bims-nenemi 2022-02-27 papers

bims-nenemi

Biomed News

on Neuroinflammation, neurodegeneration and mitochondria

Issue of 2022–02–27
twenty-one papers selected by
Marco Tigano, Thomas Jefferson University

Measurement of Cytosolic Mitochondrial DNA After NLRP3 Inflammasome Activation.
Increased Drp1 promotes autophagy and ESCC progression by mtDNA stress mediated cGAS-STING pathway.
Mechanisms of mitochondrial promoter recognition in humans and other mammalian species.
A novel mechanism for NLRP3 inflammasome activation.
Cancer/Testis Antigen 55 is required for cancer cell proliferation and mitochondrial DNA maintenance.
mito-TEMPO Attenuates Oxidative Stress and Mitochondrial Dysfunction in Noise-Induced Hearing Loss via Maintaining TFAM-mtDNA Interaction and Mitochondrial Biogenesis.
Diverse injury responses of human oligodendrocyte to mediators implicated in multiple sclerosis.
Reduced ER-mitochondria connectivity promotes neuroblastoma multidrug resistance.
PINK1-parkin-mediated neuronal mitophagy deficiency in prion disease.
Mitochondrial Neurodegeneration.
Angiotensinogen uptake and stimulation of oxidative stress in human pigment retinal epithelial cells.
A DNA repair-independent role for alkyladenine DNA glycosylase in alkylation-induced unfolded protein response.
Persistent DNA damage associated with ATM kinase deficiency promotes microglial dysfunction.
Conplastic strains for identification of retrograde effects of mitochondrial dna variation on cardiometabolic traits in the spontaneously hypertensive rat.
Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.
Genetic BACH1 deficiency alters mitochondrial function and increases NLRP3 inflammasome activation in mouse macrophages.
Mitochondria in tumour progression: a network of mtDNA variants in different types of cancer.
Organellar homeostasis and innate immune sensing.
CNS Redox Homeostasis and Dysfunction in Neurodegenerative Diseases.
Mitochondrial dysfunction associated with TANGO2 deficiency.
Development and characterization of different cell models harbouring mitochondrial DNA deletions for in vitro study of Pearson syndrome.

Methods Mol Biol. 2022 ;2459 117-129

Measurement of Cytosolic Mitochondrial DNA After NLRP3 Inflammasome Activation.

Olga M Antón, Javier Traba.

  The NLRP3 inflammasome, a key component of the innate immune system that mediates caspase-1 activation, which in turn induces cleavage of the pyroptosis executioner gasdermin D and the proinflammatory cytokines IL-1β and IL-18, requires two signals to be activated. First, inflammasome priming is achieved after activation of Toll-like receptors, which leads to NF-κB signaling and transcriptional activation of the genes for NLRP3 and IL-1β. Next, the inflammasome complex is activated by a second signal that induces extrusion of mitochondrial DNA to the cytosol of the cell, which leads to its oligomerization by a not fully understood mechanism. Here we describe a simple method that employs quantitative polymerase chain reaction (qPCR) using SYBR green to measure the presence of mitochondrial DNA (mtDNA) in the cytosol, which can be used to measure cytosolic mtDNA levels after inflammasome activation.

Keywords:  Inflammasome; Mitochondrial DNA; NLRP3; Quantitative polymerase chain reaction

DOI:  https://doi.org/10.1007/978-1-0716-2144-8_12
J Exp Clin Cancer Res. 2022 Feb 24. 41(1): 76

Increased Drp1 promotes autophagy and ESCC progression by mtDNA stress mediated cGAS-STING pathway.

Yujia Li, Hui Chen, Qi Yang, Lixin Wan, Jing Zhao, Yuanyuan Wu, Jiaxin Wang, Yating Yang, Menglan Niu, Hongliang Liu, Junqi Liu, Hushan Yang, Shaogui Wan, Yanming Wang, Dengke Bao.

   BACKGROUND: Mitochondrial dynamics homeostasis is important for cell metabolism, growth, proliferation, and immune responses. The critical GTPase for mitochondrial fission, Drp1 is frequently upregulated in many cancers and is closely implicated in tumorigenesis. However, the mechanism underling Drp1 to influence tumor progression is largely unknown, especially in esophageal squamous cell carcinoma (ESCC).
METHODS: Immunohistochemistry was used to examine Drp1 and LC3B expression in tissues of ESCC patients. Autophagic vesicles were investigated by transmission electron microscopy. Fluorescent LC3B puncta and mitochondrial nucleoid were observed by fluorescent and confocal microscopy. Mitochondrial function was evaluated by mitochondrial membrane potential, ROS and ATP levels. Xenograft tumor model was performed in BALB/c nude mice to analyze the role of Drp1 on ESCC progression.
RESULTS: We found that Drp1 high expression is correlated with poor overall survival of ESCC patients. Drp1 overexpression promotes cell proliferation and xenograft ESCC tumor growth by triggering autophagy. Furthermore, we demonstrated that Drp1 overexpression disturbs mitochondrial function and subsequent induces mitochondrial DNA (mtDNA) released into the cytosol thereby inducing cytosolic mtDNA stress. Mechanistically, cytosolic mtDNA activates the cGAS-STING pathway and facilitates autophagy, which promotes ESCC cancer growth. Moreover, mtDNA digestion with DNase I and autophagy inhibition with chloroquine attenuates the cGAS-STING pathway activation and ESCC cancer growth.
CONCLUSIONS: Our finding reveals that Drp1 overexpression induces mitochondrial dysfunction and cytosolic mtDNA stress, which subsequently activates the cGAS-STING pathway, triggers autophagy and promotes ESCC progression.

