bims-camemi 2021-05-30 papers

bims-camemi

Biomed News

on Mitochondrial metabolism in cancer

Issue of 2021‒05‒30
48 papers selected by
Christian Frezza,

Mitohormesis reprogrammes macrophage metabolism to enforce tolerance.
Mitochondrial DNA variation and cancer.
Ethyl Isopropyl Amiloride Decreases Oxidative Phosphorylation and Increases Mitochondrial Fusion in Clonal Untransformed and Cancer Cells.
Brain glycogen serves as a critical glucosamine cache required for protein glycosylation.
Medium-chain acyl CoA dehydrogenase protects mitochondria from lipid peroxidation in glioblastoma.
Single-cell metabolic imaging reveals a SLC2A3-dependent glycolytic burst in motile endothelial cells.
Autophagy in metabolism and quality control: opposing, complementary or interlinked functions?
NF1 mutation drives neuronal activity-dependent initiation of optic glioma.
Mass-spectrometry-based proteomics reveals mitochondrial supercomplexome plasticity.
SIRT5 IS A DRUGGABLE METABOLIC VULNERABILITY IN ACUTE MYELOID LEUKEMIA.
Restoration of energy homeostasis by SIRT6 extends healthy lifespan.
FLIM Imaging for Metabolic Studies in Live Cells.
Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells.
Targeting one-carbon metabolism requires mTOR inhibition: a new therapeutic approach in osteosarcoma.
Mitochondrial remodelling-a vicious cycle in diabetic complications.
Cell-free DNA captures tumor heterogeneity and driver alterations in rapid autopsies with pre-treated metastatic cancer.
Cytosolic dsDNA of mitochondrial origin induces cytotoxicity and neurodegeneration in cellular and zebrafish models of Parkinson's disease.
Unravelling the mechanisms controlling heme supply and demand.
The Trypanosome UDP-Glucose Pyrophosphorylase Is Imported by Piggybacking into Glycosomes, Where Unconventional Sugar Nucleotide Synthesis Takes Place.
Atg32 dependent mitophagy sustains spermidine and nitric oxide required for heat stress tolerance in S. cerevisiae.
Mitochondrial targeted meganuclease as a platform to eliminate mutant mtDNA in vivo.
NADPH supply and the contribution of NAD(P)+ transhydrogenase (NNT) to H2O2 balance in skeletal muscle mitochondria.
Cancer Cell Metabolism Connects Epigenetic Modifications to Transcriptional Regulation.
Elevated type I interferon responses potentiate metabolic dysfunction, inflammation, and accelerated aging in mtDNA mutator mice.
Mammary epithelial cells have lineage-rooted metabolic identities.
Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline.
Monitoring PINK1-Parkin Signaling Using Dopaminergic Neurons from iPS Cells.
Astrocyte-Neuron Metabolic Crosstalk in Neurodegeneration: A Mitochondrial Perspective.
Mitochondrial fusion and fission: The fine-tune balance for cellular homeostasis.
Mitochondrial ROS signals prevent excessive immune response.
Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis.
Mitochondrial efflux of citrate and isocitrate is fully dispensable for glucose-stimulated insulin secretion and pancreatic islet β-cell function.
Endothelial metabolism going single.
Hunger Brings Down the Tumor Fort.
Energy metabolism in brown adipose tissue.
Developing Analysis Protocols for Monitoring Intracellular Oxygenation Using Fluorescence Lifetime Imaging of Myoglobin-mCherry.
Metabolic Plasticity of Neutrophils: Relevance to Pathogen Responses and Cancer.
Methods for Studying Myofibroblast Apoptotic Pathways.
Biparental inheritance of mitochondrial DNA revisited.
Machine learning algorithms reveal the secrets of mitochondrial dynamics.
Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli.
Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer.
Epigenetic induction of mitochondrial fission is required for maintenance of liver cancer initiating cells.
Lysosome positioning and mTOR activity in Lowe syndrome.
Breast cancer has a new metabolic Achilles' heel.
The cellular-resolution revolution.
Mitochondrial Succinate Dehydrogenase in COPD: Is Complex II too Complex?
Co-occurrence and mutual exclusivity: what cross-cancer mutation patterns can tell us.

Nat Metab. 2021 May;3(5): 618-635

Mitohormesis reprogrammes macrophage metabolism to enforce tolerance.

Greg A Timblin, Kevin M Tharp, Breanna Ford, Janet M Winchester, Jerome Wang, Stella Zhu, Rida I Khan, Shannon K Louie, Anthony T Iavarone, Johanna Ten Hoeve, Daniel K Nomura, Andreas Stahl, Kaoru Saijo.

