bims-nimamd Biomed News
on Neuroimmunity and neuroinflammation in ageing and metabolic disease
Issue of 2022‒04‒24
sixty papers selected by
Fawaz Alzaïd
Sorbonne Université
  1. Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca2+ channel function.
  2. A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrid accumulation.
  3. Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF.
  4. Regulated interaction of ID2 with the anaphase-promoting complex links progression through mitosis with reactivation of cell-type-specific transcription.
  5. Somatic genomic changes in single Alzheimer's disease neurons.
  6. An evolutionarily conserved stop codon enrichment at the 5' ends of mammalian piRNAs.
  7. RNA polymerase II pausing factor NELF in CD8+ T cells promotes antitumor immunity.
  8. AKT mutant allele-specific activation dictates pharmacologic sensitivities.
  9. Intestinal fibroblastic reticular cell niches control innate lymphoid cell homeostasis and function.
  10. The Human Pangenome Project: a global resource to map genomic diversity.
  11. ESCRT-mediated membrane repair protects tumor-derived cells against T cell attack.
  12. Generation of human islet cell type-specific identity genesets.
  13. Low complexity RGG-motif sequence is required for Processing body (P-body) disassembly.
  14. Secondary structure RNA elements control the cleavage activity of DICER.
  15. Honeybee gut Lactobacillus modulates host learning and memory behaviors via regulating tryptophan metabolism.
  16. HNF4A modulates glucocorticoid action in the liver.
  17. Stearoyl-CoA Desaturase inhibition reverses immune, synaptic and cognitive impairments in an Alzheimer's disease mouse model.
  18. Single cell analyses identify a highly regenerative and homogenous human CD34+ hematopoietic stem cell population.
  19. Early age-related atrophy of cutaneous lymph nodes precipitates an early functional decline in skin immunity in mice with aging.
  20. Lateral gain is impaired in macular degeneration and can be targeted to restore vision in mice.
  21. Tension can directly suppress Aurora B kinase-triggered release of kinetochore-microtubule attachments.
  22. Programme of self-reactive innate-like T cell-mediated cancer immunity.
  23. A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.
  24. Endothelial progenitor cells stimulate neonatal lung angiogenesis through FOXF1-mediated activation of BMP9/ACVRL1 signaling.
  25. Targeting TCTP sensitizes tumor to T cell-mediated therapy by reversing immune-refractory phenotypes.
  26. Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia.
  27. Allosteric interactions prime androgen receptor dimerization and activation.
  28. Structural insights into the peptide selectivity and activation of human neuromedin U receptors.
  29. Connecting high-resolution 3D chromatin organization with epigenomics.
  30. The PPR domain of mitochondrial RNA polymerase is an exoribonuclease required for mtDNA replication in Drosophila melanogaster.
  31. Therapeutic targeting of the mevalonate-geranylgeranyl diphosphate pathway with statins overcomes chemotherapy resistance in small cell lung cancer.
  32. Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche.
  33. Niche expansion and adaptive divergence in the global radiation of crows and ravens.
  34. Human Coronary Plaque T Cells Are Clonal and Cross-React to Virus and Self.
  35. High-efficiency nonviral CRISPR/Cas9-mediated gene editing of human T cells using plasmid donor DNA.
  36. The Role of Metabolic Dysfunction in T-Cell Exhaustion During Chronic Viral Infection.
  37. PD-L1-PD-1 interactions limit effector regulatory T cell populations at homeostasis and during infection.
  38. Steroid-induced fibroblast growth factors drive an epithelial-mesenchymal inflammatory axis in severe asthma.
  39. Loss of vascular endothelial notch signaling promotes spontaneous formation of tertiary lymphoid structures.
  40. Chemotherapy-induced COX-2 upregulation by cancer cells defines their inflammatory properties and limits the efficacy of chemoimmunotherapy combinations.
  41. Supraphysiological activation of TAK1 promotes skeletal muscle growth and mitigates neurogenic atrophy.
  42. Antigen-derived peptides engage the ER stress sensor IRE1α to curb dendritic cell cross-presentation.
  43. Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole-cell mechanics.
  44. Distinct resistance mechanisms arise to allosteric vs. ATP-competitive AKT inhibitors.
  45. Central memory T cells are the most effective precursors of resident memory T cells in human skin.
  46. Evaluating ribosomal frameshifting in CCR5 mRNA decoding.
  47. Pyridine nucleotide redox potential in coronary smooth muscle couples myocardial blood flow to cardiac metabolism.
  48. ZNF117 regulates glioblastoma stem cell differentiation towards oligodendroglial lineage.
  49. CD36, a signaling receptor and fatty acid transporter that regulates immune cell metabolism and fate.
  50. Pathogenic BRCA1 variants disrupt PLK1-regulation of mitotic spindle orientation.
  51. Snf7 spirals sense and alter membrane curvature.
  52. USP22 regulates lipidome accumulation by stabilizing PPARγ in hepatocellular carcinoma.
  53. Local and substrate-specific S-palmitoylation determines subcellular localization of Gαo.
  54. Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments.
  55. Vasa nucleates asymmetric translation along the mitotic spindle during unequal cell divisions.
  56. Cooperative interaction between ERα and the EMT-inducer ZEB1 reprograms breast cancer cells for bone metastasis.
  57. An anti-influenza A virus microbial metabolite acts by degrading viral endonuclease PA.
  58. Increased Memory B Cell Potency and Breadth After a SARS-CoV-2 mRNA Boost.
  59. Skeletal Ni electrode-catalyzed C-O cleavage of diaryl ethers entails direct elimination via benzyne intermediates.
  60. Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle.
  1. Nat Commun. 2022 Apr 19. 13(1): 2033
    Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca2+ channel function.
    Serap Erdogmus, Axel R Concepcion, Megumi Yamashita, Ikjot Sidhu, Anthony Y Tao, Wenyi Li, Pedro P Rocha, Bonnie Huang, Ralph Garippa, Boram Lee, Amy Lee, Johannes W Hell, Richard S Lewis, Murali Prakriya, Stefan Feske.
      TCR stimulation triggers Ca2+ signals that are critical for T cell function and immunity. Several pore-forming α and auxiliary β subunits of voltage-gated Ca2+ channels (VGCC) were reported in T cells, but their mechanism of activation remains elusive and their contribution to Ca2+ signaling in T cells is controversial. We here identify CaVβ1, encoded by Cacnb1, as a regulator of T cell function. Cacnb1 deletion enhances apoptosis and impairs the clonal expansion of T cells after lymphocytic choriomeningitis virus (LCMV) infection. By contrast, Cacnb1 is dispensable for T cell proliferation, cytokine production and Ca2+ signaling. Using patch clamp electrophysiology and Ca2+ recordings, we are unable to detect voltage-gated Ca2+ currents or Ca2+ influx in human and mouse T cells upon depolarization with or without prior TCR stimulation. mRNAs of several VGCC α1 subunits are detectable in human (CaV3.3, CaV3.2) and mouse (CaV2.1) T cells, but they lack transcription of many 5' exons, likely resulting in N-terminally truncated and non-functional proteins. Our findings demonstrate that although CaVβ1 regulates T cell function, these effects are independent of VGCC channel activity.
    DOI:  https://doi.org/10.1038/s41467-022-29725-3
  2. Nat Commun. 2022 Apr 19. 13(1): 2012
    A POLD3/BLM dependent pathway handles DSBs in transcribed chromatin upon excessive RNA:DNA hybrid accumulation.
    S Cohen, A Guenolé, I Lazar, A Marnef, T Clouaire, D V Vernekar, N Puget, V Rocher, C Arnould, M Aguirrebengoa, M Genais, N Firmin, R A Shamanna, R Mourad, V A Bohr, V Borde, G Legube.
      Transcriptionally active loci are particularly prone to breakage and mounting evidence suggests that DNA Double-Strand Breaks arising in active genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loop accumulation and dissolution. Here, we uncover a function for the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in an R-loop dissolution-deficient background, we find that BLM promotes cell death. We report that upon excessive RNA:DNA hybrid accumulation, DNA synthesis is enhanced at DSBs, in a manner that depends on BLM and POLD3. Altogether our work unveils a role for BLM at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at transcription-associated DSBs.
    DOI:  https://doi.org/10.1038/s41467-022-29629-2
  3. Nat Commun. 2022 Apr 19. 13(1): 2139
    Analysis of sub-kilobase chromatin topology reveals nano-scale regulatory interactions with variable dependence on cohesin and CTCF.
    Abrar Aljahani, Peng Hua, Magdalena A Karpinska, Kimberly Quililan, James O J Davies, A Marieke Oudelaar.
      Enhancers and promoters predominantly interact within large-scale topologically associating domains (TADs), which are formed by loop extrusion mediated by cohesin and CTCF. However, it is unclear whether complex chromatin structures exist at sub-kilobase-scale and to what extent fine-scale regulatory interactions depend on loop extrusion. To address these questions, we present an MNase-based chromosome conformation capture (3C) approach, which has enabled us to generate the most detailed local interaction data to date (20 bp resolution) and precisely investigate the effects of cohesin and CTCF depletion on chromatin architecture. Our data reveal that cis-regulatory elements have distinct internal nano-scale structures, within which local insulation is dependent on CTCF, but which are independent of cohesin. In contrast, we find that depletion of cohesin causes a subtle reduction in longer-range enhancer-promoter interactions and that CTCF depletion can cause rewiring of regulatory contacts. Together, our data show that loop extrusion is not essential for enhancer-promoter interactions, but contributes to their robustness and specificity and to precise regulation of gene expression.
    DOI:  https://doi.org/10.1038/s41467-022-29696-5
  4. Nat Commun. 2022 Apr 19. 13(1): 2089
    Regulated interaction of ID2 with the anaphase-promoting complex links progression through mitosis with reactivation of cell-type-specific transcription.
    Sang Bae Lee, Luciano Garofano, Aram Ko, Fulvio D'Angelo, Brulinda Frangaj, Danika Sommer, Qiwen Gan, KyeongJin Kim, Timothy Cardozo, Antonio Iavarone, Anna Lasorella.
      Tissue-specific transcriptional activity is silenced in mitotic cells but it remains unclear whether the mitotic regulatory machinery interacts with tissue-specific transcriptional programs. We show that such cross-talk involves the controlled interaction between core subunits of the anaphase-promoting complex (APC) and the ID2 substrate. The N-terminus of ID2 is independently and structurally compatible with a pocket composed of core APC/C subunits that may optimally orient ID2 onto the APCCDH1 complex. Phosphorylation of serine-5 by CDK1 prevented the association of ID2 with core APC, impaired ubiquitylation and stabilized ID2 protein at the mitosis-G1 transition leading to inhibition of basic Helix-Loop-Helix (bHLH)-mediated transcription. The serine-5 phospho-mimetic mutant of ID2 that inefficiently bound core APC remained stable during mitosis, delayed exit from mitosis and reloading of bHLH transcription factors on chromatin. It also locked cells into a "mitotic stem cell" transcriptional state resembling the pluripotent program of embryonic stem cells. The substrates of APCCDH1 SKP2 and Cyclin B1 share with ID2 the phosphorylation-dependent, D-box-independent interaction with core APC. These results reveal a new layer of control of the mechanism by which substrates are recognized by APC.
    DOI:  https://doi.org/10.1038/s41467-022-29502-2
  5. Nature. 2022 Apr 20.
    Somatic genomic changes in single Alzheimer's disease neurons.
    Michael B Miller, August Yue Huang, Junho Kim, Zinan Zhou, Samantha L Kirkham, Eduardo A Maury, Jennifer S Ziegenfuss, Hannah C Reed, Jennifer E Neil, Lariza Rento, Steven C Ryu, Chanthia C Ma, Lovelace J Luquette, Heather M Ames, Derek H Oakley, Matthew P Frosch, Bradley T Hyman, Michael A Lodato, Eunjung Alice Lee, Christopher A Walsh.
