bims-nimamd 2022-10-09 papers

bims-nimamd

Biomed News

on Neuroimmunity and neuroinflammation in ageing and metabolic disease

Issue of 2022‒10‒09
forty-six papers selected by
Fawaz Alzaïd
Sorbonne Université

Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders.
Functional genomics of complex cancer genomes.
Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection thymocytes.
The γδ IEL effector API5 masks genetic susceptibility to Paneth cell death.
Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements.
Opposing roles of hepatic stellate cell subpopulations in hepatocarcinogenesis.
Tissue-specific impacts of aging and genetics on gene expression patterns in humans.
Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.
Energy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus.
The mitochondrial calcium uniporter of pulmonary type 2 cells determines severity of acute lung injury.
Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection.
Pericyte remodeling is deficient in the aged brain and contributes to impaired capillary flow and structure.
Single-cell dissection of the obesity-exercise axis in adipose-muscle tissues implies a critical role for mesenchymal stem cells.
Ebola outbreak in Uganda: how worried are researchers?
Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas.
Vitamin C epigenetically controls osteogenesis and bone mineralization.
Pancreatic islet-specific engineered Tregs exhibit robust antigen-specific and bystander immune suppression in type 1 diabetes models.
Dietary sugar lowers immunity and microbiota that protect against metabolic disease.
Ribosome specialization in glioblastoma.
Autophagy induction promoted by m6A reader YTHDF3 through translation upregulation of FOXO3 mRNA.
Molecular programming modulates hepatic lipid metabolism and adult metabolic risk in the offspring of obese mothers in a sex-specific manner.
Pluripotency factors are repurposed to shape the epigenomic landscape of neural crest cells.
Two independent respiratory chains adapt OXPHOS performance to glycolytic switch.
The immune factors driving DNA methylation variation in human blood.
Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer's disease.
GAB functions as a bioenergetic and signalling gatekeeper to control T cell inflammation.
Marker-free co-selection for successive rounds of prime editing in human cells.
XBP1-mediated activation of the STING signalling pathway in macrophages contributes to liver fibrosis progression.
Inter-organellar and systemic responses to impaired mitochondrial matrix protein import in skeletal muscle.
Precise DNA cleavage using CRISPR-SpRYgests.
Programmable RNA sensing for cell monitoring and manipulation.
Aschoff's rule on circadian rhythms orchestrated by blue light sensor CRY2 and clock component PRR9.
Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.
Chemotherapy-induced complement signaling modulates immunosuppression and metastatic relapse in breast cancer.
Past and present giant viruses diversity explored through permafrost metagenomics.
The monkeypox virus is mutating. Are scientists worried?
The diverse genetic origins of a Classical period Greek army.
Reprogramming alveolar macrophage responses to TGF-β reveals CCR2+ monocyte activity that promotes bronchiolitis obliterans syndrome.
Aging attenuates diurnal lipid uptake by brown adipose tissue.
Single-cell RNA-seq keeps cells alive.
Receptor-informed network control theory links LSD and psilocybin to a flattening of the brain's control energy landscape.
Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program.
Location bias contributes to functionally selective responses of biased CXCR3 agonists.
Mesoscale structure-function relationships in mitochondrial transcriptional condensates.
A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.
Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon.

Nat Commun. 2022 Oct 07. 13(1): 5918

Prevalence and mechanisms of somatic deletions in single human neurons during normal aging and in DNA repair disorders.

Junho Kim, August Yue Huang, Shelby L Johnson, Jenny Lai, Laura Isacco, Ailsa M Jeffries, Michael B Miller, Michael A Lodato, Christopher A Walsh, Eunjung Alice Lee.

Replication errors and various genotoxins cause DNA double-strand breaks (DSBs) where error-prone repair creates genomic mutations, most frequently focal deletions, and defective repair may lead to neurodegeneration. Despite its pathophysiological importance, the extent to which faulty DSB repair alters the genome, and the mechanisms by which mutations arise, have not been systematically examined reflecting ineffective methods. Here, we develop PhaseDel, a computational method to detect focal deletions and characterize underlying mechanisms in single-cell whole genome sequences (scWGS). We analyzed high-coverage scWGS of 107 single neurons from 18 neurotypical individuals of various ages, and found that somatic deletions increased with age and in highly expressed genes in human brain. Our analysis of 50 single neurons from DNA repair-deficient diseases with progressive neurodegeneration (Cockayne syndrome, Xeroderma pigmentosum, and Ataxia telangiectasia) reveals elevated somatic deletions compared to age-matched controls. Distinctive mechanistic signatures and transcriptional associations suggest roles for somatic deletions in neurodegeneration.

DOI: https://doi.org/10.1038/s41467-022-33642-w
Nat Commun. 2022 Oct 07. 13(1): 5908

Functional genomics of complex cancer genomes.

Francesca Menghi, Edison T Liu.

DOI: https://doi.org/10.1038/s41467-022-33717-8
Nat Commun. 2022 Oct 06. 13(1): 5901

Loss of Zfp335 triggers cGAS/STING-dependent apoptosis of post-β selection thymocytes.

Jeremy J Ratiu, William E Barclay, Elliot Lin, Qun Wang, Sebastian Wellford, Naren Mehta, Melissa J Harnois, Devon DiPalma, Sumedha Roy, Alejandra V Contreras, Mari L Shinohara, David Wiest, Yuan Zhuang.

Production of a functional peripheral T cell compartment typically involves massive expansion of the bone marrow progenitors that seed the thymus. There are two main phases of expansion during T cell development, following T lineage commitment of double-negative (DN) 2 cells and after successful rearrangement and selection for functional TCRβ chains in DN3 thymocytes, which promotes the transition of DN4 cells to the DP stage. The signals driving the expansion of DN2 thymocytes are well studied. However, factors regulating the proliferation and survival of DN4 cells remain poorly understood. Here, we uncover an unexpected link between the transcription factor Zfp335 and control of cGAS/STING-dependent cell death in post-β-selection DN4 thymocytes. Zfp335 controls survival by sustaining expression of Ankle2, which suppresses cGAS/STING-dependent cell death. Together, this study identifies Zfp335 as a key transcription factor regulating the survival of proliferating post-β-selection thymocytes and demonstrates a key role for the cGAS/STING pathway in driving apoptosis of developing T cells.

DOI: https://doi.org/10.1038/s41467-022-33610-4
Nature. 2022 Oct 05.

The γδ IEL effector API5 masks genetic susceptibility to Paneth cell death.

Yu Matsuzawa-Ishimoto, Xiaomin Yao, Akiko Koide, Beatrix M Ueberheide, Jordan E Axelrad, Bernardo S Reis, Roham Parsa, Jessica A Neil, Joseph C Devlin, Eugene Rudensky, M Zahidunnabi Dewan, Michael Cammer, Richard S Blumberg, Yi Ding, Kelly V Ruggles, Daniel Mucida, Shohei Koide, Ken Cadwell.

Loss of Paneth cells and their antimicrobial granules compromises the intestinal epithelial barrier and is associated with Crohn's disease, a major type of inflammatory bowel disease1-7. Non-classical lymphoid cells, broadly referred to as intraepithelial lymphocytes (IELs), intercalate the intestinal epithelium8,9. This anatomical position has implicated them as first-line defenders in resistance to infections, but their role in inflammatory disease pathogenesis requires clarification. The identification of mediators that coordinate crosstalk between specific IEL and epithelial subsets could provide insight into intestinal barrier mechanisms in health and disease. Here we show that the subset of IELs that express γ and δ T cell receptor subunits (γδ IELs) promotes the viability of Paneth cells deficient in the Crohn's disease susceptibility gene ATG16L1. Using an ex vivo lymphocyte-epithelium co-culture system, we identified apoptosis inhibitor 5 (API5) as a Paneth cell-protective factor secreted by γδ IELs. In the Atg16l1-mutant mouse model, viral infection induced a loss of Paneth cells and enhanced susceptibility to intestinal injury by inhibiting the secretion of API5 from γδ IELs. Therapeutic administration of recombinant API5 protected Paneth cells in vivo in mice and ex vivo in human organoids with the ATG16L1 risk allele. Thus, we identify API5 as a protective γδ IEL effector that masks genetic susceptibility to Paneth cell death.

DOI: https://doi.org/10.1038/s41586-022-05259-y
Nat Genet. 2022 Oct;54(10): 1504-1513

Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements.

Sofia Battaglia, Kevin Dong, Jingyi Wu, Zeyu Chen, Fadi J Najm, Yuanyuan Zhang, Molly M Moore, Vivian Hecht, Noam Shoresh, Bradley E Bernstein.

Epigenomic maps identify gene regulatory elements by their chromatin state. However, prevailing short-read sequencing methods cannot effectively distinguish alleles, evaluate the interdependence of elements in a locus or capture single-molecule dynamics. Here, we apply targeted nanopore sequencing to profile chromatin accessibility and DNA methylation on contiguous ~100-kb DNA molecules that span loci relevant to development, immunity and imprinting. We detect promoters, enhancers, insulators and transcription factor footprints on single molecules based on exogenous GpC methylation. We infer relationships among dynamic elements within immune loci, and order successive remodeling events during T cell stimulation. Finally, we phase primary sequence and regulatory elements across the H19/IGF2 locus, uncovering primate-specific features. These include a segmental duplication that stabilizes the imprinting control region and a noncanonical enhancer that drives biallelic IGF2 expression in specific contexts. Our study advances emerging strategies for phasing gene regulatory landscapes and reveals a mechanism that overrides IGF2 imprinting in human cells.

