bims-nenemi Biomed News
on Neuroinflammation, neurodegeneration and mitochondria
Issue of 2022‒05‒15
twelve papers selected by
Marco Tigano
Thomas Jefferson University

  1. Curr Protoc. 2022 May;2(5): e412
      Mitochondria play a very important role in many crucial cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondrial genomes. Mutant and wild-type mitochondrial DNA (mtDNA) may co-exist as heteroplasmy and cause human disease. The purpose of the protocols in this article is to simultaneously determine the mtDNA sequence and quantify the heteroplasmy level using parallel sequencing. The protocols include mitochondrial genomic DNA PCR amplification of two full-length products using two distinct sets of PCR primers. The PCR products are mixed at an equimolar ratio, and the samples are then barcoded and sequenced with high-throughput next-generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree/level of heteroplasmy. © 2022 Wiley Periodicals LLC. Basic Protocol 1: PCR amplification of mitochondrial DNA Basic Protocol 2: Analysis of next-generation sequencing of mitochondrial DNA Basic Protocol 3: Mutect2 pipeline for automated sample processing and large-scale data analysis.
    Keywords:  DNA sequence analysis; PCR; heteroplasmy; mitochondria; mitochondrial DNA; next-generation sequencing
  2. Elife. 2022 May 13. pii: e74552. [Epub ahead of print]11
      Proliferating cells undergo metabolic changes in synchrony with cell cycle progression and cell division. Mitochondria provide fuel, metabolites, and ATP during different phases of the cell cycle, however it is not completely understood how mitochondrial function and the cell cycle are coordinated. CLUH is a post-transcriptional regulator of mRNAs encoding mitochondrial proteins involved in oxidative phosphorylation and several metabolic pathways. Here, we show a role of CLUH in regulating the expression of astrin, which is involved in metaphase to anaphase progression, centrosome integrity, and mTORC1 inhibition. We find that CLUH binds both the SPAG5 mRNA and its product astrin, and controls the synthesis and the stability of the full-length astrin-1 isoform. We show that CLUH interacts with astrin-1 specifically during interphase. Astrin-depleted cells show mTORC1 hyperactivation and enhanced anabolism. On the other hand, cells lacking CLUH show decreased astrin levels and increased mTORC1 signaling, but cannot sustain anaplerotic and anabolic pathways. In absence of CLUH, cells fail to grow during G1, and progress faster through the cell cycle, indicating dysregulated matching of growth, metabolism and cell cycling. Our data reveal a role of CLUH in coupling growth signaling pathways and mitochondrial metabolism with cell cycle progression.
    Keywords:  cell biology; human
  3. FASEB J. 2022 May;36 Suppl 1
      Maintenance of the mitochondrial protein folding environment is essential for organellar and cellular homeostasis. Over 99% of mitochondrial proteins require import into mitochondria, followed by their folding and intraorganellar sorting. Mitochondrial stress can result in the accretion of misfolded proteins, establishing a requirement for mitochondrial protein quality control (MQC) strategies. The Mitochondrial Unfolded Protein Response (UPRmt ) is a compartment-specific MQC mechanism that increases the expression of protective enzymes by Activating Transcription Factor 5 (ATF5) to restore mitochondrial function. Contractile activity during acute exercise is a stressor that has the potential to temporarily disrupt organellar protein homeostasis. However, the roles of ATF5 and the UPRmt in basal mitochondrial maintenance and exercise-induced UPRmt signaling in skeletal muscle are not known. To investigate this, we subjected WT and whole-body ATF5 KO mice to a bout of acute exercise and collected skeletal muscle tissues immediately after. ATF5 KO animals exhibited 2-fold increases in phosphorylated JNK protein levels, indicative of enhanced stress signaling. Interestingly, in KO muscle, PGC-1a protein was enhanced by 50% and 40% in nuclear and cytosolic compartments, respectively, suggesting an increased drive toward mitochondrial biogenesis in the absence of ATF5. Muscle from these animals also displayed a more abundant, but dysfunctional, mitochondrial pool, with a 20% increase in mitochondrial content, 30-40% reductions in respiration, and a 20% increase in ROS emissions, corresponding with no changes in exercise performance. The UPRmt proteins mtHSP70 and LONP were upregulated 20-30% in KO muscle, while ATF4 mRNA was upregulated 2.5-3.7-fold, along with an 8% increase in its nuclear localization. Furthermore, KO muscle showed an impaired UPRmt mRNA response to acute exercise, suggesting a regulatory role for ATF5 in the maintenance of a high-quality mitochondrial pool, and in mediating the transcription of UPRmt genes during exercise.