      Dementia in Alzheimer's disease progresses alongside neurodegeneration1-4, but the specific events that cause neuronal dysfunction and death remain poorly understood. During normal ageing, neurons progressively accumulate somatic mutations5 at rates similar to those of dividing cells6,7 which suggests that genetic factors, environmental exposures or disease states might influence this accumulation5. Here we analysed single-cell whole-genome sequencing data from 319 neurons from the prefrontal cortex and hippocampus of individuals with Alzheimer's disease and neurotypical control individuals. We found that somatic DNA alterations increase in individuals with Alzheimer's disease, with distinct molecular patterns. Normal neurons accumulate mutations primarily in an age-related pattern (signature A), which closely resembles 'clock-like' mutational signatures that have been previously described in healthy and cancerous cells6-10. In neurons affected by Alzheimer's disease, additional DNA alterations are driven by distinct processes (signature C) that highlight C>A and other specific nucleotide changes. These changes potentially implicate nucleotide oxidation4,11, which we show is increased in Alzheimer's-disease-affected neurons in situ. Expressed genes exhibit signature-specific damage, and mutations show a transcriptional strand bias, which suggests that transcription-coupled nucleotide excision repair has a role in the generation of mutations. The alterations in Alzheimer's disease affect coding exons and are predicted to create dysfunctional genetic knockout cells and proteostatic stress. Our results suggest that known pathogenic mechanisms in Alzheimer's disease may lead to genomic damage to neurons that can progressively impair function. The aberrant accumulation of DNA alterations in neurodegeneration provides insight into the cascade of molecular and cellular events that occurs in the development of Alzheimer's disease.
    DOI:  https://doi.org/10.1038/s41586-022-04640-1
  6. Nat Commun. 2022 Apr 19. 13(1): 2118
    An evolutionarily conserved stop codon enrichment at the 5' ends of mammalian piRNAs.
    Susanne Bornelöv, Benjamin Czech, Gregory J Hannon.
      PIWI-interacting RNAs (piRNAs) are small RNAs required to recognize and silence transposable elements. The 5' ends of mature piRNAs are defined through cleavage of long precursor transcripts, primarily by Zucchini (Zuc). Zuc-dependent cleavage typically occurs immediately upstream of a uridine. However, Zuc lacks sequence preference in vitro, pointing towards additional unknown specificity factors. Here, we examine murine piRNAs and reveal a strong and specific enrichment of three sequences (UAA, UAG, UGA)-corresponding to stop codons-at piRNA 5' ends. Stop codon sequences are also enriched immediately after piRNA processing intermediates, reflecting their Zuc-dependent tail-to-head arrangement. Further analyses reveal that a Zuc in vivo cleavage preference at four sequences (UAA, UAG, UGA, UAC) promotes 5' end stop codons. This observation is conserved across mammals and possibly further. Our work provides new insights into Zuc-dependent cleavage and may point to a previously unrecognized connection between piRNA biogenesis and the translational machinery.
    DOI:  https://doi.org/10.1038/s41467-022-29787-3
  7. Nat Commun. 2022 Apr 20. 13(1): 2155
    RNA polymerase II pausing factor NELF in CD8+ T cells promotes antitumor immunity.
    Bogang Wu, Xiaowen Zhang, Huai-Chin Chiang, Haihui Pan, Bin Yuan, Payal Mitra, Leilei Qi, Hayk Simonyan, Colin N Young, Eric Yvon, Yanfen Hu, Nu Zhang, Rong Li.
      T cell factor 1 (TCF1) is required for memory and stem-like CD8+ T cell functions. How TCF1 partners with other transcription factors to regulate transcription remains unclear. Here we show that negative elongation factor (NELF), an RNA polymerase II (Pol II) pausing factor, cooperates with TCF1 in T cell responses to cancer. Deletion of mouse Nelfb, which encodes the NELFB subunit, in mature T lymphocytes impairs immune responses to both primary tumor challenge and tumor antigen-mediated vaccination. Nelfb deletion causes more exhausted and reduced memory T cell populations, whereas its ectopic expression boosts antitumor immunity and efficacy of chimeric antigen receptor T-cell immunotherapy. Mechanistically, NELF is associated with TCF1 and recruited preferentially to the enhancers and promoters of TCF1 target genes. Nelfb ablation reduces Pol II pausing and chromatin accessibility at these TCF1-associated loci. Our findings thus suggest an important and rate-limiting function of NELF in anti-tumor immunity.
    DOI:  https://doi.org/10.1038/s41467-022-29869-2
  8. Nat Commun. 2022 Apr 19. 13(1): 2111
    AKT mutant allele-specific activation dictates pharmacologic sensitivities.
    Tripti Shrestha Bhattarai, Tambudzai Shamu, Alexander N Gorelick, Matthew T Chang, Debyani Chakravarty, Elena I Gavrila, Mark T A Donoghue, JianJong Gao, Swati Patel, Sizhi Paul Gao, Margaret H Reynolds, Sarah M Phillips, Tara Soumerai, Wassim Abida, David M Hyman, Alison M Schram, David B Solit, Lillian M Smyth, Barry S Taylor.
      AKT- a key molecular regulator of PI-3K signaling pathway, is somatically mutated in diverse solid cancer types, and aberrant AKT activation promotes altered cancer cell growth, survival, and metabolism1-8. The most common of AKT mutations (AKT1 E17K) sensitizes affected solid tumors to AKT inhibitor therapy7,8. However, the pathway dependence and inhibitor sensitivity of the long tail of potentially activating mutations in AKT is poorly understood, limiting our ability to act clinically in prospectively characterized cancer patients. Here we show, through population-scale driver mutation discovery combined with functional, biological, and therapeutic studies that some but not all missense mutations activate downstream AKT effector pathways in a growth factor-independent manner and sensitize tumor cells to diverse AKT inhibitors. A distinct class of small in-frame duplications paralogous across AKT isoforms induce structural changes different than those of activating missense mutations, leading to a greater degree of membrane affinity, AKT activation, and cell proliferation as well as pathway dependence and hyper-sensitivity to ATP-competitive, but not allosteric AKT inhibitors. Assessing these mutations clinically, we conducted a phase II clinical trial testing the AKT inhibitor capivasertib (AZD5363) in patients with solid tumors harboring AKT alterations (NCT03310541). Twelve patients were enrolled, out of which six harbored AKT1-3 non-E17K mutations. The median progression free survival (PFS) of capivasertib therapy was 84 days (95% CI 50-not reached) with an objective response rate of 25% (n = 3 of 12) and clinical benefit rate of 42% (n = 5 of 12). Collectively, our data indicate that the degree and mechanism of activation of oncogenic AKT mutants vary, thereby dictating allele-specific pharmacological sensitivities to AKT inhibition.
    DOI:  https://doi.org/10.1038/s41467-022-29638-1
  9. Nat Commun. 2022 Apr 19. 13(1): 2027
    Intestinal fibroblastic reticular cell niches control innate lymphoid cell homeostasis and function.
    Hung-Wei Cheng, Urs Mörbe, Mechthild Lütge, Céline Engetschwiler, Lucas Onder, Mario Novkovic, Cristina Gil-Cruz, Christian Perez-Shibayama, Thomas Hehlgans, Elke Scandella, Burkhard Ludewig.
      Innate lymphoid cells (ILCs) govern immune cell homeostasis in the intestine and protect the host against microbial pathogens. Various cell-intrinsic pathways have been identified that determine ILC development and differentiation. However, the cellular components that regulate ILC sustenance and function in the intestinal lamina propria are less known. Using single-cell transcriptomic analysis of lamina propria fibroblasts, we identify fibroblastic reticular cells (FRCs) that underpin cryptopatches (CPs) and isolated lymphoid follicles (ILFs). Genetic ablation of lymphotoxin-β receptor expression in Ccl19-expressing FRCs blocks the maturation of CPs into mature ILFs. Interactome analysis shows the major niche factors and processes underlying FRC-ILC crosstalk. In vivo validation confirms that a sustained lymphotoxin-driven feedforward loop of FRC activation including IL-7 generation is critical for the maintenance of functional ILC populations. In sum, our study indicates critical fibroblastic niches within the intestinal lamina propria that control ILC homeostasis and functionality and thereby secure protective gut immunity.
    DOI:  https://doi.org/10.1038/s41467-022-29734-2
  10. Nature. 2022 Apr;604(7906): 437-446
    The Human Pangenome Project: a global resource to map genomic diversity.
    Human Pangenome Reference Consortium
      The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.
    DOI:  https://doi.org/10.1038/s41586-022-04601-8
  11. Science. 2022 Apr 22. 376(6591): 377-382
    ESCRT-mediated membrane repair protects tumor-derived cells against T cell attack.
    Alex T Ritter, Gleb Shtengel, C Shan Xu, Aubrey Weigel, David P Hoffman, Melanie Freeman, Nirmala Iyer, Nensi Alivodej, David Ackerman, Ilia Voskoboinik, Joseph Trapani, Harald F Hess, Ira Mellman.
      Cytotoxic T lymphocytes (CTLs) and natural killer cells kill virus-infected and tumor cells through the polarized release of perforin and granzymes. Perforin is a pore-forming toxin that creates a lesion in the plasma membrane of the target cell through which granzymes enter the cytosol and initiate apoptosis. Endosomal sorting complexes required for transport (ESCRT) proteins are involved in the repair of small membrane wounds. We found that ESCRT proteins were precisely recruited in target cells to sites of CTL engagement immediately after perforin release. Inhibition of ESCRT machinery in cancer-derived cells enhanced their susceptibility to CTL-mediated killing. Thus, repair of perforin pores by ESCRT machinery limits granzyme entry into the cytosol, potentially enabling target cells to resist cytolytic attack.
    DOI:  https://doi.org/10.1126/science.abl3855
  12. Nat Commun. 2022 Apr 19. 13(1): 2020
    Generation of human islet cell type-specific identity genesets.
    Léon van Gurp, Leon Fodoulian, Daniel Oropeza, Kenichiro Furuyama, Eva Bru-Tari, Anh Nguyet Vu, John S Kaddis, Iván Rodríguez, Fabrizio Thorel, Pedro L Herrera.
      Generation of surrogate cells with stable functional identities is crucial for developing cell-based therapies. Efforts to produce insulin-secreting replacement cells to treat diabetes require reliable tools to assess islet cellular identity. Here, we conduct a thorough single-cell transcriptomics meta-analysis to identify robustly expressed markers used to build genesets describing the identity of human α-, β-, γ- and δ-cells. These genesets define islet cellular identities better than previously published genesets. We show their efficacy to outline cell identity changes and unravel some of their underlying genetic mechanisms, whether during embryonic pancreas development or in experimental setups aiming at developing glucose-responsive insulin-secreting cells, such as pluripotent stem-cell differentiation or in adult islet cell reprogramming protocols. These islet cell type-specific genesets represent valuable tools that accurately benchmark gain and loss in islet cell identity traits.
    DOI:  https://doi.org/10.1038/s41467-022-29588-8
  13. Nat Commun. 2022 Apr 19. 13(1): 2077
    Low complexity RGG-motif sequence is required for Processing body (P-body) disassembly.
    Raju Roy, Gitartha Das, Ishwarya Achappa Kuttanda, Nupur Bhatter, Purusharth I Rajyaguru.
      P-bodies are conserved mRNP complexes that are implicated in determining mRNA fate by affecting translation and mRNA decay. In this report, we identify RGG-motif containing translation repressor protein Sbp1 as a disassembly factor of P-bodies since disassembly of P-bodies is defective in Δsbp1. RGG-motif is necessary and sufficient to rescue the PB disassembly defect in Δsbp1. Binding studies using purified proteins revealed that Sbp1 physically interacts with Edc3 and Sbp1-Edc3 interaction competes with Edc3-Edc3 interaction. Purified Edc3 forms assemblies, promoted by the presence of RNA and NADH and the addition of purified Sbp1, but not the RGG-deletion mutant, leads to significantly decreased Edc3 assemblies. We further note that the aggregates of human EWSR1 protein, implicated in neurodegeneration, are more persistent in the absence of Sbp1 and overexpression of EWSR1 in Δsbp1 leads to a growth defect. Taken together, our observations suggest a role of Sbp1 in disassembly, which could apply to disease-relevant heterologous protein-aggregates.
