, Boya Zhang, Mingjun Ji, Jianhuan Qi, Wei-Zhen Zhou, Wanqiu Ding, Jia-Yu Chen, Jia Yu, Li Zhang, Shaokun Shu, Baoyang Hu, Chuan-Yun Li.
      Human de novo genes can originate from neutral long non-coding RNA (lncRNA) loci and are evolutionarily significant in general, yet how and why this all-or-nothing transition to functionality happens remains unclear. Here, in 74 human/hominoid-specific de novo genes, we identified distinctive U1 elements and RNA splice-related sequences accounting for RNA nuclear export, differentiating mRNAs from lncRNAs, and driving the origin of de novo genes from lncRNA loci. The polymorphic sites facilitating the lncRNA-mRNA conversion through regulating nuclear export are selectively constrained, maintaining a boundary that differentiates mRNAs from lncRNAs. The functional new genes actively passing through it thus showed a mode of pre-adaptive origin, in that they acquire functions along with the achievement of their coding potential. As a proof of concept, we verified the regulations of splicing and U1 recognition on the nuclear export efficiency of one of these genes, the ENSG00000205704, in human neural progenitor cells. Notably, knock-out or over-expression of this gene in human embryonic stem cells accelerates or delays the neuronal maturation of cortical organoids, respectively. The transgenic mice with ectopically expressed ENSG00000205704 showed enlarged brains with cortical expansion. We thus demonstrate the key roles of nuclear export in de novo gene origin. These newly originated genes should reflect the novel uniqueness of human brain development.
    DOI:  https://doi.org/10.1038/s41559-022-01925-6
  24. Nat Genet. 2023 Jan 02.
    DNA methylation provides molecular links underlying complex traits.
      
    DOI:  https://doi.org/10.1038/s41588-022-01249-y
  25. Nat Immunol. 2023 Jan;24(1): 2
    Microbiota contributions.
    Ioana Visan.
      
    DOI:  https://doi.org/10.1038/s41590-022-01407-8
  26. Sci Transl Med. 2023 Jan 04. 15(677): eadd3949
    An autocrine signaling circuit in hepatic stellate cells underlies advanced fibrosis in nonalcoholic steatohepatitis.
    Shuang Wang, Kenneth Li, Eliana Pickholz, Ross Dobie, Kylie P Matchett, Neil C Henderson, Chris Carrico, Ian Driver, Martin Borch Jensen, Li Chen, Mathieu Petitjean, Dipankar Bhattacharya, Maria I Fiel, Xiao Liu, Tatiana Kisseleva, Uri Alon, Miri Adler, Ruslan Medzhitov, Scott L Friedman.
      Advanced hepatic fibrosis, driven by the activation of hepatic stellate cells (HSCs), affects millions worldwide and is the strongest predictor of mortality in nonalcoholic steatohepatitis (NASH); however, there are no approved antifibrotic therapies. To identify antifibrotic drug targets, we integrated progressive transcriptomic and morphological responses that accompany HSC activation in advanced disease using single-nucleus RNA sequencing and tissue clearing in a robust murine NASH model. In advanced fibrosis, we found that an autocrine HSC signaling circuit emerged that was composed of 68 receptor-ligand interactions conserved between murine and human NASH. These predicted interactions were supported by the parallel appearance of markedly increased direct stellate cell-cell contacts in murine NASH. As proof of principle, pharmacological inhibition of one such autocrine interaction, neurotrophic receptor tyrosine kinase 3-neurotrophin 3, inhibited human HSC activation in culture and reversed advanced murine NASH fibrosis. In summary, we uncovered a repertoire of antifibrotic drug targets underlying advanced fibrosis in vivo. The findings suggest a therapeutic paradigm in which stage-specific therapies could yield enhanced antifibrotic efficacy in patients with advanced hepatic fibrosis.
    DOI:  https://doi.org/10.1126/scitranslmed.add3949
  27. Cell Rep. 2022 Dec 24. pii: S2211-1247(22)01794-6. [Epub ahead of print] 111895
    PD-1highCXCR5-CD4+ peripheral helper T cells promote CXCR3+ plasmablasts in human acute viral infection.
