bims-mitper 2023-02-19 papers

bims-mitper

Biomed News

on Mitochondrial Permeabilization

Issue of 2023–02–19
seven papers selected by
Bradley Irizarry, Thomas Jefferson University

Insight into Bcl-2 proteins' functioning at mitochondrial membrane level.
Innate immune inflammatory cell death: PANoptosis and PANoptosomes in host defense and disease.
ROLE OF THE MITOCHONDRIAL PERMEABILITY TRANSITION IN BONE METABOLISM AND AGING.
Altered trafficking of miRNAs at mitochondria modulates mitochondrial functions and cell death in brain ischemia.
Large Common Mitochondrial DNA Deletions Are Associated with a Mitochondrial SNP T14798C Near the 3' Breakpoints.
The multi-tissue landscape of somatic mtdna mutations indicates tissue specific accumulation and removal in aging.
Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabolism and mitochondrial gene expression.

Biophys J. 2023 Feb 10. pii: S0006-3495(22)02282-2. [Epub ahead of print]122(3S1): 232a

Insight into Bcl-2 proteins' functioning at mitochondrial membrane level.

Luke A Clifton, Ameeq Ul Mushtaq, Jörgen Åden, Tobias Sparrman, Hanna Wacklin-Knecht, Gerhard Grobner.

DOI: https://doi.org/10.1016/j.bpj.2022.11.1366
Eur J Immunol. 2023 Feb 13. e2250235

Innate immune inflammatory cell death: PANoptosis and PANoptosomes in host defense and disease.

Wen Chen, Jessica M Gullett, Rebecca E Tweedell, Thirumala-Devi Kanneganti.

  Regulated cell death (RCD) triggered by innate immune activation is an important strategy for host survival during pathogen invasion and perturbations of cellular homeostasis. There are two main categories of RCD, including non-lytic and lytic pathways. Apoptosis is the most well-characterized non-lytic RCD, and the inflammatory pyroptosis and necroptosis pathways are among the best known lytic forms. While these were historically viewed as independent RCD pathways, extensive evidence of crosstalk among their molecular components created a knowledge gap in our mechanistic understanding of RCD and innate immune pathway components, which led to the identification of PANoptosis. PANoptosis is a unique innate immune inflammatory RCD pathway that is regulated by PANoptosome complexes upon sensing pathogens, pathogen-associated molecular patterns (PAMPs), damage-associated molecular patterns (DAMPs) or the cytokines produced downstream. Cytosolic innate immune sensors, such as ZBP1, AIM2 and RIPK1, promote the assembly of PANoptosomes to drive PANoptosis. In this review, we discuss the molecular components of the known PANoptosomes and highlight the mechanisms of PANoptosome assembly, activation and regulation identified to date. We also discuss how PANoptosomes and mutations in PANoptosome components are linked to diseases. Given the impact of RCD, and PANoptosis specifically, across the disease spectrum, improved understanding of PANoptosomes and their regulation will be critical for identifying new therapeutic targets and strategies. This article is protected by copyright. All rights reserved.

Keywords:  apoptosis; caspases; inflammasome; necroptosis; pyroptosis

DOI:  https://doi.org/10.1002/eji.202250235
J Bone Miner Res. 2023 Feb 13.

ROLE OF THE MITOCHONDRIAL PERMEABILITY TRANSITION IN BONE METABOLISM AND AGING.

Rubens Sautchuk, Chen Yu, Matthew McArthur, Christine Massie, Paul S Brookes, George A Porter, Hani Awad, Roman A Eliseev.