    DOI:  https://doi.org/10.1038/s41467-022-29715-5
  14. Nat Commun. 2022 Apr 19. 13(1): 2138
    Secondary structure RNA elements control the cleavage activity of DICER.
    Trung Duc Nguyen, Tam Anh Trinh, Sheng Bao, Tuan Anh Nguyen.
      The accurate and efficient cleavage of shRNAs and pre-miRNAs by DICER is crucial for their gene-silencing activity. Here, we conduct high-throughput DICER cleavage assays for more than ~20,000 different shRNAs and show the comprehensive cleavage activities of DICER on these sequences. We discover a single-nucleotide bulge (22-bulge), which facilitates the cleavage activity of DICER on shRNAs and human pre-miRNAs. As a result, this 22-bulge enhances the gene-silencing activity of shRNAs and the accuracy of miRNA biogenesis. In addition, various single-nucleotide polymorphism-edited 22-bulges are found to govern the cleavage sites of DICER on pre-miRNAs and thereby control their functions. Finally, we identify the single cleavage of DICER and reveal its molecular mechanism. Our findings improve the understanding of the DICER cleavage mechanism, provide a foundation for the design of accurate and efficient shRNAs for gene-silencing, and indicate the function of bulges in regulating miRNA biogenesis.
    DOI:  https://doi.org/10.1038/s41467-022-29822-3
  15. Nat Commun. 2022 Apr 19. 13(1): 2037
    Honeybee gut Lactobacillus modulates host learning and memory behaviors via regulating tryptophan metabolism.
    Zijing Zhang, Xiaohuan Mu, Qina Cao, Yao Shi, Xiaosong Hu, Hao Zheng.
      Honeybees are highly social insects with a rich behavioral repertoire and are a versatile model for neurobiological research. Their gut microbiota comprises a limited number of host-restricted bacterial phylotypes that are important for honeybee health. However, it remains unclear how specific gut members affect honeybee behaviors. Here, we find that antibiotic exposure disturbs the gut community and influences honeybee phenotypes under field conditions. Using laboratory-generated gnotobiotic bees, we show that a normal gut microbiota is required for olfactory learning and memory abilities. Brain transcriptomic profiling reveals distinct brain gene expression patterns between microbiota-free and conventional bees. Subsequent metabolomic analyses of both hemolymph and gut samples show that the microbiota mainly regulates tryptophan metabolism. Our results indicate that host-specific Lactobacillus strains promote memory behavior by transforming tryptophan to indole derivatives that activate the host aryl hydrocarbon receptor. Our findings highlight the contributions of specific gut members to honeybee neurological processes, thus providing a promising model to understand host-microbe interactions.
    DOI:  https://doi.org/10.1038/s41467-022-29760-0
  16. Cell Rep. 2022 Apr 19. pii: S2211-1247(22)00455-7. [Epub ahead of print]39(3): 110697
    HNF4A modulates glucocorticoid action in the liver.
    A Louise Hunter, Toryn M Poolman, Donghwan Kim, Frank J Gonzalez, David A Bechtold, Andrew S I Loudon, Mudassar Iqbal, David W Ray.
      The glucocorticoid receptor (GR) is a nuclear receptor critical to the regulation of energy metabolism and inflammation. The actions of GR are dependent on cell type and context. Here, we demonstrate the role of liver lineage-determining factor hepatocyte nuclear factor 4A (HNF4A) in defining liver specificity of GR action. In mouse liver, the HNF4A motif lies adjacent to the glucocorticoid response element (GRE) at GR binding sites within regions of open chromatin. In the absence of HNF4A, the liver GR cistrome is remodeled, with loss and gain of GR recruitment evident. Loss of chromatin accessibility at HNF4A-marked sites associates with loss of GR binding at weak GRE motifs. GR binding and chromatin accessibility are gained at sites characterized by strong GRE motifs, which show GR recruitment in non-liver tissues. The functional importance of these HNF4A-regulated GR sites is indicated by an altered transcriptional response to glucocorticoid treatment in the Hnf4a-null liver.
    Keywords:  CP: Molecular biology; ChIP; HNF4A; chromatin; cistrome; glucocorticoid receptor; liver; mouse; nuclear receptor; tissue specificity
    DOI:  https://doi.org/10.1016/j.celrep.2022.110697
  17. Nat Commun. 2022 Apr 20. 13(1): 2061
    Stearoyl-CoA Desaturase inhibition reverses immune, synaptic and cognitive impairments in an Alzheimer's disease mouse model.
    Laura K Hamilton, Gaël Moquin-Beaudry, Chenicka L Mangahas, Federico Pratesi, Myriam Aubin, Anne Aumont, Sandra E Joppé, Alexandre Légiot, Annick Vachon, Mélanie Plourde, Catherine Mounier, Martine Tétreault, Karl J L Fernandes.
      The defining features of Alzheimer's disease (AD) include alterations in protein aggregation, immunity, lipid metabolism, synapses, and learning and memory. Of these, lipid abnormalities are the least understood. Here, we investigate the role of Stearoyl-CoA desaturase (SCD), a crucial regulator of fatty acid desaturation, in AD pathogenesis. We show that inhibiting brain SCD activity for 1-month in the 3xTg mouse model of AD alters core AD-related transcriptomic pathways in the hippocampus, and that it concomitantly restores essential components of hippocampal function, including dendritic spines and structure, immediate-early gene expression, and learning and memory itself. Moreover, SCD inhibition dampens activation of microglia, key mediators of spine loss during AD and the main immune cells of the brain. These data reveal that brain fatty acid metabolism links AD genes to downstream immune, synaptic, and functional impairments, identifying SCD as a potential target for AD treatment.
    DOI:  https://doi.org/10.1038/s41467-022-29506-y
  18. Nat Commun. 2022 Apr 19. 13(1): 2048
    Single cell analyses identify a highly regenerative and homogenous human CD34+ hematopoietic stem cell population.
    Fernando Anjos-Afonso, Florian Buettner, Syed A Mian, Hefin Rhys, Jimena Perez-Lloret, Manuel Garcia-Albornoz, Namrata Rastogi, Linda Ariza-McNaughton, Dominique Bonnet.
      The heterogeneous nature of human CD34+ hematopoietic stem cells (HSCs) has hampered our understanding of the cellular and molecular trajectories that HSCs navigate during lineage commitment. Using various platforms including single cell RNA-sequencing and extensive xenotransplantation, we have uncovered an uncharacterized human CD34+ HSC population. These CD34+EPCR+(CD38/CD45RA)- (simply as EPCR+) HSCs have a high repopulating and self-renewal abilities, reaching a stem cell frequency of ~1 in 3 cells, the highest described to date. Their unique transcriptomic wiring in which many gene modules associated with differentiated cell lineages confers their multilineage lineage output both in vivo and in vitro. At the single cell level, EPCR+ HSCs are the most transcriptomically and functionally homogenous human HSC population defined to date and can also be easily identified in post-natal tissues. Therefore, this EPCR+ population not only offers a high human HSC resolution but also a well-structured human hematopoietic hierarchical organization at the most primitive level.
    DOI:  https://doi.org/10.1038/s41467-022-29675-w
  19. Proc Natl Acad Sci U S A. 2022 Apr 26. 119(17): e2121028119
    Early age-related atrophy of cutaneous lymph nodes precipitates an early functional decline in skin immunity in mice with aging.
    Sandip Ashok Sonar, Jennifer L Uhrlaub, Christopher P Coplen, Gregory D Sempowski, Jarrod A Dudakov, Marcel R M van den Brink, Bonnie J LaFleur, Mladen Jergović, Janko Nikolich-Žugich.
      SignificanceOlder adults are more vulnerable to infection and less capable of vigorously responding to vaccination. The contribution of peripheral T cell maintenance defects to these processes is incompletely understood. Here, we provide evidence that lymph nodes (LNs), which are critical for naive T (TN) cell maintenance and initiation of new immune responses, age asynchronously. Skin-draining LNs undergo early (6 to 9 mo) and deeper LN and spleen late-life (18 mo) atrophy, characterized by reduced ability to maintain TN cells, structural and numerical loss of LN stromal cell microenvironments, and reduced immunity to cutaneous vaccination. These results highlight the critical role of age-related LN atrophy in functional immunity and immune homeostasis.
    Keywords:  T cells; aging; homeostasis; secondary lymphoid organs
    DOI:  https://doi.org/10.1073/pnas.2121028119
  20. Nat Commun. 2022 Apr 20. 13(1): 2159
    Lateral gain is impaired in macular degeneration and can be targeted to restore vision in mice.
    M Rizzi, K Powell, M R Robinson, T Matsuki, J Hoke, R N Maswood, A Georgiadis, M Georgiou, P R Jones, C Ripamonti, F M Nadal-Nicolás, M Michaelides, G S Rubin, A J Smith, R R Ali.
      Macular degeneration is a leading cause of blindness. Treatments to rescue vision are currently limited. Here, we study how loss of central vision affects lateral feedback to spared areas of the human retina. We identify a cone-driven gain control mechanism that reduces visual function beyond the atrophic area in macular degeneration. This finding provides an insight into the negative effects of geographic atrophy on vision. Therefore, we develop a strategy to restore this feedback mechanism, through activation of laterally projecting cells. This results in improved vision in Cnga3-/- mice, which lack cone function, as well as a mouse model of geographic atrophy. Our work shows that a loss of lateral gain control contributes to the vision deficit in macular degeneration. Furthermore, in mouse models we show that lateral feedback can be harnessed to improve vision following retinal degeneration.
    DOI:  https://doi.org/10.1038/s41467-022-29666-x
  21. Nat Commun. 2022 Apr 20. 13(1): 2152
    Tension can directly suppress Aurora B kinase-triggered release of kinetochore-microtubule attachments.
    Anna K de Regt, Cordell J Clark, Charles L Asbury, Sue Biggins.
      Chromosome segregation requires sister kinetochores to attach microtubules emanating from opposite spindle poles. Proper attachments come under tension and are stabilized, but defective attachments lacking tension are released, giving another chance for correct attachments to form. This error correction process depends on Aurora B kinase, which phosphorylates kinetochores to destabilize their microtubule attachments. However, the mechanism by which Aurora B distinguishes tense versus relaxed kinetochores remains unclear because it is difficult to detect kinase-triggered detachment and to manipulate kinetochore tension in vivo. To address these challenges, we apply an optical trapping-based assay using soluble Aurora B and reconstituted kinetochore-microtubule attachments. Strikingly, the tension on these attachments suppresses their Aurora B-triggered release, suggesting that tension-dependent changes in the conformation of kinetochores can regulate Aurora B activity or its outcome. Our work uncovers the basis for a key mechano-regulatory event that ensures accurate segregation and may inform studies of other mechanically regulated enzymes.
    DOI:  https://doi.org/10.1038/s41467-022-29542-8
  22. Nature. 2022 Apr 20.
    Programme of self-reactive innate-like T cell-mediated cancer immunity.
    Chun Chou, Xian Zhang, Chirag Krishna, Briana G Nixon, Saida Dadi, Kristelle J Capistrano, Emily R Kansler, Miranda Steele, Jian Han, Amy Shyu, Jing Zhang, Efstathios G Stamatiades, Ming Liu, Shun Li, Mytrang H Do, Chaucie Edwards, Davina S Kang, Chin-Tung Chen, Iris H Wei, Emmanouil P Pappou, Martin R Weiser, J Garcia-Aguilar, J Joshua Smith, Christina S Leslie, Ming O Li.
      Cellular transformation induces phenotypically diverse populations of tumour-infiltrating T cells1-5, and immune checkpoint blockade therapies preferentially target T cells that recognize cancer cell neoantigens6,7. Yet, how other classes of tumour-infiltrating T cells contribute to cancer immunosurveillance remains elusive. Here, in a survey of T cells in mouse and human malignancies, we identified a population of αβ T cell receptor (TCR)-positive FCER1G-expressing innate-like T cells with high cytotoxic potential8 (ILTCKs). These cells were broadly reactive to unmutated self-antigens, arose from distinct thymic progenitors following early encounter with cognate antigens, and were continuously replenished by thymic progenitors during tumour progression. Notably, expansion and effector differentiation of intratumoural ILTCKs depended on interleukin-15 (IL-15) expression in cancer cells, and inducible activation of IL-15 signalling in adoptively transferred ILTCK progenitors suppressed tumour growth. Thus, the antigen receptor self-reactivity, unique ontogeny, and distinct cancer cell-sensing mechanism distinguish ILTCKs from conventional cytotoxic T cells, and define a new class of tumour-elicited immune response.