    Hiromitsu Asashima, Subhasis Mohanty, Michela Comi, William E Ruff, Kenneth B Hoehn, Patrick Wong, Jon Klein, Carolina Lucas, Inessa Cohen, Sarah Coffey, Nikhil Lele, Leissa Greta, Khadir Raddassi, Omkar Chaudhary, Avraham Unterman, Brinda Emu, Steven H Kleinstein, Ruth R Montgomery, Akiko Iwasaki, Charles S Dela Cruz, Naftali Kaminski, Albert C Shaw, David A Hafler, Tomokazu S Sumida.
      T cell-B cell interaction is the key immune response to protect the host from severe viral infection. However, how T cells support B cells to exert protective humoral immunity in humans is not well understood. Here, we use COVID-19 as a model of acute viral infections and analyze CD4+ T cell subsets associated with plasmablast expansion and clinical outcome. Peripheral helper T cells (Tph cells; denoted as PD-1highCXCR5-CD4+ T cells) are significantly increased, as are plasmablasts. Tph cells exhibit "B cell help" signatures and induce plasmablast differentiation in vitro. Interestingly, expanded plasmablasts show increased CXCR3 expression, which is positively correlated with higher frequency of activated Tph cells and better clinical outcome. Mechanistically, Tph cells help B cell differentiation and produce more interferon γ (IFNγ), which induces CXCR3 expression on plasmablasts. These results elucidate a role for Tph cells in regulating protective B cell response during acute viral infection.
    Keywords:  CP: Immunology; CXCR3(+) plasmablasts; IFNγ; PD-1(high)CXCR5(–)CD4(+) peripheral helper T cells; T cell-B cell interactions; Tph cells
    DOI:  https://doi.org/10.1016/j.celrep.2022.111895
  28. Nat Biotechnol. 2023 Jan 02.
    Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models.
    IMI DIRECT Consortium
      The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature of multi-modal data makes integration and inference a non-trivial task. We developed a deep-learning-based framework, multi-omics variational autoencoders (MOVE), to integrate such data and applied it to a cohort of 789 people with newly diagnosed type 2 diabetes with deep multi-omics phenotyping from the DIRECT consortium. Using in silico perturbations, we identified drug-omics associations across the multi-modal datasets for the 20 most prevalent drugs given to people with type 2 diabetes with substantially higher sensitivity than univariate statistical tests. From these, we among others, identified novel associations between metformin and the gut microbiota as well as opposite molecular responses for the two statins, simvastatin and atorvastatin. We used the associations to quantify drug-drug similarities, assess the degree of polypharmacy and conclude that drug effects are distributed across the multi-omics modalities.
    DOI:  https://doi.org/10.1038/s41587-022-01520-x
  29. Circulation. 2023 Jan 02.
    Targeting Epsins to Inhibit Fibroblast Growth Factor Signaling While Potentiating Transforming Growth Factor-β Signaling Constrains Endothelial-to-Mesenchymal Transition in Atherosclerosis.
    Yunzhou Dong, Beibei Wang, Mulong Du, Bo Zhu, Kui Cui, Kathryn Li, Ke Yuan, Douglas B Cowan, Sudarshan Bhattacharjee, Scott Wong, Jinjun Shi, Da-Zhi Wang, Kaifu Chen, Joyce Bischoff, MacRae F Linton, Hong Chen.
       BACKGROUND: Epsin endocytic adaptor proteins are implicated in the progression of atherosclerosis; however, the underlying molecular mechanisms have not yet been fully defined. In this study, we determined how epsins enhance endothelial-to-mesenchymal transition (EndoMT) in atherosclerosis and assessed the efficacy of a therapeutic peptide in a preclinical model of this disease.
    METHODS: Using single-cell RNA sequencing combined with molecular, cellular, and biochemical analyses, we investigated the role of epsins in stimulating EndoMT using knockout in Apoe-/- and lineage tracing/proprotein convertase subtilisin/kexin type 9 serine protease mutant viral-induced atherosclerotic mouse models. The therapeutic efficacy of a synthetic peptide targeting atherosclerotic plaques was then assessed in Apoe-/- mice.
