bims-mibica 2021-12-19 papers

bims-mibica

Biomed News

on Mitochondrial bioenergetics in cancer

Issue of 2021–12–19
25 papers selected by
Kelsey Fisher-Wellman, East Carolina University

Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I.
Enzymatic Delivery of Magnetic Nanoparticles into Mitochondria of Live Cells.
Genetically encoded biosensors for evaluating NAD+/NADH ratio in cytosolic and mitochondrial compartments.
Cristae junction as a fundamental switchboard for mitochondrial ion signaling and bioenergetics.
Copper depletion modulates mitochondrial oxidative phosphorylation to impair triple negative breast cancer metastasis.
Isolation of Mitochondria From Fresh Mice Lung Tissue.
Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes.
Loss of hexokinase 1 sensitizes ovarian cancer to high-dose metformin.
Blockade of glutamine-dependent cell survival augments antitumor efficacy of CPI-613 in head and neck cancer.
Mitochondrial-Linked De Novo Pyrimidine Biosynthesis Dictates Human T-Cell Proliferation but Not Expression of Effector Molecules.
A dynamic substrate pool revealed by cryo-EM of a lipid-preserved respiratory supercomplex.
The molecular role of Sigmar1 in regulating mitochondrial function through mitochondrial localization in cardiomyocytes.
A targetable LIFR-NF-κB-LCN2 axis controls liver tumorigenesis and vulnerability to ferroptosis.
Presynaptic Mitochondrial Volume and Packing Density Scale with Presynaptic Power Demand.
TXNRD1: A Key Regulator Involved in the Ferroptosis of CML Cells Induced by Cysteine Depletion In Vitro.
IGFBP-3 functions as a molecular switch that mediates mitochondrial and metabolic homeostasis.
TRAP1 suppresses oral squamous cell carcinoma progression by reducing oxidative phosphorylation metabolism of Cancer-associated fibroblasts.
Genetic landscape of human mitochondrial genome using whole genome sequencing.
Thiol profiling in cancer cell lines by HPLC-mass spectrometry.
Why do cells need oxygen? Insights from mitochondrial composition and function.
Identification of mitochondrial RNA polymerase as a potential therapeutic target of osteosarcoma.
Valproic acid promotes SOD2 acetylation: A potential mechanism of valproic acid-induced oxidative stress in developing systems.
The role of mitochondrial dynamics in mtDNA maintenance.
NADH inhibition of SIRT1 links energy state to transcription during time-restricted feeding.
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues.

Acc Chem Res. 2021 Dec 13.

Resolving Chemical Dynamics in Biological Energy Conversion: Long-Range Proton-Coupled Electron Transfer in Respiratory Complex I.

Ville R I Kaila.

ConspectusBiological energy conversion is catalyzed by membrane-bound proteins that transduce chemical or light energy into energy forms that power endergonic processes in the cell. At a molecular level, these catalytic processes involve elementary electron-, proton-, charge-, and energy-transfer reactions that take place in the intricate molecular machineries of cell respiration and photosynthesis. Recent developments in structural biology, particularly cryo-electron microscopy (cryoEM), have resolved the molecular architecture of several energy transducing proteins, but detailed mechanistic principles of their charge transfer reactions still remain poorly understood and a major challenge for modern biochemical research. To this end, multiscale molecular simulations provide a powerful approach to probe mechanistic principles on a broad range of time scales (femtoseconds to milliseconds) and spatial resolutions (101-106 atoms), although technical challenges also require balancing between the computational accuracy, cost, and approximations introduced within the model. Here we discuss how the combination of atomistic (aMD) and hybrid quantum/classical molecular dynamics (QM/MM MD) simulations with free energy (FE) sampling methods can be used to probe mechanistic principles of enzymes responsible for biological energy conversion. We present mechanistic explorations of long-range proton-coupled electron transfer (PCET) dynamics in the highly intricate respiratory chain enzyme Complex I, which functions as a redox-driven proton pump in bacterial and mitochondrial respiratory chains by catalyzing a 300 Å fully reversible PCET process. This process is initiated by a hydride (H-) transfer between NADH and FMN, followed by long-range (>100 Å) electron transfer along a wire of 8 FeS centers leading to a quinone biding site. The reduction of the quinone to quinol initiates dissociation of the latter to a second membrane-bound binding site, and triggers proton pumping across the membrane domain of complex I, in subunits up to 200 Å away from the active site. Our simulations across different size and time scales suggest that transient charge transfer reactions lead to changes in the internal hydration state of key regions, local electric fields, and the conformation of conserved ion pairs, which in turn modulate the dynamics of functional steps along the reaction cycle. Similar functional principles, which operate on much shorter length scales, are also found in some unrelated proteins, suggesting that enzymes may employ conserved principles in the catalysis of biological energy transduction processes.

DOI: https://doi.org/10.1021/acs.accounts.1c00524
ChemNanoMat. 2021 Oct;7(10): 1104-1107

Enzymatic Delivery of Magnetic Nanoparticles into Mitochondria of Live Cells.

Hongjian He, Jiaqi Guo, Bing Xu.

  Delivering magnetic nanoparticles (MNPs) into mitochondria provide a facile approach to manipulate cell life because mitochondria play essential roles in cell survival and death. Here we report the use of enzyme-responsive peptide assemblies to deliver MNPs into mitochondria of live cells. The mitochondria-targeting peptide (Mito-Flag), as the substrate of enterokinase (ENTK), assembles with MNPs in solution. The MNPs that are encapsulated by Mito-Flag peptides selectively accumulate to the mitochondria of cancer cells, rather than normal cells. The mitochondrial localization of MNPs reduces the viability of the cancer cells, but hardly affects the survival of the normal cell. This work demonstrates a new and facile strategy to specifically transport MNPs to the mitochondria in cancer cells for exploring the applications of MNPs as the targeted drug for biomedicine and cancer therapy.

Keywords:  Enzyme; Magnetic Nanoparticle; Mitochondria; Peptide; Self-Assembly

DOI:  https://doi.org/10.1002/cnma.202100249
Cell Rep Methods. 2021 Nov 22. pii: 100116. [Epub ahead of print]1(7):

Genetically encoded biosensors for evaluating NAD+/NADH ratio in cytosolic and mitochondrial compartments.