Macrophages generate mitochondrial reactive oxygen species and mitochondrial reactive electrophilic species as antimicrobials during Toll-like receptor (TLR)-dependent inflammatory responses. Whether mitochondrial stress caused by these molecules impacts macrophage function is unknown. Here, we demonstrate that both pharmacologically driven and lipopolysaccharide (LPS)-driven mitochondrial stress in macrophages triggers a stress response called mitohormesis. LPS-driven mitohormetic stress adaptations occur as macrophages transition from an LPS-responsive to LPS-tolerant state wherein stimulus-induced pro-inflammatory gene transcription is impaired, suggesting tolerance is a product of mitohormesis. Indeed, like LPS, hydroxyoestrogen-triggered mitohormesis suppresses mitochondrial oxidative metabolism and acetyl-CoA production needed for histone acetylation and pro-inflammatory gene transcription, and is sufficient to enforce an LPS-tolerant state. Thus, mitochondrial reactive oxygen species and mitochondrial reactive electrophilic species are TLR-dependent signalling molecules that trigger mitohormesis as a negative feedback mechanism to restrain inflammation via tolerance. Moreover, bypassing TLR signalling and pharmacologically triggering mitohormesis represents a new anti-inflammatory strategy that co-opts this stress response to impair epigenetic support of pro-inflammatory gene transcription by mitochondria.

DOI: https://doi.org/10.1038/s42255-021-00392-w
Nat Rev Cancer. 2021 May 27.

Mitochondrial DNA variation and cancer.

Piotr K Kopinski, Larry N Singh, Shiping Zhang, Marie T Lott, Douglas C Wallace.

Variation in the mitochondrial DNA (mtDNA) sequence is common in certain tumours. Two classes of cancer mtDNA variants can be identified: de novo mutations that act as 'inducers' of carcinogenesis and functional variants that act as 'adaptors', permitting cancer cells to thrive in different environments. These mtDNA variants have three origins: inherited variants, which run in families, somatic mutations arising within each cell or individual, and variants that are also associated with ancient mtDNA lineages (haplogroups) and are thought to permit adaptation to changing tissue or geographic environments. In addition to mtDNA sequence variation, mtDNA copy number and perhaps transfer of mtDNA sequences into the nucleus can contribute to certain cancers. Strong functional relevance of mtDNA variation has been demonstrated in oncocytoma and prostate cancer, while mtDNA variation has been reported in multiple other cancer types. Alterations in nuclear DNA-encoded mitochondrial genes have confirmed the importance of mitochondrial metabolism in cancer, affecting mitochondrial reactive oxygen species production, redox state and mitochondrial intermediates that act as substrates for chromatin-modifying enzymes. Hence, subtle changes in the mitochondrial genotype can have profound effects on the nucleus, as well as carcinogenesis and cancer progression.

DOI: https://doi.org/10.1038/s41568-021-00358-w
Am J Physiol Cell Physiol. 2021 05 26.

Ethyl Isopropyl Amiloride Decreases Oxidative Phosphorylation and Increases Mitochondrial Fusion in Clonal Untransformed and Cancer Cells.

Sagar S Manoli, Kyle Kisor, Bradley A Webb, Diane L Barber.

  Many cancer cells, regardless of their tissue origin or genetic landscape, have increased expression or activity of the plasma membrane Na-H exchanger NHE1 and a higher intracellular pH (pHi) compared with untransformed cells. A current perspective that remains to be validated is that increased NHE1 activity and pHi enable a Warburg-like metabolic reprogramming of increased glycolysis and decreased mitochondrial oxidative phosphorylation. We tested this perspective and find it is not accurate for clonal pancreatic and breast cancer cells. Using the pharmacological reagent ethyl isopropyl amiloride (EIPA) to inhibit NHE1 activity and decrease pHi, we observe no change in glycolysis, as indicated by secreted lactate and intracellular pyruvate, despite confirming increased activity of the glycolytic enzyme phosphofructokinase-1 at higher pH. Also, in contrast to predictions, we find a significant decrease in oxidative phosphorylation with EIPA, as indicated by oxygen consumption rate (OCR). Decreased OCR with EIPA is not associated with changes in pathways that fuel oxidative phosphorylation or with mitochondrial membrane potential but occurs with a change in mitochondrial dynamics that includes a significant increase in elongated mitochondrial networks, suggesting increased fusion. These findings conflict with current paradigms on increased pHi inhibiting oxidative phosphorylation and increased oxidative phosphorylation being associated with mitochondrial fusion. Moreover, these findings raise questions on the suggested use of EIPA-like compounds to limit metabolic reprogramming in cancer cells.

Keywords:  NHE1; cancer metabolism; glycolysis; intracellular pH; mitochondria

DOI:  https://doi.org/10.1152/ajpcell.00001.2021
Cell Metab. 2021 May 21. pii: S1550-4131(21)00220-5. [Epub ahead of print]

Brain glycogen serves as a critical glucosamine cache required for protein glycosylation.