The mitochondrial permeability transition pore (MPTP) and its positive regulator, cyclophilin D (CypD), play important pathophysiological roles in aging. In bone tissue, higher CypD expression and pore activity are found in aging, however a causal relationship between CypD/MPTP and bone degeneration needs to be established. We previously reported that CypD expression and MPTP activity are downregulated during osteoblast (OB) differentiation and that manipulations in CypD expression affect OB differentiation and function. Using a newly developed OB-specific CypD/MPTP gain-of-function (GOF) mouse model, we here present evidence that overexpression of a constitutively active K166Q mutant of CypD (caCypD) impairs OB energy metabolism and function, and bone morphological and biomechanical parameters. Specifically, in a spatial-dependent and sex-dependent manner, OB-specific CypD GOF led to a decrease in oxidative phosphorylation (OxPhos) levels, higher oxidative stress, and general metabolic adaptations coincident with the decreased bone organic matrix content in long bones. Interestingly, accelerated bone degeneration was present in vertebral bones regardless of sex. Overall, our work confirms CypD/MPTP overactivation as an important pathophysiological mechanism leading to bone degeneration and fragility in aging. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1002/jbmr.4787
Free Radic Biol Med. 2023 Feb 11. pii: S0891-5849(23)00053-9. [Epub ahead of print]

Altered trafficking of miRNAs at mitochondria modulates mitochondrial functions and cell death in brain ischemia.

Dhruv Gohel, Shatakshi Shukla, Wenson David Rajan, Bartosz Wojtas, Bozena Kaminska, Rajesh Singh.

  Stroke is one of the major causes of death and disabilities worldwide. The rapid induction of cell death by necrosis and apoptosis is observed at the ischemic core, while long lasting apoptosis and brain inflammation continue in the penumbra. The emerging evidence suggests a critical role of mitochondria in acute and chronic inflammation and cell death. Mitochondrial dysfunction may result in the release of mitokines and/or mitochondrial DNA into the cytoplasm and activate multiple cytosolic pathways which in turn triggers inflammation. The role of miRNA, specifically mitochondria-associated miRNAs (mitomiRs) in the regulation of mitochondrial functions is emerging. In the current study, we hypothesized that ischemia-induced mitomiRs may modulate the mitochondrial functions and such alterations under stress conditions may lead to mitochondrial dysfunction and cell death. We have demonstrated the specific pattern of miRNAs associated with mitochondria that is altered under ischemic condition induced by transient middle artery occlusion (tMCAo) in rats. The putative targets of altered miRNAs include several mitochondrial proteins which signifies their involvement in maintaining mitochondrial homeostasis. The alterations of selected miRNA in mitochondria was further detected in a cellular models when hypoxia is induced using a chemical agent CoCl2 in three cell lines. Two candidate mitomiRs, hsa-miR-149-3p and hsa-miR-204-5p were further analyzed for their functional role during in vitro hypoxia by transfecting mitomiR mimics into cells and determining critical mitochondrial functions and cell viability. The results here emphasize the role of certain mitomiRs as an important modulator of mitochondrial function under the ischemic condition.

Keywords:  Brain ischemia; CoCl(2); HIF-1α; Mitochondria; miRNAs; mitomiRs

DOI:  https://doi.org/10.1016/j.freeradbiomed.2023.02.004
Complex Psychiatry. 2023 Jan;8(3-4): 90-98

Large Common Mitochondrial DNA Deletions Are Associated with a Mitochondrial SNP T14798C Near the 3' Breakpoints.

Brooke E Hjelm, Christian Ramiro, Brandi L Rollins, Audrey A Omidsalar, Daniel S Gerke, Sujan C Das, Adolfo Sequeira, Ling Morgan, Alan F Schatzberg, Jack D Barchas, Francis S Lee, Richard M Myers, Stanley J Watson, Huda Akil, William E Bunney, Marquis P Vawter.

