bims-mitdis Biomed News
on Mitochondrial disorders
Issue of 2024–08–18
forty-nine papers selected by
Catalina Vasilescu, Helmholz Munich
  1. Mitochondrial-derived compartments remove surplus proteins from the outer mitochondrial membrane.
  2. Editorial: Mitochondrial bioenergetics and metabolism: implication for human health and disease.
  3. MSC-mediated mitochondrial transfer restores mitochondrial DNA and function in neural progenitor cells of Leber's hereditary optic neuropathy.
  4. OPA1 promotes ferroptosis by augmenting mitochondrial ROS and suppressing an integrated stress response.
  5. Dynamic interaction of REEP5-MFN1/2 enables mitochondrial hitchhiking on tubular ER.
  6. A spatial atlas of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.
  7. Defective mitochondrial COX1 translation due to loss of COX14 function triggers ROS-induced inflammation in mouse liver.
  8. Mitochondrial Probe for Glutathione Depletion Reveals NME3 Essentiality for Mitochondrial Redox Response.
  9. Mitochondrial-derived compartments are multilamellar domains that encase membrane cargo and cytosol.
  10. Dysregulation of mitochondria, apoptosis and mitophagy in Leber's hereditary optic neuropathy with MT-ND1 3635G>A mutation.
  11. Quantitative assessment of morphological changes in lipid droplets and lipid-mito interactions with aging in brown adipose.
  12. Both Splice Variants of Zebrafish Tmem11 Localize to the Outer Membrane of Mitochondria.
  13. Mfn2R364W, Mfn2G176S, and Mfn2H165R mutations drive Charcot-Marie-Tooth type 2A disease by inducing apoptosis and mitochondrial oxidative phosphorylation damage.
  14. Mitochondrial network reorganization and transient expansion during oligodendrocyte generation.
  15. HSP60 chaperone deficiency disrupts the mitochondrial matrix proteome and dysregulates cholesterol synthesis.
  16. Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome.
  17. Benzopyrene represses mitochondrial fission factors and PINK1/Parkin-mediated mitophagy in primary astrocytes.
  18. Effects of idebenone treatment in a patient with DNAJC30-associated Leigh Syndrome.
  19. The genomic mosaic of mitochondrial dysfunction: Decoding nuclear and mitochondrial epigenetic contributions to maternally inherited diabetes and deafness pathogenesis.
  20. Secondary mitochondrial dysfunction across the spectrum of hereditary and acquired muscle disorders.
  21. PSMF1 variants cause a phenotypic spectrum from early-onset Parkinson's disease to perinatal lethality by disrupting mitochondrial pathways.
  22. Glycogen homeostasis and mtDNA expression require motor neuron to muscle TGFβ/Activin Signaling in Drosophila.
  23. 3D Reconstruction of the Mitochondrial Network within the Neuronal Soma from SBF-SEM Volume Data.
  24. Inhibition of angiogenesis by the secretome from iPSC-derived retinal ganglion cells with Leber's hereditary optic neuropathy-like phenotypes.
  25. Mitochondrial Transfer in the Neurovascular Unit, Not Only for Energy Rescue: A Systematic Review.
  26. Mechanism of mitochondrial [2Fe2S] cluster biosynthesis.
  27. Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer.
  28. Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants.
  29. Cadmium causes cerebral mitochondrial dysfunction through regulating mitochondrial HSF1.
  30. Case report: severe hypertrophic cardiomyopathy in a female neonate caused by de novo variant in NDUFB11.
  31. Gene therapy for ultrarare diseases: a geneticist's perspective.
  32. GLUD1 determines murine muscle stem cell fate by controlling mitochondrial glutamate levels.
  33. Mfn2 induces NCLX-mediated calcium release from mitochondria.
  34. Heterogeneous brain region-specific responses to astrocytic mitochondrial DNA damage in mice.
  35. Excitotoxicity, Oxytosis/Ferroptosis, and Neurodegeneration: Emerging Insights into Mitochondrial Mechanisms.
  36. Ndufa8 promotes white fat Browning by improving mitochondrial respiratory chain complex I function to ameliorate obesity by in vitro and in vivo.
  37. Adapting cytoskeleton-mitochondria patterning with myocyte differentiation by promyogenic PRR33.
  38. Pam16 and Pam18 were repurposed during Trypanosoma brucei evolution to regulate the replication of mitochondrial DNA.
  39. Extreme mitochondrial reduction in a novel group of free-living metamonads.
  40. Generation of an Armcx1 Conditional Knockout Mouse.
  41. Inherited mitochondrial dysfunction triggered by OPA1 mutation impacts the sensory innervation fibre identity, functionality and regenerative potential in the cornea.
  42. Extracellular vesicles: opening up a new perspective for the diagnosis and treatment of mitochondrial dysfunction.
  43. A Barth Syndrome Patient-Derived D75H Point Mutation in TAFAZZIN Drives Progressive Cardiomyopathy in Mice.
  44. DNA methylation in mammalian development and disease.
  45. Unraveling cysteine deficiency-associated rapid weight loss.
  46. Protocol for monitoring fatty acid trafficking from lipid droplets to mitochondria in cultured cells.
  47. Shifting redox reaction equilibria on demand using an orthogonal redox cofactor.
  48. Rare developmental disorder caused by variants in a small RNA gene.
  49. PITX2 deficiency leads to atrial mitochondrial dysfunction.
  1. J Cell Biol. 2024 Nov 04. pii: e202307036. [Epub ahead of print]223(11):
    Mitochondrial-derived compartments remove surplus proteins from the outer mitochondrial membrane.
    Zachary N Wilson, Sai Sangeetha Balasubramaniam, Sara Wong, Max-Hinderk Schuler, Mitchell J Wopat, Adam L Hughes.
      The outer mitochondrial membrane (OMM) creates a boundary that imports most of the mitochondrial proteome while removing extraneous or damaged proteins. How the OMM senses aberrant proteins and remodels to maintain OMM integrity remains unresolved. Previously, we identified a mitochondrial remodeling mechanism called the mitochondrial-derived compartment (MDC) that removes a subset of the mitochondrial proteome. Here, we show that MDCs specifically sequester proteins localized only at the OMM, providing an explanation for how select mitochondrial proteins are incorporated into MDCs. Remarkably, selective sorting into MDCs also occurs within the OMM, as subunits of the translocase of the outer membrane (TOM) complex are excluded from MDCs unless assembly of the TOM complex is impaired. Considering that overloading the OMM with mitochondrial membrane proteins or mistargeted tail-anchored membrane proteins induces MDCs to form and sequester these proteins, we propose that one functional role of MDCs is to create an OMM-enriched trap that segregates and sequesters excess proteins from the mitochondrial surface.
    DOI:  https://doi.org/10.1083/jcb.202307036
  2. Front Mol Biosci. 2024 ;11 1468758
    Editorial: Mitochondrial bioenergetics and metabolism: implication for human health and disease.
    Sofia Ahola.
      
    Keywords:  calcium regulation; cell death; inflammation; integrated stress response; mitochondria; mitochondrial dysfunction; mitochondrial-ER communication
    DOI:  https://doi.org/10.3389/fmolb.2024.1468758
  3. Sci China Life Sci. 2024 Aug 08.
    MSC-mediated mitochondrial transfer restores mitochondrial DNA and function in neural progenitor cells of Leber's hereditary optic neuropathy.
    Rui Wang, Feixiang Bao, Manjiao Lu, Xiaoyun Jia, Jiahui Xiao, Yi Wu, Qingjiong Zhang, Xingguo Liu.
      Leber's hereditary optic neuropathy (LHON) is a debilitating mitochondrial disease associated with mutations in mitochondrial DNA (mtDNA). Unfortunately, the available treatment options for LHON patients are limited due to challenges in mitochondrial replacement. In our study, we reprogramming LHON urine cells into induced pluripotent stem cells (iPSCs) and differentiating them into neural progenitor cells (NPCs) and neurons for disease modeling. Our research revealed that LHON neurons exhibited significantly higher levels of mtDNA mutations and reduced mitochondrial function, confirming the disease phenotype. However, through co-culturing LHON iPSC-derived NPCs with mesenchymal stem cells (MSCs), we observed a remarkable rescue of mutant mtDNA and a significant improvement in mitochondrial metabolic function in LHON neurons. These findings suggest that co-culturing with MSCs can enhance mitochondrial function in LHON NPCs, even after their differentiation into neurons. This discovery holds promise as a potential therapeutic strategy for LHON patients.
    Keywords:  energy; induced pluripotent stem cells; mesenchymal stem cells; metabolism; mitochondria; mitochondrial DNA; mitochondrial diseases; stem cells
    DOI:  https://doi.org/10.1007/s11427-024-2647-8
  4. Mol Cell. 2024 Aug 09. pii: S1097-2765(24)00618-X. [Epub ahead of print]
    OPA1 promotes ferroptosis by augmenting mitochondrial ROS and suppressing an integrated stress response.
    Felix G Liang, Fereshteh Zandkarimi, Jaehoon Lee, Joshua L Axelrod, Ryan Pekson, Yisang Yoon, Brent R Stockwell, Richard N Kitsis.
      Ferroptosis, an iron-dependent form of nonapoptotic cell death mediated by lipid peroxidation, has been implicated in the pathogenesis of multiple diseases. Subcellular organelles play pivotal roles in the regulation of ferroptosis, but the mechanisms underlying the contributions of the mitochondria remain poorly defined. Optic atrophy 1 (OPA1) is a mitochondrial dynamin-like GTPase that controls mitochondrial morphogenesis, fusion, and energetics. Here, we report that human and mouse cells lacking OPA1 are markedly resistant to ferroptosis. Reconstitution with OPA1 mutants demonstrates that ferroptosis sensitization requires the GTPase activity but is independent of OPA1-mediated mitochondrial fusion. Mechanistically, OPA1 confers susceptibility to ferroptosis by maintaining mitochondrial homeostasis and function, which contributes both to the generation of mitochondrial lipid reactive oxygen species (ROS) and suppression of an ATF4-mediated integrated stress response. Together, these results identify an OPA1-controlled mitochondrial axis of ferroptosis regulation and provide mechanistic insights for therapeutically manipulating this form of cell death in diseases.
    Keywords:  ATF4; GPx4; OPA1; cell death; ferroptosis; integrated stress response; mitochondria; system X(c)(−); xCT
    DOI:  https://doi.org/10.1016/j.molcel.2024.07.020
  5. J Cell Biol. 2024 Oct 07. pii: e202304031. [Epub ahead of print]223(10):
    Dynamic interaction of REEP5-MFN1/2 enables mitochondrial hitchhiking on tubular ER.
    Shue Chen, Yang Sun, Yuling Qin, Lan Yang, Zhenhua Hao, Zhihao Xu, Mikael Björklund, Wei Liu, Zhi Hong.
