bims-mitdis 2023-12-31 papers

bims-mitdis

Biomed News

on Mitochondrial disorders

Issue of 2023–12–31
23 papers selected by
Catalina Vasilescu, Helmholz Munich

The role of lysine acetylation in the function of mitochondrial ribosomal protein L12.
Mitochondrial electron transport chain, ceramide, and coenzyme Q are linked in a pathway that drives insulin resistance in skeletal muscle.
A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass.
Neither too much nor too little: mitochondrial calcium concentration as a balance between physiological and pathological conditions.
Mutations in DNAJC19 cause altered mitochondrial structure and increased mitochondrial respiration in human iPSC-derived cardiomyocytes.
Regulation of respiratory complex I assembly by FMN cofactor targeting.
The role of mitochondrial dynamics in disease.
Chronic dietary supplementation with nicotinamide riboside reduces sleep need in the laboratory mouse.
Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings.
Protein N-myristoylation plays a critical role in the mitochondrial localization of human mitochondrial complex I accessory subunit NDUFB7.
Distinct lactate metabolism between hepatocytes and myotubes revealed by live cell imaging with genetically encoded indicators.
Case Report: A novel CYP27A1 gene variant in a patient with cerebrotendinous xanthomatosis with unusual clinical findings.
Striated preferentially expressed gene deficiency leads to mitochondrial dysfunction in developing cardiomyocytes.
TMEM135 maintains the equilibrium of osteogenesis and adipogenesis by regulating mitochondrial dynamics.
Toxicity mechanism of engineered nanomaterials: Focus on mitochondria.
Structural basis for DNA proofreading.
Applying polygenic risk score methods to pharmacogenomics GWAS: challenges and opportunities.
Heptamethine Cyanine-Based Molecule Release Triggered by Mitochondrial ROS.
HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data.
Dystonia, spastic tetraplegia, and ataxia due to a novel mutation in the dynamin domain of OPA1.
mTORC1 regulates the metabolic switch of postnatal cardiomyocytes during regeneration.
The clinical spectrum of MELAS and associated disorders across ages: a retrospective cohort study.
Whole genome sequencing to screen 100 000 newborns for treatable genetic disorders.

Proteins. 2023 Dec 25.

The role of lysine acetylation in the function of mitochondrial ribosomal protein L12.

Katelynn V Paluch, Karlie R Platz, Emma J Rudisel, Ryan R Erdmann, Taylor R Laurin, Kristin E Dittenhafer-Reed.

  Mitochondria play a central role in energy production and cellular metabolism. Mitochondria contain their own small genome (mitochondrial DNA, mtDNA) that carries the genetic instructions for proteins required for ATP synthesis. The mitochondrial proteome, including the mitochondrial transcriptional machinery, is subject to post-translational modifications (PTMs), including acetylation and phosphorylation. We set out to determine whether PTMs of proteins associated with mtDNA may provide a potential mechanism for the regulation of mitochondrial gene expression. Here, we focus on mitochondrial ribosomal protein L12 (MRPL12), which is thought to stabilize mitochondrial RNA polymerase (POLRMT) and promote transcription. Numerous acetylation sites of MRPL12 were identified by mass spectrometry. We employed amino acid mimics of the acetylated (lysine to glutamine mutants) and deacetylated (lysine to arginine mutants) versions of MRPL12 to interrogate the role of lysine acetylation in transcription initiation in vitro and mitochondrial gene expression in HeLa cells. MRPL12 acetyl and deacetyl protein mimics were purified and assessed for their ability to impact mtDNA promoter binding of POLRMT. We analyzed mtDNA content and mitochondrial transcript levels in HeLa cells upon overexpression of acetyl and deacetyl mimics of MRPL12. Our results suggest that MRPL12 single-site acetyl mimics do not change the mtDNA promoter binding ability of POLRMT or mtDNA content in HeLa cells. Individual acetyl mimics may have modest effects on mitochondrial transcript levels. We found that the mitochondrial deacetylase, Sirtuin 3, is capable of deacetylating MRPL12 in vitro, suggesting a potential role for dynamic acetylation controlling MRPL12 function in a role outside of the regulation of gene expression.

Keywords:  acetylation; mitochondrial DNA; mitochondrial genome; mitochondrial proteins; post-translational protein modification; transcription

DOI:  https://doi.org/10.1002/prot.26654
Elife. 2023 Dec 27. pii: RP87340. [Epub ahead of print]12

Mitochondrial electron transport chain, ceramide, and coenzyme Q are linked in a pathway that drives insulin resistance in skeletal muscle.

Alexis Diaz-Vegas, Søren Madsen, Kristen C Cooke, Luke Carroll, Jasmine X Y Khor, Nigel Turner, Xin Y Lim, Miro A Astore, Jonathan C Morris, Anthony S Don, Amanda Garfield, Simona Zarini, Karin A Zemski Berry, Andrew P Ryan, Bryan C Bergman, Joseph T Brozinick, David E James, James G Burchfield.