Qingxun Hu, Dan Wu, Matthew Walker, Pei Wang, Rong Tian, Wang Wang.

The ratio of oxidized to reduced NAD (NAD+/NADH) sets intracellular redox balance and antioxidant capacity. Intracellular NAD is compartmentalized and the mitochondrial NAD+/NADH ratio is intricately linked to cellular function. Here, we report the monitoring of the NAD+/NADH ratio in mitochondrial and cytosolic compartments in live cells by using a modified genetic biosensor (SoNar). The fluorescence signal of SoNar targeted to mitochondria (mt-SoNar) or cytosol (ct-SoNar) responded linearly to physiological NAD+/NADH ratios in situ. NAD+/NADH ratios in cytosol versus mitochondria responded rapidly, but differently, to acute metabolic perturbations, indicating distinct NAD pools. Subcellular NAD redox balance regained homeostasis via communications through malate-aspartate shuttle. Mitochondrial and cytosolic NAD+/NADH ratios are influenced by NAD+ precursor levels and are distinctly regulated under pathophysiological conditions. Compartment-targeted biosensors and real-time imaging allow assessment of subcellular NAD+/NADH redox signaling in live cells, enabling future mechanistic research of NAD redox in cell biology and disease development.

DOI: https://doi.org/10.1016/j.crmeth.2021.100116
Cell Calcium. 2021 Dec 10. pii: S0143-4160(21)00171-8. [Epub ahead of print]101 102517

Cristae junction as a fundamental switchboard for mitochondrial ion signaling and bioenergetics.

Benjamin Gottschalk, Corina T Madreiter-Sokolowski, Wolfgang F Graier.

OPA1 and MICU1 are both involved in the regulation of mitochondrial Ca2+ uptake and the stabilization of the cristae junction, which separates the inner mitochondrial membrane into the interboundary membrane and the cristae membrane. In this mini-review, we focus on the synergetic control of OPA1 and MICU1 on the cristae junction that serves as a fundamental regulator of multiple mitochondrial functions. In particular, we point to the critical role of an adaptive cristae junction permeability in mitochondrial Ca2+ signaling, spatial H+ gradients and mitochondrial membrane potential, metabolic activity, and apoptosis. These characteristics bear on a distinct localization of the oxidative phosphorylation machinery, the FoF1-ATPase, and mitochondrial Ca2+uniporter (MCU) within sections of the inner mitochondrial membrane isolated by the cristae junction and regulated by proteins like OPA1 and MICU1. We specifically focus on the impact of MICU1-regulated cristae junction on the activity and distribution of MCU within the complex ultrastructure of mitochondria.

DOI: https://doi.org/10.1016/j.ceca.2021.102517
Nat Commun. 2021 Dec 15. 12(1): 7311

Copper depletion modulates mitochondrial oxidative phosphorylation to impair triple negative breast cancer metastasis.

Divya Ramchandani, Mirela Berisa, Diamile A Tavarez, Zhuoning Li, Matthew Miele, Yang Bai, Sharrell B Lee, Yi Ban, Noah Dephoure, Ronald C Hendrickson, Suzanne M Cloonan, Dingcheng Gao, Justin R Cross, Linda T Vahdat, Vivek Mittal.

Copper serves as a co-factor for a host of metalloenzymes that contribute to malignant progression. The orally bioavailable copper chelating agent tetrathiomolybdate (TM) has been associated with a significant survival benefit in high-risk triple negative breast cancer (TNBC) patients. Despite these promising data, the mechanisms by which copper depletion impacts metastasis are poorly understood and this remains a major barrier to advancing TM to a randomized phase II trial. Here, using two independent TNBC models, we report a discrete subpopulation of highly metastatic SOX2/OCT4+ cells within primary tumors that exhibit elevated intracellular copper levels and a marked sensitivity to TM. Global proteomic and metabolomic profiling identifies TM-mediated inactivation of Complex IV as the primary metabolic defect in the SOX2/OCT4+ cell population. We also identify AMPK/mTORC1 energy sensor as an important downstream pathway and show that AMPK inhibition rescues TM-mediated loss of invasion. Furthermore, loss of the mitochondria-specific copper chaperone, COX17, restricts copper deficiency to mitochondria and phenocopies TM-mediated alterations. These findings identify a copper-metabolism-metastasis axis with potential to enrich patient populations in next-generation therapeutic trials.

DOI: https://doi.org/10.1038/s41467-021-27559-z
Front Physiol. 2021 ;12 748261

Isolation of Mitochondria From Fresh Mice Lung Tissue.

Dayene de Assis Fernandes Caldeira, Dahienne Ferreira de Oliveira, João Paulo Cavalcanti-de-Albuquerque, Jose Hamilton Matheus Nascimento, Walter Araujo Zin, Leonardo Maciel.

  Direct analysis of isolated mitochondria enables a better understanding of lung dysfunction. Despite well-defined mitochondrial isolation protocols applicable to other tissues, such as the brain, kidney, heart, and liver, a robust and reproductive protocol has not yet been advanced for the lung. We describe a protocol for the isolation of mitochondria from lung tissue aiming for functional analyses of mitochondrial O2 consumption, transmembrane potential, reactive oxygen species (ROS) formation, ATP production, and swelling. We compared our protocol to that used for heart mitochondrial function that is well-established in the literature, and achieved similar results.

Keywords:  ATP; O2-consumption; ROS; lung mitochondria isolation; mitochondrial assessment

DOI:  https://doi.org/10.3389/fphys.2021.748261
Zool Res. 2022 Jan 18. pii: 2095-8137(2022)01-0111-18. [Epub ahead of print]43(1): 111-128

Lack of transcriptional coordination between mitochondrial and nuclear oxidative phosphorylation genes in the presence of two divergent mitochondrial genomes.

Ran Xu, Mariangela Iannello, Justin C Havird, Liliana Milani, Fabrizio Ghiselli.

