bims-nenemi 2022-07-17 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2022‒07‒17
nine papers selected by
Marco Tigano
Thomas Jefferson University

Comparing the mitochondrial signatures in ESCs and iPSCs and their neural derivations.
Oxidized DNA fragments exit mitochondria via mPTP- and VDAC-dependent channels to activate NLRP3 inflammasome and interferon signaling.
In vitro reconstitution reveals a key role of human mitochondrial EXOG in RNA primer processing.
Mitochondrial Stress Responses in Duchenne muscular dystrophy: Metabolic Dysfunction or Adaptive Reprogramming?
Decoding endoplasmic reticulum stress signals in cancer cells and antitumor immunity.
Hijacking Cellular Stress Responses to Promote Lifespan.
Small RNAs derived from tRNA fragmentation regulate the functional maturation of neonatal β cells.
MERLIN: A BRET-Based Proximity Biosensor for Studying Mitochondria-ER Contact Sites.
Mitochondrial heterogeneity and homeostasis through the lens of a neuron.

Cell Cycle. 2022 Jul 10. 1-16

Comparing the mitochondrial signatures in ESCs and iPSCs and their neural derivations.

Cecilie Katrin Kristiansen, Anbin Chen, Lena Elise Høyland, Mathias Ziegler, Gareth John Sullivan, Laurence A Bindoff, Kristina Xiao Liang.

  Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have distinct origins: ESCs are derived from pre-implanted embryos while iPSCs are reprogrammed somatic cells. Both have their own characteristics and lineage specificity, and both are valuable tools for studying human neurological development and disease. Thus far, few studies have analyzed how differences between stem cell types influence mitochondrial function and mitochondrial DNA (mtDNA) homeostasis during differentiation into neural and glial lineages. In this study, we compared mitochondrial function and mtDNA replication in human ESCs and iPSCs at three different stages - pluripotent, neural progenitor and astrocyte. We found that while ESCs and iPSCs have a similar mitochondrial signature, neural and astrocyte derivations manifested differences. At the neural stem cell (NSC) stage, iPSC-NSCs displayed decreased ATP production and a reduction in mitochondrial respiratory chain (MRC) complex IV expression compared to ESC-NSCs. IPSC-astrocytes showed increased mitochondrial activity including elevated ATP production, MRC complex IV expression, mtDNA copy number and mitochondrial biogenesis relative to those derived from ESCs. These findings show that while ESCs and iPSCs are similar at the pluripotent stage, differences in mitochondrial function may develop during differentiation and must be taken into account when extrapolating results from different cell types.Abbreviation: BSA: Bovine serum albumin; DCFDA: 2',7'-dichlorodihydrofluorescein diacetate; DCX: Doublecortin; EAAT-1: Excitatory amino acid transporter 1; ESCs: Embryonic stem cells; GFAP: Glial fibrillary acidic protein; GS: Glutamine synthetase; iPSCs: Induced pluripotent stem cells; LC3B: Microtubule-associated protein 1 light chain 3β; LC-MS: Liquid chromatography-mass spectrometry; mito-ROS: Mitochondrial ROS; MMP: Mitochondrial membrane potential; MRC: Mitochondrial respiratory chain; mtDNA: Mitochondrial DNA; MTDR: MitoTracker Deep Red; MTG: MitoTracker Green; NSCs: Neural stem cells; PDL: Poly-D-lysine; PFA: Paraformaldehyde; PGC-1α: PPAR-γ coactivator-1 alpha; PPAR-γ: Peroxisome proliferator-activated receptor-gamma; p-SIRT1: Phosphorylated sirtuin 1; p-ULK1: Phosphorylated unc-51 like autophagy activating kinase 1; qPCR: Quantitative PCR; RT: Room temperature; RT-qPCR: Quantitative reverse transcription PCR; SEM: Standard error of the mean; TFAM: Mitochondrial transcription factor A; TMRE: Tetramethylrhodamine ethyl ester; TOMM20: Translocase of outer mitochondrial membrane 20.