    RESULTS: Single-cell RNA sequencing and lineage tracing revealed that epsins 1 and 2 promote EndoMT and that the loss of endothelial epsins inhibits EndoMT marker expression and transforming growth factor-β signaling in vitro and in atherosclerotic mice, which is associated with smaller lesions in the Apoe-/- mouse model. Mechanistically, the loss of endothelial cell epsins results in increased fibroblast growth factor receptor-1 expression, which inhibits transforming growth factor-β signaling and EndoMT. Epsins directly bind ubiquitinated fibroblast growth factor receptor-1 through their ubiquitin-interacting motif, which results in endocytosis and degradation of this receptor complex. Consequently, administration of a synthetic ubiquitin-interacting motif-containing peptide atheroma ubiquitin-interacting motif peptide inhibitor significantly attenuates EndoMT and progression of atherosclerosis.
    CONCLUSIONS: We conclude that epsins potentiate EndoMT during atherogenesis by increasing transforming growth factor-β signaling through fibroblast growth factor receptor-1 internalization and degradation. Inhibition of EndoMT by reducing epsin-fibroblast growth factor receptor-1 interaction with a therapeutic peptide may represent a novel treatment strategy for atherosclerosis.
    Keywords:  adaptor proteins, signal transducing; atherosclerosis; endocytosis; epsin; peptides; receptor, fibroblast growth factor, type 1; single-cell gene expression analysis; transforming growth factor beta; vascular diseases
    DOI:  https://doi.org/10.1161/CIRCULATIONAHA.122.063075
  30. Nature. 2023 Jan 04.
    Structural basis of regulated m7G tRNA modification by METTL1-WDR4.
    Jiazhi Li, Longfei Wang, Quentin Hahn, Radosław P Nowak, Thibault Viennet, Esteban A Orellana, Shourya S Roy Burman, Hong Yue, Moritz Hunkeler, Pietro Fontana, Hao Wu, Haribabu Arthanari, Eric S Fischer, Richard I Gregory.
      Chemical modifications of RNA have key roles in many biological processes1-3. N7-methylguanosine (m7G) is required for integrity and stability of a large subset of tRNAs4-7. The methyltransferase 1-WD repeat-containing protein 4 (METTL1-WDR4) complex is the methyltransferase that modifies G46 in the variable loop of certain tRNAs, and its dysregulation drives tumorigenesis in numerous cancer types8-14. Mutations in WDR4 cause human developmental phenotypes including microcephaly15-17. How METTL1-WDR4 modifies tRNA substrates and is regulated remains elusive18. Here we show,  through structural, biochemical and cellular studies of human METTL1-WDR4, that WDR4 serves as a scaffold for METTL1 and the tRNA T-arm. Upon tRNA binding, the αC region of METTL1 transforms into a helix, which together with the α6 helix secures both ends of the tRNA variable loop. Unexpectedly, we find that the predicted disordered N-terminal region of METTL1 is part of the catalytic pocket and essential for methyltransferase activity. Furthermore, we reveal that S27 phosphorylation in the METTL1 N-terminal region inhibits methyltransferase activity by locally disrupting the catalytic centre. Our results provide a molecular understanding of tRNA substrate recognition and phosphorylation-mediated regulation of METTL1-WDR4, and reveal the presumed disordered N-terminal region of METTL1 as a nexus of methyltransferase activity.
    DOI:  https://doi.org/10.1038/s41586-022-05566-4
  31. Cell Metab. 2023 Jan 03. pii: S1550-4131(22)00546-0. [Epub ahead of print]35(1): 3-5
    Early immune pressure makes tumors metabolically stronger.
    Sujing Yuan, Hongbo Chi.
      Metabolic communication in the tumor microenvironment underscores tumor-immune interactions and affects anti-tumor immunity, yet cell-extrinsic signals driving tumor metabolic remodeling are incompletely understood. In this issue, Tsai et al. show that during initial tumorigenesis, T cell-derived IFNγ triggers STAT3 activation and c-Myc-dependent alterations of tumor cell metabolism, which potentiates immune evasion.