Keywords:  Autophagy; Drp1; Esophageal Squamous Cell Carcinoma; Mitochondrial DNA stress; cGAS-STING signaling pathway

DOI:  https://doi.org/10.1186/s13046-022-02262-z
Nucleic Acids Res. 2022 Feb 22. pii: gkac103. [Epub ahead of print]

Mechanisms of mitochondrial promoter recognition in humans and other mammalian species.

Angelica Zamudio-Ochoa, Yaroslav I Morozov, Azadeh Sarfallah, Michael Anikin, Dmitry Temiakov.

Recognition of mammalian mitochondrial promoters requires the concerted action of mitochondrial RNA polymerase (mtRNAP) and transcription initiation factors TFAM and TFB2M. In this work, we found that transcript slippage results in heterogeneity of the human mitochondrial transcripts in vivo and in vitro. This allowed us to correctly interpret the RNAseq data, identify the bona fide transcription start sites (TSS), and assign mitochondrial promoters for > 50% of mammalian species and some other vertebrates. The divergent structure of the mammalian promoters reveals previously unappreciated aspects of mtDNA evolution. The correct assignment of TSS also enabled us to establish the precise register of the DNA in the initiation complex and permitted investigation of the sequence-specific protein-DNA interactions. We determined the molecular basis of promoter recognition by mtRNAP and TFB2M, which cooperatively recognize bases near TSS in a species-specific manner. Our findings reveal a role of mitochondrial transcription machinery in mitonuclear coevolution and speciation.

DOI: https://doi.org/10.1093/nar/gkac103
Metabol Open. 2022 Mar;13 100166

A novel mechanism for NLRP3 inflammasome activation.

Tan Zhang, Jingyao Zhao, Tiemin Liu, Wei Cheng, Yibing Wang, Shuzhe Ding, Ru Wang.

  The NLRP3 inflammasome, as an important component of the innate immune system, plays vital roles in various metabolic disorders. It has been reported that the NLRP3 inflammasome can be activated by a broad range of distinct stimuli, such as K+ efflux, mitochondrial dysfunction, lysosomal disruption and trans-Golgi disassembly, etc. However, there has been no well-established model for NLRP3 inflammasome activation so far, especially the underlying mechanisms for mitochondria in NLRP3 inflammasome activation remain elusive. Given that K+ efflux is a widely accepted nexus for triggering activation of NLRP3 inflammasome in most previous studies, we sought to elucidate the role of mitochondria in K+ efflux-induced NLRP3 inflammasome activation. Here, we demonstrated that inflammation activation by LPS evoked the expression of genes that involved in mitochondrial biogenesis and mitophagy, subsequently mitochondrial mass and mitochondrial membrane potential were also elevated, suggesting the contribution of mitochondria in inflammatory responses. Moreover, we inhibited mitochondrial biogenesis by silencing Tfam and genetic ablation of Tfam abolished the NLRP3 inflammasome activation induced by K+ efflux via release of mitochondrial DNA (mtDNA), as deprivation of cellular mtDNA by EtBr treatment could reverse inflammasome activation induced by K+ efflux. Collectively, we reveal that mtDNA release induced by K+ efflux in macrophages activates NLRP3 inflammasome, and propose that mitochondria may serve as a potential therapeutic target for NLRP3 inflammasome-related diseases.

Keywords:  K+ efflux; Mitochondria; NLRP3 inflammasome; Tfam; mtDNA

DOI:  https://doi.org/10.1016/j.metop.2022.100166
Mitochondrion. 2022 Feb 18. pii: S1567-7249(22)00012-5. [Epub ahead of print]

Cancer/Testis Antigen 55 is required for cancer cell proliferation and mitochondrial DNA maintenance.

Jade Aurrière, David Goudenege, Simone A Baechler, Shar-Yin N Huang, Naig Gueguen, Valerie Desquiret-Dumas, Floris Chabrun, Rodolphe Perrot, Arnaud Chevrollier, Majida Charif, Olivier Baris, Yves Pommier, Guy Lenaers, Salim Khiati.