    DOI:  https://doi.org/10.1038/s41586-022-04632-1
  23. Nat Commun. 2022 Apr 19. 13(1): 2042
    A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.
    Gerard Llimos, Vincent Gardeux, Ute Koch, Judith F Kribelbauer, Antonina Hafner, Daniel Alpern, Joern Pezoldt, Maria Litovchenko, Julie Russeil, Riccardo Dainese, Riccardo Moia, Abdurraouf Mokhtar Mahmoud, Davide Rossi, Gianluca Gaidano, Christoph Plass, Pavlo Lutsik, Clarissa Gerhauser, Sebastian M Waszak, Alistair Boettiger, Freddy Radtke, Bart Deplancke.
      Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of how regulatory variation might shape complex traits. To better understand the molecular mechanisms underlying VCM formation, here, we mechanistically dissect a VCM-modulating noncoding variant that is associated with reduced chronic lymphocytic leukemia (CLL) predisposition and disease progression. This common, germline variant constitutes a 5-bp indel that controls the activity of an AXIN2 gene-linked VCM by creating a MEF2 binding site, which, upon binding, activates a super-enhancer-like regulatory element. This triggers a large change in TF binding activity and chromatin state at an enhancer cluster spanning >150 kb, coinciding with subtle, long-range chromatin compaction and robust AXIN2 up-regulation. Our results support a model in which the indel acts as an AXIN2 VCM-activating TF nucleation event, which modulates CLL pathology.
    DOI:  https://doi.org/10.1038/s41467-022-29625-6
  24. Nat Commun. 2022 Apr 19. 13(1): 2080
    Endothelial progenitor cells stimulate neonatal lung angiogenesis through FOXF1-mediated activation of BMP9/ACVRL1 signaling.
    Guolun Wang, Bingqiang Wen, Zicheng Deng, Yufang Zhang, Olena A Kolesnichenko, Vladimir Ustiyan, Arun Pradhan, Tanya V Kalin, Vladimir V Kalinichenko.
      Pulmonary endothelial progenitor cells (EPCs) are critical for neonatal lung angiogenesis and represent a subset of general capillary cells (gCAPs). Molecular mechanisms through which EPCs stimulate lung angiogenesis are unknown. Herein, we used single-cell RNA sequencing to identify the BMP9/ACVRL1/SMAD1 pathway signature in pulmonary EPCs. BMP9 receptor, ACVRL1, and its downstream target genes were inhibited in EPCs from Foxf1WT/S52F mutant mice, a model of alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV). Expression of ACVRL1 and its targets were reduced in lungs of ACDMPV subjects. Inhibition of FOXF1 transcription factor reduced BMP9/ACVRL1 signaling and decreased angiogenesis in vitro. FOXF1 synergized with ETS transcription factor FLI1 to activate ACVRL1 promoter. Nanoparticle-mediated silencing of ACVRL1 in newborn mice decreased neonatal lung angiogenesis and alveolarization. Treatment with BMP9 restored lung angiogenesis and alveolarization in ACVRL1-deficient and Foxf1WT/S52F mice. Altogether, EPCs promote neonatal lung angiogenesis and alveolarization through FOXF1-mediated activation of BMP9/ACVRL1 signaling.
    DOI:  https://doi.org/10.1038/s41467-022-29746-y
  25. Nat Commun. 2022 Apr 19. 13(1): 2127
    Targeting TCTP sensitizes tumor to T cell-mediated therapy by reversing immune-refractory phenotypes.
    Hyo-Jung Lee, Kwon-Ho Song, Se Jin Oh, Suyeon Kim, Eunho Cho, Jungwon Kim, Yun Gyu Park, Kyung-Mi Lee, Cassian Yee, Seung-Hwa Song, Suhwan Chang, Jungmin Choi, Sang Taek Jung, Tae Woo Kim.
      Immunotherapy has emerged as a powerful approach to cancer treatment. However, immunotherapeutic resistance limits its clinical application. Therefore, identifying immune-resistant factors, which can be targeted by clinically available drugs and it also can be a companion diagnostic marker, is needed to develop combination strategies. Here, using the transcriptome data of patients, and immune-refractory tumor models, we identify TCTP as an immune-resistance factor that correlates with clinical outcome of anti-PD-L1 therapy and confers immune-refractory phenotypes, decreased T cell trafficking to the tumor and resistance to cytotoxic T lymphocyte-mediated tumor cell killing. Mechanistically, TCTP activates the EGFR-AKT-MCL-1/CXCL10 pathway by phosphorylation-dependent interaction with Na, K ATPase. Furthermore, treatment with dihydroartenimsinin, the most effective agent impending the TCTP-mediated-refractoriness, synergizes with T cell-mediated therapy to control immune-refractory tumors. Thus, our findings suggest a role of TCTP in promoting immune-refractoriness, thereby encouraging a rationale for combination therapies to enhance the efficacy of T cell-mediated therapy.
    DOI:  https://doi.org/10.1038/s41467-022-29611-y
  26. Nat Commun. 2022 Apr 22. 13(1): 2195
    Chromatin profiling in human neurons reveals aberrant roles for histone acetylation and BET family proteins in schizophrenia.
    Lorna A Farrelly, Shuangping Zheng, Nadine Schrode, Aaron Topol, Natarajan V Bhanu, Ryan M Bastle, Aarthi Ramakrishnan, Jennifer C Chan, Bulent Cetin, Erin Flaherty, Li Shen, Kelly Gleason, Carol A Tamminga, Benjamin A Garcia, Haitao Li, Kristen J Brennand, Ian Maze.
      Schizophrenia (SZ) is a psychiatric disorder with complex genetic risk dictated by interactions between hundreds of risk variants. Epigenetic factors, such as histone posttranslational modifications (PTMs), have been shown to play critical roles in many neurodevelopmental processes, and when perturbed may also contribute to the precipitation of disease. Here, we apply an unbiased proteomics approach to evaluate combinatorial histone PTMs in human induced pluripotent stem cell (hiPSC)-derived forebrain neurons from individuals with SZ. We observe hyperacetylation of H2A.Z and H4 in neurons derived from SZ cases, results that were confirmed in postmortem human brain. We demonstrate that the bromodomain and extraterminal (BET) protein, BRD4, is a bona fide 'reader' of H2A.Z acetylation, and further provide evidence that BET family protein inhibition ameliorates transcriptional abnormalities in patient-derived neurons. Thus, treatments aimed at alleviating BET protein interactions with hyperacetylated histones may aid in the prevention or treatment of SZ.
    DOI:  https://doi.org/10.1038/s41467-022-29922-0
  27. Mol Cell. 2022 Apr 15. pii: S1097-2765(22)00291-X. [Epub ahead of print]
    Allosteric interactions prime androgen receptor dimerization and activation.
    Elizabeth V Wasmuth, Arnaud Vanden Broeck, Justin R LaClair, Elizabeth A Hoover, Kayla E Lawrence, Navid Paknejad, Kyrie Pappas, Doreen Matthies, Biran Wang, Weiran Feng, Philip A Watson, John C Zinder, Wouter R Karthaus, M Jason de la Cruz, Richard K Hite, Katia Manova-Todorova, Zhiheng Yu, Susan T Weintraub, Sebastian Klinge, Charles L Sawyers.
      The androgen receptor (AR) is a nuclear receptor that governs gene expression programs required for prostate development and male phenotype maintenance. Advanced prostate cancers display AR hyperactivation and transcriptome expansion, in part, through AR amplification and interaction with oncoprotein cofactors. Despite its biological importance, how AR domains and cofactors cooperate to bind DNA has remained elusive. Using single-particle cryo-electron microscopy, we isolated three conformations of AR bound to DNA, showing that AR forms a non-obligate dimer, with the buried dimer interface utilized by ancestral steroid receptors repurposed to facilitate cooperative DNA binding. We identify novel allosteric surfaces which are compromised in androgen insensitivity syndrome and reinforced by AR's oncoprotein cofactor, ERG, and by DNA-binding motifs. Finally, we present evidence that this plastic dimer interface may have been adopted for transactivation at the expense of DNA binding. Our work highlights how fine-tuning AR's cooperative interactions translate to consequences in development and disease.
    Keywords:  allostery; cooperativity; nuclear receptor; prostate cancer; transcription factors
    DOI:  https://doi.org/10.1016/j.molcel.2022.03.035
  28. Nat Commun. 2022 Apr 19. 13(1): 2045
    Structural insights into the peptide selectivity and activation of human neuromedin U receptors.
    Chongzhao You, Yumu Zhang, Peiyu Xu, Sijie Huang, Wanchao Yin, H Eric Xu, Yi Jiang.
      Neuromedin U receptors (NMURs), including NMUR1 and NMUR2, are a group of Gq/11-coupled G protein-coupled receptors (GPCRs). NMUR1 and NMUR2 play distinct, pleiotropic physiological functions in peripheral tissues and in the central nervous system (CNS), respectively, according to their distinct tissue distributions. These receptors are stimulated by two endogenous neuropeptides, neuromedin U and S (NMU and NMS) with similar binding affinities. NMURs have gathered attention as potential drug targets for obesity and inflammatory disorders. Specifically, selective agonists for NMUR2 in peripheral tissue show promising long-term anti-obesity effects with fewer CNS-related side effects. However, the mechanisms of peptide binding specificity and receptor activation remain elusive. Here, we report four cryo-electron microscopy structures of Gq chimera-coupled NMUR1 and NMUR2 in complexes with NMU and NMS. These structures reveal the conserved overall peptide-binding mode and the mechanism of peptide selectivity for specific NMURs, as well as the common activation mechanism of the NMUR subfamily. Together, these findings provide insights into the molecular basis of the peptide recognition and offer an opportunity for the design of the selective drugs targeting NMURs.
    DOI:  https://doi.org/10.1038/s41467-022-29683-w
  29. Nat Commun. 2022 Apr 19. 13(1): 2054
    Connecting high-resolution 3D chromatin organization with epigenomics.
    Fan Feng, Yuan Yao, Xue Qing David Wang, Xiaotian Zhang, Jie Liu.
      The resolution of chromatin conformation capture technologies keeps increasing, and the recent nucleosome resolution chromatin contact maps allow us to explore how fine-scale 3D chromatin organization is related to epigenomic states in human cells. Using publicly available Micro-C datasets, we develop a deep learning model, CAESAR, to learn a mapping function from epigenomic features to 3D chromatin organization. The model accurately predicts fine-scale structures, such as short-range chromatin loops and stripes, that Hi-C fails to detect. With existing epigenomic datasets from ENCODE and Roadmap Epigenomics Project, we successfully impute high-resolution 3D chromatin contact maps for 91 human tissues and cell lines. In the imputed high-resolution contact maps, we identify the spatial interactions between genes and their experimentally validated regulatory elements, demonstrating CAESAR's potential in coupling transcriptional regulation with 3D chromatin organization at high resolution.
    DOI:  https://doi.org/10.1038/s41467-022-29695-6
  30. Nat Cell Biol. 2022 Apr 21.
    The PPR domain of mitochondrial RNA polymerase is an exoribonuclease required for mtDNA replication in Drosophila melanogaster.
    Yi Liu, Zhe Chen, Zong-Heng Wang, Katherine M Delaney, Juanjie Tang, Mehdi Pirooznia, Duck-Yeon Lee, Ilker Tunc, Yuesheng Li, Hong Xu.