  Insulin resistance (IR) is a complex metabolic disorder that underlies several human diseases, including type 2 diabetes and cardiovascular disease. Despite extensive research, the precise mechanisms underlying IR development remain poorly understood. Previously we showed that deficiency of coenzyme Q (CoQ) is necessary and sufficient for IR in adipocytes and skeletal muscle (Fazakerley et al., 2018). Here, we provide new insights into the mechanistic connections between cellular alterations associated with IR, including increased ceramides, CoQ deficiency, mitochondrial dysfunction, and oxidative stress. We demonstrate that elevated levels of ceramide in the mitochondria of skeletal muscle cells result in CoQ depletion and loss of mitochondrial respiratory chain components, leading to mitochondrial dysfunction and IR. Further, decreasing mitochondrial ceramide levels in vitro and in animal models (mice, C57BL/6J) (under chow and high-fat diet) increased CoQ levels and was protective against IR. CoQ supplementation also rescued ceramide-associated IR. Examination of the mitochondrial proteome from human muscle biopsies revealed a strong correlation between the respirasome system and mitochondrial ceramide as key determinants of insulin sensitivity. Our findings highlight the mitochondrial ceramide-CoQ-respiratory chain nexus as a potential foundation of an IR pathway that may also play a critical role in other conditions associated with ceramide accumulation and mitochondrial dysfunction, such as heart failure, cancer, and aging. These insights may have important clinical implications for the development of novel therapeutic strategies for the treatment of IR and related metabolic disorders.

Keywords:  biochemistry; cell biology; ceramides; chemical biology; coenzyme Q; human; insulin resistance; mitochondria; mouse; muscle; rat

DOI:  https://doi.org/10.7554/eLife.87340
Mol Cell. 2023 Dec 21. pii: S1097-2765(23)01014-6. [Epub ahead of print]

A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass.

Yuqiu Sun, Yu Cao, Huayun Wan, Adalet Memetimin, Yang Cao, Lin Li, Chongyang Wu, Meng Wang, She Chen, Qi Li, Yan Ma, Mengqiu Dong, Hui Jiang.

  Mitophagy mediated by BNIP3 and NIX critically regulates mitochondrial mass. Cellular BNIP3 and NIX levels are tightly controlled by SCFFBXL4-mediated ubiquitination to prevent excessive mitochondrial loss and lethal disease. Here, we report that knockout of PPTC7, a mitochondrial matrix protein, hyperactivates BNIP3-/NIX-mediated mitophagy and causes perinatal lethality that is rescued by NIX knockout in mice. Biochemically, the PPTC7 precursor is trapped by BNIP3 and NIX to the mitochondrial outer membrane, where PPTC7 scaffolds assembly of a substrate-PPTC7-SCFFBXL4 holocomplex to degrade BNIP3 and NIX, forming a homeostatic regulatory loop. PPTC7 possesses an unusually weak mitochondrial targeting sequence to facilitate its outer membrane retention and mitophagy control. Starvation upregulates PPPTC7 expression in mouse liver to repress mitophagy, which critically maintains hepatic mitochondrial mass, bioenergetics, and gluconeogenesis. Collectively, PPTC7 functions as a mitophagy sensor that integrates homeostatic and physiological signals to dynamically control BNIP3 and NIX degradation, thereby maintaining mitochondrial mass and cellular homeostasis.

Keywords:  Cullin; FBXL4; PPTC7; metabolism; mitochondrial mass; mitophagy receptors BNIP3 and NIX; ubiquitin

DOI:  https://doi.org/10.1016/j.molcel.2023.11.038
Front Mol Biosci. 2023 ;10 1336416

Neither too much nor too little: mitochondrial calcium concentration as a balance between physiological and pathological conditions.

Donato D'Angelo, Denis Vecellio Reane, Anna Raffaello.

  Ca2+ ions serve as pleiotropic second messengers in the cell, regulating several cellular processes. Mitochondria play a fundamental role in Ca2+ homeostasis since mitochondrial Ca2+ (mitCa2+) is a key regulator of oxidative metabolism and cell death. MitCa2+ uptake is mediated by the mitochondrial Ca2+ uniporter complex (MCUc) localized in the inner mitochondrial membrane (IMM). MitCa2+ uptake stimulates the activity of three key enzymes of the Krebs cycle, thereby modulating ATP production and promoting oxidative metabolism. As Paracelsus stated, "Dosis sola facit venenum,"in pathological conditions, mitCa2+ overload triggers the opening of the mitochondrial permeability transition pore (mPTP), enabling the release of apoptotic factors and ultimately leading to cell death. Excessive mitCa2+ accumulation is also associated with a pathological increase of reactive oxygen species (ROS). In this article, we review the precise regulation and the effectors of mitCa2+ in physiopathological processes.

Keywords:  calcium; cell death; metabolism; mitochondria; mitochondrial calcium uniporter (MCU)

DOI:  https://doi.org/10.3389/fmolb.2023.1336416
Mol Metab. 2023 Dec 23. pii: S2212-8778(23)00193-X. [Epub ahead of print] 101859

Mutations in DNAJC19 cause altered mitochondrial structure and increased mitochondrial respiration in human iPSC-derived cardiomyocytes.

Anna Janz, Katharina Walz, Alexandra Cirnu, Jessica Surjanto, Daniela Urlaub, Miriam Leskien, Michael Kohlhaas, Alexander Nickel, Theresa Brand, Naoko Nose, Philipp Wörsdörfer, Nicole Wagner, Takahiro Higuchi, Christoph Maack, Jan Dudek, Kristina Lorenz, Eva Klopocki, Süleyman Ergün, Henry J Duff, Brenda Gerull.