    DOI:  https://doi.org/10.1016/j.cmet.2022.12.009
  32. Cell Mol Immunol. 2023 Jan 05.
    β-adrenoreceptor-triggered PKA activation negatively regulates the innate antiviral response.
    Yi Guo, Xia-Nan Zhang, Shan Su, Zi-Lun Ruan, Ming-Ming Hu, Hong-Bing Shu.
      Upon viral infection, cytoplasmic pattern recognition receptors detect viral nucleic acids and activate the adaptor protein VISA/MAVS- or MITA/STING-mediated innate antiviral response. Whether and how the innate antiviral response is regulated by neuronal endocrine functions is unclear. Here, we show that viral infection reduced the serum levels of the β-adrenergic hormones epinephrine and norepinephrine as well as the cellular levels of their receptors ADRB1 and ADRB2. We further show that an increase in epinephrine/norepinephrine level inhibited the innate antiviral response in an ADRB1-/2-dependent manner. Mechanistically, epinephrine/norepinephrine stimulation activated the downstream kinase PKA, which catalyzed the phosphorylation of MITA at S241, S243 and T263, inhibiting MITA activation and suppressing the innate immune response to DNA virus. In addition, phosphorylation of VISA at T54 by PKA antagonized the innate immune response to RNA virus. These findings reveal the regulatory mechanisms of innate antiviral responses by epinephrine/norepinephrine and provide a possible explanation for increased host susceptibility to viral infection in stressful and anxiety-promoting situations.
    Keywords:  PKA; beta-adrenoreceptor; innate immunity; signal transduction; virus
    DOI:  https://doi.org/10.1038/s41423-022-00967-x
  33. Nat Biotechnol. 2023 Jan 05.
    Single-cell recording of cellular RNAs in bacteria.
      
    DOI:  https://doi.org/10.1038/s41587-022-01625-3
  34. Proc Natl Acad Sci U S A. 2023 Jan 10. 120(2): e2213056120
    Sec22b is a critical and nonredundant regulator of plasma cell maintenance.
    Amélie Bonaud, Laetitia Gargowitsch, Simon M Gilbert, Elanchezhian Rajan, Pablo Canales-Herrerias, Daniel Stockholm, Nabila F Rahman, Mark O Collins, Hakan Taskiran, Danika L Hill, Andres Alloatti, Nagham Alouche, Stéphanie Balor, Vanessa Soldan, Daniel Gillet, Julien Barbier, Françoise Bachelerie, Kenneth G C Smith, Julia Jellusova, Pierre Bruhns, Sebastian Amigorena, Karl Balabanian, Michelle A Linterman, Andrew A Peden, Marion Espéli.
      Despite the essential role of plasma cells in health and disease, the cellular mechanisms controlling their survival and secretory capacity are still poorly understood. Here, we identified the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) Sec22b as a unique and critical regulator of plasma cell maintenance and function. In the absence of Sec22b, plasma cells were hardly detectable and serum antibody titers were dramatically reduced. Accordingly, Sec22b-deficient mice fail to mount a protective immune response. At the mechanistic level, we demonstrated that Sec22b contributes to efficient antibody secretion and is a central regulator of plasma cell maintenance through the regulation of their transcriptional identity and of the morphology of the endoplasmic reticulum and mitochondria. Altogether, our results unveil an essential and nonredundant role for Sec22b as a regulator of plasma cell fitness and of the humoral immune response.
    Keywords:  SNARE; antibody; endoplasmic reticulum; mitochondria; plasma cell
    DOI:  https://doi.org/10.1073/pnas.2213056120
  35. Nature. 2023 Jan 04.
    Identification of astrocyte regulators by nucleic acid cytometry.
    Iain C Clark, Michael A Wheeler, Hong-Gyun Lee, Zhaorong Li, Liliana M Sanmarco, Shravan Thaploo, Carolina M Polonio, Seung Won Shin, Giulia Scalisi, Amy R Henry, Joseph M Rone, Federico Giovannoni, Marc Charabati, Camilo Faust Akl, Dulce M Aleman, Stephanie E J Zandee, Alexandre Prat, Daniel C Douek, Eli A Boritz, Francisco J Quintana, Adam R Abate.
      Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS)1. Astrocytes are heterogeneous CNS-resident glial cells that participate in the pathogenesis of MS and its model experimental autoimmune encephalomyelitis (EAE)2,3. However, few unique surface markers are available for the isolation of astrocyte subsets, preventing their analysis and the identification of candidate therapeutic targets; these limitations are further amplified by the rarity of pathogenic astrocytes. To address these challenges, we developed FIND-seq (Focused Interrogation of cells by Nucleic acid Detection and Sequencing), a high-throughput microfluidic cytometry method that combines encapsulation of cells in droplets, PCR-based detection of target nucleic acids, and droplet sorting to enable in-depth transcriptomic analyses of cells of interest at single-cell resolution. We applied FIND-seq to study the regulation of astrocytes characterized by the splicing-driven activation of the transcription factor XBP1, which promotes disease pathology in MS and EAE4. Using FIND-seq in combination with conditional knock-out mice, in vivo CRISPR/Cas9-driven genetic perturbation studies, and bulk and single-cell RNA-seq analyses of mouse EAE and human MS samples, we identified a new role for the nuclear receptor NR3C2 and its corepressor NCOR2 in limiting XBP1-driven pathogenic astrocyte responses. In summary, FIND-seq enabled the identification of a therapeutically targetable mechanism that limits XBP1-driven pathogenic astrocyte responses. FIND-seq allows the investigation of previously inaccessible cells, including rare cell subsets defined by unique gene expression signatures or other nucleic acid markers.
    DOI:  https://doi.org/10.1038/s41586-022-05613-0
  36. Nat Immunol. 2023 Jan 05.
    The COVID-19 immunology masterclass enters its third year.
    Daniel M Altmann.
      
    DOI:  https://doi.org/10.1038/s41590-022-01393-x
  37. Nat Immunol. 2023 Jan;24(1): 10-11
    Check(point) yourself before you wreck yourself in tumors.
    Jeong-Mi Lee, Peter T Sage.
      
    DOI:  https://doi.org/10.1038/s41590-022-01391-z
  38. Science. 2023 Jan 06. 379(6627): 110
    Tired of persevering.
    Keisha Hardeman.
      
    DOI:  https://doi.org/10.1126/science.adg4851
  39. Sci Adv. 2023 Jan 04. 9(1): eadd3216
    Lactate metabolism is essential in early-onset mitochondrial myopathy.
    Zhenkang Chen, Bogdan Bordieanu, Rushendhiran Kesavan, Nicholas P Lesner, Siva Sai Krishna Venigalla, Spencer D Shelton, Ralph J DeBerardinis, Prashant Mishra.
      Myopathies secondary to mitochondrial electron transport chain (ETC) dysfunction can result in devastating disease. While the consequences of ETC defects have been extensively studied in culture, little in vivo data are available. Using a mouse model of severe, early-onset mitochondrial myopathy, we characterized the proteomic, transcriptomic, and metabolic characteristics of disease progression. Unexpectedly, ETC dysfunction in muscle results in reduced expression of glycolytic enzymes in our animal model and patient muscle biopsies. The decrease in glycolysis was mediated by loss of constitutive Hif1α signaling, down-regulation of the purine nucleotide cycle enzyme AMPD1, and activation of AMPK. In vivo isotope tracing experiments indicated that myopathic muscle relies on lactate import to supply central carbon metabolites. Inhibition of lactate import reduced steady-state levels of tricarboxylic acid cycle intermediates and compromised the life span of myopathic mice. These data indicate an unexpected mode of metabolic reprogramming in severe mitochondrial myopathy that regulates disease progression.
    DOI:  https://doi.org/10.1126/sciadv.add3216
  40. J Clin Invest. 2023 Jan 03. pii: e165033. [Epub ahead of print]133(1):
    Liver-resident CD8+ T cells in viral hepatitis: not always good guys.
    Hendrik Luxenburger, Christoph Neumann-Haefelin.