      Mitochondrial DNA (mtDNA) replication and transcription are of paramount importance to cellular energy metabolism. Mitochondrial RNA polymerase is thought to be the primase for mtDNA replication. However, it is unclear how this enzyme, which normally transcribes long polycistronic RNAs, can produce short RNA oligonucleotides to initiate mtDNA replication. We show that the PPR domain of Drosophila mitochondrial RNA polymerase (PolrMT) has 3'-to-5' exoribonuclease activity, which is indispensable for PolrMT to synthesize short RNA oligonucleotides and prime DNA replication in vitro. An exoribonuclease-deficient mutant, PolrMTE423P, partially restores mitochondrial transcription but fails to support mtDNA replication when expressed in PolrMT-mutant flies, indicating that the exoribonuclease activity is necessary for mtDNA replication. In addition, overexpression of PolrMTE423P in adult flies leads to severe neuromuscular defects and a marked increase in mtDNA transcript errors, suggesting that exoribonuclease activity may contribute to the proofreading of mtDNA transcription.
    DOI:  https://doi.org/10.1038/s41556-022-00887-y
  31. Nat Cancer. 2022 Apr 21.
    Therapeutic targeting of the mevalonate-geranylgeranyl diphosphate pathway with statins overcomes chemotherapy resistance in small cell lung cancer.
    Chenchen Guo, Ruijie Wan, Yayi He, Shu-Hai Lin, Jiayu Cao, Ying Qiu, Tengfei Zhang, Qiqi Zhao, Yujia Niu, Yujuan Jin, Hsin-Yi Huang, Xue Wang, Li Tan, Roman K Thomas, Hua Zhang, Luonan Chen, Kwok-Kin Wong, Liang Hu, Hongbin Ji.
      Small cell lung cancer (SCLC) lacks effective treatments to overcome chemoresistance. Here we established multiple human chemoresistant xenograft models through long-term intermittent chemotherapy, mimicking clinically relevant therapeutic settings. We show that chemoresistant SCLC undergoes metabolic reprogramming relying on the mevalonate (MVA)-geranylgeranyl diphosphate (GGPP) pathway, which can be targeted using clinically approved statins. Mechanistically, statins induce oxidative stress accumulation and apoptosis through the GGPP synthase 1 (GGPS1)-RAB7A-autophagy axis. Statin treatment overcomes both intrinsic and acquired SCLC chemoresistance in vivo across different SCLC PDX models bearing high GGPS1 levels. Moreover, we show that GGPS1 expression is negatively associated with survival in patients with SCLC. Finally, we demonstrate that combined statin and chemotherapy treatment resulted in durable responses in three patients with SCLC who relapsed from first-line chemotherapy. Collectively, these data uncover the MVA-GGPP pathway as a metabolic vulnerability in SCLC and identify statins as a potentially effective treatment to overcome chemoresistance.
    DOI:  https://doi.org/10.1038/s43018-022-00358-1
  32. Cell. 2022 Apr 15. pii: S0092-8674(22)00343-9. [Epub ahead of print]
    Quiescent cancer cells resist T cell attack by forming an immunosuppressive niche.
    Pilar Baldominos, Alex Barbera-Mourelle, Olga Barreiro, Yu Huang, Andrew Wight, Jae-Won Cho, Xi Zhao, Guillem Estivill, Isam Adam, Xavier Sanchez, Shannon McCarthy, Julien Schaller, Zara Khan, Albert Ruzo, Ricardo Pastorello, Edward T Richardson, Deborah Dillon, Paula Montero-Llopis, Romualdo Barroso-Sousa, Juliet Forman, Sachet A Shukla, Sara M Tolaney, Elizabeth A Mittendorf, Ulrich H von Andrian, Kai W Wucherpfennig, Martin Hemberg, Judith Agudo.
      Immunotherapy is a promising treatment for triple-negative breast cancer (TNBC), but patients relapse, highlighting the need to understand the mechanisms of resistance. We discovered that in primary breast cancer, tumor cells that resist T cell attack are quiescent. Quiescent cancer cells (QCCs) form clusters with reduced immune infiltration. They also display superior tumorigenic capacity and higher expression of chemotherapy resistance and stemness genes. We adapted single-cell RNA-sequencing with precise spatial resolution to profile infiltrating cells inside and outside the QCC niche. This transcriptomic analysis revealed hypoxia-induced programs and identified more exhausted T cells, tumor-protective fibroblasts, and dysfunctional dendritic cells inside clusters of QCCs. This uncovered differential phenotypes in infiltrating cells based on their intra-tumor location. Thus, QCCs constitute immunotherapy-resistant reservoirs by orchestrating a local hypoxic immune-suppressive milieu that blocks T cell function. Eliminating QCCs holds the promise to counteract immunotherapy resistance and prevent disease recurrence in TNBC.
    Keywords:  T cells; TME; breast cancer; cancer-associated fibroblasts; dendritic cells; immunotherapy; resistance to therapy; single-cell RNA-sequencing; tumor dormancy; tumor immunology; tumor microenvironment
    DOI:  https://doi.org/10.1016/j.cell.2022.03.033
  33. Nat Commun. 2022 Apr 21. 13(1): 2086
    Niche expansion and adaptive divergence in the global radiation of crows and ravens.
    Joan Garcia-Porta, Daniel Sol, Matt Pennell, Ferran Sayol, Antigoni Kaliontzopoulou, Carlos A Botero.
      The processes that allow some lineages to diversify rapidly at a global scale remain poorly understood. Although earlier studies emphasized the importance of dispersal, global expansions expose populations to novel environments and may also require adaptation and diversification across new niches. In this study, we investigated the contributions of these processes to the global radiation of crows and ravens (genus Corvus). Combining a new phylogeny with comprehensive phenotypic and climatic data, we show that Corvus experienced a massive expansion of the climatic niche that was coupled with a substantial increase in the rates of species and phenotypic diversification. The initiation of these processes coincided with the evolution of traits that promoted dispersal and niche expansion. Our findings suggest that rapid global radiations may be better understood as processes in which high dispersal abilities synergise with traits that, like cognition, facilitate persistence in new environments.
    DOI:  https://doi.org/10.1038/s41467-022-29707-5
  34. Circ Res. 2022 Apr 18. 101161CIRCRESAHA121320090
    Human Coronary Plaque T Cells Are Clonal and Cross-React to Virus and Self.
    Roshni Roy Chowdhury, Jessica D'Addabbo, Xianxi Huang, Stefan Veizades, Koki Sasagawa, David M Louis, Paul Cheng, Jan Sokol, Annie Jensen, Alexandria Tso, Vishnu Shankar, Ben Shogo Wendel, Isaac Bakerman, Grace Liang, Tiffany Koyano, Robyn Fong, Allison Nau, Herra Ahmad, J K Gopakumar, Robert Wirka, Andrew Lee, Jack Boyd, Y Joseph Woo, Thomas Quertermous, Gunsagar Gulati, Siddhartha Jaiswal, Yueh-Hsiu Chien, Charles Chan, Mark M Davis, Patricia K Nguyen.
      BACKGROUND: Once considered primarily a disorder of lipid deposition, coronary artery disease is an incurable, life-threatening disease that is now also characterized by chronic inflammation notable for the buildup of atherosclerotic plaques containing immune cells in various states of activation and differentiation. Understanding how these immune cells contribute to disease progression may lead to the development of novel therapeutic strategies.METHODS: We used single-cell technology and in vitro assays to interrogate the immune microenvironment of human coronary atherosclerotic plaque at different stages of maturity.
    RESULTS: In addition to macrophages, we found a high proportion of αβ T cells in the coronary plaques. Most of these T cells lack high expression of CCR7 and L-selectin, indicating that they are primarily antigen-experienced, memory cells. Notably, nearly one-third of these cells express the HLA-DRA surface marker, signifying activation through their TCRs (T-cell receptors). Consistent with this, TCR repertoire analysis confirmed the presence of activated αβ T cells (CD4<CD8), exhibiting clonal expansion of specific TCRs. Interestingly, we found that these plaque T cells had TCRs specific for influenza, coronavirus, and other viral epitopes, which share sequence homologies to proteins found on smooth muscle cells and endothelial cells, suggesting potential autoimmune-mediated T-cell activation in the absence of active infection. To better understand the potential function of these activated plaque T cells, we then interrogated their transcriptome at the single-cell level. Of the 3 T-cell phenotypic clusters with the highest expression of the activation marker HLA-DRA identified by the Seurat algorithm, 2 clusters express a proinflammatory and cytolytic signature characteristic of CD8 cells, while the other expresses AREG (amphiregulin), which promotes smooth muscle cell proliferation and fibrosis, and, thus, contributes to plaque progression.
    CONCLUSIONS: Taken together, these findings demonstrate that plaque T cells are clonally expanded potentially by antigen engagement, are potentially reactive to self-epitopes, and may interact with smooth muscle cells and macrophages in the plaque microenvironment.
    Keywords:  HLA-DR alpha-chains; amphiregulin; coronary artery disease; endothelial cells; humans
    DOI:  https://doi.org/10.1161/CIRCRESAHA.121.320090
  35. J Exp Med. 2022 May 02. pii: e20211530. [Epub ahead of print]219(5):
    High-efficiency nonviral CRISPR/Cas9-mediated gene editing of human T cells using plasmid donor DNA.
    Soyoung A Oh, Kate Senger, Shravan Madireddi, Ilseyar Akhmetzyanova, Isabel E Ishizuka, Somayeh Tarighat, Jerry H Lo, David Shaw, Benjamin Haley, Sascha Rutz.
      Genome engineering of T lymphocytes, the main effectors of antitumor adaptive immune responses, has the potential to uncover unique insights into their functions and enable the development of next-generation adoptive T cell therapies. Viral gene delivery into T cells, which is currently used to generate CAR T cells, has limitations in regard to targeting precision, cargo flexibility, and reagent production. Nonviral methods for effective CRISPR/Cas9-mediated gene knock-out in primary human T cells have been developed, but complementary techniques for nonviral gene knock-in can be cumbersome and inefficient. Here, we report a convenient and scalable nonviral method that allows precise gene edits and transgene integration in primary human T cells, using plasmid donor DNA template and Cas9-RNP. This method is highly efficient for single and multiplex gene manipulation, without compromising T cell function, and is thus valuable for use in basic and translational research.
    DOI:  https://doi.org/10.1084/jem.20211530
  36. Front Immunol. 2022 ;13 843242
    The Role of Metabolic Dysfunction in T-Cell Exhaustion During Chronic Viral Infection.
    Kehong Zheng, Xiaojun Zheng, Wei Yang.
      T cells are important components of adaptive immunity that protect the host against invading pathogens during infection. Upon recognizing the activation signals, naïve and/or memory T cells will initiate clonal expansion, trigger differentiation into effector populations and traffic to the inflamed sites to eliminate pathogens. However, in chronic viral infections, such as those caused by human immunodeficiency virus (HIV), hepatitis B and C (HBV and HCV), T cells exhibit impaired function and become difficult to clear pathogens in a state known as T-cell exhaustion. The activation and function persistence of T cells demand for dynamic changes in cellular metabolism to meet their bioenergetic and biosynthetic demands, especially the augmentation of aerobic glycolysis, which not only provide efficient energy generation, but also fuel multiple biochemical intermediates that are essential for nucleotide, amino acid, fatty acid synthesis and mitochondria function. Changes in cellular metabolism also affect the function of effectors T cells through modifying epigenetic signatures. It is widely accepted that the dysfunction of T cell metabolism contributes greatly to T-cell exhaustion. Here, we reviewed recent findings on T cells metabolism under chronic viral infection, seeking to reveal the role of metabolic dysfunction played in T-cell exhaustion.
    Keywords:  PD-1; T-cell exhaustion; chronic viral infection; glycolysis; metabolism
    DOI:  https://doi.org/10.3389/fimmu.2022.843242
  37. Nat Immunol. 2022 Apr 18.
    PD-L1-PD-1 interactions limit effector regulatory T cell populations at homeostasis and during infection.
    Joseph A Perry, Lindsey Shallberg, Joseph T Clark, Jodi A Gullicksrud, Jonathan H DeLong, Bonnie B Douglas, Andrew P Hart, Zachary Lanzar, Keenan O'Dea, Christoph Konradt, Jeongho Park, Juhi R Kuchroo, Daniel Grubaugh, Arielle Glatman Zaretsky, Igor E Brodsky, Rene de Waal Malefyt, David A Christian, Arlene H Sharpe, Christopher A Hunter.