DOI: https://doi.org/10.1038/s41588-022-01188-8
Nature. 2022 Oct 05.

Opposing roles of hepatic stellate cell subpopulations in hepatocarcinogenesis.

Aveline Filliol, Yoshinobu Saito, Ajay Nair, Dianne H Dapito, Le-Xing Yu, Aashreya Ravichandra, Sonakshi Bhattacharjee, Silvia Affo, Naoto Fujiwara, Hua Su, Qiuyan Sun, Thomas M Savage, John R Wilson-Kanamori, Jorge M Caviglia, LiKang Chin, Dongning Chen, Xiaobo Wang, Stefano Caruso, Jin Ku Kang, Amit Dipak Amin, Sebastian Wallace, Ross Dobie, Deqi Yin, Oscar M Rodriguez-Fiallos, Chuan Yin, Adam Mehal, Benjamin Izar, Richard A Friedman, Rebecca G Wells, Utpal B Pajvani, Yujin Hoshida, Helen E Remotti, Nicholas Arpaia, Jessica Zucman-Rossi, Michael Karin, Neil C Henderson, Ira Tabas, Robert F Schwabe.

Hepatocellular carcinoma (HCC), the fourth leading cause of cancer mortality worldwide, develops almost exclusively in patients with chronic liver disease and advanced fibrosis1,2. Here we interrogated functions of hepatic stellate cells (HSCs), the main source of liver fibroblasts3, during hepatocarcinogenesis. Genetic depletion, activation or inhibition of HSCs in mouse models of HCC revealed their overall tumour-promoting role. HSCs were enriched in the preneoplastic environment, where they closely interacted with hepatocytes and modulated hepatocarcinogenesis by regulating hepatocyte proliferation and death. Analyses of mouse and human HSC subpopulations by single-cell RNA sequencing together with genetic ablation of subpopulation-enriched mediators revealed dual functions of HSCs in hepatocarcinogenesis. Hepatocyte growth factor, enriched in quiescent and cytokine-producing HSCs, protected against hepatocyte death and HCC development. By contrast, type I collagen, enriched in activated myofibroblastic HSCs, promoted proliferation and tumour development through increased stiffness and TAZ activation in pretumoural hepatocytes and through activation of discoidin domain receptor 1 in established tumours. An increased HSC imbalance between cytokine-producing HSCs and myofibroblastic HSCs during liver disease progression was associated with increased HCC risk in patients. In summary, the dynamic shift in HSC subpopulations and their mediators during chronic liver disease is associated with a switch from HCC protection to HCC promotion.

DOI: https://doi.org/10.1038/s41586-022-05289-6
Nat Commun. 2022 Oct 03. 13(1): 5803

Tissue-specific impacts of aging and genetics on gene expression patterns in humans.

Ryo Yamamoto, Ryan Chung, Juan Manuel Vazquez, Huanjie Sheng, Philippa L Steinberg, Nilah M Ioannidis, Peter H Sudmant.

Age is the primary risk factor for many common human diseases. Here, we quantify the relative contributions of genetics and aging to gene expression patterns across 27 tissues from 948 humans. We show that the predictive power of expression quantitative trait loci is impacted by age in many tissues. Jointly modelling the contributions of age and genetics to transcript level variation we find expression heritability (h2) is consistent among tissues while the contribution of aging varies by >20-fold with [Formula: see text] in 5 tissues. We find that while the force of purifying selection is stronger on genes expressed early versus late in life (Medawar's hypothesis), several highly proliferative tissues exhibit the opposite pattern. These non-Medawarian tissues exhibit high rates of cancer and age-of-expression-associated somatic mutations. In contrast, genes under genetic control are under relaxed constraint. Together, we demonstrate the distinct roles of aging and genetics on expression phenotypes.

DOI: https://doi.org/10.1038/s41467-022-33509-0
Mol Cell. 2022 Sep 30. pii: S1097-2765(22)00901-7. [Epub ahead of print]

Calcineurin dephosphorylates topoisomerase IIβ and regulates the formation of neuronal-activity-induced DNA breaks.

Ilse Delint-Ramirez, Lahiri Konada, Lance Heady, Richard Rueda, Alvaro Sebastian Vaca Jacome, Eric Marlin, Charlotte Marchioni, Amir Segev, Oleg Kritskiy, Satoko Yamakawa, Andrew H Reiter, Li-Huei Tsai, Ram Madabhushi.

  Neuronal activity induces topoisomerase IIβ (Top2B) to generate DNA double-strand breaks (DSBs) within the promoters of neuronal early response genes (ERGs) and facilitate their transcription, and yet, the mechanisms that control Top2B-mediated DSB formation are unknown. Here, we report that stimulus-dependent calcium influx through NMDA receptors activates the phosphatase calcineurin to dephosphorylate Top2B at residues S1509 and S1511, which stimulates its DNA cleavage activity and induces it to form DSBs. Exposing mice to a fear conditioning paradigm also triggers Top2B dephosphorylation at S1509 and S1511 in the hippocampus, indicating that calcineurin also regulates Top2B-mediated DSB formation following physiological neuronal activity. Furthermore, calcineurin-Top2B interactions following neuronal activity and sites that incur activity-induced DSBs are preferentially localized at the nuclear periphery in neurons. Together, these results reveal how radial gene positioning and the compartmentalization of activity-dependent signaling govern the position and timing of activity-induced DSBs and regulate gene expression patterns in neurons.

Keywords:  Top2B; activity-induced DNA breaks; calcineurin; early response genes; nuclear periphery

DOI:  https://doi.org/10.1016/j.molcel.2022.09.012
Nat Commun. 2022 Oct 01. 13(1): 5775

Energy landscape reshaped by strain-specific mutations underlies epistasis in NS1 evolution of influenza A virus.

Iktae Kim, Alyssa Dubrow, Bryan Zuniga, Baoyu Zhao, Noah Sherer, Abhishek Bastiray, Pingwei Li, Jae-Hyun Cho.

Elucidating how individual mutations affect the protein energy landscape is crucial for understanding how proteins evolve. However, predicting mutational effects remains challenging because of epistasis-the nonadditive interactions between mutations. Here, we investigate the biophysical mechanism of strain-specific epistasis in the nonstructural protein 1 (NS1) of influenza A viruses (IAVs). We integrate structural, kinetic, thermodynamic, and conformational dynamics analyses of four NS1s of influenza strains that emerged between 1918 and 2004. Although functionally near-neutral, strain-specific NS1 mutations exhibit long-range epistatic interactions with residues at the p85β-binding interface. We reveal that strain-specific mutations reshaped the NS1 energy landscape during evolution. Using NMR spin dynamics, we find that the strain-specific mutations altered the conformational dynamics of the hidden network of tightly packed residues, underlying the evolution of long-range epistasis. This work shows how near-neutral mutations silently alter the biophysical energy landscapes, resulting in diverse background effects during molecular evolution.

DOI: https://doi.org/10.1038/s41467-022-33554-9
Nat Commun. 2022 Oct 03. 13(1): 5837

The mitochondrial calcium uniporter of pulmonary type 2 cells determines severity of acute lung injury.

Mohammad Naimul Islam, Galina A Gusarova, Shonit R Das, Li Li, Eiji Monma, Murari Anjaneyulu, Liberty Mthunzi, Sadiqa K Quadri, Edward Owusu-Ansah, Sunita Bhattacharya, Jahar Bhattacharya.

Acute Lung Injury (ALI) due to inhaled pathogens causes high mortality. Underlying mechanisms are inadequately understood. Here, by optical imaging of live mouse lungs we show that a key mechanism is the viability of cytosolic Ca2+ buffering by the mitochondrial Ca2+ uniporter (MCU) in the lung's surfactant-secreting, alveolar type 2 cells (AT2). The buffering increased mitochondrial Ca2+ and induced surfactant secretion in wild-type mice, but not in mice with AT2-specific MCU knockout. In the knockout mice, ALI due to intranasal LPS instillation caused severe pulmonary edema and mortality, which were mitigated by surfactant replenishment prior to LPS instillation, indicating surfactant's protective effect against alveolar edema. In wild-type mice, intranasal LPS, or Pseudomonas aeruginosa decreased AT2 MCU. Loss of MCU abrogated buffering. The resulting mortality was reduced by spontaneous recovery of MCU expression, or by MCU replenishment. Enhancement of AT2 mitochondrial buffering, hence endogenous surfactant secretion, through MCU replenishment might be a therapy against ALI.

DOI: https://doi.org/10.1038/s41467-022-33543-y
Nat Commun. 2022 Oct 06. 13(1): 5879

Prion-like low complexity regions enable avid virus-host interactions during HIV-1 infection.