   BACKGROUND: Dilated cardiomyopathy with ataxia (DCMA) is an autosomal recessive disorder arising from truncating mutations in DNAJC19, which encodes an inner mitochondrial membrane protein. Clinical features include an early onset, often life-threatening, cardiomyopathy associated with other metabolic features. Here, we aim to understand the metabolic and pathophysiological mechanisms of mutant DNAJC19 for the development of cardiomyopathy.
METHODS: We generated induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) of two affected siblings with DCMA and a gene-edited truncation variant (tv) of DNAJC19which all lack the conserved DnaJ interaction domain. The mutant iPSC-CMs and their respective control cells were subjected to various analyses, including assessments of morphology, metabolic function, and physiological consequences such as Ca2+ kinetics, contractility, and arrhythmic potential. Validation of respiration analysis was done in a gene-edited HeLa cell line (DNAJC19tvHeLa).
RESULTS: Structural analyses revealed mitochondrial fragmentation and abnormal cristae formation associated with an overall reduced mitochondrial protein expression in mutant iPSC-CMs. Morphological alterations were associated with higher oxygen consumption rates (OCRs) in all three mutant iPSC-CMs, indicating higher electron transport chain activity to meet cellular ATP demands. Additionally, increased extracellular acidification rates suggested an increase in overall metabolic flux, while radioactive tracer uptake studies revealed decreased fatty acid uptake and utilization of glucose. Mutant iPSC-CMs also showed increased reactive oxygen species (ROS) and an elevated mitochondrial membrane potential. Increased mitochondrial respiration with pyruvate and malate as substrates was observed in mutant DNAJC19tv HeLa cells in addition to an upregulation of respiratory chain complexes, while cellular ATP-levels remain the same. Moreover, mitochondrial alterations were associated with increased beating frequencies, elevated diastolic Ca2+ concentrations, reduced sarcomere shortening and an increased beat-to-beat rate variability in mutant cell lines in response to β-adrenergic stimulation.
CONCLUSIONS: Loss of the DnaJ domain disturbs cardiac mitochondrial structure with abnormal cristae formation and mitochondrial function, which suggests that DNAJC19 plays an essential role in mitochondrial morphogenesis and biogenesis. Moreover, increased mitochondrial respiration, altered substrate utilization, increased ROS production and abnormal Ca2+ kinetics provide insights into the pathogenesis of DCMA-related cardiomyopathy.

Keywords:  Contractility; Dilated cardiomyopathy with ataxia; Genetics; Metabolism; Mitochondria; OXPHOS; ROS

DOI:  https://doi.org/10.1016/j.molmet.2023.101859
Redox Biol. 2023 Dec 20. pii: S2213-2317(23)00402-0. [Epub ahead of print]69 103001

Regulation of respiratory complex I assembly by FMN cofactor targeting.

Andrea Curtabbi, Adela Guarás, José Luis Cabrera-Alarcón, Maribel Rivero, Enrique Calvo, Marina Rosa-Moreno, Jesús Vázquez, Milagros Medina, José Antonio Enríquez.

  Respiratory complex I plays a crucial role in the mitochondrial electron transport chain and shows promise as a therapeutic target for various human diseases. While most studies focus on inhibiting complex I at the Q-site, little is known about inhibitors targeting other sites within the complex. In this study, we demonstrate that diphenyleneiodonium (DPI), a N-site inhibitor, uniquely affects the stability of complex I by reacting with its flavin cofactor FMN. Treatment with DPI blocks the final stage of complex I assembly, leading to the complete and reversible degradation of complex I in different cellular models. Growing cells in medium lacking the FMN precursor riboflavin or knocking out the mitochondrial flavin carrier gene SLC25A32 results in a similar complex I degradation. Overall, our findings establish a direct connection between mitochondrial flavin homeostasis and complex I stability and assembly, paving the way for novel pharmacological strategies to regulate respiratory complex I.

Keywords:  DPI; FMN; OXPHOS; Respiratory complex I

DOI:  https://doi.org/10.1016/j.redox.2023.103001
MedComm (2020). 2023 Dec;4(6): e462

The role of mitochondrial dynamics in disease.

Yujuan Wang, Xinyan Dai, Hui Li, Huiling Jiang, Junfu Zhou, Shiying Zhang, Jiacheng Guo, Lidu Shen, Huantao Yang, Jie Lin, Hengxiu Yan.

  Mitochondria are multifaceted and dynamic organelles regulating various important cellular processes from signal transduction to determining cell fate. As dynamic properties of mitochondria, fusion and fission accompanied with mitophagy, undergo constant changes in number and morphology to sustain mitochondrial homeostasis in response to cell context changes. Thus, the dysregulation of mitochondrial dynamics and mitophagy is unsurprisingly related with various diseases, but the unclear underlying mechanism hinders their clinical application. In this review, we summarize the recent developments in the molecular mechanism of mitochondrial dynamics and mitophagy, particularly the different roles of key components in mitochondrial dynamics in different context. We also summarize the roles of mitochondrial dynamics and target treatment in diseases related to the cardiovascular system, nervous system, respiratory system, and tumor cell metabolism demanding high-energy. In these diseases, it is common that excessive mitochondrial fission is dominant and accompanied by impaired fusion and mitophagy. But there have been many conflicting findings about them recently, which are specifically highlighted in this view. We look forward that these findings will help broaden our understanding of the roles of the mitochondrial dynamics in diseases and will be beneficial to the discovery of novel selective therapeutic targets.

Keywords:  context; disease; mitochondrial dynamics; mitophagy; target treatment

DOI:  https://doi.org/10.1002/mco2.462
Sleep Adv. 2023 ;4(1): zpad044

Chronic dietary supplementation with nicotinamide riboside reduces sleep need in the laboratory mouse.

Priyanka N Bushana, Michelle A Schmidt, Michael J Rempe, Barbara A Sorg, Jonathan P Wisor.