Ramon C Sun, Lyndsay E A Young, Ronald C Bruntz, Kia H Markussen, Zhengqiu Zhou, Lindsey R Conroy, Tara R Hawkinson, Harrison A Clarke, Alexandra E Stanback, Jessica K A Macedo, Shane Emanuelle, M Kathryn Brewer, Alberto L Rondon, Annette Mestas, William C Sanders, Krishna K Mahalingan, Buyun Tang, Vimbai M Chikwana, Dyann M Segvich, Christopher J Contreras, Elizabeth J Allenger, Christine F Brainson, Lance A Johnson, Richard E Taylor, Dustin D Armstrong, Robert Shaffer, Charles J Waechter, Craig W Vander Kooi, Anna A DePaoli-Roach, Peter J Roach, Thomas D Hurley, Richard R Drake, Matthew S Gentry.

  Glycosylation defects are a hallmark of many nervous system diseases. However, the molecular and metabolic basis for this pathology is not fully understood. In this study, we found that N-linked protein glycosylation in the brain is metabolically channeled to glucosamine metabolism through glycogenolysis. We discovered that glucosamine is an abundant constituent of brain glycogen, which functions as a glucosamine reservoir for multiple glycoconjugates. We demonstrated the enzymatic incorporation of glucosamine into glycogen by glycogen synthase, and the release by glycogen phosphorylase by biochemical and structural methodologies, in primary astrocytes, and in vivo by isotopic tracing and mass spectrometry. Using two mouse models of glycogen storage diseases, we showed that disruption of brain glycogen metabolism causes global decreases in free pools of UDP-N-acetylglucosamine and N-linked protein glycosylation. These findings revealed fundamental biological roles of brain glycogen in protein glycosylation with direct relevance to multiple human diseases of the central nervous system.

Keywords:  Lafora disease; MALDI imaging; N-linked glycosylation; antibody-enzyme therapy; brain metabolism; childhood dementia; glucosamine; glycogen metabolism; glycogen storage disease; polyglucosan body

DOI:  https://doi.org/10.1016/j.cmet.2021.05.003
Cancer Discov. 2021 May 26. pii: candisc.1437.2020. [Epub ahead of print]

Medium-chain acyl CoA dehydrogenase protects mitochondria from lipid peroxidation in glioblastoma.

Francesca Puca, Fei Yu, Caterina Bartolacci, Piergiorgio Pettazzoni, Alessandro Carugo, Emmet Huang-Hobbs, Jintan Liu, Ciro Zanca, Federica Carbone, Edoardo Del Poggetto, Joy Gumin, Pushan Dasgupta, Sahil Seth, Sanjana Srinivasan, Frederick F Lang, Erik P Sulman, Philip L Lorenzi, Lin Tan, Mengrou Shan, Zachary P Tolstyka, Maureen Kachman, Li Zhang, Sisi Gao, Angela K Deem, Giannicola Genovese, Pier Paolo Scaglioni, Costas A Lyssiotis, Andrea Viale, Giulio F Draetta.

Glioblastoma (GBM) is highly resistant to chemo- and immune-based therapies and targeted inhibitors. To identify novel drug targets, we screened orthotopically implanted, patient-derived glioblastoma sphere-forming cells (GSCs) using an RNAi library to probe essential tumor cell metabolic programs. This identified high dependence on mitochondrial fatty acid metabolism. We focused on medium-chain acyl-CoA dehydrogenase (MCAD), which oxidizes medium-chain fatty acids (MCFAs), due to its consistently high score and high expression among models and upregulation in GBM compared to normal brain. Beyond the expected energetics impairment, MCAD depletion in primary GBM models induced an irreversible cascade of detrimental metabolic effects characterized by accumulation of unmetabolized MCFAs, which induced lipid peroxidation and oxidative stress, irreversible mitochondrial damage, and apoptosis. Our data uncover a novel protective role for MCAD to clear lipid molecules that may cause lethal cell damage, suggesting that therapeutic targeting of MCFA catabolism could exploit a key metabolic feature of GBM.

DOI: https://doi.org/10.1158/2159-8290.CD-20-1437
Nat Metab. 2021 May;3(5): 714-727

Single-cell metabolic imaging reveals a SLC2A3-dependent glycolytic burst in motile endothelial cells.

David Wu, Devin L Harrison, Teodora Szasz, Chih-Fan Yeh, Tzu-Pin Shentu, Angelo Meliton, Ru-Ting Huang, Zhengjie Zhou, Gökhan M Mutlu, Jun Huang, Yun Fang.