  Cancer/Testis Antigens (CTAs) represent a group of proteins whose expression under physiological conditions is restricted to testis but activated in many human cancers. Also, it was observed that co-expression of multiple CTAs worsens the patient prognosis. Five CTAs were reported acting in mitochondria and we recently reported 147 transcripts encoded by 67 CTAs encoding for proteins potentially targeted to mitochondria. Among them, we identified the two isoforms encoded by CT55 for whom the function is poorly understood. First, we found that patients with tumors expressing wild-type CT55 are associated with poor survival. Moreover, CT55 silencing decreases dramatically cell proliferation. Second, to investigate the role of CT55 on mitochondria, we first show that CT55 is localized to both mitochondria and endoplasmic reticulum (ER) due to the presence of an ambiguous N-terminal targeting signal. Then, we show that CT55 silencing decreases mtDNA copy number and delays mtDNA recovery after an acute depletion. Moreover, demethylation of CT55 promotor increases its expression, which in turn increases mtDNA copy number. Finally, we measured the mtDNA copy number in NCI-60 cell lines and screened for genes whose expression is strongly correlated to mtDNA amount. We identified CT55 as the second highest correlated hit. Also, we show that compared to siRNA scrambled control (siCtrl) treatment, CT55 specific siRNA (siCT55) treatment down-regulates aerobic respiration, indicating that CT55 sustains mitochondrial respiration. Altogether, these data show for first time that CT55 acts on mtDNA copy number, modulates mitochondrial activity to sustain cancer cell proliferation.

Keywords:  CT55; NCI-60; cell proliferation; mitochondrial DNA

DOI:  https://doi.org/10.1016/j.mito.2022.02.005
Front Cell Neurosci. 2022 ;16 803718

mito-TEMPO Attenuates Oxidative Stress and Mitochondrial Dysfunction in Noise-Induced Hearing Loss via Maintaining TFAM-mtDNA Interaction and Mitochondrial Biogenesis.

Jia-Wei Chen, Peng-Wei Ma, Hao Yuan, Wei-Long Wang, Pei-Heng Lu, Xue-Rui Ding, Yu-Qiang Lun, Qian Yang, Lian-Jun Lu.

  The excessive generation of reactive oxygen species (ROS) and mitochondrial damage have been widely reported in noise-induced hearing loss (NIHL). However, the specific mechanism of noise-induced mitochondrial damage remains largely unclear. In this study, we showed that acoustic trauma caused oxidative damage to mitochondrial DNA (mtDNA), leading to the reduction of mtDNA content, mitochondrial gene expression and ATP level in rat cochleae. The expression level and mtDNA-binding function of mitochondrial transcription factor A (TFAM) were impaired following acoustic trauma without affecting the upstream PGC-1α and NRF-1. The mitochondria-target antioxidant mito-TEMPO (MT) was demonstrated to enter the inner ear after the systemic administration. MT treatment significantly alleviated noise-induced auditory threshold shifts 3d and 14d after noise exposure. Furthermore, MT significantly reduced outer hair cell (OHC) loss, cochlear ribbon synapse loss, and auditory nerve fiber (ANF) degeneration after the noise exposure. In addition, we found that MT treatment effectively attenuated noise-induced cochlear oxidative stress and mtDNA damage, as indicated by DHE, 4-HNE, and 8-OHdG. MT treatment also improved mitochondrial biogenesis, ATP generation, and TFAM-mtDNA interaction in the cochlea. These findings suggest that MT has protective effects against NIHL via maintaining TFAM-mtDNA interaction and mitochondrial biogenesis based on its ROS scavenging capacity.

Keywords:  mitochondrial biogenesis; mitochondrial transcription factor A; noise-induced hearing loss; rat model; reactive oxygen species; sensory hair cells

DOI:  https://doi.org/10.3389/fncel.2022.803718
Brain. 2022 Feb 24. pii: awac075. [Epub ahead of print]

Diverse injury responses of human oligodendrocyte to mediators implicated in multiple sclerosis.

Florian Pernin, Julia Luo, Qiao-Ling Cui, Manon Blain, Milton G F Fernandes, Moein Yaqubi, Myriam Srour, Jeff Hall, Roy Dudley, Hélène Jamann, Catherine Larochelle, Stephanie E J Zandee, Alexandre Prat, Jo Anne Stratton, Timothy E Kennedy, Jack P Antel.

  Early multiple sclerosis lesions feature relative preservation of oligodendrocyte cell bodies with dying back retraction of their myelinating processes. Cell loss occurs with disease progression. Putative injury mediators include metabolic stress (low glucose/nutrient), pro-inflammatory mediators (interferon γ and tumor necrosis factor α), and excitotoxins (glutamate). Our objective was to compare the impact of these disease relevant mediators on the injury responses of human mature oligodendrocytes. In the current study, we determined the effects of these mediators on process extension and survival of human brain derived mature oligodendrocytes in vitro and used bulk RNA sequencing to identify distinct effector mechanisms that underlie the responses. All mediators induced significant process retraction of the oligodendrocytes in dissociated cell culture. Only metabolic stress (low glucose/nutrient) conditions resulted in delayed (4-6 days) non-apoptotic cell death. Metabolic effects were associated with induction of the integrated stress response, which can be protective or contribute to cell injury dependent on its level and duration of activation. Addition of Sephin1, an agonist of the integrated stress response induced process retraction under control conditions and further enhanced retraction under metabolic stress conditions. The antagonist ISRIB restored process outgrowth under stress conditions, and if added to already stressed cells, reduced delayed cell death and prolonged the period in which recovery could occur. Inflammatory cytokine functional effects were associated with activation of multiple signaling pathways (including Jak/Stat-1) that regulate process outgrowth, without integrated stress response induction. Glutamate application produced limited transcriptional changes suggesting a contribution of effects directly on cell processes. Our comparative studies indicate the need to consider both the specific injury mediators and the distinct cellular mechanisms of responses to them by human oligodendrocytes to identify effective neuroprotective therapies for multiple sclerosis.