  Non-rapid eye movement sleep (NREMS) is accompanied by a reduction in cerebral glucose utilization. Enabling this metabolic change may be a central function of sleep. Since the reduction in glucose metabolism is inevitably accompanied by deceleration of downstream oxidation/reduction reactions involving nicotinamide adenine dinucleotide (NAD), we hypothesized a role for NAD in regulating the homeostatic dynamics of sleep at the biochemical level. We applied dietary nicotinamide riboside (NR), a NAD precursor, in a protocol known to improve neurological outcome measures in mice. Long-term (6-10 weeks) dietary supplementation with NR reduced the time that mice spent in NREMS by 17 percent and accelerated the rate of discharge of sleep need according to a mathematical model of sleep homeostasis (Process S). These findings suggest that increasing redox capacity by increasing nicotinamide availability reduces sleep need and increases the cortical capacity for energetically demanding high-frequency oscillations. In turn, this work demonstrates the impact of redox substrates on cortical circuit properties related to fatigue and sleep drive, implicating redox reactions in the homeostatic dynamics of cortical network events across sleep-wake cycles.

Keywords:  antioxidants; dietary supplements; electroencephalography; nicotinamide adenine dinucleotide; nicotinamide riboside; oxidation-reduction; oxidative stress; reactive oxygen species

DOI:  https://doi.org/10.1093/sleepadvances/zpad044
Front Genet. 2023 ;14 1277784

Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings.

for DDD-Africa as members of the H3Africa Consortium

  Exome sequencing (ES) is a recommended first-tier diagnostic test for many rare monogenic diseases. It allows for the detection of both single-nucleotide variants (SNVs) and copy number variants (CNVs) in coding exonic regions of the genome in a single test, and this dual analysis is a valuable approach, especially in limited resource settings. Single-nucleotide variants are well studied; however, the incorporation of copy number variant analysis tools into variant calling pipelines has not been implemented yet as a routine diagnostic test, and chromosomal microarray is still more widely used to detect copy number variants. Research shows that combined single and copy number variant analysis can lead to a diagnostic yield of up to 58%, increasing the yield with as much as 18% from the single-nucleotide variant only pipeline. Importantly, this is achieved with the consideration of computational costs only, without incurring any additional sequencing costs. This mini review provides an overview of copy number variant analysis from exome data and what the current recommendations are for this type of analysis. We also present an overview on rare monogenic disease research standard practices in resource-limited settings. We present evidence that integrating copy number variant detection tools into a standard exome sequencing analysis pipeline improves diagnostic yield and should be considered a significantly beneficial addition, with relatively low-cost implications. Routine implementation in underrepresented populations and limited resource settings will promote generation and sharing of CNV datasets and provide momentum to build core centers for this niche within genomic medicine.

Keywords:  copy number variation; exome sequencing; low-middle-income countries; monogenic disorders; rare disease; variant calling

DOI:  https://doi.org/10.3389/fgene.2023.1277784
Sci Rep. 2023 12 27. 13(1): 22991

Protein N-myristoylation plays a critical role in the mitochondrial localization of human mitochondrial complex I accessory subunit NDUFB7.

Haruna Harada, Koko Moriya, Hirotsugu Kobuchi, Naotada Ishihara, Toshihiko Utsumi.

The present study examined human N-myristoylated proteins that specifically localize to mitochondria among the 1,705 human genes listed in MitoProteome, a mitochondrial protein database. We herein employed a strategy utilizing cellular metabolic labeling with a bioorthogonal myristic acid analog in transfected COS-1 cells established in our previous studies. Four proteins, DMAC1, HCCS, NDUFB7, and PLGRKT, were identified as N-myristoylated proteins that specifically localize to mitochondria. Among these proteins, DMAC1 and NDUFB7 play critical roles in the assembly of complex I of the mitochondrial respiratory chain. DMAC1 functions as an assembly factor, and NDUFB7 is an accessory subunit of complex I. An analysis of the intracellular localization of non-myristoylatable G2A mutants revealed that protein N-myristoylation occurring on NDUFB7 was important for the mitochondrial localization of this protein. Furthermore, an analysis of the role of the CHCH domain in NDUFB7 using Cys to Ser mutants revealed that it was essential for the mitochondrial localization of NDUFB7. Therefore, the present results showed that NDUFB7, a vital component of human mitochondrial complex I, was N-myristoylated, and protein N-myrisotylation and the CHCH domain were both indispensable for the specific targeting and localization of NDUFB7 to mitochondria.

DOI: https://doi.org/10.1038/s41598-023-50390-z
Biochem Biophys Res Commun. 2023 Dec 20. pii: S0006-291X(23)01510-3. [Epub ahead of print]694 149416

Distinct lactate metabolism between hepatocytes and myotubes revealed by live cell imaging with genetically encoded indicators.

Mina Horikoshi, Kazuki Harada, Saki Tsuno, Tetsuya Kitaguchi, Masami Yokota Hirai, Mitsuharu Matsumoto, Shin Terada, Takashi Tsuboi.

  The process of glycolysis breaks down glycogen stored in muscles, producing lactate through pyruvate to generate energy. Excess lactate is then released into the bloodstream. When lactate reaches the liver, it is converted to glucose, which muscles utilize as a substrate to generate ATP. Although the biochemical study of lactate metabolism in hepatocytes and skeletal muscle cells has been extensive, the spatial and temporal dynamics of this metabolism in live cells are still unknown. We observed the dynamics of metabolism-related molecules in primary cultured hepatocytes and a skeletal muscle cell line upon lactate overload. Our observations revealed an increase in cytoplasmic pyruvate concentration in hepatocytes, which led to glucose release. Skeletal muscle cells exhibited elevated levels of lactate and pyruvate levels in both the cytoplasm and mitochondrial matrix. However, mitochondrial ATP levels remained unaffected, indicating that the increased lactate can be converted to pyruvate but is unlikely to be utilized for ATP production. The findings suggest that excess lactate in skeletal muscle cells is taken up into mitochondria with little contribution to ATP production. Meanwhile, lactate released into the bloodstream can be converted to glucose in hepatocytes for subsequent utilization in skeletal muscle cells.

