bims-minimp 2021-10-17 papers

on Mitochondria, innate immunity, proteostasis

Issue of 2021‒10‒17
thirty-six papers selected by
Hanna Salmonowicz
International Institute of Molecular Mechanisms and Machines of the Polish Academy of Sciences

Folding Mitochondrial-Mediated Cytosolic Proteostasis Into the Mitochondrial Unfolded Protein Response.
Downregulation of mitochondrial biogenesis by virus infection triggers antiviral responses by cyclic GMP-AMP synthase.
Role of the Mitochondrial Protein Import Machinery and Protein Processing in Heart Disease.
p107 mediated mitochondrial function controls muscle stem cell proliferative fates.
Targeting Mitochondrial Network Disorganization is Protective in C. elegans Models of Huntington's Disease.
Mapping the cellular response to electron transport chain inhibitors reveals selective signaling networks triggered by mitochondrial perturbation.
Macrophages, Metabolites, and Nucleosomes: Chromatin at the Intersection between Aging and Inflammation.
An anaplerotic approach to correct the mitochondrial dysfunction in ataxia-telangiectasia (A-T).
Age-related mitochondrial alterations in brain and skeletal muscle of the YAC128 model of Huntington disease.
Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity.
Hierarchical folding of the catalytic core during mitochondrial ribosome biogenesis.
Mitochondrial translation is required for sustained killing by cytotoxic T cells.
Sustained Activation of TNFα-Induced DNA Damage Response in Newly Differentiated Adipocytes.
Generating stable isolated mitochondrial recipient clones in mammalian cells using MitoPunch mitochondrial transfer.
Adaptive responses to air pollution in human dermal fibroblasts and their potential roles in aging.
Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria.
Increased CD47 and MHC Class I Inhibitory Signals Expression in Senescent CD1 Primary Mouse Lung Fibroblasts.
Glutamine restores mitochondrial respiration in bleomycin-injured epithelial cells.
A high-throughput genetic screening protocol to measure lipid bilayer stress-induced unfolded protein response in Saccharomyces cerevisiae.
The crosstalk between pattern-recognition receptor signaling and calcium signaling.
Phase separation of Nur77 mediates celastrol-induced mitophagy by promoting the liquidity of p62/SQSTM1 condensates.
Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains.
Friends and foes: Extracellular vesicles in aging and rejuvenation.
Intracellular metabolic reprogramming mediated by micro-RNAs in differentiating and proliferating cells under non-diseased conditions.
Gut bacterial metabolites modulate endoplasmic reticulum stress.
Targeting the complex I and III of mitochondrial electron transport chain as a potentially viable option in liver cancer management.
A recessive variant in TFAM causes mtDNA depletion associated with primary ovarian insufficiency, seizures, intellectual disability and hearing loss.
Biological Aspects of Inflamm-Aging in Childhood Cancer Survivors.
The Hsc70 disaggregation machinery removes monomer units directly from α-synuclein fibril ends.
No Longer A One-Trick Pony: STING Signaling Activity Beyond Interferon.
The Role of PPAR Alpha in the Modulation of Innate Immunity.
Regulation of STAT3 and its role in cardioprotection by conditioning: focus on non-genomic roles targeting mitochondrial function.
The cellular environment shapes the nuclear pore complex architecture.
ADAR1 entraps sinister cellular dsRNAs, thresholding antiviral responses.
The tumor suppression theory of aging.
Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells.

Front Cell Dev Biol. 2021 ;9 715923

Folding Mitochondrial-Mediated Cytosolic Proteostasis Into the Mitochondrial Unfolded Protein Response.

Edmund Charles Jenkins, Mrittika Chattopadhyay, Doris Germain.

  Several studies reported that mitochondrial stress induces cytosolic proteostasis. How mitochondrial stress activates proteostasis in the cytosol remains unclear. However, the cross-talk between the mitochondria and cytosolic proteostasis has far reaching implications for treatment of proteopathies including neurodegenerative diseases. This possibility appears within reach since selected drugs have begun to emerge as being able to stimulate mitochondrial-mediated cytosolic proteostasis. In this review, we focus on studies describing how mitochondrial stress activates proteostasis in the cytosol across multiple model organisms. A model is proposed linking mitochondrial-mediated regulation of cytosolic translation, folding capacity, ubiquitination, and proteasome degradation and autophagy as a multi layered control of cytosolic proteostasis that overlaps with the integrated stress response (ISR) and the mitochondrial unfolded protein response (UPRmt). By analogy to the conductor in an orchestra managing multiple instrumental sections into a dynamically integrated musical piece, the cross-talk between these signaling cascades places the mitochondria as a major conductor of cellular integrity.

Keywords:  estrogen receptor alpha; heat shock; mitochondria; mitochondrial UPR; mitochondrial integrated stress response; proteasome; translation

DOI:  https://doi.org/10.3389/fcell.2021.715923
PLoS Pathog. 2021 Oct;17(10): e1009841

Downregulation of mitochondrial biogenesis by virus infection triggers antiviral responses by cyclic GMP-AMP synthase.

Hiroki Sato, Miho Hoshi, Fusako Ikeda, Tomoko Fujiyuki, Misako Yoneda, Chieko Kai.

In general, in mammalian cells, cytosolic DNA viruses are sensed by cyclic GMP-AMP synthase (cGAS), and RNA viruses are recognized by retinoic acid-inducible gene I (RIG-I)-like receptors, triggering a series of downstream innate antiviral signaling steps in the host. We previously reported that measles virus (MeV), which possesses an RNA genome, induces rapid antiviral responses, followed by comprehensive downregulation of host gene expression in epithelial cells. Interestingly, gene ontology analysis indicated that genes encoding mitochondrial proteins are enriched among the list of downregulated genes. To evaluate mitochondrial stress after MeV infection, we first observed the mitochondrial morphology of infected cells and found that significantly elongated mitochondrial networks with a hyperfused phenotype were formed. In addition, an increased amount of mitochondrial DNA (mtDNA) in the cytosol was detected during progression of infection. Based on these results, we show that cytosolic mtDNA released from hyperfused mitochondria during MeV infection is captured by cGAS and causes consequent priming of the DNA sensing pathway in addition to canonical RNA sensing. We also ascertained the contribution of cGAS to the in vivo pathogenicity of MeV. In addition, we found that other viruses that induce downregulation of mitochondrial biogenesis as seen for MeV cause similar mitochondrial hyperfusion and cytosolic mtDNA-priming antiviral responses. These findings indicate that the mtDNA-activated cGAS pathway is critical for full innate control of certain viruses, including RNA viruses that cause mitochondrial stress.

DOI: https://doi.org/10.1371/journal.ppat.1009841
Front Cardiovasc Med. 2021 ;8 749756

Role of the Mitochondrial Protein Import Machinery and Protein Processing in Heart Disease.

Fujie Zhao, Ming-Hui Zou.

  Mitochondria are essential organelles for cellular energy production, metabolic homeostasis, calcium homeostasis, cell proliferation, and apoptosis. About 99% of mammalian mitochondrial proteins are encoded by the nuclear genome, synthesized as precursors in the cytosol, and imported into mitochondria by mitochondrial protein import machinery. Mitochondrial protein import systems function not only as independent units for protein translocation, but also are deeply integrated into a functional network of mitochondrial bioenergetics, protein quality control, mitochondrial dynamics and morphology, and interaction with other organelles. Mitochondrial protein import deficiency is linked to various diseases, including cardiovascular disease. In this review, we describe an emerging class of protein or genetic variations of components of the mitochondrial import machinery involved in heart disease. The major protein import pathways, including the presequence pathway (TIM23 pathway), the carrier pathway (TIM22 pathway), and the mitochondrial intermembrane space import and assembly machinery, related translocases, proteinases, and chaperones, are discussed here. This review highlights the importance of mitochondrial import machinery in heart disease, which deserves considerable attention, and further studies are urgently needed. Ultimately, this knowledge may be critical for the development of therapeutic strategies in heart disease.