Single-cell motility is spatially heterogeneous and driven by metabolic energy. Directly linking cell motility to cell metabolism is technically challenging but biologically important. Here, we use single-cell metabolic imaging to measure glycolysis in individual endothelial cells with genetically encoded biosensors capable of deciphering metabolic heterogeneity at subcellular resolution. We show that cellular glycolysis fuels endothelial activation, migration and contraction and that sites of high lactate production colocalize with active cytoskeletal remodelling within an endothelial cell. Mechanistically, RhoA induces endothelial glycolysis for the phosphorylation of cofilin and myosin light chain in order to reorganize the cytoskeleton and thus control cell motility; RhoA activation triggers a glycolytic burst through the translocation of the glucose transporter SLC2A3/GLUT3 to fuel the cellular contractile machinery, as demonstrated across multiple endothelial cell types. Our data indicate that Rho-GTPase signalling coordinates energy metabolism with cytoskeleton remodelling to regulate endothelial cell motility.

DOI: https://doi.org/10.1038/s42255-021-00390-y
Autophagy. 2021 May 26.

Autophagy in metabolism and quality control: opposing, complementary or interlinked functions?

Vojo Deretic, Guido Kroemer.

  The sensu stricto autophagy, macroautophagy, is considered to be both a metabolic process as well as a bona fide quality control process. The question as to how these two aspects of autophagy are coordinated and whether and why they overlap has implications for fundamental aspects, pathophysiological effects, and pharmacological manipulation of autophagy. At the top of the regulatory cascade controlling autophagy are master regulators of cellular metabolism, such as MTOR and AMPK, which render the system responsive to amino acid and glucose starvation. At the other end exists a variety of specific autophagy receptors, engaged in the selective removal of a diverse array of intracellular targets, from protein aggregates/condensates to whole organelles such as mitochondria, ER, peroxisomes, lysosomes and lipid droplets. Are the roles of autophagy in metabolism and quality control mutually exclusive, independent or interlocked? How are priorities established? What are the molecular links between both phenomena? This article will provide a starting point to formulate these questions, the responses to which should be taken into consideration in future autophagy-based interventions.

Keywords:  AMPK; ATG; Aging; Akt; Alzheimer’s disease; ESCRT; FOXO; LC3; MTOR; NAD; NASH; Obesity; Parkinson’s Disease; RagA/B; SIRT1; SIRT3; Selective autophagy; TBK1; TCA; TFEB; Tor; acetyl CoA; autophagy; calcienurin; cancer; cardiovascular; diabetes; endoplasmic reticulum; fatty acids; ferritin; galectin; glycogen; glycolysis; heart; immunity; infection; insulin; lipid droplets; liver; lysosomes; metabolism; mitochondria; mitophagy; neurodegeneration; nutrition; oxidative phosphorylation; p62 SQSTM1; peroxisome; quality control; sirtuin

DOI:  https://doi.org/10.1080/15548627.2021.1933742
Nature. 2021 May 26.

NF1 mutation drives neuronal activity-dependent initiation of optic glioma.

Yuan Pan, Jared D Hysinger, Tara Barron, Nicki F Schindler, Olivia Cobb, Xiaofan Guo, Belgin Yalçın, Corina Anastasaki, Sara B Mulinyawe, Anitha Ponnuswami, Suzanne Scheaffer, Yu Ma, Kun-Che Chang, Xin Xia, Joseph A Toonen, James J Lennon, Erin M Gibson, John R Huguenard, Linda M Liau, Jeffrey L Goldberg, Michelle Monje, David H Gutmann.

Neurons have recently emerged as essential cellular constituents of the tumour microenvironment, and their activity has been shown to increase the growth of a diverse number of solid tumours1. Although the role of neurons in tumour progression has previously been demonstrated2, the importance of neuronal activity to tumour initiation is less clear-particularly in the setting of cancer predisposition syndromes. Fifteen per cent of individuals with the neurofibromatosis 1 (NF1) cancer predisposition syndrome (in which tumours arise in close association with nerves) develop low-grade neoplasms of the optic pathway (known as optic pathway gliomas (OPGs)) during early childhood3,4, raising the possibility that postnatal light-induced activity of the optic nerve drives tumour initiation. Here we use an authenticated mouse model of OPG driven by mutations in the neurofibromatosis 1 tumour suppressor gene (Nf1)5 to demonstrate that stimulation of optic nerve activity increases optic glioma growth, and that decreasing visual experience via light deprivation prevents tumour formation and maintenance. We show that the initiation of Nf1-driven OPGs (Nf1-OPGs) depends on visual experience during a developmental period in which Nf1-mutant mice are susceptible to tumorigenesis. Germline Nf1 mutation in retinal neurons results in aberrantly increased shedding of neuroligin 3 (NLGN3) within the optic nerve in response to retinal neuronal activity. Moreover, genetic Nlgn3 loss or pharmacological inhibition of NLGN3 shedding blocks the formation and progression of Nf1-OPGs. Collectively, our studies establish an obligate role for neuronal activity in the development of some types of brain tumours, elucidate a therapeutic strategy to reduce OPG incidence or mitigate tumour progression, and underscore the role of Nf1mutation-mediated dysregulation of neuronal signalling pathways in mouse models of the NF1 cancer predisposition syndrome.