Guochao Wei, Naseer Iqbal, Valentine V Courouble, Ashwanth C Francis, Parmit K Singh, Arpa Hudait, Arun S Annamalai, Stephanie Bester, Szu-Wei Huang, Nikoloz Shkriabai, Lorenzo Briganti, Reed Haney, Vineet N KewalRamani, Gregory A Voth, Alan N Engelman, Gregory B Melikyan, Patrick R Griffin, Francisco Asturias, Mamuka Kvaratskhelia.

Cellular proteins CPSF6, NUP153 and SEC24C play crucial roles in HIV-1 infection. While weak interactions of short phenylalanine-glycine (FG) containing peptides with isolated capsid hexamers have been characterized, how these cellular factors functionally engage with biologically relevant mature HIV-1 capsid lattices is unknown. Here we show that prion-like low complexity regions (LCRs) enable avid CPSF6, NUP153 and SEC24C binding to capsid lattices. Structural studies revealed that multivalent CPSF6 assembly is mediated by LCR-LCR interactions, which are templated by binding of CPSF6 FG peptides to a subset of hydrophobic capsid pockets positioned along adjoining hexamers. In infected cells, avid CPSF6 LCR-mediated binding to HIV-1 cores is essential for functional virus-host interactions. The investigational drug lenacapavir accesses unoccupied hydrophobic pockets in the complex to potently impair HIV-1 inside the nucleus without displacing the tightly bound cellular cofactor from virus cores. These results establish previously undescribed mechanisms of virus-host interactions and antiviral action.

DOI: https://doi.org/10.1038/s41467-022-33662-6
Nat Commun. 2022 Oct 07. 13(1): 5912

Pericyte remodeling is deficient in the aged brain and contributes to impaired capillary flow and structure.

Andrée-Anne Berthiaume, Franca Schmid, Stefan Stamenkovic, Vanessa Coelho-Santos, Cara D Nielson, Bruno Weber, Mark W Majesky, Andy Y Shih.

Deterioration of brain capillary flow and architecture is a hallmark of aging and dementia. It remains unclear how loss of brain pericytes in these conditions contributes to capillary dysfunction. Here, we conduct cause-and-effect studies by optically ablating pericytes in adult and aged mice in vivo. Focal pericyte loss induces capillary dilation without blood-brain barrier disruption. These abnormal dilations are exacerbated in the aged brain, and result in increased flow heterogeneity in capillary networks. A subset of affected capillaries experience reduced perfusion due to flow steal. Some capillaries stall in flow and regress, leading to loss of capillary connectivity. Remodeling of neighboring pericytes restores endothelial coverage and vascular tone within days. Pericyte remodeling is slower in the aged brain, resulting in regions of persistent capillary dilation. These findings link pericyte loss to disruption of capillary flow and structure. They also identify pericyte remodeling as a therapeutic target to preserve capillary flow dynamics.

DOI: https://doi.org/10.1038/s41467-022-33464-w
Cell Metab. 2022 Oct 04. pii: S1550-4131(22)00394-1. [Epub ahead of print]34(10): 1578-1593.e6

Single-cell dissection of the obesity-exercise axis in adipose-muscle tissues implies a critical role for mesenchymal stem cells.

Jiekun Yang, Maria Vamvini, Pasquale Nigro, Li-Lun Ho, Kyriakitsa Galani, Marcus Alvarez, Yosuke Tanigawa, Ashley Renfro, Nicholas P Carbone, Markku Laakso, Leandro Z Agudelo, Päivi Pajukanta, Michael F Hirshman, Roeland J W Middelbeek, Kevin Grove, Laurie J Goodyear, Manolis Kellis.

  Exercise training is critical for the prevention and treatment of obesity, but its underlying mechanisms remain incompletely understood given the challenge of profiling heterogeneous effects across multiple tissues and cell types. Here, we address this challenge and opposing effects of exercise and high-fat diet (HFD)-induced obesity at single-cell resolution in subcutaneous and visceral white adipose tissue and skeletal muscle in mice with diet and exercise training interventions. We identify a prominent role of mesenchymal stem cells (MSCs) in obesity and exercise-induced tissue adaptation. Among the pathways regulated by exercise and HFD in MSCs across the three tissues, extracellular matrix remodeling and circadian rhythm are the most prominent. Inferred cell-cell interactions implicate within- and multi-tissue crosstalk centered around MSCs. Overall, our work reveals the intricacies and diversity of multi-tissue molecular responses to exercise and obesity and uncovers a previously underappreciated role of MSCs in tissue-specific and multi-tissue beneficial effects of exercise.

Keywords:  circadian rhythm pathway; exercise; extracellular matrix remodeling; mesenchymal stem cell; multi-tissue crosstalk; obesity; single-cell atlas; skeletal muscle; white adipose tissue; within-tissue crosstalk

DOI:  https://doi.org/10.1016/j.cmet.2022.09.004
Nature. 2022 Oct 07.

Ebola outbreak in Uganda: how worried are researchers?

Max Kozlov.



Keywords:  Diseases; Ebola virus; Public health

DOI:  https://doi.org/10.1038/d41586-022-03192-8
Mol Cell. 2022 Sep 29. pii: S1097-2765(22)00896-6. [Epub ahead of print]

Histone methylation antagonism drives tumor immune evasion in squamous cell carcinomas.

Yinglu Li, Elizabeth M Goldberg, Xiao Chen, Xinjing Xu, John T McGuire, Giuseppe Leuzzi, Dimitris Karagiannis, Tiffany Tate, Nargess Farhangdoost, Cynthia Horth, Esther Dai, Zhiming Li, Zhiguo Zhang, Benjamin Izar, Jianwen Que, Alberto Ciccia, Jacek Majewski, Angela J Yoon, Laurie Ailles, Cathy Lee Mendelsohn, Chao Lu.

  How cancer-associated chromatin abnormalities shape tumor-immune interaction remains incompletely understood. Recent studies have linked DNA hypomethylation and de-repression of retrotransposons to anti-tumor immunity through the induction of interferon response. Here, we report that inactivation of the histone H3K36 methyltransferase NSD1, which is frequently found in squamous cell carcinomas (SCCs) and induces DNA hypomethylation, unexpectedly results in diminished tumor immune infiltration. In syngeneic and genetically engineered mouse models of head and neck SCCs, NSD1-deficient tumors exhibit immune exclusion and reduced interferon response despite high retrotransposon expression. Mechanistically, NSD1 loss results in silencing of innate immunity genes, including the type III interferon receptor IFNLR1, through depletion of H3K36 di-methylation (H3K36me2) and gain of H3K27 tri-methylation (H3K27me3). Inhibition of EZH2 restores immune infiltration and impairs the growth of Nsd1-mutant tumors. Thus, our work uncovers a druggable chromatin cross talk that regulates the viral mimicry response and enables immune evasion of DNA hypomethylated tumors.

Keywords:  DNA methylation; EZH2; NSD1; Tazemetostat; epigenetics; head and neck cancers; histone methylation; immune evasion; squamous cell carcinomas

DOI:  https://doi.org/10.1016/j.molcel.2022.09.007
Nat Commun. 2022 Oct 06. 13(1): 5883

Vitamin C epigenetically controls osteogenesis and bone mineralization.

Roman Thaler, Farzaneh Khani, Ines Sturmlechner, Sharareh S Dehghani, Janet M Denbeigh, Xianhu Zhou, Oksana Pichurin, Amel Dudakovic, Sofia S Jerez, Jian Zhong, Jeong-Heon Lee, Ramesh Natarajan, Ivo Kalajzic, Yong-Hui Jiang, David R Deyle, Eleftherios P Paschalis, Barbara M Misof, Tamas Ordog, Andre J van Wijnen.

Vitamin C deficiency disrupts the integrity of connective tissues including bone. For decades this function has been primarily attributed to Vitamin C as a cofactor for collagen maturation. Here, we demonstrate that Vitamin C epigenetically orchestrates osteogenic differentiation and function by modulating chromatin accessibility and priming transcriptional activity. Vitamin C regulates histone demethylation (H3K9me3 and H3K27me3) and promotes TET-mediated 5hmC DNA hydroxymethylation at promoters, enhancers and super-enhancers near bone-specific genes. This epigenetic circuit licenses osteoblastogenesis by permitting the expression of all major pro-osteogenic genes. Osteogenic cell differentiation is strictly and continuously dependent on Vitamin C, whereas Vitamin C is dispensable for adipogenesis. Importantly, deletion of 5hmC-writers, Tet1 and Tet2, in Vitamin C-sufficient murine bone causes severe skeletal defects which mimic bone phenotypes of Vitamin C-insufficient Gulo knockout mice, a model of Vitamin C deficiency and scurvy. Thus, Vitamin C's epigenetic functions are central to osteoblastogenesis and bone formation and may be leveraged to prevent common bone-degenerating conditions.

DOI: https://doi.org/10.1038/s41467-022-32915-8
Sci Transl Med. 2022 Oct 05. 14(665): eabn1716

Pancreatic islet-specific engineered Tregs exhibit robust antigen-specific and bystander immune suppression in type 1 diabetes models.