Keywords:  CHCHD4 (MIA40); TIM22 complex; TIM23 complex; TOM complex; heart disease; mitochondrial protein import machinery

DOI:  https://doi.org/10.3389/fcvm.2021.749756
Nat Commun. 2021 Oct 13. 12(1): 5977

p107 mediated mitochondrial function controls muscle stem cell proliferative fates.

Debasmita Bhattacharya, Vicky Shah, Oreoluwa Oresajo, Anthony Scimè.

Muscle diseases and aging are associated with impaired myogenic stem cell self-renewal and fewer proliferating progenitors (MPs). Importantly, distinct metabolic states induced by glycolysis or oxidative phosphorylation have been connected to MP proliferation and differentiation. However, how these energy-provisioning mechanisms cooperate remain obscure. Herein, we describe a mechanism by which mitochondrial-localized transcriptional co-repressor p107 regulates MP proliferation. We show p107 directly interacts with the mitochondrial DNA, repressing mitochondrial-encoded gene transcription. This reduces ATP production by limiting electron transport chain complex formation. ATP output, controlled by the mitochondrial function of p107, is directly associated with the cell cycle rate. Sirt1 activity, dependent on the cytoplasmic glycolysis product NAD+, directly interacts with p107, impeding its mitochondrial localization. The metabolic control of MP proliferation, driven by p107 mitochondrial function, establishes a cell cycle paradigm that might extend to other dividing cell types.

DOI: https://doi.org/10.1038/s41467-021-26176-0
Aging Dis. 2021 Oct;12(7): 1753-1772

Targeting Mitochondrial Network Disorganization is Protective in C. elegans Models of Huntington's Disease.

Emily Machiela, Paige D Rudich, Annika Traa, Ulrich Anglas, Sonja K Soo, Megan M Senchuk, Jeremy M Van Raamsdonk.

  Huntington's disease (HD) is an adult-onset neurodegenerative disease caused by a trinucleotide CAG repeat expansion in the HTT gene. While the pathogenesis of HD is incompletely understood, mitochondrial dysfunction is thought to be a key contributor. In this work, we used C. elegans models to elucidate the role of mitochondrial dynamics in HD. We found that expression of a disease-length polyglutamine tract in body wall muscle, either with or without exon 1 of huntingtin, results in mitochondrial fragmentation and mitochondrial network disorganization. While mitochondria in young HD worms form elongated tubular networks as in wild-type worms, mitochondrial fragmentation occurs with age as expanded polyglutamine protein forms aggregates. To correct the deficit in mitochondrial morphology, we reduced levels of DRP-1, the GTPase responsible for mitochondrial fission. Surprisingly, we found that disrupting drp-1 can have detrimental effects, which are dependent on how much expression is decreased. To avoid potential negative side effects of disrupting drp-1, we examined whether decreasing mitochondrial fragmentation by targeting other genes could be beneficial. Through this approach, we identified multiple genetic targets that rescue movement deficits in worm models of HD. Three of these genetic targets, pgp-3, F25B5.6 and alh-12, increased movement in the HD worm model and restored mitochondrial morphology to wild-type morphology. This work demonstrates that disrupting the mitochondrial fission gene drp-1 can be detrimental in animal models of HD, but that decreasing mitochondrial fragmentation by targeting other genes can be protective. Overall, this study identifies novel therapeutic targets for HD aimed at improving mitochondrial health.

Keywords:  C. elegans; DRP1; Huntington’s disease; aggregation; animal model; genetics; mitochondria; mitochondrial dynamics; neurodegeneration; neuroprotection

DOI:  https://doi.org/10.14336/AD.2021.0404
Arch Toxicol. 2021 Oct 13.

Mapping the cellular response to electron transport chain inhibitors reveals selective signaling networks triggered by mitochondrial perturbation.

Wanda van der Stel, Huan Yang, Nanette G Vrijenhoek, Johannes P Schimming, Giulia Callegaro, Giada Carta, Salihanur Darici, Johannes Delp, Anna Forsby, Andrew White, Sylvia le Dévédec, Marcel Leist, Paul Jennings, Joost B Beltman, Bob van de Water, Erik H J Danen.

  Mitochondrial perturbation is a key event in chemical-induced organ toxicities that is incompletely understood. Here, we studied how electron transport chain (ETC) complex I, II, or III (CI, CII and CIII) inhibitors affect mitochondrial functionality, stress response activation, and cell viability using a combination of high-content imaging and TempO-Seq in HepG2 hepatocyte cells. CI and CIII inhibitors perturbed mitochondrial membrane potential (MMP) and mitochondrial and cellular ATP levels in a concentration- and time-dependent fashion and, under conditions preventing a switch to glycolysis attenuated cell viability, whereas CII inhibitors had no effect. TempO-Seq analysis of changes in mRNA expression pointed to a shared cellular response to CI and CIII inhibition. First, to define specific ETC inhibition responses, a gene set responsive toward ETC inhibition (and not to genotoxic, oxidative, or endoplasmic reticulum stress) was identified using targeted TempO-Seq in HepG2. Silencing of one of these genes, NOS3, exacerbated the impact of CI and CIII inhibitors on cell viability, indicating its functional implication in cellular responses to mitochondrial stress. Then by monitoring dynamic responses to ETC inhibition using a HepG2 GFP reporter panel for different classes of stress response pathways and applying pathway and gene network analysis to TempO-Seq data, we looked for downstream cellular events of ETC inhibition and identified the amino acid response (AAR) as being triggered in HepG2 by ETC inhibition. Through in silico approaches we provide evidence indicating that a similar AAR is associated with exposure to mitochondrial toxicants in primary human hepatocytes. Altogether, we (i) unravel quantitative, time- and concentration-resolved cellular responses to mitochondrial perturbation, (ii) identify a gene set associated with adaptation to exposure to active ETC inhibitors, and (iii) show that ER stress and an AAR accompany ETC inhibition in HepG2 and primary hepatocytes.

Keywords:  DILI; ETC complex inhibitors; High-content imaging; Mitochondrial toxicity; TempO-Seq

DOI:  https://doi.org/10.1007/s00204-021-03160-7
Int J Mol Sci. 2021 Sep 24. pii: 10274. [Epub ahead of print]22(19):

Macrophages, Metabolites, and Nucleosomes: Chromatin at the Intersection between Aging and Inflammation.

Michael C Church, Jerry L Workman, Tamaki Suganuma.

  Inflammation is the body's means of defense against harmful stimuli, with the ultimate aim being to restore homeostasis. Controlled acute inflammation transiently activates an immune response and can be beneficial as protection against infection or injury. However, dysregulated inflammatory responses, including chronic inflammation, disrupt the immune system's ability to maintain homeostatic balance, leading to increased susceptibility to infection, continuous tissue damage, and dysfunction. Aging is a risk factor for chronic inflammation; their coincidence is termed "inflammaging". Metabolic disorders including obesity, neurodegenerative diseases, and atherosclerosis are often encountered in old age. Therefore, it is important to understand the mechanistic relationship between aging, chronic inflammation, and metabolism. It has been established that the expression of inflammatory mediators is transcriptionally and translationally regulated. In addition, the post-translational modification of the mediators plays a crucial role in the response to inflammatory signaling. Chromatin regulation responds to metabolic status and controls homeostasis. However, chromatin structure is also changed by aging. In this review, we discuss the functional contributions of chromatin regulation to inflammaging.