Keywords:  ESCs; IPSCs; NSCs; astrocytes; mitochondrial biogenesis; mitochondrial function

DOI:  https://doi.org/10.1080/15384101.2022.2092185
Immunity. 2022 Jul 07. pii: S1074-7613(22)00280-1. [Epub ahead of print]

Oxidized DNA fragments exit mitochondria via mPTP- and VDAC-dependent channels to activate NLRP3 inflammasome and interferon signaling.

Hongxu Xian, Kosuke Watari, Elsa Sanchez-Lopez, Joseph Offenberger, Janset Onyuru, Harini Sampath, Wei Ying, Hal M Hoffman, Gerald S Shadel, Michael Karin.

  Mitochondrial DNA (mtDNA) escaping stressed mitochondria provokes inflammation via cGAS-STING pathway activation and, when oxidized (Ox-mtDNA), it binds cytosolic NLRP3, thereby triggering inflammasome activation. However, it is unknown how and in which form Ox-mtDNA exits stressed mitochondria in non-apoptotic macrophages. We found that diverse NLRP3 inflammasome activators rapidly stimulated uniporter-mediated calcium uptake to open mitochondrial permeability transition pores (mPTP) and trigger VDAC oligomerization. This occurred independently of mtDNA or reactive oxygen species, which induce Ox-mtDNA generation. Within mitochondria, Ox-mtDNA was either repaired by DNA glycosylase OGG1 or cleaved by the endonuclease FEN1 to 500-650 bp fragments that exited mitochondria via mPTP- and VDAC-dependent channels to initiate cytosolic NLRP3 inflammasome activation. Ox-mtDNA fragments also activated cGAS-STING signaling and gave rise to pro-inflammatory extracellular DNA. Understanding this process will advance the development of potential treatments for chronic inflammatory diseases, exemplified by FEN1 inhibitors that suppressed interleukin-1β (IL-1β) production and mtDNA release in mice.

Keywords:  FEN1; NLRP3 inflammasome; OGG1; Ox-mtDNA; VDAC; cGAS-STING; mPTP; mitochondria; mtDNA

DOI:  https://doi.org/10.1016/j.immuni.2022.06.007
Nucleic Acids Res. 2022 Jul 12. pii: gkac581. [Epub ahead of print]

In vitro reconstitution reveals a key role of human mitochondrial EXOG in RNA primer processing.

Anna Karlowicz, Andrzej B Dubiel, Jolanta Czerwinska, Adela Bledea, Piotr Purzycki, Marta Grzelewska, Ryan J McAuley, Roman J Szczesny, Gabriela Brzuska, Ewelina Krol, Bartosz Szczesny, Michal R Szymanski.

The removal of RNA primers is essential for mitochondrial DNA (mtDNA) replication. Several nucleases have been implicated in RNA primer removal in human mitochondria, however, no conclusive mechanism has been elucidated. Here, we reconstituted minimal in vitro system capable of processing RNA primers into ligatable DNA ends. We show that human 5'-3' exonuclease, EXOG, plays a fundamental role in removal of the RNA primer. EXOG cleaves short and long RNA-containing flaps but also in cooperation with RNase H1, processes non-flap RNA-containing intermediates. Our data indicate that the enzymatic activity of both enzymes is necessary to process non-flap RNA-containing intermediates and that regardless of the pathway, EXOG-mediated RNA cleavage is necessary prior to ligation by DNA Ligase III. We also show that upregulation of EXOG levels in mitochondria increases ligation efficiency of RNA-containing substrates and discover physical interactions, both in vitro and in cellulo, between RNase H1 and EXOG, Pol γA, Pol γB and Lig III but not FEN1, which we demonstrate to be absent from mitochondria of human lung epithelial cells. Together, using human mtDNA replication enzymes, we reconstitute for the first time RNA primer removal reaction and propose a novel model for RNA primer processing in human mitochondria.

DOI: https://doi.org/10.1093/nar/gkac581
Am J Physiol Cell Physiol. 2022 Jul 11.

Mitochondrial Stress Responses in Duchenne muscular dystrophy: Metabolic Dysfunction or Adaptive Reprogramming?

Catherine A Bellissimo, Madison C Garibotti, Christopher G R Perry.