      Mitochondrial functions can be regulated by membrane contact sites with the endoplasmic reticulum (ER). These mitochondria-ER contact sites (MERCs) are functionally heterogeneous and maintained by various tethers. Here, we found that REEP5, an ER tubule-shaping protein, interacts with Mitofusins 1/2 to mediate mitochondrial distribution throughout the cytosol by a new transport mechanism, mitochondrial "hitchhiking" with tubular ER on microtubules. REEP5 depletion led to reduced tethering and increased perinuclear localization of mitochondria. Conversely, increasing REEP5 expression facilitated mitochondrial distribution throughout the cytoplasm. Rapamycin-induced irreversible REEP5-MFN1/2 interaction led to mitochondrial hyperfusion, implying that the dynamic release of mitochondria from tethering is necessary for normal mitochondrial distribution and dynamics. Functionally, disruption of MFN2-REEP5 interaction dynamics by forced dimerization or silencing REEP5 modulated the production of mitochondrial reactive oxygen species (ROS). Overall, our results indicate that dynamic REEP5-MFN1/2 interaction mediates cytosolic distribution and connectivity of the mitochondrial network by "hitchhiking" and this process regulates mitochondrial ROS, which is vital for multiple physiological functions.
    DOI:  https://doi.org/10.1083/jcb.202304031
  6. bioRxiv. 2024 Aug 06. pii: 2024.08.05.604215. [Epub ahead of print]
    A spatial atlas of mitochondrial gene expression reveals dynamic translation hubs and remodeling in stress.
    Adam Begeman, John A Smolka, Ahmad Shami, Tejashree Pradip Waingankar, Samantha C Lewis.
      Mitochondrial genome expression is important for cellular bioenergetics. How mitochondrial RNA processing and translation are spatially organized across dynamic mitochondrial networks is not well understood. Here, we report that processed mitochondrial RNAs are consolidated with mitoribosome components into translation hubs distal to either nucleoids or processing granules in human cells. During stress, these hubs are remodeled into translationally repressed mesoscale bodies containing messenger, ribosomal, and double-stranded RNA. We show that the highly conserved helicase SUV3 contributes to the distribution of processed RNA within mitochondrial networks, and that stress bodies form downstream of proteostatic stress in cells lacking SUV3 unwinding activity. We propose that the spatial organization of nascent chain synthesis into discrete domains serves to throttle the flow of genetic information in stress to ensure mitochondrial quality control.
    DOI:  https://doi.org/10.1101/2024.08.05.604215
  7. Nat Commun. 2024 Aug 12. 15(1): 6914
    Defective mitochondrial COX1 translation due to loss of COX14 function triggers ROS-induced inflammation in mouse liver.
    Abhishek Aich, Angela Boshnakovska, Steffen Witte, Tanja Gall, Kerstin Unthan-Fechner, Roya Yousefi, Arpita Chowdhury, Drishan Dahal, Aditi Methi, Svenja Kaufmann, Ivan Silbern, Jan Prochazka, Zuzana Nichtova, Marcela Palkova, Miles Raishbrook, Gizela Koubkova, Radislav Sedlacek, Simon E Tröder, Branko Zevnik, Dietmar Riedel, Susann Michanski, Wiebke Möbius, Philipp Ströbel, Christian Lüchtenborg, Patrick Giavalisco, Henning Urlaub, Andre Fischer, Britta Brügger, Stefan Jakobs, Peter Rehling.
      Mitochondrial oxidative phosphorylation (OXPHOS) fuels cellular ATP demands. OXPHOS defects lead to severe human disorders with unexplained tissue specific pathologies. Mitochondrial gene expression is essential for OXPHOS biogenesis since core subunits of the complexes are mitochondrial-encoded. COX14 is required for translation of COX1, the central mitochondrial-encoded subunit of complex IV. Here we describe a COX14 mutant mouse corresponding to a patient with complex IV deficiency. COX14M19I mice display broad tissue-specific pathologies. A hallmark phenotype is severe liver inflammation linked to release of mitochondrial RNA into the cytosol sensed by RIG-1 pathway. We find that mitochondrial RNA release is triggered by increased reactive oxygen species production in the deficiency of complex IV. Additionally, we describe a COA3Y72C mouse, affected in an assembly factor that cooperates with COX14 in early COX1 biogenesis, which displays a similar yet milder inflammatory phenotype. Our study provides insight into a link between defective mitochondrial gene expression and tissue-specific inflammation.
    DOI:  https://doi.org/10.1038/s41467-024-51109-y
  8. ACS Chem Biol. 2024 Aug 12.
    Mitochondrial Probe for Glutathione Depletion Reveals NME3 Essentiality for Mitochondrial Redox Response.
    Piriththiv Dhavarasa, Tanja Sack, Carmine P Cerrato, Ashley P Cheng, Yi Y Zhang, Kangfu Chen, Shana O Kelley.
      Maintenance of the mitochondrial thiol redox state is essential for cell survival. However, we lack a comprehensive understanding of the redox response to mitochondrial glutathione depletion. We developed a mitochondria-penetrating peptide, mtCDNB, to specifically deplete mitochondrial glutathione. A genome-wide CRISPR/Cas9 screen in tandem with mtCDNB treatment was employed to uncover regulators of the redox response to mitochondrial glutathione depletion. We identified nucleoside diphosphate kinase 3 (NME3) as a regulator of mitochondrial dynamics. We show that NME3 is recruited to the mitochondrial outer membrane when under redox stress. In the absence of NME3, there is impaired mitophagy, which leads to the accumulation of dysfunctional mitochondria. NME3 knockouts depleted of mitochondrial glutathione have increased mitochondrial ROS production, accumulate mtDNA lesions, and present a senescence-associated secretory phenotype. Our findings suggest a novel role for NME3 in selecting mitochondria for degradation through mitophagy under conditions of mitochondrial redox stress.
    DOI:  https://doi.org/10.1021/acschembio.4c00287
  9. J Cell Biol. 2024 Nov 04. pii: e202307035. [Epub ahead of print]223(11):
    Mitochondrial-derived compartments are multilamellar domains that encase membrane cargo and cytosol.
    Zachary N Wilson, Matt West, Alyssa M English, Greg Odorizzi, Adam L Hughes.
      Preserving the health of the mitochondrial network is critical to cell viability and longevity. To do so, mitochondria employ several membrane remodeling mechanisms, including the formation of mitochondrial-derived vesicles (MDVs) and compartments (MDCs) to selectively remove portions of the organelle. In contrast to well-characterized MDVs, the distinguishing features of MDC formation and composition remain unclear. Here, we used electron tomography to observe that MDCs form as large, multilamellar domains that generate concentric spherical compartments emerging from mitochondrial tubules at ER-mitochondria contact sites. Time-lapse fluorescence microscopy of MDC biogenesis revealed that mitochondrial membrane extensions repeatedly elongate, coalesce, and invaginate to form these compartments that encase multiple layers of membrane. As such, MDCs strongly sequester portions of the outer mitochondrial membrane, securing membrane cargo into a protected domain, while also enclosing cytosolic material within the MDC lumen. Collectively, our results provide a model for MDC formation and describe key features that distinguish MDCs from other previously identified mitochondrial structures and cargo-sorting domains.
    DOI:  https://doi.org/10.1083/jcb.202307035
  10. Gene. 2024 Aug 13. pii: S0378-1119(24)00734-0. [Epub ahead of print] 148853
    Dysregulation of mitochondria, apoptosis and mitophagy in Leber's hereditary optic neuropathy with MT-ND1 3635G>A mutation.
    Yingqi Chen, Xiaoyang Wei, Xiaorui Ci, Yanchun Ji, Juanjuan Zhang.
      Leber's hereditary optic neuropathy (LHON) is a maternal inherited disorder, primarily due to mitochondrial DNA (mtDNA) mutations. This investigation aimed to assess the pathogenicity of m.3635G>A alteration known to confer susceptibility to LHON. The disruption of electrostatic interactions among S110 of the MT-ND1 and the side chain of E4, along with the carbonyl backbone of M1 in the NDUFA1, was observed in complex I of cybrids with m.3635G>A. This disturbance affected the complex I assembly activity by changing the mitochondrial respiratory chain composition and function. In addition, the affected cybrids exhibited notable deficiencies in complex I activities, including impaired mitochondrial respiration and depolarization of its membrane potential. Apoptosis was also stimulated in the mutant group, as witnessed by the secretion of cytochrome c and activation of PARP, caspase 3, 7, and 9 compared to the control. Furthermore, the mutant group exhibited decreased levels of autophagy protein light chain 3, accumulation of autophagic substrate P62, and impaired PINK1/Parkin-dependent mitophagy. Overall, the current study has confirmed the crucial involvement of the alteration of the m.3635G>A gene in the development of LHON. These findings contribute to a deeper comprehension of the pathophysiological mechanisms underlying LHON, providing a fundamental basis for further research.
    Keywords:  Apoptosis; Leber’s hereditary optic neuropathy (LHON); MT-ND1 mutation; Mitochondrial dysfunction; Mitophagy
    DOI:  https://doi.org/10.1016/j.gene.2024.148853
  11. J Cell Physiol. 2024 Aug 13.
    Quantitative assessment of morphological changes in lipid droplets and lipid-mito interactions with aging in brown adipose.
    Amber Crabtree, Kit Neikirk, Julia A Pinette, Aaron Whiteside, Bryanna Shao, Jessica Bedenbaugh, Zer Vue, Larry Vang, Han Le, Mert Demirci, Taseer Ahmad, Trinity Celeste Owens, Ashton Oliver, Faben Zeleke, Heather K Beasley, Edgar Garza Lopez, Estevão Scudese, Taylor Rodman, Kinuthia Kabugi, Alice Koh, Suzanne Navarro, Jacob Lam, Ben Kirk, Margaret Mungai, Mariya Sweetwyne, Ho-Jin Koh, Elma Zaganjor, Steven M Damo, Jennifer A Gaddy, Annet Kirabo, Sandra A Murray, Anthonya Cooper, Clintoria Williams, Melanie R McReynolds, Andrea G Marshall, Antentor Hinton.
      The physical characteristics of brown adipose tissue (BAT) are defined by the presence of multilocular lipid droplets (LDs) within the brown adipocytes and a high abundance of iron-containing mitochondria, which give it its characteristic color. Normal mitochondrial function is, in part, regulated by organelle-to-organelle contacts. For example, the contact sites that mediate mitochondria-LD interactions are thought to have various physiological roles, such as the synthesis and metabolism of lipids. Aging is associated with mitochondrial dysfunction, and previous studies show that there are changes in mitochondrial structure and the proteins that modulate organelle contact sites. However, how mitochondria-LD interactions change with aging has yet to be fully clarified. Therefore, we sought to define age-related changes in LD morphology and mitochondria-lipid interactions in BAT. We examined the three-dimensional morphology of mitochondria and LDs in young (3-month) and aged (2-year) murine BAT using serial block face-scanning electron microscopy and the Amira program for segmentation, analysis, and quantification. Our analyses showed reductions in LD volume, area, and perimeter in aged samples in comparison to young samples. Additionally, we observed changes in LD appearance and type in aged samples compared to young samples. Notably, we found differences in mitochondrial interactions with LDs, which could implicate that these contacts may be important for energetics in aging. Upon further investigation, we also found changes in mitochondrial and cristae structure for the mitochondria interacting with LDs. Overall, these data define the nature of LD morphology and organelle-organelle contacts during aging and provide insight into LD contact site changes that interconnect biogerontology with mitochondrial function, metabolism, and bioactivity in aged BAT.