Keywords:  aging; chromatin; chronic inflammation; histone modifications; inflammaging; metabolism; pro-inflammation; transcription

DOI:  https://doi.org/10.3390/ijms221910274
Mol Metab. 2021 Oct 09. pii: S2212-8778(21)00201-5. [Epub ahead of print] 101354

An anaplerotic approach to correct the mitochondrial dysfunction in ataxia-telangiectasia (A-T).

A J Yeo, G N Subramanian, K L Chong, M Gatei, R G Parton, D Coman, M F Lavin.

  OBJECTIVE: ATM, the protein defective in the human genetic disorder, ataxia telangiectasia (A-T) plays a central role in the response to DNA double strand breaks (DSBs) and in protecting the cell against oxidative stress. We recently showed that A-T cells are hypersensitive to metabolic stress which can be accounted for by a failure to exhibit efficient endoplasmic reticulum (ER)-mitochondrial signalling and Ca2+ transfer in response to nutrient deprivation resulting in mitochondrial dysfunction. The objective of the current study is to use an anaplerotic approach using the fatty acid, heptanoate (C7), a metabolic product of the triglyceride, triheptanoin to correct the defect in ER-mitochondrial signalling and enhance cell survival of A-T cells in response to metabolic stress.METHODS: We treated control cells and A-T cells with the anaplerotic agent, heptanoate to determine their sensitivity to metabolic stress induced by inhibition of glycolysis with 2 deoxyglucose (2DG) using live-cell imaging to monitor cell survival for 72 hours using the Incucyte system. We examined ER-mitochondrial signalling in A-T cells exposed to metabolic stress using a suite of techniques including immunofluorescence staining of Grp75, ER-mitochondrial Ca2+ channel, the VAPB-PTPIP51 ER-mitochondrial tether complexes as well as proximity ligation assays between Grp75-IP3R1 and VAPB1-PTPIP51 to establish a functional interaction between ER and mitochondria. Finally, we also performed metabolomic analysis using LC-MS/MS to determine altered levels of TCA intermediates A-T cells compared to healthy control cells.
RESULTS: We demonstrate here that heptanoate corrects all aspects of the defective ER-mitochondrial signalling observed in A-T cells. Heptanoate enhances ER-mitochondrial contacts; increases the flow of calcium from the ER to the mitochondrion; restores normal mitochondrial function and mitophagy and increases resistance of ATM-deficient cells and cells from A-T patients to metabolic stress-induced killing. The defect in mitochondrial function in ATM-deficient cells was accompanied by more reliance on aerobic glycolysis as shown by increased lactate dehydrogenase A (LDHA), accumulation of lactate and reduced levels of both acetyl CoA and ATP which are all restored by heptanoate.
CONCLUSIONS: These data together show that heptanoate corrects metabolic stress in A-T cells by restoring ER-mitochondria signalling and mitochondrial function and suggest that the parent compound, triheptanoin, has great potential as a novel therapeutic agent for patients with A-T.

Keywords:  ATM; Ataxia-telangiectasia; endoplasmic reticulum; heptanoate (C7); mitochondrial dysfunction; mitochondrial interaction; nutrient deprivation

DOI:  https://doi.org/10.1016/j.molmet.2021.101354
NPJ Aging Mech Dis. 2021 Oct 14. 7(1): 26

Age-related mitochondrial alterations in brain and skeletal muscle of the YAC128 model of Huntington disease.

Kristina Bečanović, Asghar Muhammad, Izabella Gadawska, Shiny Sachdeva, David Walker, Eduardo R Lazarowski, Sonia Franciosi, Kevin H J Park, Hélène C F Côté, Blair R Leavitt.

Mitochondrial dysfunction and bioenergetics failure are common pathological hallmarks in Huntington's disease (HD) and aging. In the present study, we used the YAC128 murine model of HD to examine the effects of mutant huntingtin on mitochondrial parameters related to aging in brain and skeletal muscle. We have conducted a cross-sectional natural history study of mitochondrial DNA changes in the YAC128 mouse. Here, we first show that the mitochondrial volume fraction appears to increase in the axons and dendrite regions adjacent to the striatal neuron cell bodies in old mice. Mitochondrial DNA copy number (mtDNAcn) was used as a proxy measure for mitochondrial biogenesis and function. We observed that the mtDNAcn changes significantly with age and genotype in a tissue-specific manner. We found a positive correlation between aging and the mtDNAcn in striatum and skeletal muscle but not in cortex. Notably, the YAC128 mice had lower mtDNAcn in cortex and skeletal muscle. We further show that mtDNA deletions are present in striatal and skeletal muscle tissue in both young and aged YAC128 and WT mice. Tracking gene expression levels cross-sectionally in mice allowed us to identify contributions of age and genotype to transcriptional variance in mitochondria-related genes. These findings provide insights into the role of mitochondrial dynamics in HD pathogenesis in both brain and skeletal muscle, and suggest that mtDNAcn in skeletal muscle tissue may be a potential biomarker that should be investigated further in human HD.

DOI: https://doi.org/10.1038/s41514-021-00079-2
Biosystems. 2021 Oct 07. pii: S0303-2647(21)00201-X. [Epub ahead of print]210 104559

Reversible and irreversible mitochondrial swelling: Effects of variable mitochondrial activity.

Igor Khmelinskii, Vladimir Makarov.

  An extended biophysical model was obtained by upgrading the previously reported one (Khmelinskii and Makarov, 2021). The upgraded model accommodates variations of solute transport rates through the inner mitochondrial membrane (IMM) within the mitochondrial population, described by a Gaussian distribution. However, the model may be used for any functional form of the distribution. The dynamics of system parameters as predicted by the current model differed from that predicted by the previous model in the same initial conditions (Khmelinskii and Makarov, 2021). The amount of change varied from one parameter to the other, remaining in the 1-38% range. The upgraded model fitted the available experimental data with a better accuracy (R = 0.993) compared to the previous model (R = 0.978) using the same experimental data (Khmelinskii and Makarov, 2021). The fitting procedure also estimated the Gaussian distribution parameters. The new model requires much larger computational resources, but given its higher accuracy, it may be used for better analysis of experimental data and for better prediction of MS dynamics in different initial conditions. Note that activities of individual mitochondria in mitochondrial populations should vary within biological tissues. Thus, the currently upgraded model is a better tool for biological and bio-medical applications. We believe that this model is much better adapted to the analysis of MS dynamics in vivo.

Keywords:  Biophysical model; Computation analysis; Irreversible swelling; Mitochondrion; Reversible swelling; Swelling

DOI:  https://doi.org/10.1016/j.biosystems.2021.104559
Trends Cell Biol. 2021 Oct 08. pii: S0962-8924(21)00183-5. [Epub ahead of print]

Hierarchical folding of the catalytic core during mitochondrial ribosome biogenesis.

Elena Lavdovskaia, Hauke S Hillen, Ricarda Richter-Dennerlein.

Final maturation steps during ribosome biogenesis require the assistance of assembly and quality control factors to ensure the folding of rRNA and proteins into a functional translation machinery. Here we integrate several recent structural snapshots of native large ribosomal subunit intermediates into the complex pathway of mitochondrial ribosome assembly.

DOI: https://doi.org/10.1016/j.tcb.2021.09.004
Science. 2021 Oct 15. 374(6565): eabe9977

Mitochondrial translation is required for sustained killing by cytotoxic T cells.