      More than twenty years ago, non-HBV-specific CD8+ T cells were found to contribute to liver immunopathology in chronic HBV infection, while HBV-specific CD8+ T cells were noted to contribute to viral control. The role of HBV-specific CD8+ T cells in viral control and the mechanisms of their failure in persistent infection have been intensively studied during the last two decades, but the exact nature of nonspecific bystander CD8+ T cells that contribute to immunopathology has remained elusive. In this issue of the JCI, Nkongolo et al. report on their application of two methodological advances, liver sampling by fine-needle aspiration (FNA) and single-cell RNA sequencing (scRNA-Seq), to define a liver-resident CD8+ T cell population that was not virus specific but associated with liver damage, thus representing hepatotoxic bystander CD8+ T cells.
    DOI:  https://doi.org/10.1172/JCI165033
  41. J Clin Invest. 2023 Jan 03. pii: e158903. [Epub ahead of print]133(1):
    Longitudinal liver sampling in patients with chronic hepatitis B starting antiviral therapy reveals hepatotoxic CD8+ T cells.
    Shirin Nkongolo, Deeqa Mahamed, Adrian Kuipery, Juan D Sanchez Vasquez, Samuel C Kim, Aman Mehrotra, Anjali Patel, Christine Hu, Ian McGilvray, Jordan J Feld, Scott Fung, Diana Chen, Jeffrey J Wallin, Anuj Gaggar, Harry LA Janssen, Adam J Gehring.
      Accumulation of activated immune cells results in nonspecific hepatocyte killing in chronic hepatitis B (CHB), leading to fibrosis and cirrhosis. This study aims to understand the underlying mechanisms in humans and to define whether these are driven by widespread activation or a subpopulation of immune cells. We enrolled CHB patients with active liver damage to receive antiviral therapy and performed longitudinal liver sampling using fine-needle aspiration to investigate mechanisms of CHB pathogenesis in the human liver. Single-cell sequencing of total liver cells revealed a distinct liver-resident, polyclonal CD8+ T cell population that was enriched at baseline and displayed a highly activated immune signature during liver damage. Cytokine combinations, identified by in silico prediction of ligand-receptor interaction, induced the activated phenotype in healthy liver CD8+ T cells, resulting in nonspecific Fas ligand-mediated killing of target cells. These results define a CD8+ T cell population in the human liver that can drive pathogenesis and a key pathway involved in their function in CHB patients.
    Keywords:  Cellular immune response; Hepatitis; Immunology; Infectious disease; T cells
    DOI:  https://doi.org/10.1172/JCI158903
  42. J Clin Invest. 2023 Jan 05. pii: e162190. [Epub ahead of print]
    Intestinal epithelial HDAC3 and MHC class II coordinate microbiota-specific immunity.
    Emily M Eshleman, Tzu-Yu Shao, Vivienne Woo, Taylor Rice, Laura Engleman, Bailey J Didriksen, Jordan Whitt, David B Haslam, Sing Sing Way, Theresa Alenghat.
      Aberrant immune responses to resident microbes promote inflammatory bowel disease and other chronic inflammatory conditions. However, how microbiota-specific immunity is controlled in mucosal tissues remains poorly understood. Here, we find that mice lacking epithelial expression of microbiota-sensitive histone deacetylase 3 (HDAC3) exhibit increased accumulation of commensal-specific CD4+ T cells in the intestine, provoking the hypothesis that epithelial HDAC3 may instruct local microbiota-specific immunity. Consistent with this, microbiota-specific CD4+ T cells and epithelial HDAC3 expression were concurrently induced following early-life microbiota colonization. Further, epithelial-intrinsic ablation of HDAC3 decreased commensal-specific Tregs, increased commensal-specific Th17 cells, and promoted T cell-driven colitis. Mechanistically, HDAC3 was essential for NFκB-dependent regulation of epithelial MHC class II (MHCII). Epithelial-intrinsic MHCII dampened local accumulation of commensal-specific Th17 cells in adult mice, and protected against microbiota-triggered inflammation. Remarkably, HDAC3 enabled the microbiota to induce MHCII on epithelial cells and limit the number of commensal-specific T cells in the intestine. Collectively, these data reveal a central role for an epithelial histone deacetylase in directing the dynamic balance of tissue-intrinsic CD4+ T cell subsets that recognize commensal microbes and control inflammation.