Soo Jung Yang, Akhilesh K Singh, Travis Drow, Tori Tappen, Yuchi Honaker, Fariba Barahmand-Pour-Whitman, Peter S Linsley, Karen Cerosaletti, Kelsey Mauk, Yufei Xiang, Jessica Smith, Emma Mortensen, Peter J Cook, Karen Sommer, Iram Khan, Denny Liggitt, David J Rawlings, Jane H Buckner.

Adoptive transfer of regulatory T cells (Tregs) is therapeutic in type 1 diabetes (T1D) mouse models. Tregs that are specific for pancreatic islets are more potent than polyclonal Tregs in preventing disease. However, the frequency of antigen-specific natural Tregs is extremely low, and ex vivo expansion may destabilize Tregs, leading to an effector phenotype. Here, we generated durable, antigen-specific engineered Tregs (EngTregs) from primary human CD4+ T cells by combining FOXP3 homology-directed repair editing and lentiviral T cell receptor (TCR) delivery. Using TCRs derived from clonally expanded CD4+ T cells isolated from patients with T1D, we generated islet-specific EngTregs that suppressed effector T cell (Teff) proliferation and cytokine production. EngTregs suppressed Teffs recognizing the same islet antigen in addition to bystander Teffs recognizing other islet antigens through production of soluble mediators and both direct and indirect mechanisms. Adoptively transferred murine islet-specific EngTregs homed to the pancreas and blocked diabetes triggered by islet-specific Teffs or diabetogenic polyclonal Teffs in recipient mice. These data demonstrate the potential of antigen-specific EngTregs as a targeted therapy for preventing T1D.

DOI: https://doi.org/10.1126/scitranslmed.abn1716
Cell Metab. 2022 Oct 04. pii: S1550-4131(22)00396-5. [Epub ahead of print]34(10): 1422-1424

Dietary sugar lowers immunity and microbiota that protect against metabolic disease.

Han Fang, Fernando F Anhê, Jonathan D Schertzer.

Diet influences intestinal microbiota, inflammation, and metabolism. Kawano et al. show that dietary sugar engaged upper gut innate lymphoid cells to replace segmented filamentous bacteria with a pathobiont. Added sugar worsened early metabolic disease by lowering protective Th17 immunity, thereby promoting intestinal lipid absorption and obesity in high-fat-diet-fed mice.

DOI: https://doi.org/10.1016/j.cmet.2022.09.006
Nat Cell Biol. 2022 Oct 03.

Ribosome specialization in glioblastoma.

Naomi R Genuth, Maria Barna.

DOI: https://doi.org/10.1038/s41556-022-01000-z
Nat Commun. 2022 Oct 04. 13(1): 5845

Autophagy induction promoted by m6A reader YTHDF3 through translation upregulation of FOXO3 mRNA.

WeiChao Hao, MeiJuan Dian, Ying Zhou, QiuLing Zhong, WenQian Pang, ZiJian Li, YaYan Zhao, JiaCheng Ma, XiaoLin Lin, RenRu Luo, YongLong Li, JunShuang Jia, HongFen Shen, ShiHao Huang, GuanQi Dai, JiaHong Wang, Yan Sun, Dong Xiao.

Autophagy is crucial for maintaining cellular energy homeostasis and for cells to adapt to nutrient deficiency, and nutrient sensors regulating autophagy have been reported previously. However, the role of eiptranscriptomic modifications such as m6A in the regulation of starvation-induced autophagy is unclear. Here, we show that the m6A reader YTHDF3 is essential for autophagy induction. m6A modification is up-regulated to promote autophagosome formation and lysosomal degradation upon nutrient deficiency. METTL3 depletion leads to a loss of functional m6A modification and inhibits YTHDF3-mediated autophagy flux. YTHDF3 promotes autophagy by recognizing m6A modification sites around the stop codon of FOXO3 mRNA. YTHDF3 also recruits eIF3a and eIF4B to facilitate FOXO3 translation, subsequently initiating autophagy. Overall, our study demonstrates that the epitranscriptome regulator YTHDF3 functions as a nutrient responder, providing a glimpse into the post-transcriptional RNA modifications that regulate metabolic homeostasis.

DOI: https://doi.org/10.1038/s41467-022-32963-0
Commun Biol. 2022 Oct 04. 5(1): 1057

Molecular programming modulates hepatic lipid metabolism and adult metabolic risk in the offspring of obese mothers in a sex-specific manner.

Christina Savva, Luisa A Helguero, Marcela González-Granillo, Tânia Melo, Daniela Couto, Bo Angelin, Maria Rosário Domingues, Xidan Li, Claudia Kutter, Marion Korach-André.

Male and female offspring of obese mothers are known to differ extensively in their metabolic adaptation and later development of complications. We investigate the sex-dependent responses in obese offspring mice with maternal obesity, focusing on changes in liver glucose and lipid metabolism. Here we show that maternal obesity prior to and during gestation leads to hepatic steatosis and inflammation in male offspring, while female offspring are protected. Females from obese mothers display important changes in hepatic transcriptional activity and triglycerides profile which may prevent the damaging effects of maternal obesity compared to males. These differences are sustained later in life, resulting in a better metabolic balance in female offspring. In conclusion, sex and maternal obesity drive differently transcriptional and posttranscriptional regulation of major metabolic processes in offspring liver, explaining the sexual dimorphism in obesity-associated metabolic risk.

DOI: https://doi.org/10.1038/s42003-022-04022-3
Dev Cell. 2022 Sep 28. pii: S1534-5807(22)00636-0. [Epub ahead of print]

Pluripotency factors are repurposed to shape the epigenomic landscape of neural crest cells.

Austin S Hovland, Debadrita Bhattacharya, Ana Paula Azambuja, Dimitrius Pramio, Jacqueline Copeland, Megan Rothstein, Marcos Simoes-Costa.

  Yamanaka factors are essential for establishing pluripotency in embryonic stem cells, but their function in multipotent stem cell populations is poorly understood. Here, we show that OCT4 and SOX2 cooperate with tissue-specific transcription factors to promote neural crest formation. By assessing avian and human neural crest cells at distinct developmental stages, we characterized the epigenomic changes that occur during their specification, migration, and early differentiation. This analysis determined that the OCT4-SOX2 dimer is required to establish a neural crest epigenomic signature that is lost upon cell fate commitment. The OCT4-SOX2 genomic targets in the neural crest differ from those of embryonic stem cells, indicating the dimer displays context-specific functions. Binding of OCT4-SOX2 to neural crest enhancers requires pioneer factor TFAP2A, which physically interacts with the dimer to modify its genomic targets. Our results demonstrate how Yamanaka factors are repurposed in multipotent cells to control chromatin organization and define their developmental potential.

Keywords:  OCT4; SOX2; TFAP2A; Yamanaka factors; epigenome; multipotency; neural crest; pioneer transcription factors; pluripotency; stem cells

DOI:  https://doi.org/10.1016/j.devcel.2022.09.006
Cell Metab. 2022 Sep 28. pii: S1550-4131(22)00395-3. [Epub ahead of print]

Two independent respiratory chains adapt OXPHOS performance to glycolytic switch.

Erika Fernández-Vizarra, Sandra López-Calcerrada, Ana Sierra-Magro, Rafael Pérez-Pérez, Luke E Formosa, Daniella H Hock, María Illescas, Ana Peñas, Michele Brischigliaro, Shujing Ding, Ian M Fearnley, Charalampos Tzoulis, Robert D S Pitceathly, Joaquín Arenas, Miguel A Martín, David A Stroud, Massimo Zeviani, Michael T Ryan, Cristina Ugalde.

  The structural and functional organization of the mitochondrial respiratory chain (MRC) remains intensely debated. Here, we show the co-existence of two separate MRC organizations in human cells and postmitotic tissues, C-MRC and S-MRC, defined by the preferential expression of three COX7A subunit isoforms, COX7A1/2 and SCAFI (COX7A2L). COX7A isoforms promote the functional reorganization of distinct co-existing MRC structures to prevent metabolic exhaustion and MRC deficiency. Notably, prevalence of each MRC organization is reversibly regulated by the activation state of the pyruvate dehydrogenase complex (PDC). Under oxidative conditions, the C-MRC is bioenergetically more efficient, whereas the S-MRC preferentially maintains oxidative phosphorylation (OXPHOS) upon metabolic rewiring toward glycolysis. We show a link between the metabolic signatures converging at the PDC and the structural and functional organization of the MRC, challenging the widespread notion of the MRC as a single functional unit and concluding that its structural heterogeneity warrants optimal adaptation to metabolic function.

Keywords:  COX7A1–2; SCAFI/COX7RP/COX7A2L; bioenergetics; glycolysis; metabolic switch; mitochondria; oxidative metabolism; pyruvate dehydrogenase; respiratory chain organizations; respiratory supercomplexes

DOI:  https://doi.org/10.1016/j.cmet.2022.09.005
Nat Commun. 2022 Oct 06. 13(1): 5895

The immune factors driving DNA methylation variation in human blood.