Miriam Lisci, Philippa R Barton, Lyra O Randzavola, Claire Y Ma, Julia M Marchingo, Doreen A Cantrell, Vincent Paupe, Julien Prudent, Jane C Stinchcombe, Gillian M Griffiths.

[Figure: see text].

DOI: https://doi.org/10.1126/science.abe9977
Int J Mol Sci. 2021 Sep 29. pii: 10548. [Epub ahead of print]22(19):

Sustained Activation of TNFα-Induced DNA Damage Response in Newly Differentiated Adipocytes.

Mahara Valverde, Aarón Sánchez-Brito.

  The response to DNA damage is the mechanism that allows the interaction between stress signals, inflammatory secretions, DNA repair, and maintenance of cell and tissue homeostasis. Adipocyte dysfunction is the cellular trigger for various disease states such as insulin resistance, diabetes, and obesity, among many others. Previously, our group demonstrated that adipogenesis per se, from mesenchymal/stromal stem cells derived from human adipose tissue (hASCs), involves an accumulation of DNA damage and a gradual loss of the repair capacity of oxidative DNA damage. Therefore, our objective was to identify whether healthy adipocytes differentiated for the first time from hASCs, when receiving inflammatory signals induced with TNFα, were able to persistently activate the DNA Damage Response and thus trigger adipocyte dysfunction. We found that TNFα at similar levels circulating in obese humans induce a sustained response to DNA damage response as part of the Senescence-Associated Secretory Phenotype. This mechanism shows the impact of inflammatory environment early affect adipocyte function, independently of aging.

Keywords:  DNA-damage response; TNFα; comet assay; hASCs; human adipocytes; pATM; γH2AX

DOI:  https://doi.org/10.3390/ijms221910548
STAR Protoc. 2021 Dec 17. 2(4): 100850

Generating stable isolated mitochondrial recipient clones in mammalian cells using MitoPunch mitochondrial transfer.

Alexander J Sercel, Alexander J Napior, Alexander N Patananan, Ting-Hsiang Wu, Pei-Yu Chiou, Michael A Teitell.

  This protocol describes the assembly and use of MitoPunch to deliver mitochondria containing mitochondrial DNA (mtDNA) into cells lacking mtDNA (ρ0 cells). MitoPunch generates stable isolated mitochondrial recipient clones with restored mtDNA and recovered respiration, enabling investigation of mtDNA mutations and mtDNA-nuclear DNA interactions in a range of cell types. For complete details on the use and execution of this protocol, please refer to Sercel et al. (2021) and Patananan et al. (2020).

Keywords:  Biotechnology and bioengineering; Cell Biology; Cell culture; Cell-based Assays; Metabolism

DOI:  https://doi.org/10.1016/j.xpro.2021.100850
FASEB Bioadv. 2021 Oct;3(10): 855-865

Adaptive responses to air pollution in human dermal fibroblasts and their potential roles in aging.

Wil J Reynolds, Amy Bowman, Peter S Hanson, Adam Critchley, Ben Griffiths, Bhaven Chavan, Mark A Birch-Machin.

  The damaging effects of air pollution on the skin are becoming increasingly researched and the outcomes of this research are now a major influence in the selection and development of protective ingredients for skincare formulations. However, extensive research has not yet been conducted into the specific cellular defense systems that are being affected after exposure to such pollutants. Research investigating the affected systems is integral to the development of suitable interventions that are capable of augmenting the systems most impacted by air pollutant exposure. The following studies involved exposing primary human dermal fibroblasts to different concentrations of particulate matter and analyzing its effects on mitochondrial complex activity, nuclear factor erythroid 2-related factor 2 localization using immunocytochemistry and protein expression of electron transport chain complex proteins, sirtuin-1 (SIRT1), and peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α) using western blotting. Particulate matter-induced alterations in both mitochondrial complex protein and activity, indicating oxidative stress, which was also complimented by increased expression of antioxidant proteins GSTP1/2 and SOD2. Particulate matter also seemed to modify expression of the proteins SIRT1 and PGC-1α which are heavily involved in the regulation of mitochondrial biogenesis and energy metabolism. Given the reported results indicating that particulate matter induces damage through oxidative stress and has a profound effect on mitochondrial homeostasis, interventions involving targeted mitochondrial antioxidants may help to minimize the damaging downstream effects of pollutant-induced oxidative stress originating from the mitochondria.

Keywords:  antioxidant; mitochondria; oxidative stress; pollution; skin

DOI:  https://doi.org/10.1096/fba.2021-00056
Nucleic Acids Res. 2021 Oct 11. pii: gkab789. [Epub ahead of print]

Translational activators and mitoribosomal isoforms cooperate to mediate mRNA-specific translation in Schizosaccharomyces pombe mitochondria.

Christopher J Herbert, Sylvie Labarre-Mariotte, David Cornu, Cyrielle Sophie, Cristina Panozzo, Thomas Michel, Geneviève Dujardin, Nathalie Bonnefoy.

Mitochondrial mRNAs encode key subunits of the oxidative phosphorylation complexes that produce energy for the cell. In Saccharomyces cerevisiae, mitochondrial translation is under the control of translational activators, specific to each mRNA. In Schizosaccharomyces pombe, which more closely resembles the human system by its mitochondrial DNA structure and physiology, most translational activators appear to be either lacking, or recruited for post-translational functions. By combining bioinformatics, genetic and biochemical approaches we identified two interacting factors, Cbp7 and Cbp8, controlling Cytb production in S. pombe. We show that their absence affects cytb mRNA stability and impairs the detection of the Cytb protein. We further identified two classes of Cbp7/Cbp8 partners and showed that they modulated Cytb or Cox1 synthesis. First, two isoforms of bS1m, a protein of the small mitoribosomal subunit, that appear mutually exclusive and confer translational specificity. Second, a complex of four proteins dedicated to Cox1 synthesis, which includes an RNA helicase that interacts with the mitochondrial ribosome. Our results suggest that S. pombe contains, in addition to complexes of translational activators, a heterogeneous population of mitochondrial ribosomes that could specifically modulate translation depending on the mRNA translated, in order to optimally balance the production of different respiratory complex subunits.

DOI: https://doi.org/10.1093/nar/gkab789
Int J Mol Sci. 2021 Sep 23. pii: 10215. [Epub ahead of print]22(19):

Increased CD47 and MHC Class I Inhibitory Signals Expression in Senescent CD1 Primary Mouse Lung Fibroblasts.

Elisa Hernández-Mercado, Jessica Lakshmi Prieto-Chávez, Lourdes Andrea Arriaga-Pizano, Salomon Hernández-Gutierrez, Fela Mendlovic, Mina Königsberg, Norma Edith López-Díazguerrero.

  Cellular senescence is more than a proliferative arrest in response to various stimuli. Senescent cells (SC) participate in several physiological processes, and their adequate removal is essential to maintain tissue and organism homeostasis. However, SC accumulation in aging and age-related diseases alters the tissue microenvironment leading to deterioration. The immune system clears the SC, but the specific scenarios and mechanisms related to recognizing and eliminating them are unknown. Hence, we aimed to evaluate the existence of three regulatory signals of phagocytic function, CD47, major histocompatibility complex class I (MHC-I), and calreticulin, present in the membrane of SC. Therefore, primary fibroblasts were isolated from CD1 female mice lungs, and stress-induced premature senescence (SIPS) was induced with hydrogen peroxide. Replicative senescence (RS) was used as a second senescent model. Our results revealed a considerable increment of CD47 and MHC-I in RS and SIPS fibroblasts. At the same time, no significant changes were found in calreticulin, suggesting that those signals might be associated with evading immune system recognition and thus averting senescent cells clearance.