    Keywords:  brown adipose tissue (BAT); lipid droplets (LD); lipids; mitochondria; mito–lipid
    DOI:  https://doi.org/10.1002/jcp.31340
  12. MicroPubl Biol. 2024 ;2024
    Both Splice Variants of Zebrafish Tmem11 Localize to the Outer Membrane of Mitochondria.
    Saron S Tadesse, Melanie Schille, Paula Collado Cordon, Susan Walsh.
      In mammalian and Drosophila systems, Transmembrane protein 11 (TMEM11) regulates mitochondrial morphology, mitophagy, and mitochondrial function. Here, we begin to expand these studies to the zebrafish model system. We identified two splice variants of tmem11 , which are both expressed during early development. In addition, we determined that both zebrafish Tmem11 proteins localize to the mitochondria using fluorescent tags and expression in cell culture. Consistent with recent data, biochemical fractionation indicates that Tmem11 is embedded in the outer membrane of mitochondria. Overall, these studies will provide new insights into the complex protein network that mediates mitochondrial physiology in the zebrafish.
    DOI:  https://doi.org/10.17912/micropub.biology.001162
  13. Int J Biol Macromol. 2024 Aug 12. pii: S0141-8130(24)05478-3. [Epub ahead of print]278(Pt 1): 134673
    Mfn2R364W, Mfn2G176S, and Mfn2H165R mutations drive Charcot-Marie-Tooth type 2A disease by inducing apoptosis and mitochondrial oxidative phosphorylation damage.
    Yuanzhu Zhang, Lerong Ma, Ziru Wang, Chuang Gao, Lin Yang, Mengjing Li, Xiaochun Tang, Hongming Yuan, Daxin Pang, Hongsheng Ouyang.
      Charcot-Marie-Tooth type 2A (CMT2A) is a single-gene motor sensory neuropathy caused by Mfn2 mutation. It is generally believed that CMT2A involves mitochondrial fusion disruption. However, how Mfn2 mutation mediates the mitochondrial membrane fusion loss and its further pathogenic mechanisms remain unclear. Here, in vivo and in vitro mouse models harboring the Mfn2R364W, Mfn2G176S and Mfn2H165R mutations were constructed. Mitochondrial membrane fusion and fission proteins analysis showed that Mfn2R364W, Mfn2G176S, and Mfn2H165R/+ mutations maintain the expression of Mfn2, but promote Drp1 upregulation and Opa1 hydrolytic cleavage. In Mfn2H165R/H165R mutation, Mfn2, Drp1, and Opa1 all play a role in inducing mitochondrial fragmentation, and the mitochondrial aggregation is affected by Mfn2 loss. Further research into the pathogenesis of CMT2A showed these three mutations all induce mitochondria-mediated apoptosis, and mitochondrial oxidative phosphorylation damage. Overall, loss of overall fusion activity affects mitochondrial DNA (mtDNA) stability and causes mitochondrial loss and dysfunction, ultimately leading to CMT2A disease. Interestingly, the differences in the pathogenesis of CMT2A between Mfn2R364W, Mfn2G176S, Mfn2H165R/+ and Mfn2H165R/H165R mutations, including the distribution of Mfn2 and mitochondria, the expression of mitochondrial outer membrane-associated proteins (Bax, VDAC1 and AIF), and the enzyme activity of mitochondrial complex I, are related to the expression of Mfn2.
    Keywords:  CMT2A; CRISPR/Cas9; Mfn2; apoptosis; mitochondria; oxidative phosphorylation
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.134673
  14. Nat Commun. 2024 Aug 14. 15(1): 6979
    Mitochondrial network reorganization and transient expansion during oligodendrocyte generation.
    Xhoela Bame, Robert A Hill.
      Oligodendrocyte precursor cells (OPCs) give rise to myelinating oligodendrocytes of the brain. This process persists throughout life and is essential for recovery from neurodegeneration. To better understand the cellular checkpoints that occur during oligodendrogenesis, we determined the mitochondrial distribution and morphometrics across the oligodendrocyte lineage in mouse and human cerebral cortex. During oligodendrocyte generation, mitochondrial content expands concurrently with a change in subcellular partitioning towards the distal processes. These changes are followed by an abrupt loss of mitochondria in the oligodendrocyte processes and myelin, coinciding with sheath compaction. This reorganization and extensive expansion and depletion take 3 days. Oligodendrocyte mitochondria are stationary over days while OPC mitochondrial motility is modulated by animal arousal state within minutes. Aged OPCs also display decreased mitochondrial size, volume fraction, and motility. Thus, mitochondrial dynamics are linked to oligodendrocyte generation, dynamically modified by their local microenvironment, and altered in the aging brain.
    DOI:  https://doi.org/10.1038/s41467-024-51016-2
  15. Mol Metab. 2024 Aug 13. pii: S2212-8778(24)00140-6. [Epub ahead of print] 102009
    HSP60 chaperone deficiency disrupts the mitochondrial matrix proteome and dysregulates cholesterol synthesis.
    Cagla Cömert, Kasper Kjær-Sørensen, Jakob Hansen, Jasper Carlsen, Jesper Just, Brandon F Meaney, Elsebet Østergaard, Yonglun Luo, Claus Oxvig, Lisbeth Schmidt-Laursen, Johan Palmfeldt, Paula Fernandez-Guerra, Peter Bross.
       OBJECTIVE: Mitochondrial proteostasis is critical for cellular function. The molecular chaperone HSP60 is essential for cell function and dysregulation of HSP60 expression has been implicated in cancer and diabetes. The few reported patients carrying HSP60 gene variants show neurodevelopmental delay and brain hypomyelination. Hsp60 interacts with more than 260 mitochondrial proteins but the mitochondrial proteins and functions affected by HSP60 deficiency are poorly characterized.
    METHODS: We studied two model systems for HSP60 deficiency: (1) engineered HEK cells carrying an inducible dominant negative HSP60 mutant protein, (2) zebrafish HSP60 knockout larvae. Both systems were analyzed by RNASeq, proteomics, and targeted metabolomics, and several functional assays relevant for the respective model. In addition, skin fibroblasts from patients with disease-associated HSP60 variants were analyzed by proteomics.
    RESULTS: We show that HSP60 deficiency leads to a differentially downregulated mitochondrial matrix proteome, transcriptional activation of stress responses, and dysregulated cholesterol biosynthesis. This leads to lipid accumulation in zebrafish knockout larvae.
    CONCLUSIONS: Our data provide a compendium of the effects of HSP60 deficiency on the mitochondrial matrix proteome. We show that HSP60 is a master regulator and modulator of mitochondrial functions and metabolic pathways. HSP60 dysfunction also affects cellular metabolism and disrupts the integrated stress response. The effect on cholesterol synthesis explains the effect of HSP60 dysfunction on myelination observed in patients carrying genetic variants of HSP60.
    Keywords:  HSP60; HSPD1; chaperone; cholesterol; folding; mitochondria; myelination; proteomics; transcriptomics; zebrafish
    DOI:  https://doi.org/10.1016/j.molmet.2024.102009
  16. Nat Struct Mol Biol. 2024 Aug 12.
    Structural basis of LRPPRC-SLIRP-dependent translation by the mitoribosome.
    Vivek Singh, J Conor Moran, Yuzuru Itoh, Iliana C Soto, Flavia Fontanesi, Mary Couvillion, Martijn A Huynen, L Stirling Churchman, Antoni Barrientos, Alexey Amunts.
      In mammalian mitochondria, mRNAs are cotranscriptionally stabilized by the protein factor LRPPRC (leucine-rich pentatricopeptide repeat-containing protein). Here, we characterize LRPPRC as an mRNA delivery factor and report its cryo-electron microscopy structure in complex with SLIRP (SRA stem-loop-interacting RNA-binding protein), mRNA and the mitoribosome. The structure shows that LRPPRC associates with the mitoribosomal proteins mS39 and the N terminus of mS31 through recognition of the LRPPRC helical repeats. Together, the proteins form a corridor for handoff of the mRNA. The mRNA is directly bound to SLIRP, which also has a stabilizing function for LRPPRC. To delineate the effect of LRPPRC on individual mitochondrial transcripts, we used RNA sequencing, metabolic labeling and mitoribosome profiling, which showed a transcript-specific influence on mRNA translation efficiency, with cyclooxygenase 1 and 2 translation being the most affected. Our data suggest that LRPPRC-SLIRP acts in recruitment of mitochondrial mRNAs to modulate their translation. Collectively, the data define LRPPRC-SLIRP as a regulator of the mitochondrial gene expression system.
    DOI:  https://doi.org/10.1038/s41594-024-01365-9
  17. Toxicology. 2024 Aug 13. pii: S0300-483X(24)00207-5. [Epub ahead of print] 153926
    Benzopyrene represses mitochondrial fission factors and PINK1/Parkin-mediated mitophagy in primary astrocytes.
    Yunn Me Me Paing, Yunkyung Eom, Sung Hoon Lee.
      Mitochondria are essential for various physiological functions in astrocytes in the brain, such as maintaining ion and pH homeostasis, regulating neurotransmission, and modulating neuroinflammation. Mitophagy, a form of autophagy specific to mitochondria, is essential for ensuring mitochondrial quality and function. Benzo[a]pyrene (BaP) accumulates in the brain, and exposure to it is recognized as an environmental risk factor for neurodegenerative diseases. However, while the toxic mechanisms of BaP have been investigated in neurons, their effects on astrocytes-the most prevalent glial cells in the brain-are not clearly understood. Therefore, this study aims to investigate the toxic effects of exposure to BaP on mitochondria in primary astrocytes. Fluorescent probes and genetically encoded indicators were utilized to visualize mitochondrial morphology and physiology, and regulatory factors involved in mitochondrial morphology and mitophagy were assessed. Additionally, the mitochondrial respiration rate was measured in BaP-exposed astrocytes. BaP exposure resulted in mitochondrial enlargement owing to the suppression of mitochondrial fission factors. Furthermore, BaP-exposed astrocytes demonstrated reduced mitophagy and exhibited aberrant mitochondrial function and physiology, such as altered mitochondrial respiration rates, increased mitochondrial superoxide, disrupted mitochondrial membrane potential, and dysregulated mitochondrial Ca2+. These findings offer insights into the underlying toxic mechanisms of BaP exposure in neurodegenerative diseases by inducing aberrant mitophagy and mitochondrial dysfunction in astrocytes.
    Keywords:  astrocytes; benzo[a]pyrene; fission factor; mitochondria; mitophagy
    DOI:  https://doi.org/10.1016/j.tox.2024.153926
  18. Neurol Neurochir Pol. 2024 Aug 12.
    Effects of idebenone treatment in a patient with DNAJC30-associated Leigh Syndrome.