DOI: https://doi.org/10.1038/s41586-021-03580-6
Cell Rep. 2021 May 25. pii: S2211-1247(21)00525-8. [Epub ahead of print]35(8): 109180

Mass-spectrometry-based proteomics reveals mitochondrial supercomplexome plasticity.

Alba Gonzalez-Franquesa, Ben Stocks, Sabina Chubanava, Helle B Hattel, Roger Moreno-Justicia, Lone Peijs, Jonas T Treebak, Juleen R Zierath, Atul S Deshmukh.

  Mitochondrial respiratory complex subunits assemble in supercomplexes. Studies of supercomplexes have typically relied upon antibody-based quantification, often limited to a single subunit per respiratory complex. To provide a deeper insight into mitochondrial and supercomplex plasticity, we combine native electrophoresis and mass spectrometry to determine the supercomplexome of skeletal muscle from sedentary and exercise-trained mice. We quantify 422 mitochondrial proteins within 10 supercomplex bands in which we show the debated presence of complexes II and V. Exercise-induced mitochondrial biogenesis results in non-stoichiometric changes in subunits and incorporation into supercomplexes. We uncover the dynamics of supercomplex-related assembly proteins and mtDNA-encoded subunits after exercise. Furthermore, exercise affects the complexing of Lactb, an obesity-associated mitochondrial protein, and ubiquinone biosynthesis proteins. Knockdown of ubiquinone biosynthesis proteins leads to alterations in mitochondrial respiration. Our approach can be applied to broad biological systems. In this instance, comprehensively analyzing respiratory supercomplexes illuminates previously undetectable complexity in mitochondrial plasticity.

Keywords:  complexome; exercise; mitochondrial respiratory complexes; mitochondrial supercomplexes; oxidative phosphorylation; protein complexes

DOI:  https://doi.org/10.1016/j.celrep.2021.109180
Blood Cancer Discov. 2021 May;2(3): 266-287

SIRT5 IS A DRUGGABLE METABOLIC VULNERABILITY IN ACUTE MYELOID LEUKEMIA.

Dongqing Yan, Anca Franzini, Anthony D Pomicter, Brayden J Halverson, Orlando Antelope, Clinton C Mason, Jonathan M Ahmann, Anna V Senina, Nadeem A Vellore, Courtney L Jones, Matthew S Zabriskie, Hein Than, Michael J Xiao, Alexandria van Scoyk, Ami B Patel, Phillip M Clair, William L Heaton, Shawn C Owen, Joshua L Andersen, Christina M Egbert, Julie A Reisz, Angelo D'Alessandro, James E Cox, Kevin C Gantz, Hannah M Redwine, Siddharth M Iyer, Jamshid S Khorashad, Nima Rajabi, Christian A Olsen, Thomas O'Hare, Michael W Deininger.

We discovered that the survival and growth of many primary acute myeloid leukemia (AML) samples and cell lines, but not normal CD34+ cells, are dependent on SIRT5, a lysine deacylase implicated in regulating multiple metabolic pathways. Dependence on SIRT5 is genotype-agnostic and extends to RAS- and p53-mutated AML. Results were comparable between SIRT5 knockdown and SIRT5 inhibition using NRD167, a potent and selective SIRT5 inhibitor. Apoptosis induced by SIRT5 disruption is preceded by reductions in oxidative phosphorylation and glutamine utilization, and an increase in mitochondrial superoxide that is attenuated by ectopic superoxide dismutase 2. These data indicate that SIRT5 controls and coordinates several key metabolic pathways in AML and implicate SIRT5 as a vulnerability in AML.

DOI: https://doi.org/10.1158/2643-3230.bcd-20-0168
Nat Commun. 2021 May 28. 12(1): 3208

Restoration of energy homeostasis by SIRT6 extends healthy lifespan.

A Roichman, S Elhanati, M A Aon, I Abramovich, A Di Francesco, Y Shahar, M Y Avivi, M Shurgi, A Rubinstein, Y Wiesner, A Shuchami, Z Petrover, I Lebenthal-Loinger, O Yaron, A Lyashkov, C Ubaida-Mohien, Y Kanfi, B Lerrer, P J Fernández-Marcos, M Serrano, E Gottlieb, R de Cabo, H Y Cohen.