Keywords:  CD47; MHC class I; calreticulin; senescent cell clearance regulation

DOI:  https://doi.org/10.3390/ijms221910215
Free Radic Biol Med. 2021 Oct 08. pii: S0891-5849(21)00754-1. [Epub ahead of print]

Glutamine restores mitochondrial respiration in bleomycin-injured epithelial cells.

Hoora Shaghaghi, Rachel Para, Cara Tran, Jesse Roman, Yemaiza Ojeda-Lassalle, Jianxin Sun, Freddy Romero, Ross Summer.

  Whether from known or unknown causes, loss of epithelial repair plays a central role in the pathogenesis of pulmonary fibrosis. Recently, diminished mitochondrial function has been implicated as a factor contributing to the loss of epithelial repair but the mechanisms mediating these changes have not been defined. Here, we investigated the factors contributing to mitochondrial respiratory dysfunction after bleomycin, a widely accepted agent for modeling pulmonary fibrosis in mice and in vitro systems. In agreement with previous reports, we found that mitochondrial respiration was decreased in lung epithelial cells exposed to bleomycin, but we also observed that responses differed depending on the type of metabolic fuel available to cells. For example, we found that mitochondrial respiration was dramatically reduced when glucose served as the primary fuel. Moreover, this associated with a marked decrease in glucose uptake, expression of glucose uptake transport 1 and capacity to augment glycolysis to either glucose or oligomycin. Conversely, mitochondrial respiration was largely preserved if glutamine was present in culture medium. The addition of glutamine also lead to increased intracellular metabolite levels, including multiple TCA cycle intermediates and the glycolytic intermediate lactate, and was associated with reduced DNA damage and cell death to bleomycin. In summary, our findings indicate that glutamine, rather than glucose, supports mitochondrial respiration and metabolite production in injured lung epithelium, and suggest that this shift away from glucose utilization serves to protect the lung epithelium from bleomycin injury.

Keywords:  13C fluxomics; 13CNMR; DNA damage; Epithelium; Glutamine; LC-MS/MS; Metabolic reprogramming; Mitochondria; Targeted metabolomics

DOI:  https://doi.org/10.1016/j.freeradbiomed.2021.10.006
STAR Protoc. 2021 Dec 17. 2(4): 100868

A high-throughput genetic screening protocol to measure lipid bilayer stress-induced unfolded protein response in Saccharomyces cerevisiae.

Nurulain Ho, Wei Sheng Yap, Guillaume Thibault.

  The endoplasmic reticulum (ER) stress is defined by the accumulation of unfolded proteins at the ER and perturbation at the ER membrane, known as lipid bilayer stress (LBS). In turn, ER stress triggers the unfolded protein response (UPR) to restore ER homeostasis. Here, we provide a modified protocol based on the synthetic genetic array analysis in Saccharomyces cerevisiae to identify genetic perturbations that induce the UPR by LBS. This method is adaptable to other canonical stress pathways. For complete details on the use and execution of this protocol, please refer to Ho et al. (2020), Jonikas et al. (2009) and Baryshnikova et al. (2010).

Keywords:  Cell Membrane; Cell-based Assays; Flow Cytometry/Mass Cytometry; Gene Expression; Genetics; High Throughput Screening; Model Organisms; Signal Transduction

DOI:  https://doi.org/10.1016/j.xpro.2021.100868
Int J Biol Macromol. 2021 Oct 08. pii: S0141-8130(21)02155-3. [Epub ahead of print]

The crosstalk between pattern-recognition receptor signaling and calcium signaling.

Fanyun Kong, Hongjuan You, Kuiyang Zheng, Renxian Tang, Chunfu Zheng.

  The innate immune system is the first line of host defense, and it is capable of resisting both exogenous pathogenic challenges and endogenous danger signals via different pattern recognition receptors (PRRs), including Toll-like receptors, retinoic acid-inducible gene-1 (RIG-1)-like receptors, cytosolic DNA sensors, as well as nucleotide-binding oligomerization domain (NOD)-like receptors. After recognizing the pathogen-associated molecular patterns from exogenous microbes or the damage-associated molecular patterns from endogenous immune-stimulatory signals, these PRRs signaling pathways can induce the expression of interferons and inflammatory factors against microbial pathogen invasion and endogenous stresses. Calcium (Ca2+) is a second messenger that participates in the modulation of various biological processes, including survival, proliferation, apoptosis, and immune response, and is involved in diverse diseases, such as autoimmune diseases and virus infection. To date, accumulating evidence elucidated that the PRR signaling exhibited a regulatory effect on Ca2+ signaling. Meanwhile, Ca2+ signaling also played a critical role in controlling biological processes mediated by the PRR adaptors. Since the importance of these two signalings, it would be interesting to clarify the deeper biological implications of their interplays. This review focuses on the crosstalk between Ca2+ signaling and PRR signaling to regulate innate immune responses.

Keywords:  Calcium signaling; DNA sensors; Janus kinase/signal transducer and activator of transcription pathway; Nuclear factor κB pathway; Nucleotide-binding oligomerization domain (NOD)-like receptors; Pattern-recognition receptor; Retinoic acid-inducible gene-1 (RIG-1)-like receptors; Toll-like receptors

DOI:  https://doi.org/10.1016/j.ijbiomac.2021.10.014
Nat Commun. 2021 Oct 13. 12(1): 5989

Phase separation of Nur77 mediates celastrol-induced mitophagy by promoting the liquidity of p62/SQSTM1 condensates.

Shuang-Zhou Peng, Xiao-Hui Chen, Si-Jie Chen, Jie Zhang, Chuan-Ying Wang, Wei-Rong Liu, Duo Zhang, Ying Su, Xiao-Kun Zhang.

Liquid-liquid phase separation promotes the formation of membraneless condensates that mediate diverse cellular functions, including autophagy of misfolded proteins. However, how phase separation participates in autophagy of dysfunctional mitochondria (mitophagy) remains obscure. We previously discovered that nuclear receptor Nur77 (also called TR3, NGFI-B, or NR4A1) translocates from the nucleus to mitochondria to mediate celastrol-induced mitophagy through interaction with p62/SQSTM1. Here, we show that the ubiquitinated mitochondrial Nur77 forms membraneless condensates capable of sequestrating damaged mitochondria by interacting with the UBA domain of p62/SQSTM1. However, tethering clustered mitochondria to the autophagy machinery requires an additional interaction mediated by the N-terminal intrinsically disordered region (IDR) of Nur77 and the N-terminal PB1 domain of p62/SQSTM1, which confers Nur77-p62/SQSTM1 condensates with the magnitude and liquidity. Our results demonstrate how composite multivalent interaction between Nur77 and p62/SQSTM1 coordinates to sequester damaged mitochondria and to connect targeted cargo mitochondria for autophagy, providing mechanistic insight into mitophagy.

DOI: https://doi.org/10.1038/s41467-021-26295-8
Immunity. 2021 Oct 12. pii: S1074-7613(21)00393-9. [Epub ahead of print]54(10): 2218-2230.e5

Ordered assembly of the cytosolic RNA-sensing MDA5-MAVS signaling complex via binding to unanchored K63-linked poly-ubiquitin chains.

Bin Song, Yun Chen, Xin Liu, Fei Yuan, Eddie Yong Jun Tan, Yixuan Lei, Ning Song, Yinqi Han, Bruce D Pascal, Patrick R Griffin, Cheng Luo, Bin Wu, Dahai Luo, Jie Zheng.