Keywords:  integrated stress response; multiple sclerosis; oligodendrocytes; process retraction

DOI:  https://doi.org/10.1093/brain/awac075
EMBO J. 2022 Feb 25. e108272

Reduced ER-mitochondria connectivity promotes neuroblastoma multidrug resistance.

Jorida Çoku, David M Booth, Jan Skoda, Madison C Pedrotty, Jennifer Vogel, Kangning Liu, Annette Vu, Erica L Carpenter, Jamie C Ye, Michelle A Chen, Peter Dunbar, Elizabeth Scadden, Taekyung D Yun, Eiko Nakamaru-Ogiso, Estela Area-Gomez, Yimei Li, Kelly C Goldsmith, C Patrick Reynolds, Gyorgy Hajnoczky, Michael D Hogarty.

  Most cancer deaths result from progression of therapy resistant disease, yet our understanding of this phenotype is limited. Cancer therapies generate stress signals that act upon mitochondria to initiate apoptosis. Mitochondria isolated from neuroblastoma cells were exposed to tBid or Bim, death effectors activated by therapeutic stress. Multidrug-resistant tumor cells obtained from children at relapse had markedly attenuated Bak and Bax oligomerization and cytochrome c release (surrogates for apoptotic commitment) in comparison with patient-matched tumor cells obtained at diagnosis. Electron microscopy identified reduced ER-mitochondria-associated membranes (MAMs; ER-mitochondria contacts, ERMCs) in therapy-resistant cells, and genetically or biochemically reducing MAMs in therapy-sensitive tumors phenocopied resistance. MAMs serve as platforms to transfer Ca2+ and bioactive lipids to mitochondria. Reduced Ca2+ transfer was found in some but not all resistant cells, and inhibiting transfer did not attenuate apoptotic signaling. In contrast, reduced ceramide synthesis and transfer was common to resistant cells and its inhibition induced stress resistance. We identify ER-mitochondria-associated membranes as physiologic regulators of apoptosis via ceramide transfer and uncover a previously unrecognized mechanism for cancer multidrug resistance.

Keywords:  ceramides; inter-organelle contacts; mitochondria-associated membranes; multidrug resistance; sphingolipids

DOI:  https://doi.org/10.15252/embj.2021108272
Cell Death Dis. 2022 Feb 18. 13(2): 162

PINK1-parkin-mediated neuronal mitophagy deficiency in prion disease.

Jie Li, Mengyu Lai, Xixi Zhang, Zhiping Li, Dongming Yang, Mengyang Zhao, Dongdong Wang, Zhixin Sun, Sharjeel Ehsan, Wen Li, Hongli Gao, Deming Zhao, Lifeng Yang.

A persistent accumulation of damaged mitochondria is part of prion disease pathogenesis. Normally, damaged mitochondria are cleared via a major pathway that involves the E3 ubiquitin ligase parkin and PTEN-induced kinase 1 (PINK1) that together initiate mitophagy, recognize and eliminate damaged mitochondria. However, the precise mechanisms underlying mitophagy in prion disease remain largely unknown. Using prion disease cell models, we observed PINK1-parkin-mediated mitophagy deficiency in which parkin depletion aggravated blocked mitochondrial colocalization with LC3-II-labeled autophagosomes, and significantly increased mitochondrial protein levels, which led to inhibited mitophagy. Parkin overexpression directly induced LC3-II colocalization with mitochondria and alleviated defective mitophagy. Moreover, parkin-mediated mitophagy was dependent on PINK1, since PINK1 depletion blocked mitochondrial Parkin recruitment and reduced optineurin and LC3-II proteins levels, thus inhibiting mitophagy. PINK1 overexpression induced parkin recruitment to the mitochondria, which then stimulated mitophagy. In addition, overexpressed parkin and PINK1 also protected neurons from apoptosis. Furthermore, we found that supplementation with two mitophagy-inducing agents, nicotinamide mononucleotide (NMN) and urolithin A (UA), significantly stimulated PINK1-parkin-mediated mitophagy. However, compared with NMN, UA could not alleviate prion-induced mitochondrial fragmentation and dysfunction, and neuronal apoptosis. These findings show that PINK1-parkin-mediated mitophagy defects lead to an accumulation of damaged mitochondria, thus suggesting that interventions that stimulate mitophagy may be potential therapeutic targets for prion diseases.

DOI: https://doi.org/10.1038/s41419-022-04613-2
Cells. 2022 Feb 11. pii: 637. [Epub ahead of print]11(4):

Mitochondrial Neurodegeneration.