  In most eukaryotes, oxidative phosphorylation (OXPHOS) is the main energy production process and it involves both mitochondrial and nuclear genomes. The close interaction between the two genomes is critical for the coordinated function of the OXPHOS process. Some bivalves show doubly uniparental inheritance (DUI) of mitochondria, where two highly divergent mitochondrial genomes, one inherited through eggs (F-type) and the other through sperm (M-type), coexist in the same individual. However, it remains a puzzle how nuclear OXPHOS genes coordinate with two divergent mitochondrial genomes in DUI species. In this study, we compared transcription, polymorphism, and synonymous codon usage in the mitochondrial and nuclear OXPHOS genes of the DUI species Ruditapes philippinarum using sex- and tissue-specific transcriptomes. Mitochondrial and nuclear OXPHOS genes showed different transcription profiles. Strong co-transcription signal was observed within mitochondrial (separate for F- and M-type) and within nuclear OXPHOS genes but the signal was weak or absent between mitochondrial and nuclear OXPHOS genes, suggesting that the coordination between mitochondrial and nuclear OXPHOS subunits is not achieved transcriptionally. McDonald-Kreitman and frequency-spectrum based tests indicated that M-type OXPHOS genes deviated significantly from neutrality, and that F-type and M-type OXPHOS genes undergo different selection patterns. Codon usage analysis revealed that mutation bias and translational selection were the major factors affecting the codon usage bias in different OXPHOS genes, nevertheless, translational selection in mitochondrial OXPHOS genes appears to be less efficient than nuclear OXPHOS genes. Therefore, we speculate that the coordination between OXPHOS genes may involve post-transcriptional/translational regulation.

Keywords:  Co-transcription; Codon usage bias; Doubly uniparental inheritance; Oxidative phosphorylation; Polymorphism; Translational selection

DOI:  https://doi.org/10.24272/j.issn.2095-8137.2021.348
Cancer Metab. 2021 Dec 11. 9(1): 41

Loss of hexokinase 1 sensitizes ovarian cancer to high-dose metformin.

Daniela Šimčíková, Dominik Gardáš, Kateřina Hložková, Martin Hruda, Petr Žáček, Lukáš Rob, Petr Heneberg.

   BACKGROUND: Hexokinases (HKs) are well-studied enzymes catalyzing the first step of glycolysis. However, non-canonical regulatory roles of HKs are still incompletely understood. Here, we hypothesized that HKs comprise one of the missing links between high-dose metformin and the inhibition of the respiratory chain in cancer.
METHODS: We tested the isoenzyme-specific regulatory roles of HKs in ovarian cancer cells by examining the effects of the deletions of HK1 and HK2 in TOV-112D ovarian adenocarcinoma cells. We reverted these effects by re-introducing wild-type HK1 and HK2, and we compared the HK1 revertant with the knock-in of catalytically dead HK1 p.D656A. We subjected these cells to a battery of metabolic and proliferation assays and targeted GC×GC-MS metabolomics.
RESULTS: We found that the HK1 depletion (but not the HK2 depletion) sensitized ovarian cancer cells to high-dose metformin during glucose starvation. We confirmed that this newly uncovered role of HK1 is glycolysis-independent by the introduction of the catalytically dead HK1. The expression of catalytically dead HK1 stimulated similar changes in levels of TCA intermediates, aspartate and cysteine, and in glutamate as were induced by the HK2 deletion. In contrast, HK1 deletion increased the levels of branched amino acids; this effect was completely eliminated by the expression of catalytically dead HK1. Furthermore, HK1 revertants but not HK2 revertants caused a strong increase of NADPH/NADP ratios independently on the presence of glucose or metformin. The HK1 deletion (but not HK2 deletion) suppressed the growth of xenotransplanted ovarian cancer cells and nearly abolished the tumor growth when the mice were fed the glucose-free diet.
CONCLUSIONS: We provided the evidence that HK1 is involved in the so far unknown glycolysis-independent HK1-metformin axis and influences metabolism even in glucose-free conditions.

Keywords:  Aerobic glycolysis; Hexokinase; Metabolism reprogramming; Metformin; Nicotinamide adenine dinucleotide phosphate; Oxidative phosphorylation

DOI:  https://doi.org/10.1186/s40170-021-00277-2
J Exp Clin Cancer Res. 2021 Dec 14. 40(1): 393

Blockade of glutamine-dependent cell survival augments antitumor efficacy of CPI-613 in head and neck cancer.

Liwei Lang, Fang Wang, Zhichun Ding, Xiangdong Zhao, Reid Loveless, Jin Xie, Chloe Shay, Peng Qiu, Yonggang Ke, Nabil F Saba, Yong Teng.

   BACKGROUND: Alterations in metabolism are one of the emerging hallmarks of cancer cells and targeting dysregulated cancer metabolism provides a new approach to developing more selective therapeutics. However, insufficient blockade critical metabolic dependencies of cancer allows the development of metabolic bypasses, thus limiting therapeutic benefits.
METHODS: A series of head and neck squamous cell carcinoma (HNSCC) cell lines and animal models were used to determine the efficacy of CPI-613 and CB-839 when given alone or in combination. Glutaminase 1 (GLS1) depletion was achieved by lentiviral shRNAs. Cell viability and apoptosis were determined in HNSCC cells cultured in 2D culture dish and SeedEZ™ 3D scaffold. Molecular alterations were examined by Western blotting and immunohistochemistry. Metabolic changes were assessed by glucose uptake, lactate production, glutathione levels, and oxygen consumption rate.
RESULTS: We show here that HNSCC cells display strong addiction to glutamine. CPI-613, a novel lipoate analog, redirects cellular activity towards tumor-promoting glutaminolysis, leading to low anticancer efficacy in HNSCC cells. Mechanistically, CPI-613 inhibits the tricarboxylic acid cycle by blocking the enzyme activities of pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, which upregulates GLS1 and eventually promotes the compensatory role of glutaminolysis in cancer cell survival. Most importantly, the addition of a GLS1 inhibitor CB-839 to CPI-613 treatment abrogates the metabolic dependency of HNSCC cells on glutamine, achieving a synergistic anticancer effect in glutamine-addicted HNSCC.
CONCLUSIONS: These findings uncover the critical role of GLS1-mediated glutaminolysis in CPI-613 treatment and suggest that the CB-839 and CPI-613 combination may potentiate synergistic anticancer activity for HNSCC therapeutic gain.