  4. FASEB J. 2022 May;36 Suppl 1
      OBJECTIVES: Heterogeneous nuclear ribonucleoprotein I (Hnrnp I) is an RNA-binding protein functions during pre-mRNA splicing and regulation of alternative splicing events. Previously we found that ablation of Hnrnp I activates NF-κB signaling in intestinal epithelial cells (IECs), resulting in increased nuclear translocation of P65 (NF-κB subunit) and upregulation of proinflammatory cytokines and chemokines. Integrated stress response (ISR) signaling was linked to activation of canonical NF-κB pathway. Therefore, in this study, we aimed to investigate ISR in the colon of Hnrnp I knockout mice. We hypothesize that cellular stress from Hnrnp I knockout triggers ISR, consequently affects the cellular dynamics among secretory cell types on colon epithelium (enteroendocrine, Paneth and goblet cells).METHODS: Total RNA was isolated from total colon cell preparations from WT and KO mice. Single-cell RNAseq libraries (biological replicates, n=3) were prepared using Chromium Single-Cell Gene Expression NextGem (v3.1, 10X Genomics). Analyses from raw counts were performed using the Seurat (v3.2.0) R package using default parameters, a computational cell calling algorithm was used to identify cell type using two published annotated mouse cell datasets. Pathway analysis was performed for secretary cell clusters including enteroendocrine cells (EECs), Paneth cells, and goblet cells RESULTS: Comparing to WT, number of EECs in colon was significantly increased in KO mice. Total mRNA level of Atf4, the principal regulator of ISR, was significantly increased in colon secretory cells in KO mice. We also examined mRNA expression of ATF4 target genes in secretory cells. Specifically, gene encoding the regulator of apoptosis and autophagy, members of Bcl2 family, Bnip3, was significantly increased in secretory cells in KO mice, while Mlx and Gabarapl2 (Atg8), both are involved in apoptosis and autophagy signaling pathways, have a trend of increase in secretory cells in KO mice, all comparing to WT.
    CONCLUSIONS: Cellular stress from Hnrnp I knockout activated ISR in IECs, specially in those secretory cell types - EECs, Paneth, and goblet cells. The activation of ISR led to both autophagy and apoptosis signaling in these cells through the upregulation of Bnip3, Mlxand Gabarapl2. Taken together, our results suggest that in response to the cellular stresses from the depletion of Hnrnp I in IECs, ISR activation in colonic secretory cells, stimulating apoptosis and autophagy pathway signaling, particularly in EECs, resulting in the proliferation of EECs in KO. The overall manipulation by ISR signaling in the colon secretary cells may present a critical early response to modulations in colon, potentially leading to perturbations to homeostasis among host colon epithelia, colon residential immunity, and gut microbiota.
  5. FASEB J. 2022 May;36 Suppl 1
      Phosphorylation has long been appreciated to influence mitochondrial metabolism via the regulation of pyruvate dehydrogenase. However, the extent to which phosphorylation broadly influences mitochondrial function remains unclear, despite the presence of multiple protein phosphatases within the organelle. We recently demonstrated that deletion of the mitochondrial matrix phosphatase Pptc7 unexpectedly caused perinatal lethality in mice, suggesting that the regulation of mitochondrial phosphorylation is essential in mammalian development. Pptc7-/- mice exhibit severe metabolic deficiencies, including hypoglycemia and lactic acidosis, and die within one day of birth. Biochemical and proteomic approaches revealed that Pptc7-/- tissues have decreased mitochondrial function concomitant with a post-transcriptional downregulation of mitochondrial proteins. Multiple elevated mitochondrial protein phosphorylation sites in Pptc7-/- tissues suggest novel functional connections between Pptc7-mediated dephosphorylation and these observed metabolic consequences. Interestingly, these modifications occur on components of the import machinery of the mitochondria and within the mitochondrial targeting sequences of select nuclear-encoded precursor proteins. Collectively, our data reveal an unappreciated role for a matrix-localized phosphatase in the post-translational regulation of the mitochondrial proteome and organismal metabolic homeostasis.
  6. Front Immunol. 2022 ;13 887054
      Porcine reproductive and respiratory syndrome virus (PRRSV) is an RNA virus that causes great economic losses globally to the swine industry. Innate immune RNA receptors mainly sense it during infection. As a DNA sensor, cyclic GMP-AMP synthase (cGAS) plays an important role in sensing cytosolic DNA and activating innate immunity to induce IFN-I and establish an antiviral cellular state. In contrast, the role of innate immune DNA sensors during PRRSV infection has not been elucidated. In this study, we found that cGAS facilitates the production of IFN-β during PRRSV infection. Western blot and virus titer assays suggested that cGAS overexpression suppressed the replication of multiple PRRSV strains, while knockout of cGAS increased viral titer and nucleocapsid protein expression. Besides, our results indicated that the mitochondria were damaged during PRRSV infection and leaked mitochondrial DNA (mtDNA) into the cytoplasm. The mtDNA in the cytoplasm co-localizes with the cGAS, and the cGAMP activity was increased when the cGAS was overexpressed during PRRSV infection. Furthermore, the cGAMP also possesses an anti-PRRSV effect. These results indicate for the first time that cGAS restricts PRRSV replication by sensing the mtDNA in the cytoplasm to increase cGAMP activity, which not only explains the molecular mechanism by which cGAS inhibits PRRSV replication but also provides research ideas for studying the role of the cGAS-STING signaling pathway in the process of RNA virus infection.