Keywords:  Cori cycle; Hepatocytes; L6 cells; Lactate metabolism; Live cell imaging

DOI:  https://doi.org/10.1016/j.bbrc.2023.149416
Int J Neurosci. 2023 Dec 28. 1-16

Case Report: A novel CYP27A1 gene variant in a patient with cerebrotendinous xanthomatosis with unusual clinical findings.

Francisco A Tama Viteri, David Cotán Marín, Francisco A Tama Sánchez, Marcia A Tama Sánchez.

  Cerebrotendinous xanthomatosis (CTX; OMIM #213700) is an autosomal recessive disease that courses with an inborn error of bile acid metabolism caused by a deficiency of the mitochondrial enzyme sterol 27-hydroxylase with clinical and molecular heterogeneity. This enzymatic failure leads to a lack of primary bile acids such as chenodeoxycholic acid and cholic acid, produces an increase in serum cholesterol and urinary excretion of biliary alcohol, and generates an accumulation of cholestanol and other sterols in tissues.The gene CYP27A1, that codes for the mitochondrial sterol 27-hydroxylase enzyme, was described as the cause of these defects and up to date, more than 50 mutations have been involved in the disease. Some adult patients with CTX may have tendon xanthomas as the only predominant feature or may not have them. In addition, sometimes the clinical manifestations of patients suggest that they are carriers of other diseases that are often confused with CTX. In this context, some patients seem to presente an "incomplete" CTX, which could be redefined as a variant of CTX with further studies.The objective of this study was to carry out a genetic study and a clinical description of a patient with unusual clinical manifestation of the disease, which indicates the possible presence of a CTX with a milder phenotype, in order to determine the possible existence of a novel mutation. The evaluation of new mutations associated with this disease allows for earlier diagnosis and greater effectiveness in its treatment.

Keywords:  Case Report; Cerebrotendinous xanthomatosis; clinical heterogeneity; neurological involvement; tendon xanthoma

DOI:  https://doi.org/10.1080/00207454.2023.2300735
Basic Res Cardiol. 2023 Dec 26.

Striated preferentially expressed gene deficiency leads to mitochondrial dysfunction in developing cardiomyocytes.

Gu Li, He Huang, Yanshuang Wu, Chang Shu, Narae Hwang, Qifei Li, Rose Zhao, Hilaire C Lam, William M Oldham, Souheil Ei-Chemaly, Pankaj B Agrawal, Jie Tian, Xiaoli Liu, Mark A Perrella.

  A deficiency of striated preferentially expressed gene (Speg), a member of the myosin light chain kinase family, results in abnormal myofibril structure and function of immature cardiomyocytes (CMs), corresponding with a dilated cardiomyopathy, heart failure and perinatal death. Mitochondrial development plays a role in cardiomyocyte maturation. Therefore, this study investigated whether Speg deficiency ( - / - ) in CMs would result in mitochondrial abnormalities. Speg wild-type and Speg-/- C57BL/6 littermate mice were utilized for assessment of mitochondrial structure by transmission electron and confocal microscopies. Speg was expressed in the first and second heart fields at embryonic (E) day 7.5, prior to the expression of mitochondrial Na+/Ca2+/Li+ exchanger (NCLX) at E8.5. Decreases in NCLX expression (E11.5) and the mitochondrial-to-nuclear DNA ratio (E13.5) were observed in Speg-/- hearts. Imaging of E18.5 Speg-/- hearts revealed abnormal mitochondrial cristae, corresponding with decreased ATP production in cells fed glucose or palmitate, increased levels of mitochondrial superoxide and depolarization of mitochondrial membrane potential. Interestingly, phosphorylated (p) PGC-1α, a key mediator of mitochondrial development, was significantly reduced in Speg-/- hearts during screening for targeted genes. Besides Z-line expression, Speg partially co-localized with PGC-1α in the sarcomeric region and was found in the same complex by co-immunoprecipitation. Overexpression of a Speg internal serine/threonine kinase domain in Speg-/- CMs promoted translocation of pPGC-1α into the nucleus, and restored ATP production that was abolished by siRNA-mediated silencing of PGC-1α. Our results demonstrate a critical role of Speg in mitochondrial development and energy metabolism in CMs, mediated in part by phosphorylation of PGC-1α.

Keywords:  Dilated cardiomyopathy; Mitochondria; PGC-1α phosphorylation; Speg

DOI:  https://doi.org/10.1007/s00395-023-01029-7
Metabolism. 2023 Dec 26. pii: S0026-0495(23)00371-2. [Epub ahead of print] 155767

TMEM135 maintains the equilibrium of osteogenesis and adipogenesis by regulating mitochondrial dynamics.

Jia Liu, Xiaogang Bao, Jian Huang, Rukun Chen, Yixuan Tan, Zheng Zhang, Bing Xiao, Fanqi Kong, Changjiang Gu, Jianhang Du, Haotian Wang, Junqiang Qi, Junming Tan, Duan Ma, Changgui Shi, Guohua Xu.