  The RNA sensor MDA5 recruits the signaling adaptor MAVS to initiate type I interferon signaling and downstream antiviral responses, a process that requires K63-linked polyubiquitin chains. Here, we examined the mechanisms whereby K63-polyUb chain regulate MDA5 activation. Only long unanchored K63-polyUbn (n ≥ 8) could mediate tetramerization of the caspase activation and recruitment domains of MDA5 (MDA5CARDs). Cryoelectron microscopy structures of a polyUb13-bound MDA5CARDs tetramer and a polyUb11-bound MDA5CARDs-MAVSCARD assembly revealed a tower-like formation, wherein eight Ubs tethered along the outer rim of the helical shell, bridging MDA5CARDs and MAVSCARD tetramers into proximity. ATP binding and hydrolysis promoted the stabilization of RNA-bound MDA5 prior to MAVS activation via allosteric effects on CARDs-polyUb complex. Abundant ATP prevented basal activation of apo MDA5. Our findings reveal the ordered assembly of a MDA5 signaling complex competent to recruit and activate MAVS and highlight differences with RIG-I in terms of CARD orientation and Ub sensing that suggest different abilities to induce antiviral responses.

Keywords:  HDX-MS; K63-polyUb chain; MAVS; MDA5; cryo-EM

DOI:  https://doi.org/10.1016/j.immuni.2021.09.008
FASEB Bioadv. 2021 Oct;3(10): 787-801

Friends and foes: Extracellular vesicles in aging and rejuvenation.

Brian V Lananna, Shin-Ichiro Imai.

  Extracellular vesicles (EVs) are released by many different cell types throughout the body and play a role in a diverse range of biological processes. EVs circulating in blood as well as in other body fluids undergo dramatic alterations over an organism's lifespan that are only beginning to be elucidated. The exact nature of these changes is an area of active and intense investigation, but lacks clear consensus due to the substantial heterogeneity in EV subpopulations and insufficiencies in current technologies. Nonetheless, emerging evidence suggests that EVs regulate systemic aging as well as the pathophysiology of age-related diseases. Here, we review the current literature investigating EVs and aging with an emphasis on consequences for the maintenance of human healthspan. Intriguingly, the biological utility of EVs both in vitro and in vivo and across contexts depends on the states of the source cells or tissues. As such, EVs secreted by cells in an aged or pathological state may impose detrimental consequences on recipient cells, while EVs secreted by youthful or healthy cells may promote functional improvement. Thus, it is critical to understand both functions of EVs and tip the balance toward their beneficial effects as an antiaging intervention.

Keywords:  NAD+ metabolism; ageing; aging; exosome; extracellular vesicle; longevity

DOI:  https://doi.org/10.1096/fba.2021-00077
Mol Biol Rep. 2021 Oct 13.

Intracellular metabolic reprogramming mediated by micro-RNAs in differentiating and proliferating cells under non-diseased conditions.

Varsha Singh.

  Intracellular metabolic reprogramming is a critical process the cells carry out to increase biomass, energy fulfillment and genome replication. Cells reprogram their demands from internal catabolic or anabolic activities in coordination with multiple genes and microRNAs which further control the critical processes of differentiation and proliferation. The microRNAs reprogram the metabolism involving mitochondria, the nucleus and the biochemical processes utilizing glucose, amino acids, lipids, and nucleic acids resulting in ATP production. The processes of glycolysis, tricarboxylic acid cycle, or oxidative phosphorylation are also mediated by micro-RNAs maintaining cells and organs in a non-diseased state. Several reports have shown practical applications of metabolic reprogramming for clinical utility to assess various diseases, mostly studying cancer and immune-related disorders. Cells under diseased conditions utilize glycolysis for abnormal growth or proliferation, respectively, affecting mitochondrial paucity and biogenesis. Similar metabolic processes also affect gene expressions and transcriptional regulation for carrying out biochemical reactions. Metabolic reprogramming is equally vital for regulating cell environment to maintain organs and tissues in non-diseased states. This review offers in depth insights and analysis of how miRNAs regulate metabolic reprogramming in four major types of cells undergoing differentiation and proliferation, i.e., immune cells, neuronal cells, skeletal satellite cells, and cardiomyocytes under a non-diseased state. Further, the work systematically summarizes and elaborates regulation of genetic switches by microRNAs through predominantly through cellular reprogramming and metabolic processes for the first time. The observations will lead to a better understanding of disease initiation during the differentiation and proliferation stages of cells, as well as fresh approaches to studying clinical onset of linked metabolic diseases targeting metabolic processes.

Keywords:  Cell differentiation; Cell proliferation; Gene regulation; Metabolic reprogramming; MicroRNAs; Signal transduction

DOI:  https://doi.org/10.1007/s11033-021-06769-0
Genome Biol. 2021 Oct 15. 22(1): 292

Gut bacterial metabolites modulate endoplasmic reticulum stress.

Xiaobo Ke, Kwontae You, Matthieu Pichaud, Henry J Haiser, Daniel B Graham, Hera Vlamakis, Jeffrey A Porter, Ramnik J Xavier.

  BACKGROUND: The endoplasmic reticulum (ER) is a membranous organelle that maintains proteostasis and cellular homeostasis, controlling the fine balance between health and disease. Dysregulation of the ER stress response has been implicated in intestinal inflammation associated with inflammatory bowel disease (IBD), a chronic condition characterized by changes to the mucosa and alteration of the gut microbiota. While the microbiota and microbially derived metabolites have also been implicated in ER stress, examples of this connection remain limited to a few observations from pathogenic bacteria. Furthermore, the mechanisms underlying the effects of bacterial metabolites on ER stress signaling have not been well established.RESULTS: Utilizing an XBP1s-GFP knock-in reporter colorectal epithelial cell line, we screened 399 microbiome-related metabolites for ER stress pathway modulation. We find both ER stress response inducers (acylated dipeptide aldehydes and bisindole methane derivatives) and suppressors (soraphen A) and characterize their activities on ER stress gene transcription and translation. We further demonstrate that these molecules modulate the ER stress pathway through protease inhibition or lipid metabolism interference.
CONCLUSIONS: Our study identified novel links between classes of gut microbe-derived metabolites and the ER stress response, suggesting the potential for these metabolites to contribute to gut ER homeostasis and providing insight into the molecular mechanisms by which gut microbes impact intestinal epithelial cell homeostasis.

Keywords:  ER stress; Intestinal epithelial homeostasis; Microbial metabolites; Unfolded protein response

DOI:  https://doi.org/10.1186/s13059-021-02496-8
Cell Death Discov. 2021 Oct 14. 7(1): 293

Targeting the complex I and III of mitochondrial electron transport chain as a potentially viable option in liver cancer management.

Qin Yang, Ling Wang, Jiaye Liu, Wanlu Cao, Qiuwei Pan, Meng Li.

Liver cancer is one of the most common and lethal types of oncological disease in the world, with limited treatment options. New treatment modalities are desperately needed, but their development is hampered by a lack of insight into the underlying molecular mechanisms of disease. It is clear that metabolic reprogramming in mitochondrial function is intimately linked to the liver cancer process, prompting the possibility to explore mitochondrial biochemistry as a potential therapeutic target. Here we report that depletion of mitochondrial DNA, pharmacologic inhibition of mitochondrial electron transport chain (mETC) complex I/complex III, or genetic of mETC complex I restricts cancer cell growth and clonogenicity in various preclinical models of liver cancer, including cell lines, mouse liver organoids, and murine xenografts. The restriction is linked to the production of reactive oxygen species, apoptosis induction and reduced ATP generation. As a result, our findings suggest that the mETC compartment of mitochondria could be a potential therapeutic target in liver cancer.