  Mitochondrial stress may be a secondary contributor to muscle weakness in inherited muscular dystrophies. Duchenne muscular dystrophy has received the majority of attention whereby most discoveries suggest mitochondrial ATP synthesis may be reduced. However, not all studies support this finding. Furthermore, some studies have reported increased mitochondrial reactive oxygen species and propensity for permeability transition pore formation as an inducer of apoptosis, although divergent findings have also been described. A closer examination of the literature suggests the degree and direction of mitochondrial stress responses may depend on the progression of the disease, the muscle type examined, the mouse model employed with regards to pre-clinical research, the precise metabolic pathways in consideration, and in some cases the in vitro technique used to assess a given mitochondrial bioenergetic function. One intent of this review is to provide careful considerations for future experimental designs to resolve the heterogeneous nature of mitochondrial stress during the progression of Duchenne muscular dystrophy. Such considerations have implications for other muscular dystrophies as well which are addressed briefly herein. A renewed perspective of the term 'mitochondrial dysfunction' is presented whereby stress responses might be re-explored in future investigations as direct contributors to myopathy vs an adaptive 'reprogramming' intended to maintain homeostasis in the face of disease stressors themselves. In so doing, the prospective development of mitochondrial enhancement therapies can be driven by advances in perspectives as much as experimental approaches when resolving the precise relationships between mitochondrial remodelling and muscle weakness in Duchenne and, indeed, other muscular dystrophies.

Keywords:  Duchenne muscular dystrophy; bioenergetics; metabolism; mitochondria; muscle

DOI:  https://doi.org/10.1152/ajpcell.00249.2022
Trends Cancer. 2022 Jul 08. pii: S2405-8033(22)00134-0. [Epub ahead of print]

Decoding endoplasmic reticulum stress signals in cancer cells and antitumor immunity.

Camilla Salvagno, Jessica K Mandula, Paulo C Rodriguez, Juan R Cubillos-Ruiz.

  The tumor microenvironment (TME) provokes endoplasmic reticulum (ER) stress in malignant cells and infiltrating immune populations. Sensing and responding to ER stress is coordinated by the unfolded protein response (UPR), an integrated signaling pathway governed by three ER stress sensors: activating transcription factor (ATF6), inositol-requiring enzyme 1α (IRE1α), and protein kinase R (PKR)-like ER kinase (PERK). Persistent UPR activation modulates malignant progression, tumor growth, metastasis, and protective antitumor immunity. Hence, therapies targeting ER stress signaling can be harnessed to elicit direct tumor killing and concomitant anticancer immunity. We highlight recent findings on the role of the ER stress responses in onco-immunology, with an emphasis on genetic vulnerabilities that render tumors highly sensitive to therapeutic UPR modulation.

Keywords:  ER stress; cancer therapy; immune cells; tumor microenvironment; unfolded protein response

DOI:  https://doi.org/10.1016/j.trecan.2022.06.006
Front Aging. 2022 ;3 860404

Hijacking Cellular Stress Responses to Promote Lifespan.

Naibedya Dutta, Gilberto Garcia, Ryo Higuchi-Sanabria.

  Organisms are constantly exposed to stress both from the external environment and internally within the cell. To maintain cellular homeostasis under different environmental and physiological conditions, cell have adapted various stress response signaling pathways, such as the heat shock response (HSR), unfolded protein responses of the mitochondria (UPRMT), and the unfolded protein response of the endoplasmic reticulum (UPRER). As cells grow older, all cellular stress responses have been shown to deteriorate, which is a major cause for the physiological consequences of aging and the development of numerous age-associated diseases. In contrast, elevated stress responses are often associated with lifespan extension and amelioration of degenerative diseases in different model organisms, including C. elegans. Activating cellular stress response pathways could be considered as an effective intervention to alleviate the burden of aging by restoring function of essential damage-clearing machinery, including the ubiquitin-proteosome system, chaperones, and autophagy. Here, we provide an overview of newly emerging concepts of these stress response pathways in healthy aging and longevity with a focus on the model organism, C. elegans.

Keywords:  C. elegans; aging; endoplasmic reticulum; heat-shock; mitochondria; stress

DOI:  https://doi.org/10.3389/fragi.2022.860404
Cell Rep. 2022 Jul 12. pii: S2211-1247(22)00867-1. [Epub ahead of print]40(2): 111069

Small RNAs derived from tRNA fragmentation regulate the functional maturation of neonatal β cells.