Massimo Zeviani, Carlo Viscomi.

  Mitochondria are cytoplasmic organelles, which generate energy as heat and ATP, the universal energy currency of the cell. This process is carried out by coupling electron stripping through oxidation of nutrient substrates with the formation of a proton-based electrochemical gradient across the inner mitochondrial membrane. Controlled dissipation of the gradient can lead to production of heat as well as ATP, via ADP phosphorylation. This process is known as oxidative phosphorylation, and is carried out by four multiheteromeric complexes (from I to IV) of the mitochondrial respiratory chain, carrying out the electron flow whose energy is stored as a proton-based electrochemical gradient. This gradient sustains a second reaction, operated by the mitochondrial ATP synthase, or complex V, which condensates ADP and Pi into ATP. Four complexes (CI, CIII, CIV, and CV) are composed of proteins encoded by genes present in two separate compartments: the nuclear genome and a small circular DNA found in mitochondria themselves, and are termed mitochondrial DNA (mtDNA). Mutations striking either genome can lead to mitochondrial impairment, determining infantile, childhood or adult neurodegeneration. Mitochondrial disorders are complex neurological syndromes, and are often part of a multisystem disorder. In this paper, we divide the diseases into those caused by mtDNA defects and those that are due to mutations involving nuclear genes; from a clinical point of view, we discuss pediatric disorders in comparison to juvenile or adult-onset conditions. The complementary genetic contributions controlling organellar function and the complexity of the biochemical pathways present in the mitochondria justify the extreme genetic and phenotypic heterogeneity of this new area of inborn errors of metabolism known as 'mitochondrial medicine'.

Keywords:  Leigh syndrome; MELAS; MERRF; OXPHOS; POLG; mitochondrial disease; mitochondrial respiratory chain

DOI:  https://doi.org/10.3390/cells11040637
Peptides. 2022 Feb 18. pii: S0196-9781(22)00036-5. [Epub ahead of print]152 170770

Angiotensinogen uptake and stimulation of oxidative stress in human pigment retinal epithelial cells.

Victor M Pulgar, Nildris Cruz-Diaz, Brian M Westwood, Mark C Chappell.

  We previously reported that isolated proximal tubules (PT) internalize the precursor protein angiotensinogen and that the 125Iodine-labeled protein accumulated in the nuclear and mitochondrial fractions of the PT cells; however, whether internalization of angiotensinogen occurs in non-renal epithelial cells is unknown. Therefore, the present study assessed the cellular uptake of 125I-angiotensinogen in human retinal pigment ARPE-19 epithelial cells, a widely utilized cell model for the assessment of retinal injury, inflammation and oxidative stress. ARPE-19 cells, maintained in serum-free media to remove extracellular sources of bovine serum angiotensinogen and renin, were incubated with 125Iodine-angiotensinogen at 37 °C and revealed the time-dependent uptake of angiotensinogen over 24 h. In contrast, incubation with labelled Ang II, Ang-(1-7) or Ang I revealed minimal cellular uptake. Subcellular fractionation following a 4-hour uptake of 125I-angiotensinogen revealed that the majority of the labeled protein localized to the nuclear fraction with lower accumulation in the mitochondrial and cytosolic fractions. Finally, we show that addition of angiotensinogen (2 nM) to the ARPE-19 cells increased oxidative stress as assessed by DCF fluorescence that was blocked by pretreatment of the cells with either the NADPH oxidase 1/4 inhibitor GKT137831, apocynin or atorvastatin, but not the AT1 receptor antagonist losartan. In contrast, treatment of the cells with Angiotensin II at an equivalent dose to angiotensinogen failed to stimulate oxidative stress. We conclude that human retinal pigment cells internalize angiotensinogen to elicit an increase in oxidative stress through a pathway that appears distinct from the Ang II-AT1 receptor axis.

Keywords:  ARPE-19 cells; Ang II; Angiotensinogen; GKT131184; NADPH oxidase; NOX4; Oxidative stress

DOI:  https://doi.org/10.1016/j.peptides.2022.170770
Proc Natl Acad Sci U S A. 2022 Mar 01. pii: e2111404119. [Epub ahead of print]119(9):

A DNA repair-independent role for alkyladenine DNA glycosylase in alkylation-induced unfolded protein response.

Larissa Milano, Clara F Charlier, Rafaela Andreguetti, Thomas Cox, Eleanor Healing, Marcos P Thomé, Ruan M Elliott, Leona D Samson, Jean-Yves Masson, Guido Lenz, João Antonio P Henriques, Axel Nohturfft, Lisiane B Meira.