    Kamil Dzwilewski, Karol Chojnowski, Magdalena Krygier, Marta Zawadzka, Magdalena Chylińska, Maria Mazurkiewicz-Bełdzińska.
      
    Keywords:  DNAJC30; Leigh Syndrome; dystonia; idebenone; mitochondrial disease; optic neuropathy
    DOI:  https://doi.org/10.5603/pjnns.100423
  19. Heliyon. 2024 Jul 30. 10(14): e34756
    The genomic mosaic of mitochondrial dysfunction: Decoding nuclear and mitochondrial epigenetic contributions to maternally inherited diabetes and deafness pathogenesis.
    Luigi Donato, Concetta Scimone, Simona Alibrandi, Maria Vadalà, Massimo Castellucci, Vincenza Maria Elena Bonfiglio, Sergio Zaccaria Scalinci, Giorgia Abate, Rosalia D'Angelo, Antonina Sidoti.
       Aims: Maternally inherited diabetes and deafness (MIDD) is a complex disorder characterized by multiorgan clinical manifestations, including diabetes, hearing loss, and ophthalmic complications. This pilot study aimed to elucidate the intricate interplay between nuclear and mitochondrial genetics, epigenetic modifications, and their potential implications in the pathogenesis of MIDD.
    Main methods: A comprehensive genomic approach was employed to analyze a Sicilian family affected by clinically characterized MIDD, negative to the only known causative m.3243 A > G variant, integrating whole-exome sequencing and whole-genome bisulfite sequencing of both nuclear and mitochondrial analyses.
    Key findings: Rare and deleterious variants were identified across multiple nuclear genes involved in retinal homeostasis, mitochondrial function, and epigenetic regulation, while complementary mitochondrial DNA analysis revealed a rich tapestry of genetic diversity across genes encoding components of the electron transport chain and ATP synthesis machinery. Epigenetic analyses uncovered significant differentially methylated regions across the genome and within the mitochondrial genome, suggesting a nuanced landscape of epigenetic modulation.
    Significance: The integration of genetic and epigenetic data highlighted the potential crosstalk between nuclear and mitochondrial regulation, with specific mtDNA variants influencing methylation patterns and potentially impacting the expression and regulation of mitochondrial genes. This pilot study provides valuable insights into the complex molecular mechanisms underlying MIDD, emphasizing the interplay between nucleus and mitochondrion, tracing the way for future research into targeted therapeutic interventions and personalized approaches for disease management.
    Keywords:  Epigenetics; MIDD; WES; WGS; mtDNA
    DOI:  https://doi.org/10.1016/j.heliyon.2024.e34756
  20. Mitochondrion. 2024 Aug 10. pii: S1567-7249(24)00103-X. [Epub ahead of print] 101945
    Secondary mitochondrial dysfunction across the spectrum of hereditary and acquired muscle disorders.
    Gloria Mak, Mark Tarnopolsky, Jian-Qiang Lu.
      Mitochondria form a dynamic network within skeletal muscle. This network is not only responsible for producing adenine triphosphate through oxidative phosphorylation, but also responds through fission, fusion and mitophagy to various factors, such as increased energy demands, oxidative stress, inflammation, and calcium dysregulation. Mitochondrial dysfunction in skeletal muscle not only occurs in primary mitochondrial myopathies, but also other hereditary and acquired myopathies. As such, this review attempts to highlight the clinical and histopathologic aspects of mitochondrial dysfunction seen in hereditary and acquired myopathies, as well as discuss potential mechanisms leading to mitochondrial dysfunction and therapies to restore mitochondrial function.
    Keywords:  Congenital myopathies; Inflammatory myopathies; Mitochondrial dysfunction; Muscular dystrophies
    DOI:  https://doi.org/10.1016/j.mito.2024.101945
  21. medRxiv. 2024 Jun 20. pii: 2024.06.19.24308302. [Epub ahead of print]
    PSMF1 variants cause a phenotypic spectrum from early-onset Parkinson's disease to perinatal lethality by disrupting mitochondrial pathways.
    Francesca Magrinelli, Christelle Tesson, Plamena R Angelova, Ainara Salazar-Villacorta, Jose A Rodriguez, Annarita Scardamaglia, Brian Hon-Yin Chung, Matthew Jaconelli, Barbara Vona, Noemi Esteras, Anna Ka-Yee Kwong, Thomas Courtin, Reza Maroofian, Shahryar Alavi, Raja Nirujogi, Mariasavina Severino, Patrick A Lewis, Stephanie Efthymiou, Benjamin O'Callaghan, Rebecca Buchert, Linda Sofan, Pawel Lis, Chloé Pinon, Guido J Breedveld, Martin Man-Chun Chui, David Murphy, Vanessa Pitz, Mary B Makarious, Marlene Cassar, Bassem A Hassan, Sana Iftikhar, Clarissa Rocca, Peter Bauer, Michele Tinazzi, Marina Svetel, Bedia Samanci, Haşmet A Hanağası, Basar Bilgiç, José A Obeso, Monica M Kurtis, Guillaume Cogan, Ayşe Nazlı Başak, Güneş Kiziltan, Tuğçe Gül, Gül Yalçın, Bülent Elibol, Nina Barišić, Earny Wei-Sen Ng, Sze-Shing Fan, Tova Hershkovitz, Karin Weiss, Javeria Raza Alvi, Tipu Sultan, Issam Azmi Alkhawaja, Tawfiq Froukh, Hadeel Abdollah E Alrukban, Christine Fauth, Ulrich A Schatz, Thomas Zöggeler, Michael Zech, Karen Stals, Vinod Varghese, Sonia Gandhi, Cornelis Blauwendraat, John A Hardy, Suzanne Lesage, Vincenzo Bonifati, Tobias B Haack, Aida M Bertoli-Avella, Robert Steinfeld, Dario R Alessi, Hermann Steller, Alexis Brice, Andrey Y Abramov, Kailash P Bhatia, Henry Houlden.
      Dissecting biological pathways highlighted by Mendelian gene discovery has provided critical insights into the pathogenesis of Parkinson's disease (PD) and neurodegeneration. This approach ultimately catalyzes the identification of potential biomarkers and therapeutic targets. Here, we identify PSMF1 as a new gene implicated in PD and childhood neurodegeneration. We find that biallelic PSMF1 missense and loss-of-function variants co-segregate with phenotypes from early-onset PD and parkinsonism to perinatal lethality with neurological manifestations across 15 unrelated pedigrees with 22 affected subjects, showing clear genotype-phenotype correlation. PSMF1 encodes the proteasome regulator PSMF1/PI31, a highly conserved, ubiquitously expressed partner of the 20S proteasome and neurodegeneration-associated F-box-O 7 and valosin-containing proteins. We demonstrate that PSMF1 variants impair mitochondrial membrane potential, dynamics and mitophagy in patient-derived fibroblasts. Additionally, we develop models of psmf1 knockdown Drosophila and Psmf1 conditional knockout mouse exhibiting age-dependent motor impairment, with diffuse gliosis in mice. These findings unequivocally link defective PSMF1 to early-onset PD and neurodegeneration and suggest mitochondrial dysfunction as a mechanistic contributor.
    DOI:  https://doi.org/10.1101/2024.06.19.24308302
  22. bioRxiv. 2024 Jul 31. pii: 2024.06.25.600699. [Epub ahead of print]
    Glycogen homeostasis and mtDNA expression require motor neuron to muscle TGFβ/Activin Signaling in Drosophila.
    Heidi Bretscher, Michael B O'Connor.
      Maintaining metabolic homeostasis requires coordinated nutrient utilization between intracellular organelles and across multiple organ systems. Many organs rely heavily on mitochondria to generate (ATP) from glucose, or stored glycogen. Proteins required for ATP generation are encoded in both nuclear and mitochondrial DNA (mtDNA). We show that motoneuron to muscle signaling by the TGFβ/Activin family member Actβ positively regulates glycogen levels during Drosophila development. Remarkably, we find that levels of stored glycogen are unaffected by altering cytoplasmic glucose catabolism. Instead, Actβ loss reduces levels of mtDNA and nuclearly encoded genes required for mtDNA replication, transcription and translation. Direct RNAi mediated knockdown of these same nuclearly encoded mtDNA expression factors also results in decreased glycogen stores. Lastly, we find that expressing an activated form of the type I receptor Baboon in muscle restores both glycogen and mtDNA levels in actβ mutants, thereby confirming a direct link between Actβ signaling, glycogen homeostasis and mtDNA expression.
    Key Points: The Drosophila TGFβ family member Actβ signals from motor neuron to muscle positively regulating glycogen levelsActβ positively regulates nuclearly encoded factors required for mtDNA expressionGenes involved in mtDNA expression directly regulate glycogen stores Expressing an activated receptor in muscle restores glycogen and mtDNA in actβ mutants.
    Abstract Figure:
    DOI:  https://doi.org/10.1101/2024.06.25.600699
  23. Methods Mol Biol. 2024 ;2831 145-177
    3D Reconstruction of the Mitochondrial Network within the Neuronal Soma from SBF-SEM Volume Data.
    Jane Tweedy, Ross Laws, George Merces, Tracey Davey, Amy K Reeve, Amy E Vincent.
      Neurons contain three compartments, the soma, long axon, and dendrites, which have distinct energetic and biochemical requirements. Mitochondria feature in all compartments and regulate neuronal activity and survival, including energy generation and calcium buffering alongside other roles including proapoptotic signaling and steroid synthesis. Their dynamicity allows them to undergo constant fusion and fission events in response to the changing energy and biochemical requirements. These events, termed mitochondrial dynamics, impact their morphology and a variety of three-dimensional (3D) morphologies exist within the neuronal mitochondrial network. Distortions in the morphological profile alongside mitochondrial dysfunction may begin in the neuronal soma in ageing and common neurodegenerative disorders. However, 3D morphology cannot be comprehensively examined in flat, two-dimensional (2D) images. This highlights a need to segment mitochondria within volume data to provide a representative snapshot of the processes underpinning mitochondrial dynamics and mitophagy within healthy and diseased neurons. The advent of automated high-resolution volumetric imaging methods such as Serial Block Face Scanning Electron Microscopy (SBF-SEM) as well as the range of image software packages allow this to be performed.We describe and evaluate a method for randomly sampling mitochondria and manually segmenting their whole morphologies within randomly generated regions of interest of the neuronal soma from SBF-SEM image stacks. These 3D reconstructions can then be used to generate quantitative data about mitochondrial and cellular morphologies. We further describe the use of a macro that automatically dissects the soma and localizes 3D mitochondria into the subregions created.