      Phenotypic and transcriptional profiling of regulatory T (Treg) cells at homeostasis reveals that T cell receptor activation promotes Treg cells with an effector phenotype (eTreg) characterized by the production of interleukin-10 and expression of the inhibitory receptor PD-1. At homeostasis, blockade of the PD-1 pathway results in enhanced eTreg cell activity, whereas during infection with Toxoplasma gondii, early interferon-γ upregulates myeloid cell expression of PD-L1 associated with reduced Treg cell populations. In infected mice, blockade of PD-L1, complete deletion of PD-1 or lineage-specific deletion of PD-1 in Treg cells prevents loss of eTreg cells. These interventions resulted in a reduced ratio of pathogen-specific effector T cells: eTreg cells and increased levels of interleukin-10 that mitigated the development of immunopathology, but which could compromise parasite control. Thus, eTreg cell expression of PD-1 acts as a sensor to rapidly tune the pool of eTreg cells at homeostasis and during inflammatory processes.
    DOI:  https://doi.org/10.1038/s41590-022-01170-w
  38. Sci Transl Med. 2022 Apr 20. 14(641): eabl8146
    Steroid-induced fibroblast growth factors drive an epithelial-mesenchymal inflammatory axis in severe asthma.
    Riccardo Guidi, Daqi Xu, David F Choy, Thirumalai R Ramalingam, Wyne P Lee, Zora Modrusan, Yuxin Liang, Scot Marsters, Avi Ashkenazi, Alison Huynh, Jessica Mills, Sean Flanagan, Shannon Hambro, Victor Nunez, Laurie Leong, Ashley Cook, Tiffany Hao Tran, Cary D Austin, Yi Cao, Christine Clarke, Reynold A Panettieri, Cynthia Koziol-White, William F Jester, Fen Wang, Mark S Wilson.
      Asthma and inflammatory airway diseases restrict airflow in the lung, compromising gas exchange and lung function. Inhaled corticosteroids (ICSs) can reduce inflammation, control symptoms, and improve lung function; however, a growing number of patients with severe asthma do not benefit from ICS. Using bronchial airway epithelial brushings from patients with severe asthma or primary human cells, we delineated a corticosteroid-driven fibroblast growth factor (FGF)-dependent inflammatory axis, with FGF-responsive fibroblasts promoting downstream granulocyte colony-stimulating factor (G-CSF) production, hyaluronan secretion, and neutrophilic inflammation. Allergen challenge studies in mice demonstrate that the ICS, fluticasone propionate, inhibited type 2-driven eosinophilia but induced a concomitant increase in FGFs, G-CSF, hyaluronan, and neutrophil infiltration. We developed a model of steroid-induced neutrophilic inflammation mediated, in part, by induction of an FGF-dependent epithelial-mesenchymal axis, which may explain why some individuals do not benefit from ICS. In further proof-of-concept experiments, we found that combination therapy with pan-FGF receptor inhibitors and corticosteroids prevented both eosinophilic and steroid-induced neutrophilic inflammation. Together, these results establish FGFs as therapeutic targets for severe asthma patients who do not benefit from ICS.
    DOI:  https://doi.org/10.1126/scitranslmed.abl8146
  39. Nat Commun. 2022 Apr 19. 13(1): 2022
    Loss of vascular endothelial notch signaling promotes spontaneous formation of tertiary lymphoid structures.
    Susanne Fleig, Tamar Kapanadze, Jeremiah Bernier-Latmani, Julia K Lill, Tania Wyss, Jaba Gamrekelashvili, Dustin Kijas, Bin Liu, Anne M Hüsing, Esther Bovay, Adan Chari Jirmo, Stephan Halle, Melanie Ricke-Hoch, Ralf H Adams, Daniel R Engel, Sibylle von Vietinghoff, Reinhold Förster, Denise Hilfiker-Kleiner, Hermann Haller, Tatiana V Petrova, Florian P Limbourg.
      Tertiary lymphoid structures (TLS) are lymph node-like immune cell clusters that emerge during chronic inflammation in non-lymphoid organs like the kidney, but their origin remains not well understood. Here we show, using conditional deletion strategies of the canonical Notch signaling mediator Rbpj, that loss of endothelial Notch signaling in adult mice induces the spontaneous formation of bona fide TLS in the kidney, liver and lung, based on molecular, cellular and structural criteria. These TLS form in a stereotypical manner around parenchymal arteries, while secondary lymphoid structures remained largely unchanged. This effect is mediated by endothelium of blood vessels, but not lymphatics, since a lymphatic endothelial-specific targeting strategy did not result in TLS formation, and involves loss of arterial specification and concomitant acquisition of a high endothelial cell phenotype, as shown by transcriptional analysis of kidney endothelial cells. This indicates a so far unrecognized role for vascular endothelial cells and Notch signaling in TLS initiation.
    DOI:  https://doi.org/10.1038/s41467-022-29701-x
  40. Nat Commun. 2022 Apr 19. 13(1): 2063
    Chemotherapy-induced COX-2 upregulation by cancer cells defines their inflammatory properties and limits the efficacy of chemoimmunotherapy combinations.
    Charlotte R Bell, Victoria S Pelly, Agrin Moeini, Shih-Chieh Chiang, Eimear Flanagan, Christian P Bromley, Christopher Clark, Charles H Earnshaw, Maria A Koufaki, Eduardo Bonavita, Santiago Zelenay.
      Cytotoxic therapies, besides directly inducing cancer cell death, can stimulate immune-dependent tumor growth control or paradoxically accelerate tumor progression. The underlying mechanisms dictating these opposing outcomes are poorly defined. Here, we show that cytotoxic therapy acutely upregulates cyclooxygenase (COX)-2 expression and prostaglandin E2 (PGE2) production in cancer cells with pre-existing COX-2 activity. Screening a compound library of 1280 approved drugs, we find that all classes of chemotherapy drugs enhance COX-2 transcription whilst arresting cancer cell proliferation. Genetic manipulation of COX-2 expression or its gene promoter region uncover how augmented COX-2/PGE2 activity post-treatment profoundly alters the inflammatory properties of chemotherapy-treated cancer cells in vivo. Pharmacological COX-2 inhibition boosts the efficacy of the combination of chemotherapy and PD-1 blockade. Crucially, in a poorly immunogenic breast cancer model, only the triple therapy unleashes tumor growth control and significantly reduces relapse and spontaneous metastatic spread in an adjuvant setting. Our findings suggest COX-2/PGE2 upregulation by dying cancer cells acts as a major barrier to cytotoxic therapy-driven tumor immunity and uncover a strategy to improve the outcomes of immunotherapy and chemotherapy combinations.
    DOI:  https://doi.org/10.1038/s41467-022-29606-9
  41. Nat Commun. 2022 Apr 22. 13(1): 2201
    Supraphysiological activation of TAK1 promotes skeletal muscle growth and mitigates neurogenic atrophy.
    Anirban Roy, Ashok Kumar.
      Skeletal muscle mass is regulated through coordinated activation of multiple signaling pathways. TAK1 signalosome has been found to be activated in various conditions of muscle atrophy and hypertrophy. However, the role and mechanisms by which TAK1 regulates skeletal muscle mass remain less understood. Here, we demonstrate that supraphysiological activation of TAK1 in skeletal muscle of adult mice stimulates translational machinery, protein synthesis, and myofiber growth. TAK1 causes phosphorylation of elongation initiation factor 4E (eIF4E) independent of mTOR. Inactivation of TAK1 disrupts neuromuscular junction morphology and causes deregulation of Smad signaling. Using genetic approaches, we demonstrate that TAK1 prevents excessive loss of muscle mass during denervation. TAK1 favors the nuclear translocation of Smad4 and cytoplasmic retention of Smad6. TAK1 is also required for the phosphorylation of eIF4E in denervated skeletal muscle. Collectively, our results demonstrate that TAK1 supports skeletal muscle growth and prevents neurogenic muscle atrophy in adult mice.
    DOI:  https://doi.org/10.1038/s41467-022-29752-0
  42. J Cell Biol. 2022 Jun 06. pii: e202111068. [Epub ahead of print]221(6):
    Antigen-derived peptides engage the ER stress sensor IRE1α to curb dendritic cell cross-presentation.
    Ofer Guttman, Adrien Le Thomas, Scot Marsters, David A Lawrence, Lauren Gutgesell, Iratxe Zuazo-Gaztelu, Jonathan M Harnoss, Simone M Haag, Aditya Murthy, Geraldine Strasser, Zora Modrusan, Thomas Wu, Ira Mellman, Avi Ashkenazi.
      Dendritic cells (DCs) promote adaptive immunity by cross-presenting antigen-based epitopes to CD8+ T cells. DCs process internalized protein antigens into peptides that enter the endoplasmic reticulum (ER), bind to major histocompatibility type I (MHC-I) protein complexes, and are transported to the cell surface for cross-presentation. DCs can exhibit activation of the ER stress sensor IRE1α without ER stress, but the underlying mechanism remains obscure. Here, we show that antigen-derived hydrophobic peptides can directly engage ER-resident IRE1α, masquerading as unfolded proteins. IRE1α activation depletes MHC-I heavy-chain mRNAs through regulated IRE1α-dependent decay (RIDD), curtailing antigen cross-presentation. In tumor-bearing mice, IRE1α disruption increased MHC-I expression on tumor-infiltrating DCs and enhanced recruitment and activation of CD8+ T cells. Moreover, IRE1α inhibition synergized with anti-PD-L1 antibody treatment to cause tumor regression. Our findings identify an unexpected cell-biological mechanism of antigen-driven IRE1α activation in DCs, revealing translational potential for cancer immunotherapy.
    DOI:  https://doi.org/10.1083/jcb.202111068
  43. Proc Natl Acad Sci U S A. 2022 Apr 26. 119(17): e2121816119
    Nuclear lamin isoforms differentially contribute to LINC complex-dependent nucleocytoskeletal coupling and whole-cell mechanics.
    Amir Vahabikashi, Suganya Sivagurunathan, Fiona Ann Sadsad Nicdao, Yu Long Han, Chan Young Park, Mark Kittisopikul, Xianrong Wong, Joseph R Tran, Gregg G Gundersen, Karen L Reddy, G W Gant Luxton, Ming Guo, Jeffrey J Fredberg, Yixian Zheng, Stephen A Adam, Robert D Goldman.
      SignificanceInteractions between the cell nucleus and cytoskeleton regulate cell mechanics and are facilitated by the interplay between the nuclear lamina and linker of nucleoskeleton and cytoskeleton (LINC) complexes. To date, the specific contribution of the four lamin isoforms to nucleocytoskeletal connectivity and whole-cell mechanics remains unknown. We discover that A- and B-type lamins distinctively interact with LINC complexes that bind F-actin and vimentin filaments to differentially modulate cortical stiffness, cytoplasmic stiffness, and contractility of mouse embryonic fibroblasts (MEFs). We propose and experimentally verify an integrated lamin-LINC complex-cytoskeleton model that explains cellular mechanical phenotypes in lamin-deficient MEFs. Our findings uncover potential mechanisms for cellular defects in human laminopathies and many cancers associated with mutations or modifications in lamin isoforms.
    Keywords:  LINC complex; cell mechanics; cytoskeleton; mechanobiology; nuclear lamins
    DOI:  https://doi.org/10.1073/pnas.2121816119
  44. Nat Commun. 2022 Apr 19. 13(1): 2057
    Distinct resistance mechanisms arise to allosteric vs. ATP-competitive AKT inhibitors.
    Kristin M Zimmerman Savill, Brian B Lee, Jason Oeh, Jie Lin, Eva Lin, Wei-Jen Chung, Amy Young, Wennie Chen, Monika Miś, Kathryn Mesh, Jeffrey Eastham, Florian Gnad, Zhaoshi Jiang, Eric W Stawiski, Benjamin Haley, Anneleen Daemen, Xiaojing Wang, Hartmut Koeppen, Zora Modrusan, Scott E Martin, Deepak Sampath, Kui Lin.