   Introduction: Large somatic deletions of mitochondrial DNA (mtDNA) accumulate with aging in metabolically active tissues such as the brain. We have cataloged the breakpoints and frequencies of large mtDNA deletions in the human brain.
Methods: We quantified 112 high-frequency mtDNA somatic deletions across four human brain regions with the Splice-Break2 pipeline. In addition, we utilized PLINK/Seq to test the association of mitochondrial genotypes with the abundance of these high-frequency mtDNA deletions. A conservative p value threshold of 5E-08 was used to find the significant loci.
Results: One mtDNA SNP (T14798C) was significantly associated with mtDNA deletions in two brain regions, the dorsolateral prefrontal cortex (DLPFC) and the superior temporal gyrus. Since the DLPFC showed the most robust association between T14798C and two deletion breakpoints (7816-14807 and 5462-14807), this association was tested in the DLPFC of a replication sample and validated the first results. Incorporating the C allele at 14,798 bp increased the perfect/imperfect length of the repeat at the 3' breakpoint of the two associated deletions.
Conclusion: This is the first study to identify the association of mtDNA SNP with large mtDNA deletions in the human brain. The T14798C allele located in the MT-CYB gene is a common polymorphism that occurs in several mitochondrial haplogroups. We hypothesize that the T14798C association with two deletions occurs by extending the repeat length around the 3' deletion breakpoints. This simple mechanism suggests that mtDNA SNPs can affect the mitochondrial genome structure, especially in brain where high levels of reactive oxygen species lead to deletion accumulation with aging.

Keywords:  Dorsolateral prefrontal cortex; Mitochondrial DNA somatic deletion; Primary visual cortex; Superior temporal gyrus

DOI:  https://doi.org/10.1159/000528051
Elife. 2023 Feb 17. pii: e83395. [Epub ahead of print]12

The multi-tissue landscape of somatic mtdna mutations indicates tissue specific accumulation and removal in aging.

Monica Sanchez-Contreras, Mariya T Sweetwyne, Kristine A Tsantilas, Jeremy A Whitson, Matthew D Campbell, Brenden F Kohrn, Hyeon Jeong Kim, Michael J Hipp, Jeanne Fredrickson, Megan M Nguyen, James B Hurley, David J Marcinek, Peter S Rabinovitch, Scott R Kennedy.

  Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue and mutation type dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with Elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.

Keywords:  genetics; genomics; mouse

DOI:  https://doi.org/10.7554/eLife.83395
bioRxiv. 2023 Feb 11. pii: 2023.02.11.528118. [Epub ahead of print]

Genome-wide screens for mitonuclear co-regulators uncover links between compartmentalized metabolism and mitochondrial gene expression.

Nicholas J Kramer, Gyan Prakash, Karine Choquet, Iliana Soto, Boryana Petrova, Hope E Merens, Naama Kanarek, L Stirling Churchman.

Mitochondrial oxidative phosphorylation (OXPHOS) complexes are assembled from proteins encoded by both nuclear and mitochondrial DNA. These dual-origin enzymes pose a complex gene regulatory challenge for cells, in which gene expression must be coordinated across organelles using distinct pools of ribosomes. How cells produce and maintain the accurate subunit stoichiometries for these OXPHOS complexes remains largely unknown. To identify genes involved in dual-origin protein complex synthesis, we performed FACS-based genome-wide screens analyzing mutant cells with unbalanced levels of mitochondrial- and nuclear-encoded subunits of cytochrome c oxidase (Complex IV). We identified novel genes involved in OXPHOS biogenesis, including two uncharacterized genes: PREPL and NME6 . We found that PREPL specifically regulates Complex IV biogenesis by interacting with mitochondrial protein synthesis machinery, while NME6, an uncharacterized nucleoside diphosphate kinase (NDPK), controls OXPHOS complex biogenesis through multiple mechanisms reliant on its NDPK domain. First, NME6 maintains local mitochondrial pyrimidine triphosphate levels essential for mitochondrial RNA abundance. Second, through stabilizing interactions with RCC1L, NME6 modulates the activity of mitoribosome regulatory complexes, leading to disruptions in mitoribosome assembly and mitochondrial RNA pseudouridylation. Taken together, we propose that NME6 acts as a link between compartmentalized mitochondrial metabolites and mitochondrial gene expression. Finally, we present these screens as a resource, providing a catalog of genes involved in mitonuclear gene regulation and OXPHOS biogenesis.

DOI: https://doi.org/10.1101/2023.02.11.528118