Keywords:  CB-839; CPI-613; Combined targeting; GLS1; Glutaminolysis; HNSCC

DOI:  https://doi.org/10.1186/s13046-021-02207-y
Front Immunol. 2021 ;12 718863

Mitochondrial-Linked De Novo Pyrimidine Biosynthesis Dictates Human T-Cell Proliferation but Not Expression of Effector Molecules.

Marlies J W Peeters, Pia Aehnlich, Adriano Pizzella, Kasper Mølgaard, Tina Seremet, Özcan Met, Lene Juel Rasmussen, Per Thor Straten, Claus Desler.

  T-cell activation upon antigen stimulation is essential for the continuation of the adaptive immune response. Impairment of mitochondrial oxidative phosphorylation is a well-known disruptor of T-cell activation. Dihydroorotate dehydrogenase (DHODH) is a component of the de novo synthesis of pyrimidines, the activity of which depends on functional oxidative phosphorylation. Under circumstances of an inhibited oxidative phosphorylation, DHODH becomes rate-limiting. Inhibition of DHODH is known to block clonal expansion and expression of effector molecules of activated T cells. However, this effect has been suggested to be caused by downstream impairment of oxidative phosphorylation rather than a lower rate of pyrimidine synthesis. In this study, we successfully inhibit the DHODH of T cells with no residual effect on oxidative phosphorylation and demonstrate a dose-dependent inhibition of proliferation of activated CD3+ T cells. This block is fully rescued when uridine is supplemented. Inhibition of DHODH does not alter expression of effector molecules but results in decreased intracellular levels of deoxypyrimidines without decreasing cell viability. Our results clearly demonstrate the DHODH and mitochondrial linked pyrimidine synthesis as an independent and important cytostatic regulator of activated T cells.

Keywords:  T-cell activation; T-cell metabolism; immunosenescence and exhaustion; mitochondrial respiration and oxidative respiration; pyrimidine de novo synthesis

DOI:  https://doi.org/10.3389/fimmu.2021.718863
Antioxid Redox Signal. 2021 Dec 16.

A dynamic substrate pool revealed by cryo-EM of a lipid-preserved respiratory supercomplex.

Tae Jin Jeon, Seong-Gyu Lee, Suk Hyun Yoo, Myeongbin Kim, Dabin Song, Joong Hyun Ryu, Hwangseo Park, Deok Soo Kim, Jaekyung Hyun, Ho Min Kim, Seong Eon Ryu.

AIMS: Mitochondrial respiratory supercomplexes mediate redox electron transfer, generating a proton gradient for ATP synthesis. To provide structural information on the function of supercomplexes in physiologically relevant conditions, we conducted cryo-electron microscopy studies with supercomplexes in a lipid-preserving state.
RESULTS: Here, we present cryo-electron microscopy structures of bovine respiratory supercomplex I1III2IV1 by using a lipid-preserving sample preparation. The preparation greatly enhances the inter-complex quinone transfer activity. The structures reveal large inter-complex motions that result in different shapes and sizes of the inter-complex space between complexes I and III, forming a dynamic substrate pool. Biochemical and structural analyses indicated that inter-complex phospholipids mediate the inter-complex motions. An analysis of the different classes of focus-refined complex I showed that structural switches due to quinone reduction led to the formation of a novel channel that could transfer reduced quinones to the inter-complex substrate pool. Innovation and Conclusion: Our results indicate potential mechanism for the facilitated electron transfer involving a dynamic substrate pool and inter-complex movement by which supercomplexes play an active role in the regulation of metabolic flux and reactive oxygen species.

DOI: https://doi.org/10.1089/ars.2021.0114
Mitochondrion. 2021 Dec 10. pii: S1567-7249(21)00169-0. [Epub ahead of print]

The molecular role of Sigmar1 in regulating mitochondrial function through mitochondrial localization in cardiomyocytes.

Chowdhury S Abdullah, Richa Aishwarya, Shafiul Alam, Naznin Sultana Remex, Mahboob Morshed, Sadia Nitu, Sumitra Miriyala, Manikandan Panchatcharam, Brandon Hartman, Judy King, Mohammad Alfrad Nobel Bhuiyan, James Traylor, Christopher G Kevil, A Wayne Orr, Shenuarin Bhuiyan.

  Sigmar1 is a widely expressed molecular chaperone protein in mammalian cell systems. Accumulating research demonstrated the cardioprotective roles of pharmacologic Sigmar1 activation by ligands in preclinical rodent models of cardiac injury. Extensive biochemical and immuno-electron microscopic research demonstrated Sigmar1's sub-cellular localization largely depends on cell and organ types. Despite comprehensive studies, Sigmar1's direct molecular role in cardiomyocytes remains elusive. In the present study, we determined Sigmar1's subcellular localization, transmembrane topology, and function using complementary microscopy, biochemical, and functional assays in cardiomyocytes. Quantum dots in transmission electron microscopy showed Sigmar1 labeled quantum dots on the mitochondrial membranes, lysosomes, and sarcoplasmic reticulum-mitochondrial interface. Subcellular fractionation of heart cell lysates confirmed Sigmar1's localization in purified mitochondria fraction and lysosome fraction. Immunocytochemistry confirmed Sigmar1 colocalization with mitochondrial proteins in isolated adult mouse cardiomyocytes. Sigmar1's mitochondrial localization was further confirmed by Sigmar1 colocalization with Mito-Tracker in isolated mouse heart mitochondria. A series of biochemical experiments, including alkaline extraction and proteinase K treatment of purified heart mitochondria, demonstrated Sigmar1 as an integral mitochondrial membrane protein. Sigmar1's structural requirement for mitochondrial localization was determined by expressing FLAG-tagged Sigmar1 fragments in cells. Full-length Sigmar1 and Sigmar1's C terminal-deletion fragments were able to localize to the mitochondrial membrane, whereas N- terminal deletion fragment was unable to incorporate into the mitochondria. Finally, functional assays using extracellular flux analyzer and high-resolution respirometry showed Sigmar1 siRNA knockdown significantly altered mitochondrial respiration in cardiomyocytes. Overall, we found that Sigmar1 localizes to mitochondrial membranes and is indispensable for maintaining mitochondrial respiratory homeostasis in cardiomyocytes.