    Keywords:  3D reconstruction; Ageing; Mitochondria; Morphology; Neurodegeneration; SBF-SEM; Three-dimensional; Two-dimensional; mtDNA
    DOI:  https://doi.org/10.1007/978-1-0716-3969-6_11
  24. Biomed Pharmacother. 2024 Aug 09. pii: S0753-3322(24)01154-5. [Epub ahead of print]178 117270
    Inhibition of angiogenesis by the secretome from iPSC-derived retinal ganglion cells with Leber's hereditary optic neuropathy-like phenotypes.
    Shih-Yuan Peng, Chih-Ying Chen, Hsin Chen, Yi-Ping Yang, Mong-Lien Wang, Fu-Ting Tsai, Chian-Shiu Chien, Pei-Yu Weng, En-Tung Tsai, I-Chieh Wang, Chih-Chien Hsu, Tai-Chi Lin, De-Kuang Hwang, Shih-Jen Chen, Shih-Hwa Chiou, Chuan-Chin Chiao, Yueh Chien.
      The blood supply in the retina ensures photoreceptor function and maintains regular vision. Leber's hereditary optic neuropathy (LHON), caused by the mitochondrial DNA mutations that deteriorate complex I activity, is characterized by progressive vision loss. Although some reports indicated retinal vasculature abnormalities as one of the comorbidities in LHON, the paracrine influence of LHON-affected retinal ganglion cells (RGCs) on vascular endothelial cell physiology remains unclear. To address this, we established an in vitro model of mitochondrial complex I deficiency using induced pluripotent stem cell-derived RGCs (iPSC-RGCs) treated with a mitochondrial complex I inhibitor rotenone (Rot) to recapitulate LHON pathologies. The secretomes from Rot-treated iPSC-RGCs (Rot-iPSC-RGCs) were collected, and their treatment effect on human umbilical vein endothelial cells (HUVECs) was studied. Rot induced LHON-like characteristics in iPSC-RGCs, including decreased mitochondrial complex I activity and membrane potential, and increased mitochondrial reactive oxygen species (ROS) and apoptosis, leading to mitochondrial dysfunction. When HUVECs were exposed to conditioned media (CM) from Rot-iPSC-RGCs, the angiogenesis of HUVECs was suppressed compared to those treated with CM from control iPSC-RGCs (Ctrl-iPSC-RGCs). Angiogenesis-related proteins were altered in the secretomes from Rot-iPSC-RGC-derived CM, particularly angiopoietin, MMP-9, uPA, collagen XVIII, and VEGF were reduced. Notably, GeneMANIA analysis indicated that VEGFA emerged as the pivotal angiogenesis-related protein among the identified proteins secreted by health iPSC-RGCs but reduced in the secretomes from Rot-iPSC-RGCs. Quantitative real-time PCR and western blots confirmed the reduction of VEGFA at both transcription and translation levels, respectively. Our study reveals that Rot-iPSC-RGCs establish a microenvironment to diminish the angiogenic potential of vascular cells nearby, shedding light on the paracrine regulation of LHON-affected RGCs on retinal vasculature.
    Keywords:  Angiogenesis; Human umbilical vein endothelial cells; Leber’s hereditary optic neuropathy; Retinal ganglion cells (RGCs); Rotenone
    DOI:  https://doi.org/10.1016/j.biopha.2024.117270
  25. Aging Dis. 2024 Jul 30.
    Mitochondrial Transfer in the Neurovascular Unit, Not Only for Energy Rescue: A Systematic Review.
    Daqiang Zhou, Sibo Yang, Jiehong Wu, Yanan Li, Huijuan Jin, Yan Luo, Feng Zhang, Junjie Jiang, Bo Hu, Yifan Zhou.
      Despite substantial evidence highlighting molecular communication within the components of neurovascular units (NVU), the interactions at the organelle level have been insufficiently explored in recent decades. Mitochondria, for instance, beyond their traditional role as energy supply for intracellular metabolism and survival, provide a novel perspective on intercellular connections through mitochondrial transfer. These transferred mitochondria not only carry bioactive molecules but also signal to mitigate risks in both healthy and pathological conditions. In this review, we summarized mitochondrial transfer events, relevant routes, and underlying molecular mechanisms originating from diverse cell populations within NVU. We particularly focus on the therapeutic potential of this mechanism in treating central nervous system disorders, notably neurodegenerative diseases marked by mitochondrial dysfunction and then highlight the promising prospects of exogenous mitochondrial supplementation as a treatment target.
    DOI:  https://doi.org/10.14336/AD.2024.0461
  26. Biochim Biophys Acta Mol Cell Res. 2024 Aug 09. pii: S0167-4889(24)00154-X. [Epub ahead of print] 119811
    Mechanism of mitochondrial [2Fe2S] cluster biosynthesis.
    Kristian Want, Benoit D'Autréaux.
      Iron‑sulfur (FeS) clusters constitute ancient cofactors that accompany a versatile range of fundamental biological reactions across eukaryotes and prokaryotes. Several cellular pathways exist to coordinate iron acquisition and sulfur mobilization towards a scaffold protein during the tightly regulated synthesis of FeS clusters. The mechanism of mitochondrial eukaryotic [2Fe-2S] cluster synthesis is coordinated by the Iron-Sulfur Cluster (ISC) machinery and its aberrations herein have strong implications to the field of disease and medicine which is therefore of particular interest. Here, we describe our current knowledge on the step-by-step mechanism leading to the production of mitochondrial [2Fe2S] clusters while highlighting the recent developments in the field alongside the challenges that are yet to be overcome.
    Keywords:  FeS cluster; Frataxin; ISC persulfide; Iron; [2Fe-2S]
    DOI:  https://doi.org/10.1016/j.bbamcr.2024.119811
  27. Nat Commun. 2024 Aug 15. 15(1): 7016
    Fast and deep phosphoproteome analysis with the Orbitrap Astral mass spectrometer.
    Noah M Lancaster, Pavel Sinitcyn, Patrick Forny, Trenton M Peters-Clarke, Caroline Fecher, Andrew J Smith, Evgenia Shishkova, Tabiwang N Arrey, Anna Pashkova, Margaret Lea Robinson, Nicholas Arp, Jing Fan, Juli Hansen, Andrea Galmozzi, Lia R Serrano, Julie Rojas, Audrey P Gasch, Michael S Westphall, Hamish Stewart, Christian Hock, Eugen Damoc, David J Pagliarini, Vlad Zabrouskov, Joshua J Coon.
      Owing to its roles in cellular signal transduction, protein phosphorylation plays critical roles in myriad cell processes. That said, detecting and quantifying protein phosphorylation has remained a challenge. We describe the use of a novel mass spectrometer (Orbitrap Astral) coupled with data-independent acquisition (DIA) to achieve rapid and deep analysis of human and mouse phosphoproteomes. With this method, we map approximately 30,000 unique human phosphorylation sites within a half-hour of data collection. The technology is benchmarked to other state-of-the-art MS platforms using both synthetic peptide standards and with EGF-stimulated HeLa cells. We apply this approach to generate a phosphoproteome multi-tissue atlas of the mouse. Altogether, we detect 81,120 unique phosphorylation sites within 12 hours of measurement. With this unique dataset, we examine the sequence, structural, and kinase specificity context of protein phosphorylation. Finally, we highlight the discovery potential of this resource with multiple examples of phosphorylation events relevant to mitochondrial and brain biology.
    DOI:  https://doi.org/10.1038/s41467-024-51274-0
  28. NAR Genom Bioinform. 2024 Sep;6(3): lqae095
    Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants.
    Benjamin Story, Lars Velten, Gregor Mönke, Ahrmad Annan, Lars Steinmetz.
      Clonal cell population dynamics play a critical role in both disease and development. Due to high mitochondrial mutation rates under both healthy and diseased conditions, mitochondrial genomic variability is a particularly useful resource in facilitating the identification of clonal population structure. Here we present mitoClone2, an all-inclusive R package allowing for the identification of clonal populations through integration of mitochondrial heteroplasmic variants discovered from single-cell sequencing experiments. Our package streamlines the investigation of this phenomenon by providing: built-in compatibility with commonly used tools for the delineation of clonal structure, the ability to directly use multiplexed BAM files as input, annotations for both human and mouse mitochondrial genomes, and helper functions for calling, filtering, clustering, and visualizing variants.
    DOI:  https://doi.org/10.1093/nargab/lqae095
  29. Environ Pollut. 2024 Aug 08. pii: S0269-7491(24)01391-5. [Epub ahead of print]360 124677
    Cadmium causes cerebral mitochondrial dysfunction through regulating mitochondrial HSF1.
    Chen-Xi Li, Milton Talukder, Ya-Ru Xu, Shi-Yong Zhu, Yu-Xiang Wang, Jin-Long Li.
      Mitochondria, as the powerhouse of the cell, play a vital role in maintaining cellular energy homeostasis and are known to be a primary target of cadmium (Cd) toxicity. The improper targeting of proteins to mitochondria can compromise the normal functions of the mitochondria. However, the precise mechanism by which protein localization contributes to the development of mitochondrial dysfunction induced by Cd is still not fully understood. For this research, Hy-Line white variety chicks (1-day-old) were used and equally distributed into 4 groups: the Control group (fed with a basic diet), the Cd35 group (basic diet with 35 mg/kg CdCl2), the Cd70 group (basic diet with 70 mg/kg CdCl2) and the Cd140 group (basic diet with 140 mg/kg CdCl2), respectively for 90 days. It was found that Cd caused the accumulation of heat shock factor 1 (HSF1) in the mitochondria, and the overexpression of HSF1 in the mitochondria led to mitochondrial dysfunction and neuronal damage. This process is due to the mitochondrial HSF1 (mtHSF1), causing mitochondrial fission through the upregulation of dynamin-related protein 1 (Drp1) content, while inhibiting oligomer formation of single-stranded DNA-binding protein 1 (SSBP1), resulting in the mitochondrial DNA (mtDNA) deletion. The findings unveil an unforeseen role of HSF1 in triggering mitochondrial dysfunction.
    Keywords:  Cadmium; Cerebrum; Dynamin-related protein 1; Mitochondrial dysfunction; Mitochondrial heat shock factor 1; Single-stranded DNA-Binding protein 1
    DOI:  https://doi.org/10.1016/j.envpol.2024.124677
  30. Eur Heart J Case Rep. 2024 Aug;8(8): ytae377
    Case report: severe hypertrophic cardiomyopathy in a female neonate caused by de novo variant in NDUFB11.
    Javeria Tariq, Madeleine Townsend, Sumit Parikh, Jeffrey Bennett.
       Background: Hypertrophic cardiomyopathy in the neonate has a diverse genetic background, and non-sarcomeric variants may not be identified on commercial genetic testing panels. NDUFB11 is an X-linked mitochondrial Complex I protein and is known to cause histiocytoid cardiomyopathy but has not been described in female infants with hypertrophic cardiomyopathy. We present this first reported case of obstructive hypertrophic cardiomyopathy in a female neonate secondary to a pathogenic variant in NDUFB11.