  Alkylating agents damage DNA and proteins and are widely used in cancer chemotherapy. While cellular responses to alkylation-induced DNA damage have been explored, knowledge of how alkylation affects global cellular stress responses is sparse. Here, we examined the effects of the alkylating agent methylmethane sulfonate (MMS) on gene expression in mouse liver, using mice deficient in alkyladenine DNA glycosylase (Aag), the enzyme that initiates the repair of alkylated DNA bases. MMS induced a robust transcriptional response in wild-type liver that included markers of the endoplasmic reticulum (ER) stress/unfolded protein response (UPR) known to be controlled by XBP1, a key UPR effector. Importantly, this response is significantly reduced in the Aag knockout. To investigate how AAG affects alkylation-induced UPR, the expression of UPR markers after MMS treatment was interrogated in human glioblastoma cells expressing different AAG levels. Alkylation induced the UPR in cells expressing AAG; conversely, AAG knockdown compromised UPR induction and led to a defect in XBP1 activation. To verify the requirements for the DNA repair activity of AAG in this response, AAG knockdown cells were complemented with wild-type Aag or with an Aag variant producing a glycosylase-deficient AAG protein. As expected, the glycosylase-defective Aag does not fully protect AAG knockdown cells against MMS-induced cytotoxicity. Remarkably, however, alkylation-induced XBP1 activation is fully complemented by the catalytically inactive AAG enzyme. This work establishes that, besides its enzymatic activity, AAG has noncanonical functions in alkylation-induced UPR that contribute to cellular responses to alkylation.

Keywords:  DNA damage; ER stress; alkylating agents; base excision repair; unfolded protein response

DOI:  https://doi.org/10.1073/pnas.2111404119
Nucleic Acids Res. 2022 Feb 25. pii: gkac104. [Epub ahead of print]

Persistent DNA damage associated with ATM kinase deficiency promotes microglial dysfunction.

Julie Bourseguin, Wen Cheng, Emily Talbot, Liana Hardy, Jenny Lai, Ailsa M Jeffries, Michael A Lodato, Eunjung Alice Lee, Svetlana V Khoronenkova.

The autosomal recessive genome instability disorder Ataxia-telangiectasia, caused by mutations in ATM kinase, is characterized by the progressive loss of cerebellar neurons. We find that DNA damage associated with ATM loss results in dysfunctional behaviour of human microglia, immune cells of the central nervous system. Microglial dysfunction is mediated by the pro-inflammatory RELB/p52 non-canonical NF-κB transcriptional pathway and leads to excessive phagocytic clearance of neuronal material. Activation of the RELB/p52 pathway in ATM-deficient microglia is driven by persistent DNA damage and is dependent on the NIK kinase. Activation of non-canonical NF-κB signalling is also observed in cerebellar microglia of individuals with Ataxia-telangiectasia. These results provide insights into the underlying mechanisms of aberrant microglial behaviour in ATM deficiency, potentially contributing to neurodegeneration in Ataxia-telangiectasia.

DOI: https://doi.org/10.1093/nar/gkac104
Physiol Res. 2021 Dec 30. 70(Suppl4): S471-S484

Conplastic strains for identification of retrograde effects of mitochondrial dna variation on cardiometabolic traits in the spontaneously hypertensive rat.

M Pravenec, J Šilhavý, P Mlejnek, M Šimáková, T Mráček, A Pecinová, K Tauchmannová, M Hütl, H Malínská, L Kazdová, J Neckář, F Kolář, J Žurmanová, J Novotný, J Houštěk.

Mitochondrial retrograde signaling is a pathway of communication from mitochondria to the nucleus. Recently, natural mitochondrial genome (mtDNA) polymorphisms (haplogroups) received increasing attention in the pathophysiology of human common diseases. However, retrograde effects of mtDNA variants on such traits are difficult to study in humans. The conplastic strains represent key animal models to elucidate regulatory roles of mtDNA haplogroups on defined nuclear genome background. To analyze the relationship between mtDNA variants and cardiometabolic traits, we derived a set of rat conplastic strains (SHR-mtBN, SHR-mtF344 and SHR-mtLEW), harboring all major mtDNA haplotypes present in common inbred strains on the nuclear background of the spontaneously hypertensive rat (SHR). The BN, F344 and LEW mtDNA differ from the SHR in multiple amino acid substitutions in protein coding genes and also in variants of tRNA and rRNA genes. Different mtDNA haplotypes were found to predispose to various sets of cardiometabolic phenotypes which provided evidence for significant retrograde effects of mtDNA in the SHR. In the future, these animals could be used to decipher individual biochemical components involved in the retrograde signaling.
Nat Biotechnol. 2022 Feb 24.

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations.

Tyler E Miller, Caleb A Lareau, Julia A Verga, Erica A K DePasquale, Vincent Liu, Daniel Ssozi, Katalin Sandor, Yajie Yin, Leif S Ludwig, Chadi A El Farran, Duncan M Morgan, Ansuman T Satpathy, Gabriel K Griffin, Andrew A Lane, J Christopher Love, Bradley E Bernstein, Vijay G Sankaran, Peter van Galen.

The combination of single-cell transcriptomics with mitochondrial DNA variant detection can be used to establish lineage relationships in primary human cells, but current methods are not scalable to interrogate complex tissues. Here, we combine common 3' single-cell RNA-sequencing protocols with mitochondrial transcriptome enrichment to increase coverage by more than 50-fold, enabling high-confidence mutation detection. The method successfully identifies skewed immune-cell expansions in primary human clonal hematopoiesis.