Milieu Intérieur Consortium

Epigenetic changes are required for normal development, yet the nature and respective contribution of factors that drive epigenetic variation in humans remain to be fully characterized. Here, we assessed how the blood DNA methylome of 884 adults is affected by DNA sequence variation, age, sex and 139 factors relating to life habits and immunity. Furthermore, we investigated whether these effects are mediated or not by changes in cellular composition, measured by deep immunophenotyping. We show that DNA methylation differs substantially between naïve and memory T cells, supporting the need for adjustment on these cell-types. By doing so, we find that latent cytomegalovirus infection drives DNA methylation variation and provide further support that the increased dispersion of DNA methylation with aging is due to epigenetic drift. Finally, our results indicate that cellular composition and DNA sequence variation are the strongest predictors of DNA methylation, highlighting critical factors for medical epigenomics studies.

DOI: https://doi.org/10.1038/s41467-022-33511-6
Nat Aging. 2021 Oct;1(10): 919-931

Effect of APOE alleles on the glial transcriptome in normal aging and Alzheimer's disease.

Alberto Serrano-Pozo, Zhaozhi Li, Ayush Noori, Huong N Nguyen, Aziz Mezlini, Liang Li, Eloise Hudry, Rosemary J Jackson, Bradley T Hyman, Sudeshna Das.

The roles of APOEε4 and APOEε2-the strongest genetic risk and protective factors for Alzheimer's disease-in glial responses remain elusive. We tested the hypothesis that APOE alleles differentially impact glial responses by investigating their effects on the glial transcriptome from elderly control brains with no neuritic amyloid plaques. We identified a cluster of microglial genes that are upregulated in APOEε4 and downregulated in APOEε2 carriers relative to APOEε3 homozygotes. This microglia-APOE cluster is enriched in phagocytosis-including TREM2 and TYROBP-and proinflammatory genes, and is also detectable in brains with frequent neuritic plaques. Next, we tested these findings in APOE knock-in mice exposed to acute (lipopolysaccharide challenge) and chronic (cerebral β-amyloidosis) insults and found that these mice partially recapitulate human APOE-linked expression patterns. Thus, the APOEε4 allele might prime microglia towards a phagocytic and proinflammatory state through an APOE-TREM2-TYROBP axis in normal aging as well as in Alzheimer's disease.

DOI: https://doi.org/10.1038/s43587-021-00123-6
Nat Metab. 2022 Oct 03.

GAB functions as a bioenergetic and signalling gatekeeper to control T cell inflammation.

Siwen Kang, Lingling Liu, Tingting Wang, Matthew Cannon, Penghui Lin, Teresa W-M Fan, David A Scott, Hsin-Jung Joyce Wu, Andrew N Lane, Ruoning Wang.

γ-Aminobutyrate (GAB), the biochemical form of (GABA) γ-aminobutyric acid, participates in shaping physiological processes, including the immune response. How GAB metabolism is controlled to mediate such functions remains elusive. Here we show that GAB is one of the most abundant metabolites in CD4+ T helper 17 (TH17) and induced T regulatory (iTreg) cells. GAB functions as a bioenergetic and signalling gatekeeper by reciprocally controlling pro-inflammatory TH17 cell and anti-inflammatory iTreg cell differentiation through distinct mechanisms. 4-Aminobutyrate aminotransferase (ABAT) funnels GAB into the tricarboxylic acid (TCA) cycle to maximize carbon allocation in promoting TH17 cell differentiation. By contrast, the absence of ABAT activity in iTreg cells enables GAB to be exported to the extracellular environment where it acts as an autocrine signalling metabolite that promotes iTreg cell differentiation. Accordingly, ablation of ABAT activity in T cells protects against experimental autoimmune encephalomyelitis (EAE) progression. Conversely, ablation of GABAA receptor in T cells worsens EAE. Our results suggest that the cell-autonomous control of GAB on CD4+ T cells is bimodal and consists of the sequential action of two processes, ABAT-dependent mitochondrial anaplerosis and the receptor-dependent signalling response, both of which are required for T cell-mediated inflammation.

DOI: https://doi.org/10.1038/s42255-022-00638-1
Nat Commun. 2022 Oct 07. 13(1): 5909

Marker-free co-selection for successive rounds of prime editing in human cells.

Sébastien Levesque, Diana Mayorga, Jean-Philippe Fiset, Claudia Goupil, Alexis Duringer, Andréanne Loiselle, Eva Bouchard, Daniel Agudelo, Yannick Doyon.

Prime editing enables the introduction of precise point mutations, small insertions, or short deletions without requiring donor DNA templates. However, efficiency remains a key challenge in a broad range of human cell types. In this work, we design a robust co-selection strategy through coediting of the ubiquitous and essential sodium/potassium pump (Na+/K+ ATPase). We readily engineer highly modified pools of cells and clones with homozygous modifications for functional studies with minimal pegRNA optimization. This process reveals that nicking the non-edited strand stimulates multiallelic editing but often generates tandem duplications and large deletions at the target site, an outcome dictated by the relative orientation of the protospacer adjacent motifs. Our approach streamlines the production of cell lines with multiple genetic modifications to create cellular models for biological research and lays the foundation for the development of cell-type specific co-selection strategies.

DOI: https://doi.org/10.1038/s41467-022-33669-z
JHEP Rep. 2022 Nov;4(11): 100555

XBP1-mediated activation of the STING signalling pathway in macrophages contributes to liver fibrosis progression.

Qi Wang, Qingfa Bu, Mu Liu, Rui Zhang, Jian Gu, Lei Li, Jinren Zhou, Yuan Liang, Wantong Su, Zheng Liu, Mingming Wang, Zhexiong Lian, Ling Lu, Haoming Zhou.

  Background & Aims: XBP1 modulates the macrophage proinflammatory response, but its function in macrophage stimulator of interferon genes (STING) activation and liver fibrosis is unknown. X-box binding protein 1 (XBP1) has been shown to promote macrophage nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing 3 (NLRP3) activation in steatohepatitis. Herein, we aimed to explore the underlying mechanism of XBP1 in the regulation of STING signalling and the subsequent NLRP3 activation during liver fibrosis.Methods: XBP1 expression was measured in the human fibrotic liver tissue samples. Liver fibrosis was induced in myeloid-specific Xbp1-, STING-, and Nlrp3-deficient mice by carbon tetrachloride injection, bile duct ligation, or a methionine/choline-deficient diet.
Results: Although increased XBP1 expression was observed in the fibrotic liver macrophages of mice and clinical patients, myeloid-specific Xbp1 deficiency or pharmacological inhibition of XBP1 protected the liver against fibrosis. Furthermore, it inhibited macrophage NLPR3 activation in a STING/IRF3-dependent manner. Oxidative mitochondrial injury facilitated cytosolic leakage of macrophage self-mtDNA and cGAS/STING/NLRP3 signalling activation to promote liver fibrosis. Mechanistically, RNA sequencing analysis indicated a decreased mtDNA expression and an increased BCL2/adenovirus E1B interacting protein 3 (BNIP3)-mediated mitophagy activation in Xbp1-deficient macrophages. Chromatin immunoprecipitation (ChIP) assays further suggested that spliced XBP1 bound directly to the Bnip3 promoter and inhibited the transcription of Bnip3 in macrophages. Xbp1 deficiency decreased the mtDNA cytosolic release and STING/NLRP3 activation by promoting BNIP3-mediated mitophagy activation in macrophages, which was abrogated by Bnip3 knockdown. Moreover, macrophage XBP1/STING signalling contributed to the activation of hepatic stellate cells.
Conclusions: Our findings demonstrate that XBP1 controls macrophage cGAS/STING/NLRP3 activation by regulating macrophage self-mtDNA cytosolic leakage via BNIP3-mediated mitophagy modulation, thus providing a novel target against liver fibrosis.
Lay summary: Liver fibrosis is a typical progressive process of chronic liver disease, driven by inflammatory and immune responses, and is characterised by an excess of extracellular matrix in the liver. Currently, there is no effective therapeutic strategy for the treatment of liver fibrosis, resulting in high mortality worldwide. In this study, we found that myeloid-specific Xbp1 deficiency protected the liver against fibrosis in mice, while XBP1 inhibition ameliorated liver fibrosis in mice. This study concluded that targeting XBP1 signalling in macrophages may provide a novel strategy for protecting the liver against fibrosis.