   BACKGROUND: Disturbance in the differentiation process of bone marrow mesenchymal stem cells (BMSCs) leads to osteoporosis. Mitochondrial dynamics plays a pivotal role in the metabolism and differentiation of BMSCs. However, the mechanisms underlying mitochondrial dynamics and their impact on the differentiation equilibrium of BMSCs remain unclear.
METHODS: We investigated the mitochondrial morphology and markers related to mitochondrial dynamics during BMSCs osteogenic and adipogenic differentiation. Bioinformatics was used to screen potential genes regulating BMSCs differentiation through mitochondrial dynamics. Subsequently, we evaluated the impact of Transmembrane protein 135 (TMEM135) deficiency on bone homeostasis by comparing Tmem135 knockout mice with their littermates. The mechanism of TMEM135 in mitochondrial dynamics and BMSCs differentiation was also investigated in vivo and in vitro.
RESULTS: Distinct changes in mitochondrial morphology were observed between osteogenic and adipogenic differentiation of BMSCs, manifesting as fission in the late stage of osteogenesis and fusion in adipogenesis. Additionally, we revealed that TMEM135, a modulator of mitochondrial dynamics, played a functional role in regulating the equilibrium between adipogenesis and osteogenesis. The TMEM135 deficiency impaired mitochondrial fission and disrupted crucial mitochondrial energy metabolism during osteogenesis. Tmem135 knockout mice showed osteoporotic phenotype, characterized by reduced osteogenesis and increased adipogenesis. Mechanistically, TMEM135 maintained intracellular calcium ion homeostasis and facilitated the dephosphorylation of dynamic-related protein 1 at Serine 637 in BMSCs.
CONCLUSIONS: Our findings underscore the significant role of TMEM135 as a modulator in orchestrating the differentiation trajectory of BMSCs and promoting a shift in mitochondrial dynamics toward fission. This ultimately contributes to the osteogenesis process. This work has provided promising biological targets for the treatment of osteoporosis.

Keywords:  Adipogenesis; Energy metabolism; Mitochondrial dynamics; Osteogenesis; Osteoporosis; Transmembrane proteins

DOI:  https://doi.org/10.1016/j.metabol.2023.155767
Environ Pollut. 2023 Dec 26. pii: S0269-7491(23)02233-9. [Epub ahead of print] 123231

Toxicity mechanism of engineered nanomaterials: Focus on mitochondria.

Yongshuai Yao, Ting Zhang, Meng Tang.

  With the rapid development of nanotechnology, engineered nanomaterials (ENMs) are widely used in various fields. This has exacerbated the environmental pollution and human exposure of ENMs. The study of toxicity of ENMs and its mechanism has become a hot research topic in recent years. Mitochondrial damage plays an important role in the toxicity of ENMs. This paper reviews the structural damage, dysfunction, and molecular level perturbations caused by different ENMs to mitochondria, including ZnO NPs, Ag NPs, TiO2 NPs, iron oxide NPs, cadmium-based quantum dots, CuO NPs, silica NPs, carbon-based nanomaterials. Among them, mitochondrial quality control plays an important role in mitochondrial damage. We further summarize the cellular level outcomes caused by mitochondrial damage, mainly including, apoptosis, ferroptosis, pyroptosis and inflammation response. In addition, we concluded that reducing mitochondrial damage at source as well as accelerating recovery from mitochondrial damage through ENMs modification and pharmacological intervention are two feasible strategies. This review further provides new insights into the mitochondrial toxicity mechanisms of ENMs and provides a new foothold for predicting human health and environmental risks of ENMs.

Keywords:  ENMs design strategies; Engineered nanomaterials (ENMs); Ferroptosis; Inflammation; Mitochondrial quality control; Mitochondrial toxicity

DOI:  https://doi.org/10.1016/j.envpol.2023.123231
Nat Commun. 2023 Dec 27. 14(1): 8501

Structural basis for DNA proofreading.

Gina Buchel, Ashok R Nayak, Karl Herbine, Azadeh Sarfallah, Viktoriia O Sokolova, Angelica Zamudio-Ochoa, Dmitry Temiakov.

DNA polymerase (DNAP) can correct errors in DNA during replication by proofreading, a process critical for cell viability. However, the mechanism by which an erroneously incorporated base translocates from the polymerase to the exonuclease site and the corrected DNA terminus returns has remained elusive. Here, we present an ensemble of nine high-resolution structures representing human mitochondrial DNA polymerase Gamma, Polγ, captured during consecutive proofreading steps. The structures reveal key events, including mismatched base recognition, its dissociation from the polymerase site, forward translocation of DNAP, alterations in DNA trajectory, repositioning and refolding of elements for primer separation, DNAP backtracking, and displacement of the mismatched base into the exonuclease site. Altogether, our findings suggest a conserved 'bolt-action' mechanism of proofreading based on iterative cycles of DNAP translocation without dissociation from the DNA, facilitating primer transfer between catalytic sites. Functional assays and mutagenesis corroborate this mechanism, connecting pathogenic mutations to crucial structural elements in proofreading steps.

DOI: https://doi.org/10.1038/s41467-023-44198-8
Brief Bioinform. 2023 Nov 22. pii: bbad470. [Epub ahead of print]25(1):

Applying polygenic risk score methods to pharmacogenomics GWAS: challenges and opportunities.

Song Zhai, Devan V Mehrotra, Judong Shen.