DOI: https://doi.org/10.1038/s41587-022-01210-8
Redox Biol. 2022 Feb 10. pii: S2213-2317(22)00037-4. [Epub ahead of print]51 102265

Genetic BACH1 deficiency alters mitochondrial function and increases NLRP3 inflammasome activation in mouse macrophages.

Pooja Pradhan, Vijith Vijayan, Karsten Cirksena, Falk F R Buettner, Kazuhiko Igarashi, Roberto Motterlini, Roberta Foresti, Stephan Immenschuh.

  BTB-and-CNC homologue 1 (BACH1), a heme-regulated transcription factor, mediates innate immune responses via its functional role in macrophages. BACH1 has recently been shown to modulate mitochondrial metabolism in cancer cells. In the current study, we utilized a proteomics approach and demonstrate that genetic deletion of BACH1 in mouse macrophages is associated with decreased levels of various mitochondrial proteins, particularly mitochondrial complex I. Bioenergetic studies revealed alterations of mitochondrial energy metabolism in BACH1-/- macrophages with a shift towards increased glycolysis and decreased oxidative phosphorylation. Moreover, these cells exhibited enhanced mitochondrial membrane potential and generation of mitochondrial reactive oxygen species (mtROS) along with lower levels of mitophagy. Notably, a higher inducibility of NLRP3 inflammasome activation in response to ATP and nigericin following challenge with lipopolysaccharide (LPS) was observed in BACH1-deficient macrophages compared to wild-type cells. Mechanistically, pharmacological inhibition of mtROS markedly attenuated inflammasome activation. In addition, it is shown that inducible nitric oxide synthase and cyclooxygenase-2, both of which are markedly induced by LPS in macrophages, are directly implicated in BACH1-dependent regulation of NLRP3 inflammasome activation. Taken together, the current findings indicate that BACH1 is critical for immunomodulation of macrophages and may serve as a target for therapeutic approaches in inflammatory disorders.

Keywords:  BACH1; Inflammation; Macrophages; Mitochondrial complex 1; Mitochondrial metabolism; NLRP3 inflammasome

DOI:  https://doi.org/10.1016/j.redox.2022.102265
BMC Genom Data. 2022 Feb 18. 23(1): 16

Mitochondria in tumour progression: a network of mtDNA variants in different types of cancer.

Giovanna C Cavalcante, Ândrea Ribeiro-Dos-Santos, Gilderlanio S de Araújo.

   BACKGROUND: Mitochondrial participation in tumorigenesis and metastasis has been studied for many years, but several aspects of this mechanism remain unclear, such as the association of mitochondrial DNA (mtDNA) with different cancers. Here, based on two independent datasets, we modelled an mtDNA mutation-cancer network by systematic integrative analysis including 37 cancer types to identify the mitochondrial variants found in common among them.
RESULTS: Our network showed mtDNA associations between gastric cancer and other cancer types, particularly kidney, liver, and prostate cancers, which is suggestive of a potential role of such variants in the metastatic processes among these cancer types. A graph-based interactive web tool was made available at www2.lghm.ufpa.br/mtdna. We also highlighted that most shared variants were in the MT-ND4, MT-ND5 and D-loop, and that some of these variants were nonsynonymous, indicating a special importance of these variants and regions regarding cancer progression, involving genomic and epigenomic alterations.
CONCLUSIONS: This study reinforces the importance of studying mtDNA in cancer and offers new perspectives on the potential involvement of different mitochondrial variants in cancer development and metastasis.

Keywords:  Cancer; Genetic overlap; Interactive variant networks; Mitochondrial genome; Oxidative stress

DOI:  https://doi.org/10.1186/s12863-022-01032-2
Nat Rev Immunol. 2022 Feb 23.

Organellar homeostasis and innate immune sensing.

Cassandra R Harapas, Elina Idiiatullina, Mahmoud Al-Azab, Katja Hrovat-Schaale, Thomas Reygaerts, Annemarie Steiner, Pawat Laohamonthonkul, Sophia Davidson, Chien-Hsiung Yu, Lee Booty, Seth L Masters.

A cell is delimited by numerous borders that define specific organelles. The walls of some organelles are particularly robust, such as in mitochondria or endoplasmic reticulum, but some are more fluid such as in phase-separated stress granules. Either way, all organelles can be damaged at times, leading their contents to leak out into the surrounding environment. Therefore, an elegant way to construct an innate immune defence system is to recognize host molecules that do not normally reside within a particular compartment. Here, we provide several examples where organellar homeostasis is lost, leading to the activation of a specific innate immune sensor; these include NLRP3 activation owing to a disrupted trans-Golgi network, Pyrin activation due to cytoskeletal damage, and cGAS-STING activation following the leakage of nuclear or mitochondrial DNA. Frequently, organelle damage is observed downstream of pathogenic infection but it can also occur in sterile settings as associated with auto-inflammatory disease. Therefore, understanding organellar homeostasis is central to efforts that will identify new innate immune pathways, and therapeutics that balance organellar homeostasis, or target the breakdown pathways that trigger innate immune sensors, could be useful treatments for infection and chronic inflammatory diseases.