Keywords:  Acta2/α-SMA, actin, alpha 2, smooth muscle, aorta; BDL, bile duct ligation; BMDMs, bone marrow-derived macrophages; BNIP3; BNIP3, BCL2/adenovirus E1B interacting protein 3; CCl4, carbon tetrachloride; CM, conditional media; ChIP, chromatin immunoprecipitation; Col1a1, collagen, type I, alpha 1; DMXAA, 5,6-dimethylxanthenone-4-acetic acid; ER, endoplasmic reticulum; EtBr, ethidium bromide; HSC, hepatic stellate cell; IRE1α, inositol-requiring enzyme-1α; IRF3, interferon regulatory factor 3; KEGG, Kyoto Encyclopedia of Genes and Genomes; LC3B, microtubule-associated protein 1 light chain 3 beta; LPS, lipopolysaccharide; Liver fibrosis; MCD, methionine/choline-deficient diet; Macrophage; Mitophagy; MnSOD, manganese superoxide dismutase; NAFLD, non-alcoholic fatty liver disease; NASH, non-alcoholic steatohepatitis; NLRP3, nucleotide-binding oligomerization domain, leucine-rich repeat and pyrin domain-containing 3; PBMCs, peripheral blood mononuclear cells; ROS, reactive oxygen species; STING; STING, stimulator of interferon genes; TBK1, TANK binding kinase 1; TGF-β1, transforming growth factor beta 1; TLR, Toll-like receptor; TNF-α, tumour necrosis factor alpha; Timp1, tissue inhibitor of matrix metalloproteinase 1; WT, wild-type; XBP1; XBP1, X-box binding protein 1; cGAS, cyclic GMP-AMP synthase; mtDNA; mtDNA, mitochondrial DNA; p62, sequestosome 1; sXBP1, spliced XBP1; shRNAs, short hairpin RNAs; uXBP1, unspliced XBP1

DOI:  https://doi.org/10.1016/j.jhepr.2022.100555
Commun Biol. 2022 Oct 05. 5(1): 1060

Inter-organellar and systemic responses to impaired mitochondrial matrix protein import in skeletal muscle.

Nirajan Neupane, Jayasimman Rajendran, Jouni Kvist, Sandra Harjuhaahto, Bowen Hu, Veijo Kinnunen, Yang Yang, Anni I Nieminen, Henna Tyynismaa.

Effective protein import from cytosol is critical for mitochondrial functions and metabolic regulation. We describe here the mammalian muscle-specific and systemic consequences to disrupted mitochondrial matrix protein import by targeted deletion of the mitochondrial HSP70 co-chaperone GRPEL1. Muscle-specific loss of GRPEL1 caused rapid muscle atrophy, accompanied by shut down of oxidative phosphorylation and mitochondrial fatty acid oxidation, and excessive triggering of proteotoxic stress responses. Transcriptome analysis identified new responders to mitochondrial protein import toxicity, such as the neurological disease-linked intermembrane space protein CHCHD10. Besides communication with ER and nucleus, we identified crosstalk of distressed mitochondria with peroxisomes, in particular the induction of peroxisomal Acyl-CoA oxidase 2 (ACOX2), which we propose as an ATF4-regulated peroxisomal marker of integrated stress response. Metabolic profiling indicated fatty acid enrichment in muscle, a shift in TCA cycle intermediates in serum and muscle, and dysregulated bile acids. Our results demonstrate the fundamental importance of GRPEL1 and provide a robust model for detecting mammalian inter-organellar and systemic responses to impaired mitochondrial matrix protein import and folding.

DOI: https://doi.org/10.1038/s42003-022-04034-z
Nat Biotechnol. 2022 Oct 06.

Precise DNA cleavage using CRISPR-SpRYgests.

Kathleen A Christie, Jimmy A Guo, Rachel A Silverstein, Roman M Doll, Megumu Mabuchi, Hannah E Stutzman, Jiecong Lin, Linyuan Ma, Russell T Walton, Luca Pinello, G Brett Robb, Benjamin P Kleinstiver.

Methods for in vitro DNA cleavage and molecular cloning remain unable to precisely cleave DNA directly adjacent to bases of interest. Restriction enzymes (REs) must bind specific motifs, whereas wild-type CRISPR-Cas9 or CRISPR-Cas12 nucleases require protospacer adjacent motifs (PAMs). Here we explore the utility of our previously reported near-PAMless SpCas9 variant, named SpRY, to serve as a universal DNA cleavage tool for various cloning applications. By performing SpRY DNA digests (SpRYgests) using more than 130 guide RNAs (gRNAs) sampling a wide diversity of PAMs, we discovered that SpRY is PAMless in vitro and can cleave DNA at practically any sequence, including sites refractory to cleavage with wild-type SpCas9. We illustrate the versatility and effectiveness of SpRYgests to improve the precision of several cloning workflows, including those not possible with REs or canonical CRISPR nucleases. We also optimize a rapid and simple one-pot gRNA synthesis protocol to streamline SpRYgest implementation. Together, SpRYgests can improve various DNA engineering applications that benefit from precise DNA breaks.

DOI: https://doi.org/10.1038/s41587-022-01492-y
Nature. 2022 Oct 05.

Programmable RNA sensing for cell monitoring and manipulation.

Yongjun Qian, Jiayun Li, Shengli Zhao, Elizabeth A Matthews, Michael Adoff, Weixin Zhong, Xu An, Michele Yeo, Christine Park, Xiaolu Yang, Bor-Shuen Wang, Derek G Southwell, Z Josh Huang.

RNA is a central and universal mediator of genetic information underlying the diversity of cell types and cell states, which together shape tissue organization and organismal function across species and lifespans. Despite numerous advances in RNA sequencing technologies and the massive accumulation of transcriptome datasets across the life sciences1,2, the dearth of technologies that use RNAs to observe and manipulate cell types remains a bottleneck in biology and medicine. Here we describe CellREADR (Cell access through RNA sensing by Endogenous ADAR), a programmable RNA-sensing technology that leverages RNA editing mediated by ADAR to couple the detection of cell-defining RNAs with the translation of effector proteins. Viral delivery of CellREADR conferred specific cell-type access in mouse and rat brains and in ex vivo human brain tissues. Furthermore, CellREADR enabled the recording and control of specific types of neurons in behaving mice. CellREADR thus highlights the potential for RNA-based monitoring and editing of animal cells in ways that are specific, versatile, simple and generalizable across organ systems and species, with wide applications in biology, biotechnology and programmable RNA medicine.

DOI: https://doi.org/10.1038/s41586-022-05280-1
Nat Commun. 2022 Oct 05. 13(1): 5869

Aschoff's rule on circadian rhythms orchestrated by blue light sensor CRY2 and clock component PRR9.

Yuqing He, Yingjun Yu, Xiling Wang, Yumei Qin, Chen Su, Lei Wang.

Circadian pace is modulated by light intensity, known as the Aschoff's rule, with largely unrevealed mechanisms. Here we report that photoreceptor CRY2 mediates blue light input to the circadian clock by directly interacting with clock core component PRR9 in blue light dependent manner. This physical interaction dually blocks the accessibility of PRR9 protein to its co-repressor TPL/TPRs and the resulting kinase PPKs. Notably, phosphorylation of PRR9 by PPKs is critical for its DNA binding and repressive activity, hence to ensure proper circadian speed. Given the labile nature of CRY2 in strong blue light, our findings provide a mechanistic explanation for Aschoff's rule in plants, i.e., blue light triggers CRY2 turnover in proportional to its intensity, which accordingly releasing PRR9 to fine tune circadian speed. Our findings not only reveal a network mediating light input into the circadian clock, but also unmask a mechanism by which the Arabidopsis circadian clock senses light intensity.

DOI: https://doi.org/10.1038/s41467-022-33568-3
Commun Biol. 2022 10 03. 5(1): 1032

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

Núria Mach, Cédric Midoux, Sébastien Leclercq, Samuel Pennarun, Laurence Le Moyec, Olivier Rué, Céline Robert, Guillaume Sallé, Eric Barrey.

Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance. Still, the extent of its functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built an integrated horse gut gene catalog comprising ~25 million unique genes and 372 metagenome-assembled genomes. This catalog represents 4179 genera spanning 95 phyla and functional capacities primed to exploit energy from dietary, microbial, and host resources. The holo-omics approach shows that gut microbiomes enriched in Lachnospiraceae taxa are negatively associated with cardiovascular capacity. Conversely, more complex and functionally diverse microbiomes are associated with higher glucose concentrations and reduced accumulation of long-chain acylcarnitines and non-esterified fatty acids in plasma, suggesting increased ß-oxidation capacity in the mitochondria. In line with this hypothesis, more fit athletes show upregulation of mitochondrial-related genes involved in energy metabolism, biogenesis, and Ca2+ cytosolic transport, all of which are necessary to improve aerobic work power, spare glycogen usage, and enhance cardiovascular capacity. The results identify an associative link between endurance performance and gut microbiome composition and gene function, laying the basis for nutritional interventions that could benefit horse athletes.

DOI: https://doi.org/10.1038/s42003-022-03977-7
Nat Commun. 2022 Oct 02. 13(1): 5797

Chemotherapy-induced complement signaling modulates immunosuppression and metastatic relapse in breast cancer.

Lea Monteran, Nour Ershaid, Hila Doron, Yael Zait, Ye'ela Scharff, Shahar Ben-Yosef, Camila Avivi, Iris Barshack, Amir Sonnenblick, Neta Erez.

Mortality from breast cancer is almost exclusively a result of tumor metastasis and resistance to therapy and therefore understanding the underlying mechanisms is an urgent challenge. Chemotherapy, routinely used to treat breast cancer, induces extensive tissue damage, eliciting an inflammatory response that may hinder efficacy and promote metastatic relapse. Here we show that systemic treatment with doxorubicin, but not cisplatin, following resection of a triple-negative breast tumor induces the expression of complement factors in lung fibroblasts and modulates an immunosuppressive metastatic niche that supports lung metastasis. Complement signaling derived from cancer-associated fibroblasts (CAFs) mediates the recruitment of myeloid-derived suppressor cells (MDSCs) to the metastatic niche, thus promoting T cell dysfunction. Pharmacological targeting of complement signaling in combination with chemotherapy alleviates immune dysregulation and attenuates lung metastasis. Our findings suggest that combining cytotoxic treatment with blockade of complement signaling in triple-negative breast cancer patients may attenuate the adverse effects of chemotherapy, thus offering a promising approach for clinical use.