Keywords:  Sigma-1 receptor; mitochondria; subcellular localization

DOI:  https://doi.org/10.1016/j.mito.2021.12.002
Nat Commun. 2021 Dec 17. 12(1): 7333

A targetable LIFR-NF-κB-LCN2 axis controls liver tumorigenesis and vulnerability to ferroptosis.

Fan Yao, Yalan Deng, Yang Zhao, Ying Mei, Yilei Zhang, Xiaoguang Liu, Consuelo Martinez, Xiaohua Su, Roberto R Rosato, Hongqi Teng, Qinglei Hang, Shannon Yap, Dahu Chen, Yumeng Wang, Mei-Ju May Chen, Mutian Zhang, Han Liang, Dong Xie, Xin Chen, Hao Zhu, Jenny C Chang, M James You, Yutong Sun, Boyi Gan, Li Ma.

The growing knowledge of ferroptosis has suggested the role and therapeutic potential of ferroptosis in cancer, but has not been translated into effective therapy. Liver cancer, primarily hepatocellular carcinoma (HCC), is highly lethal with limited treatment options. LIFR is frequently downregulated in HCC. Here, by studying hepatocyte-specific and inducible Lifr-knockout mice, we show that loss of Lifr promotes liver tumorigenesis and confers resistance to drug-induced ferroptosis. Mechanistically, loss of LIFR activates NF-κB signaling through SHP1, leading to upregulation of the iron-sequestering cytokine LCN2, which depletes iron and renders insensitivity to ferroptosis inducers. Notably, an LCN2-neutralizing antibody enhances the ferroptosis-inducing and anticancer effects of sorafenib on HCC patient-derived xenograft tumors with low LIFR expression and high LCN2 expression. Thus, anti-LCN2 therapy is a promising way to improve liver cancer treatment by targeting ferroptosis.

DOI: https://doi.org/10.1038/s41467-021-27452-9
J Neurosci. 2021 Dec 10. pii: JN-RM-1236-21. [Epub ahead of print]

Presynaptic Mitochondrial Volume and Packing Density Scale with Presynaptic Power Demand.

Karlis A Justs, Zhongmin Lu, Amit K Chouhan, Jolanta A Borycz, Zhiyuan Lu, Ian A Meinertzhagen, Gregory T Macleod.

Stable neural function requires an energy supply that can meet the intense episodic power demands of neuronal activity. Neurons have presumably optimized the volume of their bioenergetic machinery to ensure these power demands are met, but the relationship between presynaptic power demands and the volume available to the bioenergetic machinery has never been quantified. Here we estimated the power demands of six motor nerve terminals in female Drosophila larvae through direct measurements of neurotransmitter release and Ca2+ entry, and via theoretical estimates of Na+ entry and power demands at rest. Electron microscopy revealed that terminals with the highest power demands contained the greatest volume of mitochondria, indicating that mitochondria are allocated according to presynaptic power demands. In addition, terminals with the greatest power demand-to-volume ratio (∼66 nmol·min-1·μL-1) harbor the largest mitochondria packed at the greatest density. If we assume sequential and complete oxidation of glucose by glycolysis and oxidative phosphorylation, then these mitochondria are required to produce ATP at a rate of 52 nmol·min-1·μL-1 at rest, rising to 963 during activity. Glycolysis would contribute ATP at 0.24 nmol·min-1·μL-1 of cytosol at rest, rising to 4.36 during activity. These data provide a quantitative framework for presynaptic bioenergetics in situ, and reveal that, beyond an immediate capacity to accelerate ATP output from glycolysis and oxidative phosphorylation, over longer time periods presynaptic terminals optimize mitochondrial volume and density to meet power demand.Significance StatementThe remarkable energy demands of the brain are supported by the complete oxidation of its fuel but debate continues regarding a division of labor between glycolysis and oxidative phosphorylation across different cell types. Here we exploit the neuromuscular synapse, a model for studying neurophysiology, to elucidate fundamental aspects of neuronal energy metabolism that ultimately constrain rates of neural processing. We quantified energy production rates required to sustain activity at individual nerve terminals and compared these with the volume capable of oxidative phosphorylation (mitochondria) and glycolysis (cytosol). We find strong support for oxidative phosphorylation playing a primary role in presynaptic terminals and provide the first in vivo estimates of energy production rates per unit volume of presynaptic mitochondria and cytosol.

DOI: https://doi.org/10.1523/JNEUROSCI.1236-21.2021
Oxid Med Cell Longev. 2021 ;2021 7674565

TXNRD1: A Key Regulator Involved in the Ferroptosis of CML Cells Induced by Cysteine Depletion In Vitro.

Shuhan Liu, Wei Wu, Qiaoqian Chen, Zhiyuan Zheng, Xiandong Jiang, Yan Xue, Donghong Lin.

Cysteine metabolism plays a critical role in cancer cell survival. Cysteine depletion was reported to inhibit tumor growth and induce pancreatic cancer cell ferroptosis. Nevertheless, the effect of cysteine depletion in chronic myeloid leukemia (CML) remains to be explored. In this work, we showed that cysteine depletion can induce K562/G01 but not K562 cell death in the form of ferroptosis. However, the glutathione (GSH)/glutathione peroxidase 4 (GPX4) pathways of the two CML cell lines were both blocked after cysteine depletion. This unexpected outcome guided us to perform RNA-Seq to screen the key genes that affect the sensitivity of CML cells to cysteine depletion. Excitingly, thioredoxin reductase 1 (TXNRD1), which related to cell redox metabolism, was significantly upregulated in K562/G01 cells after cysteine depletion. We further inferred that the upregulation is negatively feedback by the enzyme activity decrease of TXNRD1. Then, we triggered the ferroptosis by applying TXNRD1 shRNA and TXNRD1 inhibitor auranofin in K562 cells after cysteine depletion. In summary, we have reason to believe that TXNRD1 is a key regulator involved in the ferroptosis of CML cells induced by cysteine depletion in vitro. These findings highlight that cysteine depletion serves as a potential therapeutic strategy for overcoming chemotherapy resistance CML.