  Polygenic risk scores (PRSs) have emerged as promising tools for the prediction of human diseases and complex traits in disease genome-wide association studies (GWAS). Applying PRSs to pharmacogenomics (PGx) studies has begun to show great potential for improving patient stratification and drug response prediction. However, there are unique challenges that arise when applying PRSs to PGx GWAS beyond those typically encountered in disease GWAS (e.g. Eurocentric or trans-ethnic bias). These challenges include: (i) the lack of knowledge about whether PGx or disease GWAS/variants should be used in the base cohort (BC); (ii) the small sample sizes in PGx GWAS with corresponding low power and (iii) the more complex PRS statistical modeling required for handling both prognostic and predictive effects simultaneously. To gain insights in this landscape about the general trends, challenges and possible solutions, we first conduct a systematic review of both PRS applications and PRS method development in PGx GWAS. To further address the challenges, we propose (i) a novel PRS application strategy by leveraging both PGx and disease GWAS summary statistics in the BC for PRS construction and (ii) a new Bayesian method (PRS-PGx-Bayesx) to reduce Eurocentric or cross-population PRS prediction bias. Extensive simulations are conducted to demonstrate their advantages over existing PRS methods applied in PGx GWAS. Our systematic review and methodology research work not only highlights current gaps and key considerations while applying PRS methods to PGx GWAS, but also provides possible solutions for better PGx PRS applications and future research.

Keywords:  Bayesian; Eurocentric bias; challenges and opportunities; multiple traits; pharmacogenomics GWAS; polygenic risk score

DOI:  https://doi.org/10.1093/bib/bbad470
ACS Appl Bio Mater. 2023 Dec 27.

Heptamethine Cyanine-Based Molecule Release Triggered by Mitochondrial ROS.

Jing Liu, Pu Yan, Xiangjun Liu, Zhenhao Long, Tao Bing, Nan Zhang, Dihua Shangguan.

  Conditionally activated molecule release in live cells would provide spatiotemporal control for the study and intervention of biological processes, e.g., bioactive molecule monitoring and controlled drug release. Mitochondria are the main sites of reactive oxygen species (ROS) production in cells. Here, we report an ROS-triggered molecule release strategy in mitochondria. A molecule IRTO with dual targeting groups was designed by covalently linking IR-780 (a mitochondrial targeted heptamethine cyanine) and 4-aminobutyl-thiazole orange (NH2-TO, a nuclear dye). IRTO diffused into live cells and first accumulated in mitochondria. As the cyanine moiety reacted with mitochondrial ROS directly or with the help of mitochondrial cytochromes, NH2-TO was released, escaped from mitochondria, and finally located in the nucleus. This process could be visualized by fluorescent imaging, i.e., red fluorescence (from the cyanine moiety of IRTO) first located in mitochondria, and green fluorescence (from NH2-TO) appeared and gradually enhanced in the nucleus with the increase of incubation time. The addition of H2O2 or lipopolysaccharide (LPS, an ROS accelerator) could accelerate the release of NH2-TO, whereas N-acetyl-l-cysteine (NAC, an ROS inhibitor) and mitoquinone mesylate (MitoQ, a mitochondrial ROS scavenger) could obviously decrease the release of NH2-TO. These results suggest that IRTO could serve as a fluorescent probe for monitoring ROS in mitochondria and that IR-780 might be a promising endogenous ROS-triggered molecule release platform.

Keywords:  heptamethine cyanine; mitochondrial ROS; molecular probe; molecule release; thiazole orange

DOI:  https://doi.org/10.1021/acsabm.3c00955
Nucleic Acids Res. 2023 Dec 28. pii: gkad1223. [Epub ahead of print]

HMZDupFinder: a robust computational approach for detecting intragenic homozygous duplications from exome sequencing data.

Haowei Du, Zain Dardas, Angad Jolly, Christopher M Grochowski, Shalini N Jhangiani, He Li, Donna Muzny, Jawid M Fatih, Gozde Yesil, Nursel H Elçioglu, Alper Gezdirici, Dana Marafi, Davut Pehlivan, Daniel G Calame, Claudia M B Carvalho, Jennifer E Posey, Tomasz Gambin, Zeynep Coban-Akdemir, James R Lupski.

Homozygous duplications contribute to genetic disease by altering gene dosage or disrupting gene regulation and can be more deleterious to organismal biology than heterozygous duplications. Intragenic exonic duplications can result in loss-of-function (LoF) or gain-of-function (GoF) alleles that when homozygosed, i.e. brought to homozygous state at a locus by identity by descent or state, could potentially result in autosomal recessive (AR) rare disease traits. However, the detection and functional interpretation of homozygous duplications from exome sequencing data remains a challenge. We developed a framework algorithm, HMZDupFinder, that is designed to detect exonic homozygous duplications from exome sequencing (ES) data. The HMZDupFinder algorithm can efficiently process large datasets and accurately identifies small intragenic duplications, including those associated with rare disease traits. HMZDupFinder called 965 homozygous duplications with three or less exons from 8,707 ES with a recall rate of 70.9% and a precision of 16.1%. We experimentally confirmed 8/10 rare homozygous duplications. Pathogenicity assessment of these copy number variant alleles allowed clinical genomics contextualization for three homozygous duplications alleles, including two affecting known OMIM disease genes EDAR (MIM# 224900), TNNT1(MIM# 605355), and one variant in a novel candidate disease gene: PAAF1.

DOI: https://doi.org/10.1093/nar/gkad1223
Ann Clin Transl Neurol. 2023 Dec 26.

Dystonia, spastic tetraplegia, and ataxia due to a novel mutation in the dynamin domain of OPA1.

YuZhi Shi, Kang Zhang, GeHong Dong, Hua Pan, Bin Chen, An Wang, SongTao Niu, XinGao Wang, ZaiQiang Zhang.

Movement disorders manifest in various hereditary neurodegenerative diseases. We reported a young man who presented with progressive upper limb dystonia, spastic tetraplegia, and ataxia. Whole-exome sequencing (WES) revealed a novel variant, c.2357A > G, in the dynamin domain of OPA1. No mtDNA deletion was detected in muscle by long-range PCR. Atrophy and decreased glucose metabolism of the basal ganglia were discovered. Decreased mtDNA copy number, fragmented mitochondria, slightly impaired oxidative phosphorylation, and increased autophagy were detected in mutant fibroblasts. Evident oxidative phosphorylation impairment and mtDNA deletions were not involved in the pathogenicity of this mutation unlike mutations in the GTPase domain of OPA1.