DOI: https://doi.org/10.1038/s41420-021-00675-x
Hum Genet. 2021 Oct 13.

A recessive variant in TFAM causes mtDNA depletion associated with primary ovarian insufficiency, seizures, intellectual disability and hearing loss.

Farid Ullah, Waqar Rauf, Kamal Khan, Sheraz Khan, Katrina M Bell, Vanessa Cristina de Oliveira, Muhammad Tariq, Shabnam Bakhshalizadeh, Philippe Touraine, Nicholas Katsanis, Andrew Sinclair, Sijie He, Elena J Tucker, Shahid M Baig, Erica E Davis.

Mitochondrial disorders are collectively common, genetically heterogeneous disorders in both pediatric and adult populations. They are caused by molecular defects in oxidative phosphorylation, failure of essential bioenergetic supply to mitochondria, and apoptosis. Here, we present three affected individuals from a consanguineous family of Pakistani origin with variable seizures and intellectual disability. Both females display primary ovarian insufficiency (POI), while the male shows abnormal sex hormone levels. We performed whole exome sequencing and identified a recessive missense variant c.694C > T, p.Arg232Cys in TFAM that segregates with disease. TFAM (mitochondrial transcription factor A) is a component of the mitochondrial replisome machinery that maintains mtDNA transcription and replication. In primary dermal fibroblasts, we show depletion of mtDNA and significantly altered mitochondrial function and morphology. Moreover, we observed reduced nucleoid numbers with significant changes in nucleoid size or shape in fibroblasts from an affected individual compared to controls. We also investigated the effect of tfam impairment in zebrafish; homozygous tfam mutants carrying an in-frame c.141_149 deletion recapitulate the mtDNA depletion and ovarian dysgenesis phenotypes observed in affected humans. Together, our genetic and functional data confirm that TFAM plays a pivotal role in gonad development and expands the repertoire of mitochondrial disease phenotypes.

DOI: https://doi.org/10.1007/s00439-021-02380-2
Cancers (Basel). 2021 Sep 30. pii: 4933. [Epub ahead of print]13(19):

Biological Aspects of Inflamm-Aging in Childhood Cancer Survivors.

Francesca Rossi, Alessandra Di Paola, Elvira Pota, Maura Argenziano, Daniela Di Pinto, Maria Maddalena Marrapodi, Caterina Di Leva, Martina Di Martino, Chiara Tortora.

  Anti-cancer treatments improve survival in children with cancer. A total of 80% of children treated for childhood cancer achieve 5-year survival, becoming long-term survivors. However, they undergo several chronic late effects related to treatments. In childhood cancer survivors a chronic low-grade inflammation, known as inflamm-aging, is responsible for frailty, a condition characterized by vital organ failure and by premature aging processes. Inflamm-aging is closely related to chemotherapy and radiotherapy, which induce inflammation, accumulation of senescent cells, DNA mutations, and the production of reactive oxygen species. All these conditions are responsible for the onset of secondary diseases, such as osteoporosis, cardiovascular diseases, obesity, and infertility. Considering that the pathobiology of frailty among childhood cancer survivors is still unknown, investigations are needed to better understand frailty's biological and molecular processes and to identify inflamm-aging key biomarkers in order to facilitate the screening of comorbidities and to clarify whether treatments, normally used to modulate inflamm-aging, may be beneficial. This review offers an overview of the possible biological mechanisms involved in the development of inflamm-aging, focusing our attention on immune system alteration, oxidative stress, cellular senescence, and therapeutic strategies.

Keywords:  childhood cancer survivors; frailty; immune system; inflamm-aging; oxidative stress; senescence; therapeutic strategies

DOI:  https://doi.org/10.3390/cancers13194933
Nat Commun. 2021 Oct 14. 12(1): 5999

The Hsc70 disaggregation machinery removes monomer units directly from α-synuclein fibril ends.

Matthias M Schneider, Saurabh Gautam, Therese W Herling, Ewa Andrzejewska, Georg Krainer, Alyssa M Miller, Victoria A Trinkaus, Quentin A E Peter, Francesco Simone Ruggeri, Michele Vendruscolo, Andreas Bracher, Christopher M Dobson, F Ulrich Hartl, Tuomas P J Knowles.

Molecular chaperones contribute to the maintenance of cellular protein homoeostasis through assisting de novo protein folding and preventing amyloid formation. Chaperones of the Hsp70 family can further disaggregate otherwise irreversible aggregate species such as α-synuclein fibrils, which accumulate in Parkinson's disease. However, the mechanisms and kinetics of this key functionality are only partially understood. Here, we combine microfluidic measurements with chemical kinetics to study α-synuclein disaggregation. We show that Hsc70 together with its co-chaperones DnaJB1 and Apg2 can completely reverse α-synuclein aggregation back to its soluble monomeric state. This reaction proceeds through first-order kinetics where monomer units are removed directly from the fibril ends with little contribution from intermediate fibril fragmentation steps. These findings extend our mechanistic understanding of the role of chaperones in the suppression of amyloid proliferation and in aggregate clearance, and inform on possibilities and limitations of this strategy in the development of therapeutics against synucleinopathies.

DOI: https://doi.org/10.1038/s41467-021-25966-w
J Mol Biol. 2021 Oct 07. pii: S0022-2836(21)00490-3. [Epub ahead of print] 167257

No Longer A One-Trick Pony: STING Signaling Activity Beyond Interferon.

Jianjun Wu, Nan Yan.

  Stimulator of interferon genes (STING) plays an important role in infection, autoimmune disease and cancer. STING-mediated type I interferon (IFN) signaling is well recognized and extensively studied. Several IFN-independent activities of STING were also discovered in recent years and their physiological importance has begun to be appreciated. Here, we review recent advance in the evolutionary origin and molecular mechanisms of STING-mediated IFN-independent activities. New insights from these studies suggest that STING functions as a hub that converts multiple environmental cues into diverse cellular responses rather than acts as a simple IFN-producing machine. This expanded view of STING biology should guide future clinical testing of STING agonists and treatment of STING-associated human diseases.

Keywords:  STING evolution; STING trafficking; STING-mediated IFN-independent activities; STING-mediated autophagy; STING-mediated cell death

DOI:  https://doi.org/10.1016/j.jmb.2021.167257
Int J Mol Sci. 2021 Sep 29. pii: 10545. [Epub ahead of print]22(19):

The Role of PPAR Alpha in the Modulation of Innate Immunity.

Maja Grabacka, Małgorzata Pierzchalska, Przemysław M Płonka, Piotr Pierzchalski.

  Peroxisome proliferator-activated receptor α is a potent regulator of systemic and cellular metabolism and energy homeostasis, but it also suppresses various inflammatory reactions. In this review, we focus on its role in the regulation of innate immunity; in particular, we discuss the PPARα interplay with inflammatory transcription factor signaling, pattern-recognition receptor signaling, and the endocannabinoid system. We also present examples of the PPARα-specific immunomodulatory functions during parasitic, bacterial, and viral infections, as well as approach several issues associated with innate immunity processes, such as the production of reactive nitrogen and oxygen species, phagocytosis, and the effector functions of macrophages, innate lymphoid cells, and mast cells. The described phenomena encourage the application of endogenous and pharmacological PPARα agonists to alleviate the disorders of immunological background and the development of new solutions that engage PPARα activation or suppression.

Keywords:  fenofibrate; nitric oxide synthase; oleoylethanolamide; palmitoylethanolamide; pattern-recognition receptors; phagocytosis

DOI:  https://doi.org/10.3390/ijms221910545
Basic Res Cardiol. 2021 Oct 12. 116(1): 56

Regulation of STAT3 and its role in cardioprotection by conditioning: focus on non-genomic roles targeting mitochondrial function.