DOI: https://doi.org/10.1038/s41467-022-33598-x
Nat Commun. 2022 Oct 07. 13(1): 5853

Past and present giant viruses diversity explored through permafrost metagenomics.

Sofia Rigou, Sébastien Santini, Chantal Abergel, Jean-Michel Claverie, Matthieu Legendre.

Giant viruses are abundant in aquatic environments and ecologically important through the metabolic reprogramming of their hosts. Less is known about giant viruses from soil even though two of them, belonging to two different viral families, were reactivated from 30,000-y-old permafrost samples. This suggests an untapped diversity of Nucleocytoviricota in this environment. Through permafrost metagenomics we reveal a unique diversity pattern and a high heterogeneity in the abundance of giant viruses, representing up to 12% of the sum of sequence coverage in one sample. Pithoviridae and Orpheoviridae-like viruses were the most important contributors. A complete 1.6 Mb Pithoviridae-like circular genome was also assembled from a 42,000-y-old sample. The annotation of the permafrost viral sequences revealed a patchwork of predicted functions amidst a larger reservoir of genes of unknown functions. Finally, the phylogenetic reconstructions not only revealed gene transfers between cells and viruses, but also between viruses from different families.

DOI: https://doi.org/10.1038/s41467-022-33633-x
Nature. 2022 Oct 05.

The monkeypox virus is mutating. Are scientists worried?

Max Kozlov.



Keywords:  Diseases; Genomics; Public health; Virology

DOI:  https://doi.org/10.1038/d41586-022-03171-z
Proc Natl Acad Sci U S A. 2022 Oct 11. 119(41): e2205272119

The diverse genetic origins of a Classical period Greek army.

Laurie J Reitsema, Alissa Mittnik, Britney Kyle, Giulio Catalano, Pier Francesco Fabbri, Adam C S Kazmi, Katherine L Reinberger, Luca Sineo, Stefano Vassallo, Rebecca Bernardos, Nasreen Broomandkhoshbacht, Kim Callan, Francesca Candilio, Olivia Cheronet, Elizabeth Curtis, Daniel Fernandes, Martina Lari, Ann Marie Lawson, Matthew Mah, Swapan Mallick, Kirsten Mandl, Adam Micco, Alessandra Modi, Jonas Oppenheimer, Kadir Toykan Özdogan, Nadin Rohland, Kristin Stewardson, Stefania Vai, Chiara Vergata, J Noah Workman, Fatma Zalzala, Valentina Zaro, Alessandro Achilli, Achilles Anagnostopoulos, Cristian Capelli, Varnavas Constantinou, Hovirag Lancioni, Anna Olivieri, Anastasia Papadopoulou, Nikoleta Psatha, Ornella Semino, John Stamatoyannopoulos, Ioanna Valliannou, Evangelia Yannaki, Iosif Lazaridis, Nick Patterson, Harald Ringbauer, David Caramelli, Ron Pinhasi, David Reich.

  Trade and colonization caused an unprecedented increase in Mediterranean human mobility in the first millennium BCE. Often seen as a dividing force, warfare is in fact another catalyst of culture contact. We provide insight into the demographic dynamics of ancient warfare by reporting genome-wide data from fifth-century soldiers who fought for the army of the Greek Sicilian colony of Himera, along with representatives of the civilian population, nearby indigenous settlements, and 96 present-day individuals from Italy and Greece. Unlike the rest of the sample, many soldiers had ancestral origins in northern Europe, the Steppe, and the Caucasus. Integrating genetic, archaeological, isotopic, and historical data, these results illustrate the significant role mercenaries played in ancient Greek armies and highlight how participation in war contributed to continental-scale human mobility in the Classical world.

Keywords:  Classical world; ancient DNA; ancient warfare; archaeology; history

DOI:  https://doi.org/10.1073/pnas.2205272119
J Clin Invest. 2022 10 03. pii: e159229. [Epub ahead of print]132(19):

Reprogramming alveolar macrophage responses to TGF-β reveals CCR2+ monocyte activity that promotes bronchiolitis obliterans syndrome.

Zhiyi Liu, Fuyi Liao, Jihong Zhu, Dequan Zhou, Gyu Seong Heo, Hannah P Leuhmann, Davide Scozzi, Antanisha Parks, Ramsey Hachem, Derek E Byers, Laneshia K Tague, Hrishikesh S Kulkarni, Marlene Cano, Brian W Wong, Wenjun Li, Howard J Huang, Alexander S Krupnick, Daniel Kreisel, Yongjian Liu, Andrew E Gelman.

  Bronchiolitis obliterans syndrome (BOS) is a major impediment to lung transplant survival and is generally resistant to medical therapy. Extracorporeal photophoresis (ECP) is an immunomodulatory therapy that shows promise in stabilizing BOS patients, but its mechanisms of action are unclear. In a mouse lung transplant model, we show that ECP blunts alloimmune responses and inhibits BOS through lowering airway TGF-β bioavailability without altering its expression. Surprisingly, ECP-treated leukocytes were primarily engulfed by alveolar macrophages (AMs), which were reprogrammed to become less responsive to TGF-β and reduce TGF-β bioavailability through secretion of the TGF-β antagonist decorin. In untreated recipients, high airway TGF-β activity stimulated AMs to express CCL2, leading to CCR2+ monocyte-driven BOS development. Moreover, we found TGF-β receptor 2-dependent differentiation of CCR2+ monocytes was required for the generation of monocyte-derived AMs, which in turn promoted BOS by expanding tissue-resident memory CD8+ T cells that inflicted airway injury through Blimp-1-mediated granzyme B expression. Thus, through studying the effects of ECP, we have identified an AM functional plasticity that controls a TGF-β-dependent network that couples CCR2+ monocyte recruitment and differentiation to alloimmunity and BOS.

Keywords:  Adaptive immunity; Immunology; Inflammation; Monocytes; Organ transplantation

DOI:  https://doi.org/10.1172/JCI159229
Aging (Albany NY). 2022 Oct 04. 14(undefined):

Aging attenuates diurnal lipid uptake by brown adipose tissue.

Wietse In Het Panhuis, Milena Schönke, Ricky Siebeler, Salwa Afkir, Rianne Baelde, Amanda C M Pronk, Trea C M Streefland, Hetty C M Sips, Reshma A Lalai, Patrick C N Rensen, Sander Kooijman.

  Brown adipose tissue (BAT) contributes to cardiometabolic health by taking up glucose and lipids for oxidation, a process that displays a strong diurnal rhythm. While aging has been shown to reduce thermogenic characteristics of BAT, it is as yet unknown whether this reduction is specific to the time of day. Therefore, we assessed whole-body and BAT energy metabolism in young and middle-aged male and female C57BL/6J mice and studied the consequences for lipid metabolism in humanized APOE*3-Leiden.CETP mice (also on a C57BL/6J background). We demonstrate that in middle-aged versus young mice body temperature is lower in both male and female mice, while uptake of triglyceride (TG)-derived fatty acids (FAs) by BAT, reflecting metabolic activity, is attenuated at its peak at the onset of the dark (wakeful) phase in female mice. This coincided with delayed plasma clearance of TG-rich lipoproteins and TG-depleted lipoprotein core remnants, and elevated plasma TGs at the same time point. Furthermore, middle-aged female mice showed increased adiposity, accompanied by lipid accumulation, increased expression of genes involved in lipogenesis, and reduced expression of genes involved in fat oxidation and the intracellular clock machinery in BAT. Peak abundance of lipoprotein lipase (LPL), a crucial regulator of FA uptake, was attenuated in BAT. Our findings suggest that LPL is a potential therapeutic target for restoring diurnal metabolic BAT activity, and that efficiency of strategies targeting BAT may be improved by including time of day as an important factor.

Keywords:  APOE*3-Leiden.CETP mice; aging; brown adipose tissue; diurnal rhythm; lipoprotein metabolism

DOI:  https://doi.org/10.18632/aging.204318
Nat Biotechnol. 2022 Oct;40(10): 1432

Single-cell RNA-seq keeps cells alive.

Eleni Kotsiliti.

DOI: https://doi.org/10.1038/s41587-022-01515-8
Nat Commun. 2022 Oct 03. 13(1): 5812

Receptor-informed network control theory links LSD and psilocybin to a flattening of the brain's control energy landscape.

S Parker Singleton, Andrea I Luppi, Robin L Carhart-Harris, Josephine Cruzat, Leor Roseman, David J Nutt, Gustavo Deco, Morten L Kringelbach, Emmanuel A Stamatakis, Amy Kuceyeski.