    Keywords:  Adaptive immunity; Antigen presentation; Gastroenterology; Immunology; Inflammatory bowel disease
    DOI:  https://doi.org/10.1172/JCI162190
  43. Nat Biotechnol. 2023 Jan 05.
    Solid-phase capture and profiling of open chromatin by spatial ATAC.
    Enric Llorens-Bobadilla, Margherita Zamboni, Maja Marklund, Nayanika Bhalla, Xinsong Chen, Johan Hartman, Jonas Frisén, Patrik L Ståhl.
      Current methods for epigenomic profiling are limited in their ability to obtain genome-wide information with spatial resolution. We introduce spatial ATAC, a method that integrates transposase-accessible chromatin profiling in tissue sections with barcoded solid-phase capture to perform spatially resolved epigenomics. We show that spatial ATAC enables the discovery of the regulatory programs underlying spatial gene expression during mouse organogenesis, lineage differentiation and in human pathology.
    DOI:  https://doi.org/10.1038/s41587-022-01603-9
  44. Cell Metab. 2023 Jan 03. pii: S1550-4131(22)00541-1. [Epub ahead of print]35(1): 166-183.e11
    Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins.
    Thomas F Martinez, Sally Lyons-Abbott, Angie L Bookout, Eduardo V De Souza, Cynthia Donaldson, Joan M Vaughan, Calvin Lau, Ariel Abramov, Arian F Baquero, Karalee Baquero, Dave Friedrich, Justin Huard, Ray Davis, Bong Kim, Ty Koch, Aaron J Mercer, Ayesha Misquith, Sara A Murray, Sakara Perry, Lindsay K Pino, Christina Sanford, Alex Simon, Yu Zhang, Garrett Zipp, Cristiano V Bizarro, Maxim N Shokhirev, Andrew J Whittle, Brian C Searle, Michael J MacCoss, Alan Saghatelian, Christopher A Barnes.
      Microproteins (MPs) are a potentially rich source of uncharacterized metabolic regulators. Here, we use ribosome profiling (Ribo-seq) to curate 3,877 unannotated MP-encoding small ORFs (smORFs) in primary brown, white, and beige mouse adipocytes. Of these, we validated 85 MPs by proteomics, including 33 circulating MPs in mouse plasma. Analyses of MP-encoding mRNAs under different physiological conditions (high-fat diet) revealed that numerous MPs are regulated in adipose tissue in vivo and are co-expressed with established metabolic genes. Furthermore, Ribo-seq provided evidence for the translation of Gm8773, which encodes a secreted MP that is homologous to human and chicken FAM237B. Gm8773 is highly expressed in the arcuate nucleus of the hypothalamus, and intracerebroventricular administration of recombinant mFAM237B showed orexigenic activity in obese mice. Together, these data highlight the value of this adipocyte MP database in identifying MPs with roles in fundamental metabolic and physiological processes such as feeding.
    Keywords:  Ribo-seq; brown adipose tissue; data-independent acquisition mass spectrometry; diet-induced obesity; microproteins; ribosome profiling; secreted microproteins; small ORFs; white adipose tissue
    DOI:  https://doi.org/10.1016/j.cmet.2022.12.004
  45. Cell Mol Immunol. 2023 Jan 05.
    The neuropeptide CGRP enters the macrophage cytosol to suppress the NLRP3 inflammasome during pulmonary infection.
    Fangrui Zhu, Dou Yu, Xiwen Qin, Yan Qian, Juan Ma, Weitao Li, Qiannv Liu, Chunlei Wang, Yan Zhang, Yi Li, Dong Jiang, Shuo Wang, Pengyan Xia.