    Case summary: A term female neonate presented following a prenatal diagnosis of biventricular hypertrophy and growth restriction. She developed lactic acidosis after birth and whole-genome sequencing identified a de novo variant in the mitochondrial Complex I gene, NDUFB11 (c.391G>A, p.Glu131Lys). There was progression of left ventricular hypertrophy and obstruction, with rapid development of heart failure symptoms. She was unresponsive to beta-blocker medical therapy and was not suitable for advanced mechanical support. There was subsequent clinical deterioration resulting in death by 3 months of age.
    Discussion: Hemizygous variants in NDUFB11 have been associated with hypertrophic cardiomyopathy in male infants previously, and skewed X-linked inactivation likely resulted in the presentation described here in a female infant. This variant was not identifiable by commercial cardiomyopathy panels. We highlight the importance of rapid whole-genome sequencing in cases of infantile hypertrophic cardiomyopathy and the importance of genetic diagnosis in guiding prognosis and care for these individuals.
    Keywords:  Case report; Hypertrophic cardiomyopathy; Mitochondrial; Neonatal; Whole genome
    DOI:  https://doi.org/10.1093/ehjcr/ytae377
  31. J Biomed Sci. 2024 Aug 13. 31(1): 79
    Gene therapy for ultrarare diseases: a geneticist's perspective.
    Wuh-Liang Hwu.
      Gene therapy has made considerable strides in recent years. More than 4000 protein-coding genes have been implicated in more than 6000 genetic diseases; next-generation sequencing has dramatically revolutionized the diagnosis of genetic diseases. Most genetic diseases are considered very rare or ultrarare, defined here as having fewer than 1:100,000 cases, but only one of the 12 approved gene therapies (excluding RNA therapies) targets an ultrarare disease. This article explores three gene supplementation therapy approaches suitable for various rare genetic diseases: lentiviral vector-modified autologous CD34+ hematopoietic stem cell transplantation, systemic delivery of adeno-associated virus (AAV) vectors to the liver, and local AAV delivery to the cerebrospinal fluid and brain. Together with RNA therapies, we propose a potential business model for these gene therapies.
    Keywords:  Adeno-associated viral vector; Gene therapy; Lentiviral vector; Ultrarare
    DOI:  https://doi.org/10.1186/s12929-024-01070-1
  32. Dev Cell. 2024 Aug 02. pii: S1534-5807(24)00455-6. [Epub ahead of print]
    GLUD1 determines murine muscle stem cell fate by controlling mitochondrial glutamate levels.
    Inés Soro-Arnáiz, Gillian Fitzgerald, Sarah Cherkaoui, Jing Zhang, Paola Gilardoni, Adhideb Ghosh, Ori Bar-Nur, Evi Masschelein, Pierre Maechler, Nicola Zamboni, Martin Poms, Alessio Cremonesi, Juan Carlos Garcia-Cañaveras, Katrien De Bock, Raphael Johannes Morscher.
      Muscle stem cells (MuSCs) enable muscle growth and regeneration after exercise or injury, but how metabolism controls their regenerative potential is poorly understood. We describe that primary metabolic changes can determine murine MuSC fate decisions. We found that glutamine anaplerosis into the tricarboxylic acid (TCA) cycle decreases during MuSC differentiation and coincides with decreased expression of the mitochondrial glutamate deaminase GLUD1. Deletion of Glud1 in proliferating MuSCs resulted in precocious differentiation and fusion, combined with loss of self-renewal in vitro and in vivo. Mechanistically, deleting Glud1 caused mitochondrial glutamate accumulation and inhibited the malate-aspartate shuttle (MAS). The resulting defect in transporting NADH-reducing equivalents into the mitochondria induced compartment-specific NAD+/NADH ratio shifts. MAS activity restoration or directly altering NAD+/NADH ratios normalized myogenesis. In conclusion, GLUD1 prevents deleterious mitochondrial glutamate accumulation and inactivation of the MAS in proliferating MuSCs. It thereby acts as a compartment-specific metabolic brake on MuSC differentiation.
    Keywords:  GLUD1; glutamine metabolism; malate aspartate shuttle; metabolite compartmentalization; muscle stem cells; tricarboxylic acid cycle
    DOI:  https://doi.org/10.1016/j.devcel.2024.07.015
  33. bioRxiv. 2024 Aug 13. pii: 2024.08.05.606704. [Epub ahead of print]
    Mfn2 induces NCLX-mediated calcium release from mitochondria.
    Panagiota Kolitsida, Akash Saha, Andrew W Caliri, Essam Assali, Alejandro Martorell Riera, Samuel Itskanov, Catalina S Magana, Bjorn Stork, Orian S Shirihai, Israel Sekler, Carla M Koehler, Alexander M van der Bliek.
      Mfn2 is a mitochondrial outer membrane fusion protein with the additional role of tethering mitochondria to the ER. Here, we describe a novel connection between Mfn2 and calcium release from mitochondria. We show that Mfn2 controls the mitochondrial inner membrane sodium-calcium exchange protein NCLX, which is a major source for calcium release from mitochondria. This discovery was made with the fungal toxin Phomoxanthone (PXA), which induces calcium release from mitochondria. PXA-induced calcium release is blocked by a chemical inhibitor of NCLX, while NCLX and Mfn2 deletions both also prevent PXA-induced calcium release. CETSA experiments show that PXA directly targets Mfn2, which likely controls NCLX through physical interactions since co-immunoprecipitation and proximity ligation assays show increased association between Mfn2 and NCLX upon treatment with PXA. Interactions between Mfn2 and NCLX also increase when cells are treated with mitochondrial ROS-inducing conditions, such as oligomycin treatment of respiring cells, while the interactions do not increase in Oma1 -/- cells. It seems likely that opening of cristae by Oma1-mediated cleavage of Opa1 promotes translocation of NCLX from cristae to the rim where it can come into contact with Mfn2 thus promoting PXA-induced calcium release from mitochondria. These results therefore delineate a pathway that connects ROS produced inside mitochondria with calcium release and signaling in the cytosol.
    DOI:  https://doi.org/10.1101/2024.08.05.606704
  34. Sci Rep. 2024 08 10. 14(1): 18586
    Heterogeneous brain region-specific responses to astrocytic mitochondrial DNA damage in mice.
    Daniela A Ayala, Anthony Matarazzo, Bonnie L Seaberg, Misha Patel, Eliana Tijerina, Camryn Matthews, Gabriel Bizi, Ashton Brown, Alan Ta, Mendell Rimer, Rahul Srinivasan.
      Astrocytes display context-specific diversity in their functions and respond to noxious stimuli between brain regions. Astrocytic mitochondria have emerged as key players in governing astrocytic functional heterogeneity, given their ability to dynamically adapt their morphology to regional demands on ATP generation and Ca2+ buffering functions. Although there is reciprocal regulation between mitochondrial dynamics and mitochondrial Ca2+ signaling in astrocytes, the extent of this regulation in astrocytes from different brain regions remains unexplored. Brain-wide, experimentally induced mitochondrial DNA (mtDNA) loss in astrocytes showed that mtDNA integrity is critical for astrocyte function, however, possible diverse responses to this noxious stimulus between brain areas were not reported in these experiments. To selectively damage mtDNA in astrocytes in a brain-region-specific manner, we developed a novel adeno-associated virus (AAV)-based tool, Mito-PstI expressing the restriction enzyme PstI, specifically in astrocytic mitochondria. Here, we applied Mito-PstI to two brain regions, the dorsolateral striatum and dentate gyrus, and we show that Mito-PstI induces astrocytic mtDNA loss in vivo, but with remarkable brain-region-dependent differences on mitochondrial dynamics, Ca2+ fluxes, and astrocytic and microglial reactivity. Thus, AAV-Mito-PstI is a novel tool to explore the relationship between astrocytic mitochondrial network dynamics and astrocytic mitochondrial Ca2+ signaling in a brain-region-selective manner.
    Keywords:  Astrocyte mitochondrial DNA; Calcium influx; Heterogenous; Hippocampus; Mitochondrial dynamics; Striatum
    DOI:  https://doi.org/10.1038/s41598-024-69499-w
  35. Aging Dis. 2024 Aug 08.
    Excitotoxicity, Oxytosis/Ferroptosis, and Neurodegeneration: Emerging Insights into Mitochondrial Mechanisms.
    Sameera Khan, Nargis Bano, Shakir Ahamad, Urmilla John, Nawab John Dar, Shahnawaz Ali Bhat.
      Mitochondrial dysfunction plays a pivotal role in the development of age-related diseases, particularly neurodegenerative disorders. The etiology of mitochondrial dysfunction involves a multitude of factors that remain elusive. This review centers on elucidating the role(s) of excitotoxicity, oxytosis/ferroptosis and neurodegeneration within the context of mitochondrial bioenergetics, biogenesis, mitophagy and oxidative stress and explores their intricate interplay in the pathogenesis of neurodegenerative diseases. The effective coordination of mitochondrial turnover processes, notably mitophagy and biogenesis, is assumed to be critically important for cellular resilience and longevity. However, the age-associated decrease in mitophagy impedes the elimination of dysfunctional mitochondria, consequently impairing mitochondrial biogenesis. This deleterious cascade results in the accumulation of damaged mitochondria and deterioration of cellular functions. Both excitotoxicity and oxytosis/ferroptosis have been demonstrated to contribute significantly to the pathophysiology of neurodegenerative diseases, including Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's Disease (HD), Amyotrophic Lateral Sclerosis (ALS) and Multiple Sclerosis (MS). Excitotoxicity, characterized by excessive glutamate signaling, initiates a cascade of events involving calcium dysregulation, energy depletion, and oxidative stress and is intricately linked to mitochondrial dysfunction. Furthermore, emerging concepts surrounding oxytosis/ferroptosis underscore the importance of iron-dependent lipid peroxidation and mitochondrial engagement in the pathogenesis of neurodegeneration. This review not only discusses the individual contributions of excitotoxicity and ferroptosis but also emphasizes their convergence with mitochondrial dysfunction, a key driver of neurodegenerative diseases. Understanding the intricate crosstalk between excitotoxicity, oxytosis/ferroptosis, and mitochondrial dysfunction holds potential to pave the way for mitochondrion-targeted therapeutic strategies. Such strategies, with a focus on bioenergetics, biogenesis, mitophagy, and oxidative stress, emerge as promising avenues for therapeutic intervention.
    DOI:  https://doi.org/10.14336/AD.2024.0125-1
  36. Cell Signal. 2024 Aug 08. pii: S0898-6568(24)00308-5. [Epub ahead of print]122 111340
    Ndufa8 promotes white fat Browning by improving mitochondrial respiratory chain complex I function to ameliorate obesity by in vitro and in vivo.
    Qinghua Fu, Rui Lv, Simeng Wang, Wentao Wang, Yizhou Li, Guiping Qiu, Xinhao Chen, Chao Sun.