Aging leads to a gradual decline in physical activity and disrupted energy homeostasis. The NAD+-dependent SIRT6 deacylase regulates aging and metabolism through mechanisms that largely remain unknown. Here, we show that SIRT6 overexpression leads to a reduction in frailty and lifespan extension in both male and female B6 mice. A combination of physiological assays, in vivo multi-omics analyses and 13C lactate tracing identified an age-dependent decline in glucose homeostasis and hepatic glucose output in wild type mice. In contrast, aged SIRT6-transgenic mice preserve hepatic glucose output and glucose homeostasis through an improvement in the utilization of two major gluconeogenic precursors, lactate and glycerol. To mediate these changes, mechanistically, SIRT6 increases hepatic gluconeogenic gene expression, de novo NAD+ synthesis, and systemically enhances glycerol release from adipose tissue. These findings show that SIRT6 optimizes energy homeostasis in old age to delay frailty and preserve healthy aging.

DOI: https://doi.org/10.1038/s41467-021-23545-7
Methods Mol Biol. 2021 ;2304 339-346

FLIM Imaging for Metabolic Studies in Live Cells.

Heejun Choi.

  Fluorescent biochemical sensors allow probing metabolic states in a living cell with high spatiotemporal dynamics. This chapter describes a method for the in situ detection of changes in NAD+ level in living cells using fluorescence lifetime imaging (FLIM).

Keywords:  Biosensors; Cytosolic NAD+; FLIM; FRET; Metabolism; Mitochondrial NAD+; NAD+; Nuclear NAD+

DOI:  https://doi.org/10.1007/978-1-0716-1402-0_18
Elife. 2021 May 26. pii: e67624. [Epub ahead of print]10

Genome-wide CRISPRi screening identifies OCIAD1 as a prohibitin client and regulatory determinant of mitochondrial Complex III assembly in human cells.

Maxence Le Vasseur, Jonathan Friedman, Marco Jost, Jiawei Xu, Justin Yamada, Martin Kampmann, Max A Horlbeck, Michelle R Salemi, Brett S Phinney, Jonathan S Weissman, Jodi Nunnari.

  Dysfunction of the mitochondrial electron transport chain (mETC) is a major cause of human mitochondrial diseases. To identify determinants of mETC function, we screened a genome-wide human CRISPRi library under oxidative metabolic conditions with selective inhibition of mitochondrial Complex III and identified ovarian carcinoma immunoreactive antigen (OCIA) domain-containing protein 1 (OCIAD1) as a Complex III assembly factor. We find that OCIAD1 is an inner mitochondrial membrane protein that forms a complex with supramolecular prohibitin assemblies. Our data indicate that OCIAD1 is required for maintenance of normal steady-state levels of Complex III and the proteolytic processing of the catalytic subunit cytochrome c1 (CYC1). In OCIAD1 depleted mitochondria, unprocessed CYC1 is hemylated and incorporated into Complex III. We propose that OCIAD1 acts as an adaptor within prohibitin assemblies to stabilize and/or chaperone CYC1 and to facilitate its proteolytic processing by the IMMP2L protease.

Keywords:  Complex III; cell biology; cytochrome c1; electron transport chain; human; mitochondria; prohibitin; protease

DOI:  https://doi.org/10.7554/eLife.67624
Mol Cell Oncol. 2021 Mar 25. 8(3): 1902250

Targeting one-carbon metabolism requires mTOR inhibition: a new therapeutic approach in osteosarcoma.

Richa Rathore, Brian Van Tine.

  The rate-limiting enzyme of serine biosynthesis, 3-phosphoglycerate dehydrogenase (PHGDH), contributes to rapid growth and proliferation when it is overexpressed in cancer. We recently described the metabolic adaptations that occur upon PHGDH inhibition in osteosarcoma. PHGDH inhibition causes metabolite accumulation that activates the mechanistic target of rapamycin (mTOR) signaling, sensitizing osteosarcoma to non-rapalog mTOR inhibition.

Keywords:  PHGDH; mTORC1; methotrexate; osteosarcoma; perhexiline; serine

DOI:  https://doi.org/10.1080/23723556.2021.1902250
Mol Biol Rep. 2021 May 22.

Mitochondrial remodelling-a vicious cycle in diabetic complications.

Bhoomika Sherkhane, Gundu Chayanika, Anika Sood, Dharmendra Kumar Khatri, Shashi Bala Singh.