      The NLRP3 inflammasome plays an essential role in resistance to bacterial infection. The nervous system secretes multiple neuropeptides affecting the nervous system as well as immune cells. The precise impact of the neuropeptide CGRP on NLRP3 inflammasome activation is still unclear. Here, we show that CGRP negatively regulates the antibacterial process of host cells. CGRP prevents NLRP3 inflammasome activation and reduces mature IL-1β secretion. Following NLRP3 inflammasome stimulation that triggers endosome leakage, CGRP internalized to endosomal compartments is released into the cell cytosol. Cytosolic CGRP binds directly to NLRP3 and dismantles the NLRP3-NEK7 complex, which is crucial for NLRP3 inflammasome activation. CGRP administration exacerbates bacterial infection, while the treatment with a CGRP antagonist has the opposite effect. Our study uncovers a unique role of CGRP in inhibiting inflammasome activation during infections, which might shed new light on antibacterial therapies in the future.
    Keywords:  CGRP; Inflammasome; NLRP3; Neuropeptide; Suppressor
    DOI:  https://doi.org/10.1038/s41423-022-00968-w
  46. Commun Biol. 2023 Jan 04. 6(1): 9
    Profilin 1 deficiency drives mitotic defects and reduces genome stability.
    Federica Scotto di Carlo, Sharon Russo, Francesc Muyas, Maria Mangini, Lorenza Garribba, Laura Pazzaglia, Rita Genesio, Flavia Biamonte, Anna Chiara De Luca, Stefano Santaguida, Katia Scotlandi, Isidro Cortés-Ciriano, Fernando Gianfrancesco.
      Profilin 1-encoded by PFN1-is a small actin-binding protein with a tumour suppressive role in various adenocarcinomas and pagetic osteosarcomas. However, its contribution to tumour development is not fully understood. Using fix and live cell imaging, we report that Profilin 1 inactivation results in multiple mitotic defects, manifested prominently by anaphase bridges, multipolar spindles, misaligned and lagging chromosomes, and cytokinesis failures. Accordingly, next-generation sequencing technologies highlighted that Profilin 1 knock-out cells display extensive copy-number alterations, which are associated with complex genome rearrangements and chromothripsis events in primary pagetic osteosarcomas with Profilin 1 inactivation. Mechanistically, we show that Profilin 1 is recruited to the spindle midzone at anaphase, and its deficiency reduces the supply of actin filaments to the cleavage furrow during cytokinesis. The mitotic defects are also observed in mouse embryonic fibroblasts and mesenchymal cells deriving from a newly generated knock-in mouse model harbouring a Pfn1 loss-of-function mutation. Furthermore, nuclear atypia is also detected in histological sections of mutant femurs. Thus, our results indicate that Profilin 1 has a role in regulating cell division, and its inactivation triggers mitotic defects, one of the major mechanisms through which tumour cells acquire chromosomal instability.
    DOI:  https://doi.org/10.1038/s42003-022-04392-8
  47. Nat Rev Cancer. 2023 Jan 03.
    STAT proteins in cancer: orchestration of metabolism.
    Yi-Jia Li, Chunyan Zhang, Antons Martincuks, Andreas Herrmann, Hua Yu.
      Reprogrammed metabolism is a hallmark of cancer. However, the metabolic dependency of cancer, from tumour initiation through disease progression and therapy resistance, requires a spectrum of distinct reprogrammed cellular metabolic pathways. These pathways include aerobic glycolysis, oxidative phosphorylation, reactive oxygen species generation, de novo lipid synthesis, fatty acid β-oxidation, amino acid (notably glutamine) metabolism and mitochondrial metabolism. This Review highlights the central roles of signal transducer and activator of transcription (STAT) proteins, notably STAT3, STAT5, STAT6 and STAT1, in orchestrating the highly dynamic metabolism not only of cancer cells but also of immune cells and adipocytes in the tumour microenvironment. STAT proteins are able to shape distinct metabolic processes that regulate tumour progression and therapy resistance by transducing signals from metabolites, cytokines, growth factors and their receptors; defining genetic programmes that regulate a wide range of molecules involved in orchestration of metabolism in cancer and immune cells; and regulating mitochondrial activity at multiple levels, including energy metabolism and lipid-mediated mitochondrial integrity. Given the central role of STAT proteins in regulation of metabolic states, they are potential therapeutic targets for altering metabolic reprogramming in cancer.
    DOI:  https://doi.org/10.1038/s41568-022-00537-3
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