Stefano Comità, Saveria Femmino, Cecilia Thairi, Giuseppe Alloatti, Kerstin Boengler, Pasquale Pagliaro, Claudia Penna.

  Ischemia-reperfusion injury (IRI) is one of the biggest challenges for cardiovascular researchers given the huge death toll caused by myocardial ischemic disease. Cardioprotective conditioning strategies, namely pre- and post-conditioning maneuvers, represent the most important strategies for stimulating pro-survival pathways essential to preserve cardiac health. Conditioning maneuvers have proved to be fundamental for the knowledge of the molecular basis of both IRI and cardioprotection. Among this evidence, the importance of signal transducer and activator of transcription 3 (STAT3) emerged. STAT3 is not only a transcription factor but also exhibits non-genomic pro-survival functions preserving mitochondrial function from IRI. Indeed, STAT3 is emerging as an influencer of mitochondrial function to explain the cardioprotection phenomena. Studying cardioprotection, STAT3 proved to be crucial as an element of the survivor activating factor enhancement (SAFE) pathway, which converges on mitochondria and influences their function by cross-talking with other cardioprotective pathways. Clearly there are still some functional properties of STAT3 to be discovered. Therefore, in this review, we highlight the evidence that places STAT3 as a promoter of the metabolic network. In particular, we focus on the possible interactions of STAT3 with processes aimed at maintaining mitochondrial functions, including the regulation of the electron transport chain, the production of reactive oxygen species, the homeostasis of Ca2+ and the inhibition of opening of mitochondrial permeability transition pore. Then we consider the role of STAT3 and the parallels between STA3/STAT5 in cardioprotection by conditioning, giving emphasis to the human heart and confounders.

Keywords:  Ca2+ regulation; Ischemia reperfusion injury; Mitochondrial permeability transition pore; RISK pathway; Reactive oxygen species; SAFE pathway; STAT3; STAT5

DOI:  https://doi.org/10.1007/s00395-021-00898-0
Nature. 2021 Oct 13.

The cellular environment shapes the nuclear pore complex architecture.

Anthony P Schuller, Matthias Wojtynek, David Mankus, Meltem Tatli, Rafael Kronenberg-Tenga, Saroj G Regmi, Phat V Dip, Abigail K R Lytton-Jean, Edward J Brignole, Mary Dasso, Karsten Weis, Ohad Medalia, Thomas U Schwartz.

Nuclear pore complexes (NPCs) create large conduits for cargo transport between the nucleus and cytoplasm across the nuclear envelope (NE)1-3. These multi-megadalton structures are composed of about thirty different nucleoporins that are distributed in three main substructures (the inner, cytoplasmic and nucleoplasmic rings) around the central transport channel4-6. Here we use cryo-electron tomography on DLD-1 cells that were prepared using cryo-focused-ion-beam milling to generate a structural model for the human NPC in its native environment. We show that-compared with previous human NPC models obtained from purified NEs-the inner ring in our model is substantially wider; the volume of the central channel is increased by 75% and the nucleoplasmic and cytoplasmic rings are reorganized. Moreover, the NPC membrane exhibits asymmetry around the inner-ring complex. Using targeted degradation of Nup96, a scaffold nucleoporin of the cytoplasmic and nucleoplasmic rings, we observe the interdependence of each ring in modulating the central channel and maintaining membrane asymmetry. Our findings highlight the inherent flexibility of the NPC and suggest that the cellular environment has a considerable influence on NPC dimensions and architecture.

DOI: https://doi.org/10.1038/s41586-021-03985-3
Trends Immunol. 2021 Oct 09. pii: S1471-4906(21)00204-0. [Epub ahead of print]

ADAR1 entraps sinister cellular dsRNAs, thresholding antiviral responses.

Liam P Keegan, Dragana Vukić, Mary A O'Connell.

ADAR1 edits adenosines to inosines in cellular double-stranded (ds)RNA, thereby preventing aberrant activation of antiviral dsRNA sensors, as well as interferon (IFN) induction in Aicardi-Goutières syndrome (AGS) encephalopathy. Recently, Nakahama et al., Tang et al., Maurano et al., and de Reuver et al. demonstrated that Adar1 Zα domain-mutant mice show aberrant MDA5 and PKR activation, developing encephalopathies; short Z-RNA patches within cellular dsRNA are unexpectedly crucial in causing aberrant antiviral responses.

DOI: https://doi.org/10.1016/j.it.2021.09.013
Mech Ageing Dev. 2021 Oct 09. pii: S0047-6374(21)00155-X. [Epub ahead of print] 111583

The tumor suppression theory of aging.

Alexander M Wolf.

  Despite continued increases in human life expectancy, the factors determining the rate of human biological aging remain unknown. Without understanding the molecular mechanisms underlying aging, efforts to prevent aging are unlikely to succeed. The tumor suppression theory of aging introduced here proposes somatic mutation as the proximal cause of aging, but postulates that oncogenic transformation and clonal expansion, not functional impairment, are the relevant consequences of somatic mutation. Obesity and caloric restriction accelerate and decelerate aging due to their effect on cell proliferation, during which most mutations arise. Most phenotypes of aging are merely tumor-suppressive mechanisms that evolved to limit malignant growth, the dominant age-related cause of death in early and middle life. Cancer limits life span for most long-lived mammals, a phenomenon known as Peto's paradox. Its conservation across species demonstrates that mutation is a fundamental but hard limit on mammalian longevity. Cell senescence and apoptosis and differentiation induced by oncogenes, telomere shortening or DNA damage evolved as a second line of defense to limit the tumorigenic potential of clonally expanding cells, but accumulating senescent cells, senescence-associated secretory phenotypes and stem cell exhaustion eventually cause tissue dysfunction and the majority, if not most, phenotypes of aging.

Keywords:  aging; cancer; cell senescence; somatic mutation; tumor suppression

DOI:  https://doi.org/10.1016/j.mad.2021.111583
J Proteome Res. 2021 Oct 12.

Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells.

Alireza Delfarah, Nicolas G Hartel, DongQing Zheng, Jesse Yang, Nicholas A Graham.

  Senescence is a permanent cell cycle arrest that occurs in response to cellular stress and promotes age-related disease. Because senescence differs greatly depending on cell type and senescence inducer, continued progress in the characterization of senescent cells is needed. Here, we analyzed primary human mammary epithelial cells (HMECs), a model system for aging and cancer, using mass spectrometry-based proteomics. By integrating data from replicative senescence, immortalization by telomerase reactivation, and quiescence, we identified a robust proteomic signature of HMEC senescence consisting of 34 upregulated and 10 downregulated proteins. This approach identified known senescence biomarkers including β-galactosidase (GLB1) as well as novel senescence biomarkers including catechol O-methyltransferase (COMT), synaptic vesicle membrane protein VAT-1 homolog (VAT1), and plastin-1/3 (PLS1/PLS3). Gene ontology enrichment analysis demonstrated that senescent HMECs upregulated lysosomal proteins and downregulated RNA metabolic processes. In addition, a classification model based on our proteomic signature successfully discriminated proliferating and senescent HMECs at the transcriptional level. Finally, we found that the HMEC senescence signature was positively and negatively correlated with proteomic alterations in HMEC aging and breast cancer, respectively. Taken together, our results demonstrate the power of proteomics to identify cell type-specific signatures of senescence and advance the understanding of senescence in HMECs.

Keywords:  aging; breast cancer; data integration; mammary epithelial cell; proteomics; replicative senescence

DOI:  https://doi.org/10.1021/acs.jproteome.1c00659