DOI: https://doi.org/10.1038/s41577-022-00682-8
Antioxidants (Basel). 2022 Feb 16. pii: 405. [Epub ahead of print]11(2):

CNS Redox Homeostasis and Dysfunction in Neurodegenerative Diseases.

Gundars Goldsteins, Vili Hakosalo, Merja Jaronen, Meike Hedwig Keuters, Šárka Lehtonen, Jari Koistinaho.

  A single paragraph of about 200 words maximum. Neurodegenerative diseases (ND), such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis, pose a global challenge in the aging population due to the lack of treatments for their cure. Despite various disease-specific clinical symptoms, ND have some fundamental common pathological mechanisms involving oxidative stress and neuroinflammation. The present review focuses on the major causes of central nervous system (CNS) redox homeostasis imbalance comprising mitochondrial dysfunction and endoplasmic reticulum (ER) stress. Mitochondrial disturbances, leading to reduced mitochondrial function and elevated reactive oxygen species (ROS) production, are thought to be a major contributor to the pathogenesis of ND. ER dysfunction has been implicated in ND in which protein misfolding evidently causes ER stress. The consequences of ER stress ranges from an increase in ROS production to altered calcium efflux and proinflammatory signaling in glial cells. Both pathological pathways have links to ferroptotic cell death, which has been implicated to play an important role in ND. Pharmacological targeting of these pathological pathways may help alleviate or slow down neurodegeneration.

Keywords:  Alzheimer’s disease; Parkinson’s disease; amyotrophic lateral sclerosis; endoplasmic reticulum (ER) stress; ferroptosis; mitochondria; neuroinflammation; reactive oxygen species (ROS); unfolded protein response (UPR)

DOI:  https://doi.org/10.3390/antiox11020405
Sci Rep. 2022 02 23. 12(1): 3045

Mitochondrial dysfunction associated with TANGO2 deficiency.

Paige Heiman, Al-Walid Mohsen, Anuradha Karunanidhi, Claudette St Croix, Simon Watkins, Erik Koppes, Richard Haas, Jerry Vockley, Lina Ghaloul-Gonzalez.

Transport and Golgi Organization protein 2 Homolog (TANGO2)-related disease is an autosomal recessive disorder caused by mutations in the TANGO2 gene. Symptoms typically manifest in early childhood and include developmental delay, stress-induced episodic rhabdomyolysis, and cardiac arrhythmias, along with severe metabolic crises including hypoglycemia, lactic acidosis, and hyperammonemia. Severity varies among and within families. Previous studies have reported contradictory evidence of mitochondrial dysfunction. Since the clinical symptoms and metabolic abnormalities are suggestive of a broad dysfunction of mitochondrial energy metabolism, we undertook a broad examination of mitochondrial bioenergetics in TANGO2 deficient patients utilizing skin fibroblasts derived from three patients exhibiting TANGO2-related disease. Functional studies revealed that TANGO2 protein was present in mitochondrial extracts of control cells but not patient cells. Superoxide production was increased in patient cells, while oxygen consumption rate, particularly under stress, along with relative ATP levels and β-oxidation of oleate were reduced. Our findings suggest that mitochondrial function should be assessed and monitored in all patients with TANGO2 mutation as targeted treatment of the energy dysfunction could improve outcome in this condition.

DOI: https://doi.org/10.1038/s41598-022-07076-9
Dis Model Mech. 2022 Feb 22. pii: dmm.049083. [Epub ahead of print]

Development and characterization of different cell models harbouring mitochondrial DNA deletions for in vitro study of Pearson syndrome.

Carmen Hernández-Ainsa, Ester López-Gallardo, María Concepción García-Jiménez, Francisco José Climent-Alcalá, Carmen Rodríguez-Vigil, Marta García Fernández de Villalta, Rafael Artuch, Julio Montoya, Eduardo Ruiz-Pesini, Sonia Emperador.

  Pearson syndrome (PS) is a rare multisystem disease caused by single large scale mitochondrial DNA deletions (SLSMDs). PS presents early in infancy and it is mainly characterized by refractory sideroblastic anaemia. Prognosis is poor and treatment is supportive, thus development of new models for the study of PS and new therapy strategies is essential. In this work we report three different cell models carrying a SLMSD: fibroblasts, transmitochondrial cybrids and induced pluripotent stem cells (iPSC). All studied models exhibited an aberrant mitochondrial ultrastructure and defective OXPHOS function, showing a decrease in different parameters such as mitochondrial ATP, respiratory complex IV activity and quantity or oxygen consumption. Despite that, iPSC harbouring "common deletion" were able to differentiate into three germ layers. Besides, cybrids clones only showed mitochondrial dysfunction when heteroplasmy level reached 70%. Some differences observed among models may depend on their metabolic profile, therefore we consider these three models are useful for the in vitro study of the PS as well as for testing new specific therapies.

Keywords:  Cybrid; IPSC; Mitochondrial DNA; Mitochondrial disease; MtDNA deletion; Pearson syndrome

DOI:  https://doi.org/10.1242/dmm.049083