  Diabetes mellitus (DM) is a chronic, metabolic condition characterized by excessive blood glucose that causes perturbations in physiological functioning of almost all the organs of human body. This devastating metabolic disease has its implications in cognitive decline, heart damage, renal, retinal and neuronal complications that severely affects quality of life and associated with decreased life expectancy. Mitochondria possess adaptive mechanisms to meet the cellular energy demand and combat cellular stress. In recent years mitochondrial homeostasis has been point of focus where several mechanisms regulating mitochondrial health and function are evaluated. Mitochondrial dynamics plays crucial role in maintaining healthy mitochondria in cell under physiological as well as stress condition. Mitochondrial dynamics and corresponding regulating mechanisms have been implicated in progression of metabolic disorders including diabetes and its complications. In current review we have discussed about role of mitochondrial dynamics under physiological and pathological conditions. Also, modulation of mitochondrial fission and fusion in diabetic complications are described. The available literature supports mitochondrial remodelling as reliable target for diabetic complications.

Keywords:  Diabetic complications; Mitochondria; Mitochondrial dynamics; Mitochondrial fission; Mitochondrial fusion; Mitochondrial morphology

DOI:  https://doi.org/10.1007/s11033-021-06408-8
Nat Commun. 2021 May 27. 12(1): 3199

Cell-free DNA captures tumor heterogeneity and driver alterations in rapid autopsies with pre-treated metastatic cancer.

Bernard Pereira, Christopher T Chen, Lipika Goyal, Charlotte Walmsley, Christopher J Pinto, Islam Baiev, Read Allen, Laura Henderson, Supriya Saha, Stephanie Reyes, Martin S Taylor, Donna M Fitzgerald, Maida Williams Broudo, Avinash Sahu, Xin Gao, Wendy Winckler, A Rose Brannon, Jeffrey A Engelman, Rebecca Leary, James R Stone, Catarina D Campbell, Dejan Juric.

In patients with metastatic cancer, spatial heterogeneity of somatic alterations may lead to incomplete assessment of a cancer's mutational profile when analyzing a single tumor biopsy. In this study, we perform sequencing of cell-free DNA (cfDNA) and distinct metastatic tissue samples from ten rapid autopsy cases with pre-treated metastatic cancer. We show that levels of heterogeneity in genetic biomarkers vary between patients but that gene expression signatures representative of the tumor microenvironment are more consistent. Across nine patients with plasma samples available, we are able to detect 62/62 truncal and 47/121 non-truncal point mutations in cfDNA. We observe that mutation clonality in cfDNA is correlated with the number of metastatic lesions in which the mutation is detected and use this result to derive a clonality threshold to classify truncal and non-truncal driver alterations with reasonable specificity. In contrast, mutation truncality is more often incorrectly assigned when studying single tissue samples. Our results demonstrate the utility of a single cfDNA sample relative to that of single tissue samples when treating patients with metastatic cancer.

DOI: https://doi.org/10.1038/s41467-021-23394-4
Nat Commun. 2021 May 25. 12(1): 3101

Cytosolic dsDNA of mitochondrial origin induces cytotoxicity and neurodegeneration in cellular and zebrafish models of Parkinson's disease.

Hideaki Matsui, Junko Ito, Noriko Matsui, Tamayo Uechi, Osamu Onodera, Akiyoshi Kakita.

Mitochondrial dysfunction and lysosomal dysfunction have been implicated in Parkinson's disease (PD), but the links between these dysfunctions in PD pathogenesis are still largely unknown. Here we report that cytosolic dsDNA of mitochondrial origin escaping from lysosomal degradation was shown to induce cytotoxicity in cultured cells and PD phenotypes in vivo. The depletion of PINK1, GBA and/or ATP13A2 causes increases in cytosolic dsDNA of mitochondrial origin and induces type I interferon (IFN) responses and cell death in cultured cell lines. These phenotypes are rescued by the overexpression of DNase II, a lysosomal DNase that degrades discarded mitochondrial DNA, or the depletion of IFI16, which acts as a sensor for cytosolic dsDNA of mitochondrial origin. Reducing the abundance of cytosolic dsDNA by overexpressing human DNase II ameliorates movement disorders and dopaminergic cell loss in gba mutant PD model zebrafish. Furthermore, IFI16 and cytosolic dsDNA puncta of mitochondrial origin accumulate in the brain of patients with PD. These results support a common causative role for the cytosolic leakage of mitochondrial DNA in PD pathogenesis.

DOI: https://doi.org/10.1038/s41467-021-23452-x
Proc Natl Acad Sci U S A. 2021 Jun 01. pii: e2104008118. [Epub ahead of print]118(22):

Unravelling the mechanisms controlling heme supply and demand.

Galvin C-H Leung, Simon S-P Fung, Andrea E Gallio, Robert Blore, Dominic Alibhai, Emma L Raven, Andrew J Hudson.