      Obesity and its complications have become a global health problem that needs to be addressed urgently. White adipose tissue (WAT) browning contributes to consuming excess energy in WAT, which is important for improving obesity and maintaining a healthy energy homeostasis. Mitochondria, as the energy metabolism center of cells, are extensively involved in many metabolic processes, including the browning of WAT. NADH: Ubiquinone oxidoreductase subunit A8 (NDUFA8) is a constituent subunit of respiratory chain complex I (CI), which has been found to participate in a wide range of physiological processes by affecting the activity of respiratory CI. However, the regulatory effect of Ndufa8 on the browning of WAT has not been reported. Here, we used β3-adrenergic agonis CL316, 243 to construct WAT browning models in vivo and in vitro to investigate the role and mechanism of Ndufa8 in the regulation of WAT browning. Briefly, Ndufa8 significantly increased CI activity and suppressed mitochondrial ROS levels in vitro, thereby improving mitochondrial function. Ndufa8 also increased the transcriptional levels and protein levels of UCP1 in vitro and in vivo, which promoted WAT browning. Our findings provide a new molecular approach for the research of browning of WAT in animals, as well as a new target for animal metabolism improvement and obesity treatments.
    Keywords:  Mitochondrial function; Ndufa8; Oxidative stress; Respiratory chain complex I; White adipose tissue browning
    DOI:  https://doi.org/10.1016/j.cellsig.2024.111340
  37. Cell Death Differ. 2024 Aug 15.
    Adapting cytoskeleton-mitochondria patterning with myocyte differentiation by promyogenic PRR33.
    Xuyang Fu, Feng Zhang, Xiaoxuan Dong, Linbin Pu, Yan Feng, Yang Xu, Feng Gao, Tian Liang, Jianmeng Kang, Hongke Sun, Tingting Hong, Yunxia Liu, Hongmei Zhou, Jun Jiang, Deling Yin, Xinyang Hu, Da-Zhi Wang, Jian Ding, Jinghai Chen.
      Coordinated cytoskeleton-mitochondria organization during myogenesis is crucial for muscle development and function. Our understanding of the underlying regulatory mechanisms remains inadequate. Here, we identified a novel muscle-enriched protein, PRR33, which is upregulated during myogenesis and acts as a promyogenic factor. Depletion of Prr33 in C2C12 represses myoblast differentiation. Genetic deletion of Prr33 in mice reduces myofiber size and decreases muscle strength. The Prr33 mutant mice also exhibit impaired myogenesis and defects in muscle regeneration in response to injury. Interactome and transcriptome analyses reveal that PRR33 regulates cytoskeleton and mitochondrial function. Remarkably, PRR33 interacts with DESMIN, a key regulator of cytoskeleton-mitochondria organization in muscle cells. Abrogation of PRR33 in myocytes substantially abolishes the interaction of DESMIN filaments with mitochondria, leading to abnormal intracellular accumulation of DESMIN and mitochondrial disorganization/dysfunction in myofibers. Together, our findings demonstrate that PRR33 and DESMIN constitute an important regulatory module coordinating mitochondrial organization with muscle differentiation.
    DOI:  https://doi.org/10.1038/s41418-024-01363-w
  38. PLoS Biol. 2024 Aug 15. 22(8): e3002449
    Pam16 and Pam18 were repurposed during Trypanosoma brucei evolution to regulate the replication of mitochondrial DNA.
    Corinne von Känel, Philip Stettler, Carmela Esposito, Stephan Berger, Simona Amodeo, Silke Oeljeklaus, Salvatore Calderaro, Ignacio M Durante, Vendula Rašková, Bettina Warscheid, André Schneider.
      Protein import and genome replication are essential processes for mitochondrial biogenesis and propagation. The J-domain proteins Pam16 and Pam18 regulate the presequence translocase of the mitochondrial inner membrane. In the protozoan Trypanosoma brucei, their counterparts are TbPam16 and TbPam18, which are essential for the procyclic form (PCF) of the parasite, though not involved in mitochondrial protein import. Here, we show that during evolution, the 2 proteins have been repurposed to regulate the replication of maxicircles within the intricate kDNA network, the most complex mitochondrial genome known. TbPam18 and TbPam16 have inactive J-domains suggesting a function independent of heat shock proteins. However, their single transmembrane domain is essential for function. Pulldown of TbPam16 identifies a putative client protein, termed MaRF11, the depletion of which causes the selective loss of maxicircles, akin to the effects observed for TbPam18 and TbPam16. Moreover, depletion of the mitochondrial proteasome results in increased levels of MaRF11. Thus, we have discovered a protein complex comprising TbPam18, TbPam16, and MaRF11, that controls maxicircle replication. We propose a working model in which the matrix protein MaRF11 functions downstream of the 2 integral inner membrane proteins TbPam18 and TbPam16. Moreover, we suggest that the levels of MaRF11 are controlled by the mitochondrial proteasome.
    DOI:  https://doi.org/10.1371/journal.pbio.3002449
  39. Nat Commun. 2024 Aug 09. 15(1): 6805
    Extreme mitochondrial reduction in a novel group of free-living metamonads.
    Shelby K Williams, Jon Jerlström Hultqvist, Yana Eglit, Dayana E Salas-Leiva, Bruce Curtis, Russell J S Orr, Courtney W Stairs, Tuğba N Atalay, Naomi MacMillan, Alastair G B Simpson, Andrew J Roger.
      Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.
    DOI:  https://doi.org/10.1038/s41467-024-50991-w
  40. Genesis. 2024 Aug;62(4): e23615
    Generation of an Armcx1 Conditional Knockout Mouse.
    Cora L Bright, Howard M Bomze, Mantu Bhaumik, Jeremy N Kay, Romain Cartoni, Sidney M Gospe.
      Armadillo repeat-containing X-linked protein-1 (Armcx1) is a poorly characterized transmembrane protein that regulates mitochondrial transport in neurons. Its overexpression has been shown to induce neurite outgrowth in embryonic neurons and to promote retinal ganglion cell (RGC) survival and axonal regrowth in a mouse optic nerve crush model. In order to evaluate the functions of endogenous Armcx1 in vivo, we have created a conditional Armcx1 knockout mouse line in which the entire coding region of the Armcx1 gene is flanked by loxP sites. This Armcx1fl line was crossed with mouse strains in which Cre recombinase expression is driven by the promoters for β-actin and Six3, in order to achieve deletion of Armcx1 globally and in retinal neurons, respectively. Having confirmed deletion of the gene, we proceeded to characterize the abundance and morphology of RGCs in Armcx1 knockout mice aged to 15 months. Under normal physiological conditions, no evidence of aberrant retinal or optic nerve development or RGC degeneration was observed in these mice. The Armcx1fl mouse should be valuable for future studies investigating mitochondrial morphology and transport in the absence of Armcx1 and in determining the susceptibility of Armcx1-deficient neurons to degeneration in the setting of additional heritable or environmental stressors.
    Keywords:  armadillo repeat‐containing X‐linked protein‐1; conditional knockout; mitochondria; retinal ganglion cell
    DOI:  https://doi.org/10.1002/dvg.23615
  41. Sci Rep. 2024 08 13. 14(1): 18794
    Inherited mitochondrial dysfunction triggered by OPA1 mutation impacts the sensory innervation fibre identity, functionality and regenerative potential in the cornea.
    Léna Meneux, Nadège Feret, Sarah Pernot, Mélissa Girard, Solange Sarkis, Alicia Caballero Megido, Melanie Quiles, Agnès Müller, Laura Fichter, Jerome Vialaret, Christophe Hirtz, Cecile Delettre, Frederic Michon.
      Mitochondrial dysfunctions are detrimental to organ metabolism. The cornea, transparent outmost layer of the eye, is prone to environmental aggressions, such as UV light, and therefore dependent on adequate mitochondrial function. While several reports have linked corneal defects to mitochondrial dysfunction, the impact of OPA1 mutation, known to induce such dysfunction, has never been studied in this context. We used the mouse line carrying OPA1delTTAG mutation to investigate its impact on corneal biology. To our surprise, neither the tear film composition nor the corneal epithelial transcriptomic signature were altered upon OPA1 mutation. However, when analyzing the corneal innervation, we discovered an undersensitivity of the cornea upon the mutation, but an increased innervation volume at 3 months. Furthermore, the fibre identity changed with a decrease of the SP + axons. Finally, we demonstrated that the innervation regeneration was less efficient and less functional in OPA1+/- corneas. Altogether, our study describes the resilience of the corneal epithelial biology, reflecting the mitohormesis induced by the OPA1 mutation, and the adaptation of the corneal innervation to maintain its functionality despite its morphogenesis defects. These findings will participate to a better understanding of the mitochondrial dysfunction on peripheral innervation.
    Keywords:  Cornea; Epithelium; Innervation; Mitochondria; OPA1; Proteomic; Tear film; Transcriptomic
    DOI:  https://doi.org/10.1038/s41598-024-68994-4
  42. J Nanobiotechnology. 2024 Aug 14. 22(1): 487
    Extracellular vesicles: opening up a new perspective for the diagnosis and treatment of mitochondrial dysfunction.
    Jiali Li, Tangrong Wang, Xiaomei Hou, Yu Li, Jiaxin Zhang, Wenhuan Bai, Hui Qian, Zixuan Sun.
      Mitochondria are crucial organelles responsible for energy generation in eukaryotic cells. Oxidative stress, calcium disorders, and mitochondrial DNA abnormalities can all cause mitochondrial dysfunction. It is now well documented that mitochondrial dysfunction significantly contributes to the pathogenesis of numerous illnesses. Hence, it is vital to investigate innovative treatment methods targeting mitochondrial dysfunction. Extracellular vesicles (EVs) are cell-derived nanovesicles that serve as intercellular messengers and are classified into small EVs (sEVs, < 200 nm) and large EVs (lEVs, > 200 nm) based on their sizes. It is worth noting that certain subtypes of EVs are rich in mitochondrial components (even structurally intact mitochondria) and possess the ability to transfer them or other contents including proteins and nucleic acids to recipient cells to modulate their mitochondrial function. Specifically, EVs can modulate target cell mitochondrial homeostasis as well as mitochondria-controlled apoptosis and ROS generation by delivering relevant substances. In addition, the artificial modification of EVs as delivery carriers for therapeutic goods targeting mitochondria is also a current research hotspot. In this article, we will focus on the ability of EVs to modulate the mitochondrial function of target cells, aiming to offer novel perspectives on therapeutic approaches for diverse conditions linked to mitochondrial dysfunction.
    Keywords:  Biomarkers; Extracellular vesicles; Mitochondrial dysfunction; Pathogenesis; Targeted therapies
    DOI:  https://doi.org/10.1186/s12951-024-02750-8
  43. Int J Mol Sci. 2024 Jul 27. pii: 8201. [Epub ahead of print]25(15):
    A Barth Syndrome Patient-Derived D75H Point Mutation in TAFAZZIN Drives Progressive Cardiomyopathy in Mice.
    Paige L Snider, Elizabeth A Sierra Potchanant, Zejin Sun, Donna M Edwards, Ka-Kui Chan, Catalina Matias, Junya Awata, Aditya Sheth, P Melanie Pride, R Mark Payne, Michael Rubart, Jeffrey J Brault, Michael T Chin, Grzegorz Nalepa, Simon J Conway.