    Keywords:  PRRSV; antiviral activity; cGAMP; cGAS; mtDNA; replication
  7. FASEB J. 2022 May;36 Suppl 1
      Mitochondrial ATPase ATAD3A is essential for cholesterol transport, mitochondrial structure, and cell survival. However, the relationship between ATAD3A and non-alcoholic fatty liver disease (NAFLD) is largely unknown. In this study, we found that ATAD3A was upregulated in the progression of NAFLD in livers from rats with diet-induced non-alcoholic steatohepatitis (NASH) and in human livers with NAFLD. CRISPR-Cas9 was used to delete ATAD3A function in Huh7 human hepatocellular carcinoma cells to assess the influence of ATAD3A deletion on liver cells with free cholesterol (FC) overload induced by treatment with cholesterol plus 58035, an inhibitor for acetyl-CoA acetyltransferase, the enzyme converting FC to cholesterol ester. The results showed that ATAD3A KO exacerbated FC accumulation under FC overload in Huh7 cells. Triglyceride (TG) levels were also significantly increased in ATAD3A KO Huh7 cells under FC overload and control conditions via inhibited lipolysis mediated by upregulation of perilipin 2. Moreover, loss of ATAD3A downregulated mitophagy-associated PTEN-induced kinase 1 expression in Huh7 cells under FC overload and control conditions, suggesting that ATAD3A KO blocks mitophagy. Consistently, mitochondrial mass was increased in ATAD3A KO cells under FC overload as indicated by mitochondrial protein translocase of outer mitochondrial membrane 20 (TOM20). The results also showed that loss of ATAD3A impaired mitochondrial basal respiration and ATP production in Huh7 cells under FC overload, accompanied by downregulation of mitochondrial ATP synthase. In conclusion, loss of ATAD3A promotes the progression of NAFLD through the accumulation of FC, TG, and damaged mitochondria in hepatocytes.
  8. FASEB J. 2022 May;36 Suppl 1
      Air pollution is a sustained problem of public health for the general population. Accumulating evidence has confirmed a significant association between exposure to fine ambient particulate matter with aerodynamic diameters < 2.5 μm (PM2.5 ) and the increase of morbidity and mortality associated with cardiovascular and metabolic diseases. Chronic inflammation and dysregulated energy metabolism have been identified as the driving force of the PM2.5 -caused pathogenesis. However, a precise understanding of the molecular and cellular mechanisms by which PM2.5 induces inflammatory stress responses and impairs energy homeostasis remains elusive. Research in our laboratory has addressed the mechanistic basis underlying the pathophysiologic effects of PM2.5 exposure on liver and adipose tissues with mouse models under inhalation exposure to environmentally relevant PM2.5 . Proteomics analysis with PM2.5 -exposed mouse liver tissues indicated that mitochondria and endoplasmic reticulum (ER) are the most sensitive organelles in transducing signaling cascades upon PM2.5 stimulation. Further investigation revealed that inhalation exposure to PM2.5 induces an integrated ER stress and mitochondrial stress response in mouse livers. Under PM2.5 exposure, the ER and mitochondria interact and build up a platform through Mitochondria-Associated Membranes (MAMs) to augment an integrated inflammatory stress response, mediated through the primary ER stress sensor IRE1α and Toll-like receptor (TLR) 2 and 4. This integrated organelle stress response pathway promoted non-alcoholic steatohepatitis (NASH), characterized by hepatic inflammation, steatosis and fibrogenesis, hepatic glycogen depletion, and insulin resistance in PM2.5 -exposed mice. Disruption of MAMs by knockdown of the MAM-residing ER chaperone Sigma-1 Receptor (Sig-1R) or mitofusin (MNF2) in Kupffer cells or hepatocytes suppressed PM2.5- induced NASH and insulin resistance in mice. Together, our studies suggested that exposure to airborne PM2.5 pollution activates an integrated ER and mitochondrial stress response in the liver, which promotes NASH, disrupts energy homeostasis, and impairs insulin signaling associated with the development of metabolic syndrome. These findings provide significant insights into the hepatic pathways underlying PM2.5 -triggered liver pathology, and have important implications in the understanding, prevention, and treatment of air pollution-associated metabolic disease.