Psychedelics including lysergic acid diethylamide (LSD) and psilocybin temporarily alter subjective experience through their neurochemical effects. Serotonin 2a (5-HT2a) receptor agonism by these compounds is associated with more diverse (entropic) brain activity. We postulate that this increase in entropy may arise in part from a flattening of the brain's control energy landscape, which can be observed using network control theory to quantify the energy required to transition between recurrent brain states. Using brain states derived from existing functional magnetic resonance imaging (fMRI) datasets, we show that LSD and psilocybin reduce control energy required for brain state transitions compared to placebo. Furthermore, across individuals, reduction in control energy correlates with more frequent state transitions and increased entropy of brain state dynamics. Through network control analysis that incorporates the spatial distribution of 5-HT2a receptors (obtained from publicly available positron emission tomography (PET) data under non-drug conditions), we demonstrate an association between the 5-HT2a receptor and reduced control energy. Our findings provide evidence that 5-HT2a receptor agonist compounds allow for more facile state transitions and more temporally diverse brain activity. More broadly, we demonstrate that receptor-informed network control theory can model the impact of neuropharmacological manipulation on brain activity dynamics.

DOI: https://doi.org/10.1038/s41467-022-33578-1
Cell Metab. 2022 Sep 30. pii: S1550-4131(22)00403-X. [Epub ahead of print]

Understanding islet dysfunction in type 2 diabetes through multidimensional pancreatic phenotyping: The Human Pancreas Analysis Program.

Suzanne N Shapira, Ali Naji, Mark A Atkinson, Alvin C Powers, Klaus H Kaestner.

  In this perspective, we provide an overview of a recently established National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) initiative, the Human Pancreas Analysis Program for Type 2 Diabetes (HPAP-T2D). This program is designed to define the molecular pathogenesis of islet dysfunction by studying human pancreatic tissue samples from organ donors with T2D. HPAP-T2D generates detailed datasets of physiological, histological, transcriptomic, epigenomic, and genomic information. Importantly, all data collected, generated, and analyzed by HPAP-T2D are made immediately and freely available through a centralized database, PANC-DB, thus providing a comprehensive data resource for the diabetes research community.

Keywords:  T2D; epigenomics; islets; pancreas; type 2 diabetes

DOI:  https://doi.org/10.1016/j.cmet.2022.09.013
Nat Commun. 2022 Oct 04. 13(1): 5846

Location bias contributes to functionally selective responses of biased CXCR3 agonists.

Dylan Scott Eiger, Noelia Boldizsar, Christopher Cole Honeycutt, Julia Gardner, Stephen Kirchner, Chloe Hicks, Issac Choi, Uyen Pham, Kevin Zheng, Anmol Warman, Jeffrey S Smith, Jennifer Y Zhang, Sudarshan Rajagopal.

Some G protein-coupled receptor (GPCR) ligands act as "biased agonists" that preferentially activate specific signaling transducers over others. Although GPCRs are primarily found at the plasma membrane, GPCRs can traffic to and signal from many subcellular compartments. Here, we determine that differential subcellular signaling contributes to the biased signaling generated by three endogenous ligands of the GPCR CXC chemokine receptor 3 (CXCR3). The signaling profile of CXCR3 changes as it traffics from the plasma membrane to endosomes in a ligand-specific manner. Endosomal signaling is critical for biased activation of G proteins, β-arrestins, and extracellular-signal-regulated kinase (ERK). In CD8 + T cells, the chemokines promote unique transcriptional responses predicted to regulate inflammatory pathways. In a mouse model of contact hypersensitivity, β-arrestin-biased CXCR3-mediated inflammation is dependent on receptor internalization. Our work demonstrates that differential subcellular signaling is critical to the overall biased response observed at CXCR3, which has important implications for drugs targeting chemokine receptors and other GPCRs.

DOI: https://doi.org/10.1038/s41467-022-33569-2
Proc Natl Acad Sci U S A. 2022 Oct 11. 119(41): e2207303119

Mesoscale structure-function relationships in mitochondrial transcriptional condensates.

Marina Feric, Azadeh Sarfallah, Furqan Dar, Dmitry Temiakov, Rohit V Pappu, Tom Misteli.

  In live cells, phase separation is thought to organize macromolecules into membraneless structures known as biomolecular condensates. Here, we reconstituted transcription in condensates from purified mitochondrial components using optimized in vitro reaction conditions to probe the structure-function relationships of biomolecular condensates. We find that the core components of the mt-transcription machinery form multiphasic, viscoelastic condensates in vitro. Strikingly, the rates of condensate-mediated transcription are substantially lower than in solution. The condensate-mediated decrease in transcriptional rates is associated with the formation of vesicle-like structures that are driven by the production and accumulation of RNA during transcription. The generation of RNA alters the global phase behavior and organization of transcription components within condensates. Coarse-grained simulations of mesoscale structures at equilibrium show that the components stably assemble into multiphasic condensates and that the vesicles formed in vitro are the result of dynamical arrest. Overall, our findings illustrate the complex phase behavior of transcribing, multicomponent condensates, and they highlight the intimate, bidirectional interplay of structure and function in transcriptional condensates.

Keywords:  biomolecular condensates; mitochondrial genome; phase separation; transcription; vesicles

DOI:  https://doi.org/10.1073/pnas.2207303119
Commun Biol. 2022 Oct 07. 5(1): 1066

A multi-omic analysis of MCF10A cells provides a resource for integrative assessment of ligand-mediated molecular and phenotypic responses.

Sean M Gross, Mark A Dane, Rebecca L Smith, Kaylyn L Devlin, Ian C McLean, Daniel S Derrick, Caitlin E Mills, Kartik Subramanian, Alexandra B London, Denis Torre, John Erol Evangelista, Daniel J B Clarke, Zhuorui Xie, Cemal Erdem, Nicholas Lyons, Ted Natoli, Sarah Pessa, Xiaodong Lu, James Mullahoo, Jonathan Li, Miriam Adam, Brook Wassie, Moqing Liu, David F Kilburn, Tiera A Liby, Elmar Bucher, Crystal Sanchez-Aguila, Kenneth Daily, Larsson Omberg, Yunguan Wang, Connor Jacobson, Clarence Yapp, Mirra Chung, Dusica Vidovic, Yiling Lu, Stephan Schurer, Albert Lee, Ajay Pillai, Aravind Subramanian, Malvina Papanastasiou, Ernest Fraenkel, Heidi S Feiler, Gordon B Mills, Jake D Jaffe, Avi Ma'ayan, Marc R Birtwistle, Peter K Sorger, James E Korkola, Joe W Gray, Laura M Heiser.

The phenotype of a cell and its underlying molecular state is strongly influenced by extracellular signals, including growth factors, hormones, and extracellular matrix proteins. While these signals are normally tightly controlled, their dysregulation leads to phenotypic and molecular states associated with diverse diseases. To develop a detailed understanding of the linkage between molecular and phenotypic changes, we generated a comprehensive dataset that catalogs the transcriptional, proteomic, epigenomic and phenotypic responses of MCF10A mammary epithelial cells after exposure to the ligands EGF, HGF, OSM, IFNG, TGFB and BMP2. Systematic assessment of the molecular and cellular phenotypes induced by these ligands comprise the LINCS Microenvironment (ME) perturbation dataset, which has been curated and made publicly available for community-wide analysis and development of novel computational methods ( synapse.org/LINCS_MCF10A ). In illustrative analyses, we demonstrate how this dataset can be used to discover functionally related molecular features linked to specific cellular phenotypes. Beyond these analyses, this dataset will serve as a resource for the broader scientific community to mine for biological insights, to compare signals carried across distinct molecular modalities, and to develop new computational methods for integrative data analysis.

DOI: https://doi.org/10.1038/s42003-022-03975-9
Nat Commun. 2022 Oct 02. 13(1): 5792

Structure of the TnsB transposase-DNA complex of type V-K CRISPR-associated transposon.

Francisco Tenjo-Castaño, Nicholas Sofos, Blanca López-Méndez, Luisa S Stutzke, Anders Fuglsang, Stefano Stella, Guillermo Montoya.

CRISPR-associated transposons (CASTs) are mobile genetic elements that co-opted CRISPR-Cas systems for RNA-guided transposition. Here we present the 2.4 Å cryo-EM structure of the Scytonema hofmannii (sh) TnsB transposase from Type V-K CAST, bound to the strand transfer DNA. The strand transfer complex displays an intertwined pseudo-symmetrical architecture. Two protomers involved in strand transfer display a catalytically competent active site composed by DDE residues, while other two, which play a key structural role, show active sites where the catalytic residues are not properly positioned for phosphodiester hydrolysis. Transposon end recognition is accomplished by the NTD1/2 helical domains. A singular in trans association of NTD1 domains of the catalytically competent subunits with the inactive DDE domains reinforces the assembly. Collectively, the structural features suggest that catalysis is coupled to protein-DNA assembly to secure proper DNA integration. DNA binding residue mutants reveal that lack of specificity decreases activity, but it could increase transposition in some cases. Our structure sheds light on the strand transfer reaction of DDE transposases and offers new insights into CAST transposition.

DOI: https://doi.org/10.1038/s41467-022-33504-5