      Cardiomyopathy is the predominant defect in Barth syndrome (BTHS) and is caused by a mutation of the X-linked Tafazzin (TAZ) gene, which encodes an enzyme responsible for remodeling mitochondrial cardiolipin. Despite the known importance of mitochondrial dysfunction in BTHS, how specific TAZ mutations cause diverse BTHS heart phenotypes remains poorly understood. We generated a patient-tailored CRISPR/Cas9 knock-in mouse allele (TazPM) that phenocopies BTHS clinical traits. As TazPM males express a stable mutant protein, we assessed cardiac metabolic dysfunction and mitochondrial changes and identified temporally altered cardioprotective signaling effectors. Specifically, juvenile TazPM males exhibit mild left ventricular dilation in systole but have unaltered fatty acid/amino acid metabolism and normal adenosine triphosphate (ATP). This occurs in concert with a hyperactive p53 pathway, elevation of cardioprotective antioxidant pathways, and induced autophagy-mediated early senescence in juvenile TazPM hearts. However, adult TazPM males exhibit chronic heart failure with reduced growth and ejection fraction, cardiac fibrosis, reduced ATP, and suppressed fatty acid/amino acid metabolism. This biphasic changeover from a mild-to-severe heart phenotype coincides with p53 suppression, downregulation of cardioprotective antioxidant pathways, and the onset of terminal senescence in adult TazPM hearts. Herein, we report a BTHS genotype/phenotype correlation and reveal that absent Taz acyltransferase function is sufficient to drive progressive cardiomyopathy.
    Keywords:  Barth syndrome; mitochondria; p53 pathway; patient-tailored Tafazzin mutant allele; progressive cardiomyopathy
    DOI:  https://doi.org/10.3390/ijms25158201
  44. Nat Rev Genet. 2024 Aug 12.
    DNA methylation in mammalian development and disease.
    Zachary D Smith, Sara Hetzel, Alexander Meissner.
      The DNA methylation field has matured from a phase of discovery and genomic characterization to one seeking deeper functional understanding of how this modification contributes to development, ageing and disease. In particular, the past decade has seen many exciting mechanistic discoveries that have substantially expanded our appreciation for how this generic, evolutionarily ancient modification can be incorporated into robust epigenetic codes. Here, we summarize the current understanding of the distinct DNA methylation landscapes that emerge over the mammalian lifespan and discuss how they interact with other regulatory layers to support diverse genomic functions. We then review the rising interest in alternative patterns found during senescence and the somatic transition to cancer. Alongside advancements in single-cell and long-read sequencing technologies, the collective insights made across these fields offer new opportunities to connect the biochemical and genetic features of DNA methylation to cell physiology, developmental potential and phenotype.
    DOI:  https://doi.org/10.1038/s41576-024-00760-8
  45. bioRxiv. 2024 Jul 31. pii: 2024.07.30.605703. [Epub ahead of print]
    Unraveling cysteine deficiency-associated rapid weight loss.
    Alan Varghese, Ivan Gusarov, Begoña Gamallo-Lana, Daria Dolgonos, Yatin Mankan, Ilya Shamovsky, Mydia Phan, Rebecca Jones, Maria Gomez-Jenkins, Eileen White, Rui Wang, Drew Jones, Thales Papagiannakopoulos, Michael E Pacold, Adam C Mar, Dan R Littman, Evgeny Nudler.
      Forty percent of the US population and 1 in 6 individuals worldwide are obese, and the incidence of this disease is surging globally1,2. Various dietary interventions, including carbohydrate and fat restriction, and more recently amino acid restriction, have been explored to combat this epidemic3-6. We sought to investigate the impact of removing individual amino acids on the weight profiles of mice. Compared to essential amino acid restriction, induction of conditional cysteine restriction resulted in the most dramatic weight loss, amounting to 20% within 3 days and 30% within one week, which was readily reversed. This weight loss occurred despite the presence of substantial cysteine reserves stored in glutathione (GSH) across various tissues7. Further analysis demonstrated that the weight reduction primarily stemmed from an increase in the utilization of fat mass, while locomotion, circadian rhythm and histological appearance of multiple other tissues remained largely unaffected. Cysteine deficiency activated the integrated stress response (ISR) and NRF2-mediated oxidative stress response (OSR), which amplify each other, leading to the induction of GDF15 and FGF21, hormones associated with increased lipolysis, energy homeostasis and food aversion8-10. We additionally observed rapid tissue coenzyme A (CoA) depletion, resulting in energetically inefficient anaerobic glycolysis and TCA cycle, with sustained urinary excretion of pyruvate, orotate, citrate, α-ketoglutarate, nitrogen rich compounds and amino acids. In summary, our investigation highlights that cysteine restriction, by depleting GSH and CoA, exerts a maximal impact on weight loss, metabolism, and stress signaling compared to other amino acid restrictions. These findings may pave the way for innovative strategies for addressing a range of metabolic diseases and the growing obesity crisis.
    DOI:  https://doi.org/10.1101/2024.07.30.605703
  46. STAR Protoc. 2024 Aug 13. pii: S2666-1667(24)00401-5. [Epub ahead of print]5(3): 103236
    Protocol for monitoring fatty acid trafficking from lipid droplets to mitochondria in cultured cells.
    Gregory E Miner, Sarah Cohen.
      Intracellular trafficking of fatty acids (FAs) between organelles is critical for cells to adjust their metabolism in response to stimuli such as exercise, fasting, and cold exposure. Here, we describe a protocol to monitor trafficking of FAs from lipid droplets to mitochondria. We describe the labeling of organelles in cultured C2C12 myoblasts with transfection and dyes. We detail a pulse-chase labeling paradigm using a fluorescent FA analog, live-cell imaging to visualize trafficking of FAs, and steps to quantify FA trafficking. For complete details on the use and execution of this protocol, please refer to Miner et al.1.
    Keywords:  Cell Biology; Metabolism; Microscopy
    DOI:  https://doi.org/10.1016/j.xpro.2024.103236
  47. Nat Chem Biol. 2024 Aug 13.
    Shifting redox reaction equilibria on demand using an orthogonal redox cofactor.
    Derek Aspacio, Yulai Zhang, Youtian Cui, Emma Luu, Edward King, William B Black, Sean Perea, Qiang Zhu, Yongxian Wu, Ray Luo, Justin B Siegel, Han Li.
      Nature's two redox cofactors, nicotinamide adenine dinucleotide (NAD+) and nicotinamide adenine dinucleotide phosphate (NADP+), are held at different reduction potentials, driving catabolism and anabolism in opposite directions. In biomanufacturing, there is a need to flexibly control redox reaction direction decoupled from catabolism and anabolism. We established nicotinamide mononucleotide (NMN+) as a noncanonical cofactor orthogonal to NAD(P)+. Here we present the development of Nox Ortho, a reduced NMN+ (NMNH)-specific oxidase, that completes the toolkit to modulate NMNH:NMN+ ratio together with an NMN+-specific glucose dehydrogenase (GDH Ortho). The design principle discovered from Nox Ortho engineering and modeling is facilely translated onto six different enzymes to create NMN(H)-orthogonal biocatalysts with a consistent ~103-106-fold cofactor specificity switch from NAD(P)+ to NMN+. We assemble these enzymes to produce stereo-pure 2,3-butanediol in cell-free systems and in Escherichia coli, enabled by NMN(H)'s distinct redox ratio firmly set by its designated driving forces, decoupled from both NAD(H) and NADP(H).
    DOI:  https://doi.org/10.1038/s41589-024-01702-5
  48. Nature. 2024 Aug 12.
    Rare developmental disorder caused by variants in a small RNA gene.
    Henrike Heyne.
      
    Keywords:  DNA sequencing; Diseases; Genomics; Non-coding RNAs
    DOI:  https://doi.org/10.1038/d41586-024-02434-1
  49. Cardiovasc Res. 2024 Aug 12. pii: cvae169. [Epub ahead of print]
    PITX2 deficiency leads to atrial mitochondrial dysfunction.
    Jasmeet S Reyat, Laura C Sommerfeld, Molly O'Reilly, Victor R Cardoso, Ellen Thiemann, Abdullah O Khan, Christopher O'Shea, Sönke Harder, Christian Müller, Jonathan Barlow, Rachel J Stapley, Winnie Chua, S Nashitha Kabir, Olivia Grech, Oliver Hummel, Norbert Hübner, Stefan Kääb, Lluis Mont, Stéphane N Hatem, Joris Winters, Stef Zeemering, Neil V Morgan, Julie Rayes, Katja Gehmlich, Monika Stoll, Theresa Brand, Michaela Schweizer, Angelika Piasecki, Ulrich Schotten, Georgios V Gkoutos, Kristina Lorenz, Friederike Cuello, Paulus Kirchhof, Larissa Fabritz.
       AIM: Reduced left atrial PITX2 is associated with atrial cardiomyopathy and atrial fibrillation. PITX2 is restricted to left atrial cardiomyocytes in the adult heart. The links between PITX2 deficiency, atrial cardiomyopathy and atrial fibrillation are not fully understood.
    METHODS AND RESULTS: To identify mechanisms linking PITX2 deficiency to atrial fibrillation, we generated and characterized PITX2-deficient human atrial cardiomyocytes derived from human induced pluripotent stem cells (hiPSC) and their controls. PITX2-deficient hiPSC-derived atrial cardiomyocytes showed shorter and disorganised sarcomeres and increased mononucleation. Electron microscopy found an increased number of smaller mitochondria compared to the control. Mitochondrial protein expression was altered in PITX2-deficient hiPSC-derived atrial cardiomyocytes. Single-nuclear RNA-sequencing found differences in cellular respiration pathways and differentially expressed mitochondrial and ion channel genes in PITX2-deficient hiPSC-derived atrial cardiomyocytes. PITX2 repression in hiPSC-derived atrial cardiomyocytes replicated dysregulation of cellular respiration. Mitochondrial respiration was shifted to increased glycolysis in PITX2-deficient hiPSC-derived atrial cardiomyocytes. PITX2-deficient human hiPSC-derived atrial cardiomyocytes showed higher spontaneous beating rates. Action potential duration was more variable with an overall prolongation of early repolarization, consistent with metabolic defects. Gene expression analyses confirmed changes in mitochondrial genes in left atria from 42 patients with atrial fibrillation compared to 43 patients in sinus rhythm. Dysregulation of left atrial mitochondrial (COX7C) and metabolic (FOXO1) genes was associated with PITX2 expression in human left atria.
    CONCLUSIONS: In summary, PITX2 deficiency causes mitochondrial dysfunction and a metabolic shift to glycolysis in human atrial cardiomyocytes. PITX2-dependent metabolic changes can contribute to the structural and functional defects found in PITX2-deficient atria.
    Keywords:   PITX2 ; atrial fibrillation; human heart tissue; human induced pluripotent stem cells; metabolic shift; mitochondrial dysfunction
    DOI:  https://doi.org/10.1093/cvr/cvae169
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