DOI: https://doi.org/10.1155/2021/7674565
FASEB J. 2022 Jan;36(1): e22062

IGFBP-3 functions as a molecular switch that mediates mitochondrial and metabolic homeostasis.

Whitney L Stuard, Rossella Titone, Danielle M Robertson.

  Mitochondrial dysfunction or loss of homeostasis is a central hallmark of many human diseases. Mitochondrial homeostasis is mediated by multiple quality control mechanisms including mitophagy, a form of selective autophagy that recycles terminally ill or dysfunctional mitochondria in order to preserve mitochondrial integrity. Our prior studies have shown that members of the insulin-like growth factor (IGF) family localize to the mitochondria and may play important roles in mediating mitochondrial health in the corneal epithelium, an integral tissue that is required for the maintenance of optical transparency and vision. Importantly, the IGF-binding protein-3, IGFBP-3, is secreted by corneal epithelial cells in response to stress and functions to mediate intracellular receptor trafficking in this cell type. In this study, we demonstrate a novel role for IGFBP-3 in mitochondrial homeostasis through regulation of the short isoform (s)BNIP3L/NIX mitophagy receptor in corneal epithelial cells and extend this finding to non-ocular epithelial cells. We further show that IGFBP-3-mediated control of mitochondrial homeostasis is associated with alterations in lamellar cristae morphology and mitochondrial dynamics. Interestingly, both loss and gain of function of IGFBP-3 drive an increase in mitochondrial respiration. This increase in respiration is associated with nuclear accumulation of IGFBP-3. Taken together, these findings support a novel role for IGFBP-3 as a key mediator of mitochondrial health in mucosal epithelia through the regulation of mitophagy and mitochondrial morphology.

Keywords:  autophagy; insulin-like growth factor type 1 receptor; mTOR; metabolism; mitochondria

DOI:  https://doi.org/10.1096/fj.202100710RR
BMC Cancer. 2021 Dec 14. 21(1): 1329

TRAP1 suppresses oral squamous cell carcinoma progression by reducing oxidative phosphorylation metabolism of Cancer-associated fibroblasts.

Li Xiao, Qiannan Hu, Yanshuang Peng, Kaiyue Zheng, Ting Zhang, Lianjie Yang, Zhi Wang, Wanrong Tang, Jie Yu, Qian Xiao, Dandan Zhang, Weifang Zhang, Chanjuan He, Dengxun Wu, Yanyan Zheng, Ying Liu.

   BACKGROUND: Glucose metabolism in cancer associated fibroblasts (CAFs) within the tumor microenvironment is a material and energy source for tumorigenesis and tumor development. However, the characteristics and important regulatory mechanisms of glucose metabolism in fibroblasts associated with oral squamous cell carcinoma (OSCC) are still unknown.
METHODS: We successfully isolated, cultured, purified and identified CAFs and normal fibroblasts (NFs). Cell culture, immunohistochemistry (IHC) and CCK8, flow cytometry, Seahorse XF Analyzer, MitoTracker assay, western blotting (WB), transmission electron microscope, Quantitative real-time PCR (qPCR), immunofluorescence (IF), and Label-free quantitative proteomics assay, animal xenograft model studies and statistical analysis were applied in this study.
RESULTS: We demonstrated that the proliferation activity of CAFs was significantly enhanced as compared to NFs, while the apoptosis rate was significantly decreased. CAFs in OSCC preferentially use oxidative phosphorylation (OXPHOS) rather than glycolysis. Moreover, CAFs showed stronger maximal respiration, a larger substantial mitochondrial spare respiratory capacity (SRC) and higher adenosine triphosphate (ATP) production capacity than NFs. The results of mitotracker green fluorescence staining showed that compared with NFs, CAFs exhibited stronger green fluorescence. The results of WB showed the expression level of Peroxisome proliferator-activated receptor γ coactivator-1α (PGC-1α) obviously increased in CAFs compared to NFs. These results confirmed that CAFs have greater mitochondrial activity and function than NFs. Furthermore, Label-free quantitative proteomics assays showed that both ATP synthase subunit O (ATP5O) and tumor necrosis factor receptor-associated protein 1 (TRAP1) are important differentially expressed proteins in the mitochondria of CAFs/NFs. Overexpression of TRAP1 in CAFs increased basal oxygen consumption rate (OCR), maximal respiration, ATP production and SRC. In vivo, overexpression TRAP1 expression in CAFs suppress tumor growth.
CONCLUSION: Taken together, the results indicated that TRAP1 is an important regulatory molecule of CAFs glucose metabolism and promotes OSCC progression by regulating the OXPHOS of CAFs.

Keywords:  Cancer associated fibroblasts; Oral squamous cell carcinoma; Oxidative phosphorylation; Proteomics; TRAP1

DOI:  https://doi.org/10.1186/s12885-021-09049-z
Hum Mol Genet. 2021 Dec 13. pii: ddab358. [Epub ahead of print]

Genetic landscape of human mitochondrial genome using whole genome sequencing.

Yijing Wang, Guihu Zhao, Zhenghuan Fang, Hongxu Pan, Yuwen Zhao, Yige Wang, Xun Zhou, Xiaomeng Wang, Tengfei Luo, Yi Zhang, Zheng Wang, Qian Chen, Lijie Dong, Yuanfeng Huang, Qiao Zhou, Lu Xia, Bin Li, Jifeng Guo, Kun Xia, Beisha Tang, Jinchen Li.

Increasing evidences suggest that mitochondrial dysfunction is implicated in diseases and aging, and whole-genome sequencing (WGS) is the most unbiased method in analyzing the mitochondrial genome (mtDNA). However, the genetic landscape of mtDNA in the Chinese population has not been fully examined. Here, we described the genetic landscape of mtDNA using WGS data from Chinese individuals (n = 3241). We identified 3892 mtDNA variants, of which 3349 (86%) were rare variants. Interestingly, we observed a trend toward extreme heterogeneity of mtDNA variants. Our study observed a distinct purifying selection on mtDNA, which inhibits the accumulation of harmful heteroplasmies at the individual level: (1) mitochondrial dN/dS ratios were much less than 1; (2) the dN/dS ratio of heteroplasmies was higher than homoplasmies; (3) heteroplasmies had more indels and predicted deleterious variants than homoplasmies. Furthermore, we found that haplogroup M (20.27%) and D (20.15%) had the highest frequencies in the Chinese population, followed by B (18.51%) and F (16.45%). The number of variants per individual differed across haplogroup groups, with a higher number of homoplasmies for the M lineage. Meanwhile, mtDNA copy number was negatively correlated with age but positively correlated with the female sex. Finally, we developed an mtDNA variation database of Chinese populations called MTCards (http://genemed.tech/mtcards/) to facilitate the query of mtDNA variants in this study. In summary, these findings contribute to different aspects of understanding mtDNA, providing a better understanding of the genetic basis of mitochondrial-related diseases.