Mustafa Bilal Bayazit, Cécile Jacovetti, Cristina Cosentino, Jonathan Sobel, Kejing Wu, Flora Brozzi, Adriana Rodriguez-Trejo, Lisa Stoll, Claudiane Guay, Romano Regazzi.

  tRNA-derived fragments (tRFs) are an emerging class of small non-coding RNAs with distinct cellular functions. Here, we studied the contribution of tRFs to the regulation of postnatal β cell maturation, a critical process that may lead to diabetes susceptibility in adulthood. We identified three tRFs abundant in neonatal rat islets originating from 5' halves (tiRNA-5s) of histidine and glutamate tRNAs. Their inhibition in these islets reduced β cell proliferation and insulin secretion. Mitochondrial respiration was also perturbed, fitting with the mitochondrial enrichment of nuclear-encoded tiRNA-5HisGTG and tiRNA-5GluCTC. Notably, tiRNA-5 inhibition reduced Mpc1, a mitochondrial pyruvate carrier whose knock down largely phenocopied tiRNA-5 inhibition. tiRNA-5HisGTG interactome revealed binding to Musashi-1, which was essential for the mitochondrial enrichment of tiRNA-5HisGTG. Finally, tiRNA-5s were dysregulated in the islets of diabetic and diabetes-prone animals. Altogether, tiRNA-5s represent a class of regulators of β cell maturation, and their deregulation in neonatal islets may lead to diabetes susceptibility in adulthood.

Keywords:  CP: Developmental biology; CP: Metabolism; diabetes; insulin; metabolism; pancreatic islet; transfer RNA

DOI:  https://doi.org/10.1016/j.celrep.2022.111069
Methods Mol Biol. 2022 ;2525 197-205

MERLIN: A BRET-Based Proximity Biosensor for Studying Mitochondria-ER Contact Sites.

Hector Flores-Romero, Ana J García-Sáez.

  The contacts between the endoplasmic reticulum (ER) and mitochondria play a fundamental role in a wide variety of cellular processes, like the exchange of calcium and lipids between both organelles, as well as in apoptosis and in autophagy signaling. Despite their importance, due to their dynamic and heterogeneous nature, we still lack understanding of the molecular composition, structure, and regulation of these structures. In this chapter, we introduce a new bioluminescence resonance energy transfer (BRET)-based biosensor for the quantitative analysis of mitochondria-ER interorganellar distances without perturbing their natural environment, which we call MERLIN (mitochondria ER length indicator nanosensor). Here, we describe the rationale behind the MERLIN biosensor, detail the experimental setup and methodology, and provide tips for troubleshooting.

Keywords:  Bioluminescence resonance energy transfer (BRET); Biosensor; Endoplasmic reticulum (ER); Mitochondria; Mitochondria ER contact sites (MERCs); Mitochondria ER length indicator nanosensor (MERLIN)

DOI:  https://doi.org/10.1007/978-1-0716-2473-9_14
Nat Metab. 2022 Jul 11.

Mitochondrial heterogeneity and homeostasis through the lens of a neuron.

Gulcin Pekkurnaz, Xinnan Wang.

Mitochondria are vital organelles with distinct morphological features and functional properties. The dynamic network of mitochondria undergoes structural and functional adaptations in response to cell-type-specific metabolic demands. Even within the same cell, mitochondria can display wide diversity and separate into functionally distinct subpopulations. Mitochondrial heterogeneity supports unique subcellular functions and is crucial to polarized cells, such as neurons. The spatiotemporal metabolic burden within the complex shape of a neuron requires precisely localized mitochondria. By travelling great lengths throughout neurons and experiencing bouts of immobility, mitochondria meet distant local fuel demands. Understanding mitochondrial heterogeneity and homeostasis mechanisms in neurons provides a framework to probe their significance to many other cell types. Here, we put forth an outline of the multifaceted role of mitochondria in regulating neuronal physiology and cellular functions more broadly.

DOI: https://doi.org/10.1038/s42255-022-00594-w