      The AKT kinases have emerged as promising therapeutic targets in oncology and both allosteric and ATP-competitive AKT inhibitors have entered clinical investigation. However, long-term efficacy of such inhibitors will likely be challenged by the development of resistance. We have established prostate cancer models of acquired resistance to the allosteric inhibitor MK-2206 or the ATP-competitive inhibitor ipatasertib following prolonged exposure. While alterations in AKT are associated with acquired resistance to MK-2206, ipatasertib resistance is driven by rewired compensatory activity of parallel signaling pathways. Importantly, MK-2206 resistance can be overcome by treatment with ipatasertib, while ipatasertib resistance can be reversed by co-treatment with inhibitors of pathways including PIM signaling. These findings demonstrate that distinct resistance mechanisms arise to the two classes of AKT inhibitors and that combination approaches may reverse resistance to ATP-competitive inhibition.
    DOI:  https://doi.org/10.1038/s41467-022-29655-0
  45. Sci Immunol. 2022 Apr 22. 7(70): eabn1889
    Central memory T cells are the most effective precursors of resident memory T cells in human skin.
    Tiago R Matos, Ahmed Gehad, Jessica E Teague, Beatrice Dyring-Andersen, Theresa Benezeder, Mitra Dowlatshahi, Jack Crouch, Yoshinori Watanabe, John T O'Malley, Thomas S Kupper, Chao Yang, Rei Watanabe, Rachael A Clark.
      The circulating precursor cells that give rise to human resident memory T cells (TRM) are poorly characterized. We used an in vitro differentiation system and human skin-grafted mice to study TRM generation from circulating human memory T cell subsets. In vitro TRM differentiation was associated with functional changes, including enhanced IL-17A production and FOXP3 expression in CD4+ T cells and granzyme B production in CD8+ T cells, changes that mirrored the phenotype of T cells in healthy human skin. Effector memory T cells (TEM) had the highest conversion rate to TRM in vitro and in vivo, but central memory T cells (TCM) persisted longer in the circulation, entered the skin in larger numbers, and generated increased numbers of TRM. In summary, TCM are highly efficient precursors of human skin TRM, a feature that may underlie their known association with effective long-term immunity.
    DOI:  https://doi.org/10.1126/sciimmunol.abn1889
  46. Nature. 2022 Apr;604(7906): E16-E23
    Evaluating ribosomal frameshifting in CCR5 mRNA decoding.
    Yousuf A Khan, Gary Loughran, Anna-Lena Steckelberg, Katherine Brown, Stephen J Kiniry, Hazel Stewart, Pavel V Baranov, Jeffrey S Kieft, Andrew E Firth, John F Atkins.
      
    DOI:  https://doi.org/10.1038/s41586-022-04627-y
  47. Nat Commun. 2022 Apr 19. 13(1): 2051
    Pyridine nucleotide redox potential in coronary smooth muscle couples myocardial blood flow to cardiac metabolism.
    Marc M Dwenger, Sean M Raph, Michelle L Reyzer, M Lisa Manier, Daniel W Riggs, Zachary B Wohl, Vahagn Ohanyan, Gregory Mack, Thomas Pucci, Joseph B Moore, Bradford G Hill, William M Chilian, Richard M Caprioli, Aruni Bhatnagar, Matthew A Nystoriak.
      Adequate oxygen delivery to the heart during stress is essential for sustaining cardiac function. Acute increases in myocardial oxygen demand evoke coronary vasodilation and enhance perfusion via functional upregulation of smooth muscle voltage-gated K+ (Kv) channels. Because this response is controlled by Kv1 accessory subunits (i.e., Kvβ), which are NAD(P)(H)-dependent aldo-keto reductases, we tested the hypothesis that oxygen demand modifies arterial [NAD(H)]i, and that resultant cytosolic pyridine nucleotide redox state influences Kv1 activity. High-resolution imaging mass spectrometry and live-cell imaging reveal cardiac workload-dependent increases in NADH:NAD+ in intramyocardial arterial myocytes. Intracellular NAD(P)(H) redox ratios reflecting elevated oxygen demand potentiate native coronary Kv1 activity in a Kvβ2-dependent manner. Ablation of Kvβ2 catalysis suppresses redox-dependent increases in Kv1 activity, vasodilation, and the relationship between cardiac workload and myocardial blood flow. Collectively, this work suggests that the pyridine nucleotide sensitivity and enzymatic activity of Kvβ2 controls coronary vasoreactivity and myocardial blood flow during metabolic stress.
    DOI:  https://doi.org/10.1038/s41467-022-29745-z
  48. Nat Commun. 2022 Apr 22. 13(1): 2196
    ZNF117 regulates glioblastoma stem cell differentiation towards oligodendroglial lineage.
    Jun Liu, Xiaoying Wang, Ann T Chen, Xingchun Gao, Benjamin T Himes, Hongyi Zhang, Zeming Chen, Jianhui Wang, Wendy C Sheu, Gang Deng, Yang Xiao, Pan Zou, Shenqi Zhang, Fuyao Liu, Yong Zhu, Rong Fan, Toral R Patel, W Mark Saltzman, Jiangbing Zhou.
      Glioblastoma (GBM) is a deadly disease without effective treatment. Because glioblastoma stem cells (GSCs) contribute to tumor resistance and recurrence, improved treatment of GBM can be achieved by eliminating GSCs through inducing their differentiation. Prior efforts have been focused on studying GSC differentiation towards the astroglial lineage. However, regulation of GSC differentiation towards the neuronal and oligodendroglial lineages is largely unknown. To identify genes that control GSC differentiation to all three lineages, we performed an image-based genome-wide RNAi screen, in combination with single-cell RNA sequencing, and identified ZNF117 as a major regulator of GSC differentiation. Using patient-derived GSC cultures, we show that ZNF117 controls GSC differentiation towards the oligodendroglial lineage via the Notch pathway. We demonstrate that ZNF117 is a promising target for GSC differentiation therapy through targeted delivery of CRISPR/Cas9 gene-editing nanoparticles. Our study suggests a direction to improve GBM treatment through differentiation of GSCs towards various lineages.
    DOI:  https://doi.org/10.1038/s41467-022-29884-3
  49. J Exp Med. 2022 Jun 06. pii: e20211314. [Epub ahead of print]219(6):
    CD36, a signaling receptor and fatty acid transporter that regulates immune cell metabolism and fate.
    Yiliang Chen, Jue Zhang, Weiguo Cui, Roy L Silverstein.
      CD36 is a type 2 cell surface scavenger receptor widely expressed in many immune and non-immune cells. It functions as both a signaling receptor responding to DAMPs and PAMPs, as well as a long chain free fatty acid transporter. Recent studies have indicated that CD36 can integrate cell signaling and metabolic pathways through its dual functions and thereby influence immune cell differentiation and activation, and ultimately help determine cell fate. Its expression along with its dual functions in both innate and adaptive immune cells contribute to pathogenesis of common diseases, including atherosclerosis and tumor progression, which makes CD36 and its downstream effectors potential therapeutic targets. This review comprehensively examines the dual functions of CD36 in a variety of immune cells, especially macrophages and T cells. We also briefly discuss CD36 function in non-immune cells, such as adipocytes and platelets, which impact the immune system via intercellular communication. Finally, outstanding questions in this field are provided for potential directions of future studies.
    DOI:  https://doi.org/10.1084/jem.20211314
  50. Nat Commun. 2022 Apr 22. 13(1): 2200
    Pathogenic BRCA1 variants disrupt PLK1-regulation of mitotic spindle orientation.
    Zhengcheng He, Ryan Ghorayeb, Susanna Tan, Ke Chen, Amanda C Lorentzian, Jack Bottyan, Syed Mohammed Musheer Aalam, Miguel Angel Pujana, Philipp F Lange, Nagarajan Kannan, Connie J Eaves, Christopher A Maxwell.
      Preneoplastic mammary tissues from human female BRCA1 mutation carriers, or Brca1-mutant mice, display unexplained abnormalities in luminal differentiation. We now study the division characteristics of human mammary cells purified from female BRCA1 mutation carriers or non-carrier donors. We show primary BRCA1 mutant/+ cells exhibit defective BRCA1 localization, high radiosensitivity and an accelerated entry into cell division, but fail to orient their cell division axis. We also analyse 15 genetically-edited BRCA1 mutant/+ human mammary cell-lines and find that cells carrying pathogenic BRCA1 mutations acquire an analogous defect in their division axis accompanied by deficient expression of features of mature luminal cells. Importantly, these alterations are independent of accumulated DNA damage, and specifically dependent on elevated PLK1 activity induced by reduced BRCA1 function. This essential PLK1-mediated role of BRCA1 in controlling the cell division axis provides insight into the phenotypes expressed during BRCA1 tumorigenesis.
    DOI:  https://doi.org/10.1038/s41467-022-29885-2
  51. Nat Commun. 2022 Apr 21. 13(1): 2174
    Snf7 spirals sense and alter membrane curvature.
    Nebojsa Jukic, Alma P Perrino, Frédéric Humbert, Aurélien Roux, Simon Scheuring.
      Endosomal Sorting Complex Required for Transport III (ESCRT-III) is a conserved protein system involved in many cellular processes resulting in membrane deformation and scission, topologically away from the cytoplasm. However, little is known about the transition of the planar membrane-associated protein assembly into a 3D structure. High-speed atomic force microscopy (HS-AFM) provided insights into assembly, structural dynamics and turnover of Snf7, the major ESCRT-III component, on planar supported lipid bilayers. Here, we develop HS-AFM experiments that remove the constraints of membrane planarity, crowdedness, and support rigidity. On non-planar membranes, Snf7 monomers are curvature insensitive, but Snf7-spirals selectively adapt their conformation to membrane geometry. In a non-crowded system, Snf7-spirals reach a critical radius, and remodel to minimize internal stress. On non-rigid supports, Snf7-spirals compact and buckle, deforming the underlying bilayer. These experiments provide direct evidence that Snf7 is sufficient to mediate topological transitions, in agreement with the loaded spiral spring model.
    DOI:  https://doi.org/10.1038/s41467-022-29850-z
  52. Nat Commun. 2022 Apr 21. 13(1): 2187
    USP22 regulates lipidome accumulation by stabilizing PPARγ in hepatocellular carcinoma.
    Zhen Ning, Xin Guo, Xiaolong Liu, Chang Lu, Aman Wang, Xiaolin Wang, Wen Wang, Huan Chen, Wangshu Qin, Xinyu Liu, Lina Zhou, Chi Ma, Jian Du, Zhikun Lin, Haifeng Luo, Wuxiyar Otkur, Huan Qi, Di Chen, Tian Xia, Jiwei Liu, Guang Tan, Guowang Xu, Hai-Long Piao.
      Elevated de novo lipogenesis is considered to be a crucial factor in hepatocellular carcinoma (HCC) development. Herein, we identify ubiquitin-specific protease 22 (USP22) as a key regulator for de novo fatty acid synthesis, which directly interacts with deubiquitinates and stabilizes peroxisome proliferator-activated receptor gamma (PPARγ) through K48-linked deubiquitination, and in turn, this stabilization increases acetyl-CoA carboxylase (ACC) and ATP citrate lyase (ACLY) expressions. In addition, we find that USP22 promotes de novo fatty acid synthesis and contributes to HCC tumorigenesis, however, this tumorigenicity is suppressed by inhibiting the expression of PPARγ, ACLY, or ACC in in vivo tumorigenesis experiments. In HCC, high expression of USP22 positively correlates with PPARγ, ACLY or ACC expression, and associates with a poor prognosis. Taken together, we identify a USP22-regulated lipogenesis mechanism that involves the PPARγ-ACLY/ACC axis in HCC tumorigenesis and provide a rationale for therapeutic targeting of lipogenesis via USP22 inhibition.
    DOI:  https://doi.org/10.1038/s41467-022-29846-9
  53. Nat Commun. 2022 Apr 19. 13(1): 2072
    Local and substrate-specific S-palmitoylation determines subcellular localization of Gαo.
    Gonzalo P Solis, Arghavan Kazemzadeh, Laurence Abrami, Jana Valnohova, Cecilia Alvarez, F Gisou van der Goot, Vladimir L Katanaev.