DOI: https://doi.org/10.1093/hmg/ddab358
STAR Protoc. 2021 Dec 17. 2(4): 100977

Thiol profiling in cancer cell lines by HPLC-mass spectrometry.

Xiaoguang Liu, Pranavi Koppula, Kellen Olszewski, Boyi Gan.

  We describe a protocol for identifying cellular thiol metabolites such as cysteine and cystine in adherent cells using high performance liquid chromatography (HPLC) tandem mass spectrometry-based metabolomics. We applied a modified extraction and sample derivatization protocol to accurately quantify the intracellular levels of labile thiol species and to inhibit oxidation prior to analysis. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020) and Koppula et al. (2021).

Keywords:  Cancer; Mass Spectrometry; Metabolism

DOI:  https://doi.org/10.1016/j.xpro.2021.100977
Cell Biol Int. 2021 Dec 17.

Why do cells need oxygen? Insights from mitochondrial composition and function.

Kelath Murali Manoj, Daniel Andrew Gideon, Laurent Jaeken.

  Mitochondrial membrane-embedded redox proteins are classically perceived as deterministic 'electron transport chain' (ETC) arrays cum proton pumps; and oxygen is seen as an 'immobile terminal electron acceptor'. This is untenable because: (1) there are little free protons to be pumped out of the matrix; (2) proton pumping would be highly endergonic; (3) ETC-chemiosmosis-rotary ATP synthesis proposal is 'irreducibly complex'/'non-evolvable' and does not fit with mitochondrial architecture or structural/distribution data of the concerned proteins/components; (4) a plethora of experimental observations do not conform to the postulates/requisites; e.g. there is little evidence for viable proton-pumps/pH-gradient in mitochondria, trans-membrane potential (TMP) is non-fluctuating/non-trappable, oxygen is seen to give copious 'diffusible reactive (oxygen) species' (DRS/DROS) in milieu, etc. Quite contrarily, the newly proposed murburn model's tenets agree with known principles of energetics/kinetics, and build on established structural data and reported observations. In this purview, oxygen is needed to make DRS, the principal component of mitochondrial function. Complex V and porins respectively serve as proton-inlet and turgor-based water-exodus portals, thereby achieving organellar homeostasis. Complexes I to IV possess ADP-binding sites and their redox-centres react/interact with O2 /DRS. At/around these complexes, DRS cross-react or activate/oxidize ADP/Pi via fast thermogenic one-electron reaction(s), condensing to form two-electron stabilized products (H2 O2 /H2 O/ATP). The varied architecture and distribution of components in mitochondria validate DRS as the- (i) the coupling agent of oxidative reactions and phosphorylations, and (ii) the primary reason for manifestation of TMP in steady-state. Explorations along the new precepts stand to provide greater insights on mitochondrial function and pathophysiology. This article is protected by copyright. All rights reserved.

Keywords:  energetics; homeostasis; mitochondrial physiology; murburn concept; thermogenesis

DOI:  https://doi.org/10.1002/cbin.11746
Cell Death Discov. 2021 Dec 14. 7(1): 393

Identification of mitochondrial RNA polymerase as a potential therapeutic target of osteosarcoma.

Qi-Cai Han, Xiang-Yang Zhang, Peng-Hui Yan, Song-Feng Chen, Fei-Fei Liu, Yun-Rong Zhu, Qing Tian.

POLRMT (RNA polymerase mitochondrial) is essential for transcription of mitochondrial genome encoding components of oxidative phosphorylation process. The current study tested POLRMT expression and its potential function in osteosarcoma (OS). The Cancer Genome Atlas (TCGA) cohorts and Gene Expression Profiling Interactive Analysis (GEPIA) database both show that POLRMT transcripts are elevated in OS tissues. In addition, POLRMT mRNA and protein levels were upregulated in local OS tissues as well as in established and primary human OS cells. In different OS cells, shRNA-induced stable knockdown of POLRMT decreased cell viability, proliferation, migration, and invasion, whiling inducing apoptosis activation. CRISPR/Cas9-induced POLRMT knockout induced potent anti-OS cell activity as well. Conversely, in primary OS cells ectopic POLRMT overexpression accelerated cell proliferation and migration. In vivo, intratumoral injection of adeno-associated virus-packed POLRMT shRNA potently inhibited U2OS xenograft growth in nude mice. Importantly, levels of mitochondrial DNA, mitochondrial transcripts and expression of respiratory chain complex subunits were significantly decreased in U2OS xenografts with POLRMT shRNA virus injection. Together, POLRMT is overexpressed in human OS, promoting cell growth in vitro and in vivo. POLRMT could be a novel therapeutic target for OS.

DOI: https://doi.org/10.1038/s41420-021-00780-x
Free Radic Res. 2021 Dec 13. 1-34

Valproic acid promotes SOD2 acetylation: A potential mechanism of valproic acid-induced oxidative stress in developing systems.

Jason M Hansen, S Marc Lucas, Catania D Ramos, Eli J Green, Dakota J Nuttall, David S Clark, Erik D Marchant, Chad R Hancock, Ted B Piorczynski.