DOI: https://doi.org/10.1002/acn3.51981
J Mol Cell Cardiol. 2023 Dec 22. pii: S0022-2828(23)00198-0. [Epub ahead of print]187 15-25

mTORC1 regulates the metabolic switch of postnatal cardiomyocytes during regeneration.

Wyatt G Paltzer, Timothy J Aballo, Jiyoung Bae, Corey G K Flynn, Kayla N Wanless, Katharine A Hubert, Dakota J Nuttall, Cassidy Perry, Raya Nahlawi, Ying Ge, Ahmed I Mahmoud.

  The metabolic switch from glycolysis to fatty acid oxidation in postnatal cardiomyocytes contributes to the loss of the cardiac regenerative potential of the mammalian heart. However, the mechanisms that regulate this metabolic switch remain unclear. The protein kinase complex mechanistic target of rapamycin complex 1 (mTORC1) is a central signaling hub that regulates cellular metabolism and protein synthesis, yet its role during mammalian heart regeneration and postnatal metabolic maturation is undefined. Here, we use immunoblotting, rapamycin treatment, myocardial infarction, and global proteomics to define the role of mTORC1 in postnatal heart development and regeneration. Our results demonstrate that the activity of mTORC1 is dynamically regulated between the regenerating and the non-regenerating hearts. Acute inhibition of mTORC1 by rapamycin or everolimus reduces cardiomyocyte proliferation and inhibits neonatal heart regeneration following injury. Our quantitative proteomic analysis demonstrates that transient inhibition of mTORC1 during neonatal heart injury did not reduce protein synthesis, but rather shifts the cardiac proteome of the neonatal injured heart from glycolysis towards fatty acid oxidation. This indicates that mTORC1 inhibition following injury accelerates the postnatal metabolic switch, which promotes metabolic maturation and impedes cardiomyocyte proliferation and heart regeneration. Taken together, our results define an important role for mTORC1 in regulating postnatal cardiac metabolism and may represent a novel target to modulate cardiac metabolism and promote heart regeneration.

Keywords:  Cardiomyocyte proliferation; Heart regeneration; Mechanistic target of rapamycin complex 1; Metabolism; Proteomics

DOI:  https://doi.org/10.1016/j.yjmcc.2023.12.004
Front Neurol. 2023 ;14 1298569

The clinical spectrum of MELAS and associated disorders across ages: a retrospective cohort study.

Benjamin C Cox, Jennifer Y Pearson, Jay Mandrekar, Ralitza H Gavrilova.

   Objective: Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) is a severe multisystemic disease, although some have a milder phenotype. We aimed to evaluate the clinical spectrum of this disease from MELAS patients to asymptomatic carriers and identify predictors of severity.
Methods: We reviewed 81 patients, who had MELAS or had positive genetics without meeting clinical criteria. Patients who met criteria including lactic acidosis, encephalomyopathy, and stroke-like episodes (SLE) were categorized as MELAS, symptomatic non-MELAS, and asymptomatic. MELAS was further categorized as "standard-onset" if the first stroke-like episode (SLE) occurred before age 40 or "late-onset."
Results: Eighty-one patients were included: 42 MELAS (13 late-onset), 30 symptomatic non-MELAS, and 9 asymptomatic. MELAS patients had lower BMI at onset (mean 18.6 vs. 25.1 asymptomatic and 22.0 symptomatic non-MELAS, p < 0.05). There was a trend toward higher serum heteroplasmy in MELAS compared to symptomatic non-MELAS and asymptomatic (means 39.3, 29.3, and 21.8% p = 0.09). Symptomatic non-MELAS had more sensorineural hearing loss as first presenting symptom (51.6% vs. 24.4%, p < 0.05). MELAS had higher prevalence of seizures (88.1% vs. 16.7%, p < 0.05) and shorter survival from onset to death (50% mortality at 25 years vs. 10%, p < 0.05). Late-onset MELAS had longer disease duration from first symptom to first SLE (mean 16.6 vs. 9.3 yrs) and also lived longer (mean age at death 62 vs. 30). Standard-onset MELAS had more neurologic involvement at onset than late-onset (51.7% vs. 15.4%). Late-onset patients had more prevalent diabetes (69.2% vs. 13.8%) and nephropathy (53.8% vs. 10.3%). Patients with late-onset MELAS also had more organ systems involved (mean 4.1 vs. 2.7, p < 0.05). There was a trend toward higher heteroplasmy levels in standard-onset (mean 44.8% vs. 25.3%, p = 0.18).
Discussion: Our study highlights the spectrum of MELAS. The lower BMI in MELAS at presentation as well as higher rates of sensorineural hearing loss as initial symptom in symptomatic non-MELAS may be useful clinical markers. While many patients present before age 40 with SLE, some can present with SLE later in life. Standard onset MELAS is more likely to present with neurologic symptoms. Late-onset is more likely to suffer diabetes or nephropathy and have more organ systems involved.

Keywords:  MELAS; epilepsy; genetics; mitochondrial disease; myopathy; stroke

DOI:  https://doi.org/10.3389/fneur.2023.1298569
J Inherit Metab Dis. 2023 Dec 26.

Whole genome sequencing to screen 100 000 newborns for treatable genetic disorders.

Shamima Rahman, David Bick, Richard H Scott.

DOI: https://doi.org/10.1002/jimd.12704