      Peripheral membrane proteins (PMPs) associate with cellular membranes through post-translational modifications like S-palmitoylation. The Golgi apparatus is generally viewed as the transitory station where palmitoyl acyltransferases (PATs) modify PMPs, which are then transported to their ultimate destinations such as the plasma membrane (PM). However, little substrate specificity among the many PATs has been determined. Here we describe the inherent partitioning of Gαo - α-subunit of heterotrimeric Go proteins - to PM and Golgi, independent from Golgi-to-PM transport. A minimal code within Gαo N-terminus governs its compartmentalization and re-coding produces G protein versions with shifted localization. We establish the S-palmitoylation at the outer nuclear membrane assay ("SwissKASH") to probe substrate specificity of PATs in intact cells. With this assay, we show that PATs localizing to different membrane compartments display remarkable substrate selectivity, which is the basis for PMP compartmentalization. Our findings uncover a mechanism governing protein localization and establish the basis for innovative drug discovery.
    DOI:  https://doi.org/10.1038/s41467-022-29685-8
  54. Immunity. 2022 Apr 12. pii: S1074-7613(22)00143-1. [Epub ahead of print]
    Combined protein and nucleic acid imaging reveals virus-dependent B cell and macrophage immunosuppression of tissue microenvironments.
    Sizun Jiang, Chi Ngai Chan, Xavier Rovira-Clavé, Han Chen, Yunhao Bai, Bokai Zhu, Erin McCaffrey, Noah F Greenwald, Candace Liu, Graham L Barlow, Jason L Weirather, John Paul Oliveria, Tsuguhisa Nakayama, Ivan T Lee, Matthias S Matter, Anne E Carlisle, Darci Philips, Gustavo Vazquez, Nilanjan Mukherjee, Kathleen Busman-Sahay, Michael Nekorchuk, Margaret Terry, Skyler Younger, Marc Bosse, Janos Demeter, Scott J Rodig, Alexandar Tzankov, Yury Goltsev, David Robert McIlwain, Michael Angelo, Jacob D Estes, Garry P Nolan.
      Understanding the mechanisms of HIV tissue persistence necessitates the ability to visualize tissue microenvironments where infected cells reside; however, technological barriers limit our ability to dissect the cellular components of these HIV reservoirs. Here, we developed protein and nucleic acid in situ imaging (PANINI) to simultaneously quantify DNA, RNA, and protein levels within these tissue compartments. By coupling PANINI with multiplexed ion beam imaging (MIBI), we measured over 30 parameters simultaneously across archival lymphoid tissues from healthy or simian immunodeficiency virus (SIV)-infected nonhuman primates. PANINI enabled the spatial dissection of cellular phenotypes, functional markers, and viral events resulting from infection. SIV infection induced IL-10 expression in lymphoid B cells, which correlated with local macrophage M2 polarization. This highlights a potential viral mechanism for conditioning an immunosuppressive tissue environment for virion production. The spatial multimodal framework here can be extended to decipher tissue responses in other infectious diseases and tumor biology.
    Keywords:  HIV; SIV; immunosuppression; multiplexed imaging; single-cell biology; spatial multiomics; viral pathogenesis; viral reservoir; virus-host interactions
    DOI:  https://doi.org/10.1016/j.immuni.2022.03.020
  55. Nat Commun. 2022 Apr 20. 13(1): 2145
    Vasa nucleates asymmetric translation along the mitotic spindle during unequal cell divisions.
    Ana Fernandez-Nicolas, Alicia Uchida, Jessica Poon, Mamiko Yajima.
      mRNA translation on the spindle is hypothesized to be an essential strategy for the localized production of cell regulators. This mechanism may be important particularly in early embryonic cells, which have a large diffusion volume and that undergo rapid cell divisions. Evidence to test such a hypothesis has been, however, limited. Here, we use an embryo with both symmetric and asymmetric cell divisions and manipulate Vasa protein, an RNA-helicase, on the spindle in live sea urchin embryos. We learned that the spindle serves as a major site of translation and that protein synthesis within a single spindle can be unequal and help drive asymmetric cell divisions during embryogenesis. Recruiting Vasa to the ectopic sub-cellular region induced a new site of translation, disturbed asymmetric translation on the spindle, and changed the cell fate. Based on these observations, we conclude that Vasa functions in localized translation, which provides a spatiotemporal control in protein synthesis and is essential for rapidly developing embryonic cells.
    DOI:  https://doi.org/10.1038/s41467-022-29855-8
  56. Nat Commun. 2022 Apr 19. 13(1): 2104
    Cooperative interaction between ERα and the EMT-inducer ZEB1 reprograms breast cancer cells for bone metastasis.
    Nastaran Mohammadi Ghahhari, Magdalena K Sznurkowska, Nicolas Hulo, Lilia Bernasconi, Nicola Aceto, Didier Picard.
      The epithelial to mesenchymal transition (EMT) has been proposed to contribute to the metastatic spread of breast cancer cells. EMT-promoting transcription factors determine a continuum of different EMT states. In contrast, estrogen receptor α (ERα) helps to maintain the epithelial phenotype of breast cancer cells and its expression is crucial for effective endocrine therapies. Determining whether and how EMT-associated transcription factors such as ZEB1 modulate ERα signaling during early stages of EMT could promote the discovery of therapeutic approaches to suppress metastasis. Here we show that, shortly after induction of EMT and while cells are still epithelial, ZEB1 modulates ERα-mediated transcription induced by estrogen or cAMP signaling in breast cancer cells. Based on these findings and our ex vivo and xenograft results, we suggest that the functional interaction between ZEB1 and ERα may alter the tissue tropism of metastatic breast cancer cells towards bone.
    DOI:  https://doi.org/10.1038/s41467-022-29723-5
  57. Nat Commun. 2022 Apr 19. 13(1): 2079
    An anti-influenza A virus microbial metabolite acts by degrading viral endonuclease PA.
    Jianyuan Zhao, Jing Wang, Xu Pang, Zhenlong Liu, Quanjie Li, Dongrong Yi, Yongxin Zhang, Xiaomei Fang, Tao Zhang, Rui Zhou, Tao Zhang, Zhe Guo, Wancang Liu, Xiaoyu Li, Chen Liang, Tao Deng, Fei Guo, Liyan Yu, Shan Cen.
      The emergence of new highly pathogenic and drug-resistant influenza strains urges the development of novel therapeutics for influenza A virus (IAV). Here, we report the discovery of an anti-IAV microbial metabolite called APL-16-5 that was originally isolated from the plant endophytic fungus Aspergillus sp. CPCC 400735. APL-16-5 binds to both the E3 ligase TRIM25 and IAV polymerase subunit PA, leading to TRIM25 ubiquitination of PA and subsequent degradation of PA in the proteasome. This mode of action conforms to that of a proteolysis targeting chimera which employs the cellular ubiquitin-proteasome machinery to chemically induce the degradation of target proteins. Importantly, APL-16-5 potently inhibits IAV and protects mice from lethal IAV infection. Therefore, we have identified a natural microbial metabolite with potent in vivo anti-IAV activity and the potential of becoming a new IAV therapeutic. The antiviral mechanism of APL-16-5 opens the possibility of improving its anti-IAV potency and specificity by adjusting its affinity for TRIM25 and viral PA protein through medicinal chemistry.
    DOI:  https://doi.org/10.1038/s41467-022-29690-x
  58. Nature. 2022 Apr 21.
    Increased Memory B Cell Potency and Breadth After a SARS-CoV-2 mRNA Boost.
    Frauke Muecksch, Zijun Wang, Alice Cho, Christian Gaebler, Tarek Ben Tanfous, Justin DaSilva, Eva Bednarski, Victor Ramos, Shuai Zong, Brianna Johnson, Raphael Raspe, Dennis Schaefer-Babajew, Irina Shimeliovich, Mridushi Daga, Kai-Hui Yao, Fabian Schmidt, Katrina G Millard, Martina Turroja, Mila Jankovic, Thiago Y Oliveira, Anna Gazumyan, Marina Caskey, Theodora Hatziioannou, Paul D Bieniasz, Michel C Nussenzweig.
      The omicron variant of SARS-CoV-2 infected many vaccinated and convalescent individuals1-3. Despite the reduced protection from infection, individuals that received 3 doses of an mRNA vaccine were highly protected from more serious consequences of infection4. Here we examine the memory B cell repertoire in a longitudinal cohort of individuals receiving 3 mRNA vaccine doses5,6. We find that the 3rd dose is accompanied by an increase in, and evolution of, anti-receptor binding domain-specific memory B cells. The increase is due to expansion of memory B cell clones that were present after the 2nd dose as well as the emergence of new clones. The antibodies encoded by these cells showed significantly increased potency and breadth when compared to antibodies obtained after the 2nd dose. Notably, the increase in potency was especially evident among newly developing clones of memory cells that differed from the persisting clones in targeting more conserved regions of the RBD. Overall, more than 50% of the analyzed neutralizing antibodies in the memory compartment after a 3rd mRNA vaccine dose neutralized Omicron. Thus, individuals receiving 3 doses of an mRNA vaccine, have a diverse memory B cell repertoire that can respond rapidly and produce antibodies capable of clearing even diversified variants such as Omicron. These data help explain why a 3rd dose of a vaccine that was not specifically designed to protect against variants is effective against variant-induced serious disease.
    DOI:  https://doi.org/10.1038/s41586-022-04778-y
  59. Nat Commun. 2022 Apr 19. 13(1): 2050
    Skeletal Ni electrode-catalyzed C-O cleavage of diaryl ethers entails direct elimination via benzyne intermediates.
    Yuting Zhou, Grace E Klinger, Eric L Hegg, Christopher M Saffron, James E Jackson.
      Diaryl ethers undergo electrocatalytic hydrogenolysis (ECH) over skeletal Ni cathodes in a mild, aqueous process that achieves direct C-O cleavage without initial benzene ring saturation. Mechanistic studies find that aryl phenyl ethers with a single para or meta functional group (methyl, methoxy, or hydroxy) are selectively cleaved to the substituted benzene and phenol, in contrast to recently reported homogeneous catalytic cleavage processes. Ortho positioning of substituents reverses this C-O bond selectivity, except for the 2-phenoxyphenol case. Together with isotope labeling and co-solvent studies, these results point to two distinct cleavage mechanisms: (a) dual-ring coordination and C-H activation, leading to vicinal elimination to form phenol and a surface-bound aryne intermediate which is then hydrogenated and released as the arene; and (b) surface binding in keto form by the phenolic ring of the hydroxy-substituted substrates, followed by direct displacement of the departing phenol. Notably, acetone inhibits the well-known reduction of phenol to cyclohexanol, affording control of product ring saturation. A byproduct of this work is the discovery that the ECH treatment completely defluorinates substrates bearing aromatic C-F and C-CF3 groupings.
    DOI:  https://doi.org/10.1038/s41467-022-29555-3
  60. Nat Commun. 2022 Apr 19. 13(1): 2025
    Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle.
    Daniel J Ham, Anastasiya Börsch, Kathrin Chojnowska, Shuo Lin, Aurel B Leuchtman, Alexander S Ham, Marco Thürkauf, Julien Delezie, Regula Furrer, Dominik Burri, Michael Sinnreich, Christoph Handschin, Lionel A Tintignac, Mihaela Zavolan, Nitish Mittal, Markus A Rüegg.
      Preserving skeletal muscle function is essential to maintain life quality at high age. Calorie restriction (CR) potently extends health and lifespan, but is largely unachievable in humans, making "CR mimetics" of great interest. CR targets nutrient-sensing pathways centering on mTORC1. The mTORC1 inhibitor, rapamycin, is considered a potential CR mimetic and is proven to counteract age-related muscle loss. Therefore, we tested whether rapamycin acts via similar mechanisms as CR to slow muscle aging. Here we show that long-term CR and rapamycin unexpectedly display distinct gene expression profiles in geriatric mouse skeletal muscle, despite both benefiting aging muscles. Furthermore, CR improves muscle integrity in mice with nutrient-insensitive, sustained muscle mTORC1 activity and rapamycin provides additive benefits to CR in naturally aging mouse muscles. We conclude that rapamycin and CR exert distinct, compounding effects in aging skeletal muscle, thus opening the possibility of parallel interventions to counteract muscle aging.
    DOI:  https://doi.org/10.1038/s41467-022-29714-6
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