  9. Nat Commun. 2022 May 13. 13(1): 2673
      The folded mitochondria inner membrane-cristae is the structural foundation for oxidative phosphorylation (OXPHOS) and energy production. By mechanically simulating mitochondria morphogenesis, we speculate that efficient sculpting of the cristae is organelle non-autonomous. It has long been inferred that folding requires buckling in living systems. However, the tethering force for cristae formation and regulation has not been identified. Combining electron tomography, proteomics strategies, super resolution live cell imaging and mathematical modeling, we reveal that the mitochondria localized actin motor-myosin 19 (Myo19) is critical for maintaining cristae structure, by associating with the SAM-MICOS super complex. We discover that depletion of Myo19 or disruption of its motor activity leads to altered mitochondria membrane potential and decreased OXPHOS. We propose that Myo19 may act as a mechanical tether for effective ridging of the mitochondria cristae, thus sustaining the energy homeostasis essential for various cellular functions.
  10. STAR Protoc. 2022 03 18. 3(1): 101165
      DNA damage caused by genetic instability or extrinsic treatment can induce DNA leakage from the nucleus or mitochondria into the cytosol and activate innate and adaptive immunity. To enable characterization of these endogenous cytosolic DNAs and the mechanisms that produce them, we developed an approach for isolation of cytosolic DNA with no detectable mitochondrial contamination. Here we describe cytosolic compartment separation followed by DNA purification from colorectal cancer cells and illustrate how this may be expanded to other cell types.
    Keywords:  Behavioral neuroscience; Biological sciences; Neuroscience
  11. Transl Res. 2022 May 08. pii: S1931-5244(22)00100-1. [Epub ahead of print]
      Doxorubicin (Dox), as a widely used anthracycline antitumor drug, can cause severe cardiotoxicity. Cardiomyocyte death and inflammation are involved in the pathophysiology of Dox-induced cardiotoxicity (DIC). Gasdermin D (GSDMD) is known as a key executioner of pyroptosis, which is a pro-inflammatory programmed cell death. We aimed to investigate the impact of GSDMD on DIC and systematically reveal its underlying mechanisms. Our findings indicated that Dox induced cardiomyocyte pyroptosis in a GSDMD-dependent manner by utilizing siRNA or overexpression-plasmid technique. We then generated GSDMD global knockout mice via CRISPR/Cas9 system and found that GSDMD deficiency reduced Dox-induced cardiomyopathy. Dox induced the activation of inflammatory caspases, which subsequently mediated GSDMD-N generation indirectly. Using molecular dynamics simulation and cell-free systems, we confirmed that Dox directly bound to GSDMD and facilitated GSDMD-N-mediated pyroptosis. Furthermore, GSDMD also mediated Dox-induced mitochondrial damage via Bnip3 and mitochondrial perforation in cardiomyocytes. These findings provide fresh insights into the mechanism of how Dox-engaged GSDMD orchestrates adverse cardiotoxicity and highlight the prospects of GSDMD as a potential target for DIC.
    Keywords:  Gasdermin D; cardiotoxicity; doxorubicin; inflammation; pyroptosis
  12. Curr Cancer Drug Targets. 2022 May 11.
      AIM: Mitochondria are essential for energy metabolism in the tumor microenvironment and the survival of cancer cells.BACKGROUND: ADP-ribosylation factor-like GTPase 5b (ARL5B) has been found to be associated with mitochondrial dysfunction and breast cancer (BC) progression, but the underlying mechanism needs to be further understood.
    OBJECTIVE: We investigated the effects of ARL5B on the apoptosis and glycolysis of breast cancer cells and its underlying mechanisms.
    METHOD: Quantitative reverse transcription-PCR (qRT-PCR) and western blot assays were used to detect the expression of ARL5B in breast cancer tissues and cells. An ARL5B loss-of-function assay was performed to verify its role in BC development.
    RESULTS: ARL5B was upregulated in breast cancer tissues and cell lines. ARL5B knockdown induced apoptosis and activated the mitochondrial pathway in breast cancer cells. Interestingly, the inhibition of ARL5B repressed the aerobic glycolysis of breast cancer cells. The role of ARL5B in breast cancer cells was exerted by mediating the activation of viral RNA sensor MDA5-evoked signaling. Silencing ARL5B triggered MDA5 signaling by upregulating the key proteins involved in the MDA5 pathway. Importantly, MDA5 silencing reversed the effects of ARL5B knockdown on mitochondrial-mediated apoptosis and glycolysis, whereas poly(I:C), as a ligand for MDA5, further enhanced ARL5B knockdown-facilitated mitochondrial apoptosis and the inhibition of glycolysis. Conclusion The knockdown of ARL5B activated MDA5 signaling and thus led to the enhanced mitochondrial-mediated apoptosis and glycolysis inhibition in breast cancer cells. Our study suggested that ARL5B might be a potential therapy target for BC.
    Keywords:  ARL5B; apoptosis; breast cancer; energy metabolism