  Valproic acid (VPA) is an antiepileptic, bipolar and migraine medication, which is associated with embryonic dysmorphology, more specifically neural tube defects (NTDs), if taken while pregnant. One mechanism by which VPA may cause NTDs is through oxidative stress that cause disruption of cell signaling. However, mechanisms of VPA-induced oxidative stress are not fully understood. Since VPA is a deacetylase inhibitor, we propose that VPA promotes mitochondrial superoxide dismutase-2 (SOD2) acetylation, decreasing SOD2 activity and increasing oxidant levels. Using the pluripotent embryonal carcinoma cell line, P19, VPA effects were evaluated in undifferentiated and neurodifferentiated cells. VPA treatments increased oxidant levels, oxidized the glutathione (GSH)/glutathione disulfide (GSSG) redox couple, and decreased total SOD and SOD2 activity in undifferentiated P19 cells but not in differentiated P19 cells. VPA caused a specific increase in mitochondrial oxidants in undifferentiated P19 cells, VPA did not alter respirometry measurements. Immunoblot analyses demonstrated that VPA increased acetylation of SOD2 at lysine68 (AcK68 SOD2) in undifferentiated P19 cells but not in differentiated P19 cells. Pretreatments with the Nrf2 inducer, dithiol-3-thione (D3T), in undifferentiated P19 cells prevented increased oxidant levels, GSH/GSSG redox oxidation and restored total SOD and SOD2 activity, correlating with a decrease in AcK68 SOD2 levels. In embryos, VPA decreased total SOD and SOD2 activity and increased levels of AcK68 SOD2, and D3T pretreatments prevented VPA effects, increasing total SOD and SOD2 activity and lowering levels of AcK68 SOD2. These data demonstrate a potential, contributing oxidizing mechanism by which VPA incites teratogenesis in developing systems. Moreover, these data also suggest that Nrf2 interventions may serve as a means to protect developmental signaling and inhibit VPA-induced malformations.

Keywords:  Oxidative stress; acetylation; mitochondria; neural tube defect; superoxide dismutase; valproic acid

DOI:  https://doi.org/10.1080/10715762.2021.2017913
J Cell Sci. 2021 Dec 15. pii: jcs258944. [Epub ahead of print]134(24):

The role of mitochondrial dynamics in mtDNA maintenance.

Rasha Sabouny, Timothy E Shutt.

  The dynamic nature of mitochondria, which can fuse, divide and move throughout the cell, allows these critical organelles to adapt their function in response to cellular demands, and is also important for regulating mitochondrial DNA (mtDNA). While it is established that impairments in mitochondrial fusion and fission impact the mitochondrial genome and can lead to mtDNA depletion, abnormal nucleoid organization or accumulation of deletions, it is not entirely clear how or why remodeling mitochondrial network morphology affects mtDNA. Here, we focus on recent advances in our understanding of how mitochondrial dynamics contribute to the regulation of mtDNA and discuss links to human disease.

Keywords:  Fission; Fusion; Mitochondria; Mitochondrial dynamics; Mitophagy; mtDNA

DOI:  https://doi.org/10.1242/jcs.258944
Nat Metab. 2021 Dec 13.

NADH inhibition of SIRT1 links energy state to transcription during time-restricted feeding.

Daniel C Levine, Hsin-Yu Kuo, Hee-Kyung Hong, Jonathan Cedernaes, Chelsea Hepler, Alexandra G Wright, Meredith A Sommars, Yumiko Kobayashi, Biliana Marcheva, Peng Gao, Olga R Ilkayeva, Chiaki Omura, Kathryn M Ramsey, Christopher B Newgard, Grant D Barish, Clara Bien Peek, Navdeep S Chandel, Milan Mrksich, Joseph Bass.

In mammals, circadian rhythms are entrained to the light cycle and drive daily oscillations in levels of NAD+, a cosubstrate of the class III histone deacetylase sirtuin 1 (SIRT1) that associates with clock transcription factors. Although NAD+ also participates in redox reactions, the extent to which NAD(H) couples nutrient state with circadian transcriptional cycles remains unknown. Here we show that nocturnal animals subjected to time-restricted feeding of a calorie-restricted diet (TRF-CR) only during night-time display reduced body temperature and elevated hepatic NADH during daytime. Genetic uncoupling of nutrient state from NADH redox state through transduction of the water-forming NADH oxidase from Lactobacillus brevis (LbNOX) increases daytime body temperature and blood and liver acyl-carnitines. LbNOX expression in TRF-CR mice induces oxidative gene networks controlled by brain and muscle Arnt-like protein 1 (BMAL1) and peroxisome proliferator-activated receptor alpha (PPARα) and suppresses amino acid catabolic pathways. Enzymatic analyses reveal that NADH inhibits SIRT1 in vitro, corresponding with reduced deacetylation of SIRT1 substrates during TRF-CR in vivo. Remarkably, Sirt1 liver nullizygous animals subjected to TRF-CR display persistent hypothermia even when NADH is oxidized by LbNOX. Our findings reveal that the hepatic NADH cycle links nutrient state to whole-body energetics through the rhythmic regulation of SIRT1.

DOI: https://doi.org/10.1038/s42255-021-00498-1
Nature. 2021 Dec 15.

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues.

Tongtong Zhao, Zachary D Chiang, Julia W Morriss, Lindsay M LaFave, Evan M Murray, Isabella Del Priore, Kevin Meli, Caleb A Lareau, Naeem M Nadaf, Jilong Li, Andrew S Earl, Evan Z Macosko, Tyler Jacks, Jason D Buenrostro, Fei Chen.

The state and behaviour of a cell can be influenced by both genetic and environmental factors. In particular, tumour progression is determined by underlying genetic aberrations1-4 as well as the makeup of the tumour microenvironment5,6. Quantifying the contributions of these factors requires new technologies that can accurately measure the spatial location of genomic sequence together with phenotypic readouts. Here we developed slide-DNA-seq, a method for capturing spatially resolved DNA sequences from intact tissue sections. We demonstrate that this method accurately preserves local tumour architecture and enables the de novo discovery of distinct tumour clones and their copy number alterations. We then apply slide-DNA-seq to a mouse model of metastasis and a primary human cancer, revealing that clonal populations are confined to distinct spatial regions. Moreover, through integration with spatial transcriptomics, we uncover distinct sets of genes that are associated with clone-specific genetic aberrations, the local tumour microenvironment, or both. Together, this multi-modal spatial genomics approach provides a versatile platform for quantifying how cell-intrinsic and cell-extrinsic factors contribute to gene expression, protein abundance and other cellular phenotypes.

DOI: https://doi.org/10.1038/s41586-021-04217-4