  In addition to heme's role as the prosthetic group buried inside many different proteins that are ubiquitous in biology, there is new evidence that heme has substantive roles in cellular signaling and regulation. This means that heme must be available in locations distant from its place of synthesis (mitochondria) in response to transient cellular demands. A longstanding question has been to establish the mechanisms that control the supply and demand for cellular heme. By fusing a monomeric heme-binding peroxidase (ascorbate peroxidase, mAPX) to a monomeric form of green-fluorescent protein (mEGFP), we have developed a heme sensor (mAPXmEGFP) that can respond to heme availability. By means of fluorescence lifetime imaging, this heme sensor can be used to quantify heme concentrations; values of the mean fluorescence lifetime (τMean) for mAPX-mEGFP are shown to be responsive to changes in free (unbound) heme concentration in cells. The results demonstrate that concentrations are typically limited to one molecule or less within cellular compartments. These miniscule amounts of free heme are consistent with a system that sequesters the heme and is able to buffer changes in heme availability while retaining the capability to mobilize heme when and where it is needed. We propose that this exchangeable supply of heme can operate using mechanisms for heme transfer that are analogous to classical ligand-exchange mechanisms. This exquisite control, in which heme is made available for transfer one molecule at a time, protects the cell against the toxic effect of excess heme and offers a simple mechanism for heme-dependent regulation in single-molecule steps.

Keywords:  biosensing; fluorescence lifetime imaging; heme biology

DOI:  https://doi.org/10.1073/pnas.2104008118
mBio. 2021 May 28. e0037521

The Trypanosome UDP-Glucose Pyrophosphorylase Is Imported by Piggybacking into Glycosomes, Where Unconventional Sugar Nucleotide Synthesis Takes Place.

Oriana Villafraz, Hélène Baudouin, Muriel Mazet, Hanna Kulyk, Jean-William Dupuy, Erika Pineda, Cyrille Botté, Daniel Ken Inaoka, Jean-Charles Portais, Frédéric Bringaud.

  Glycosomes are peroxisome-related organelles of trypanosomatid parasites containing metabolic pathways, such as glycolysis and biosynthesis of sugar nucleotides, usually present in the cytosol of other eukaryotes. UDP-glucose pyrophosphorylase (UGP), the enzyme responsible for the synthesis of the sugar nucleotide UDP-glucose, is localized in the cytosol and glycosomes of the bloodstream and procyclic trypanosomes, despite the absence of any known peroxisome-targeting signal (PTS1 and PTS2). The questions that we address here are (i) is the unusual glycosomal biosynthetic pathway of sugar nucleotides functional and (ii) how is the PTS-free UGP imported into glycosomes? We showed that UGP is imported into glycosomes by piggybacking on the glycosomal PTS1-containing phosphoenolpyruvate carboxykinase (PEPCK) and identified the domains involved in the UGP/PEPCK interaction. Proximity ligation assays revealed that this interaction occurs in 3 to 10% of glycosomes, suggesting that these correspond to organelles competent for protein import. We also showed that UGP is essential for the growth of trypanosomes and that both the glycosomal and cytosolic metabolic pathways involving UGP are functional, since the lethality of the knockdown UGP mutant cell line (RNAiUGP, where RNAi indicates RNA interference) was rescued by expressing a recoded UGP (rUGP) in the organelle (RNAiUGP/EXPrUGP-GPDH, where GPDH is glycerol-3-phosphate dehydrogenase). Our conclusion was supported by targeted metabolomic analyses (ion chromatography-high-resolution mass spectrometry [IC-HRMS]) showing that UDP-glucose is no longer detectable in the RNAiUGP mutant, while it is still produced in cells expressing UGP exclusively in the cytosol (PEPCK null mutant) or glycosomes (RNAiUGP/EXPrUGP-GPDH). Trypanosomatids are the only known organisms to have selected functional peroxisomal (glycosomal) sugar nucleotide biosynthetic pathways in addition to the canonical cytosolic ones. IMPORTANCE Unusual compartmentalization of metabolic pathways within organelles is one of the most enigmatic features of trypanosomatids. These unicellular eukaryotes are the only organisms that sequestered glycolysis inside peroxisomes (glycosomes), although the selective advantage of this compartmentalization is still not clear. Trypanosomatids are also unique for the glycosomal localization of enzymes of the sugar nucleotide biosynthetic pathways, which are also present in the cytosol. Here, we showed that the cytosolic and glycosomal pathways are functional. As in all other eukaryotes, the cytosolic pathways feed glycosylation reactions; however, the role of the duplicated glycosomal pathways is currently unknown. We also showed that one of these enzymes (UGP) is imported into glycosomes by piggybacking on another glycosomal enzyme (PEPCK); they are not functionally related. The UGP/PEPCK association is unique since all piggybacking examples reported to date involve functionally related interacting partners, which broadens the possible combinations of carrier-cargo proteins being imported as hetero-oligomers.

Keywords:  Trypanosoma brucei; UDP-glucose pyrophosphorylase; glycosomes; peroxisomes; piggybacking; procyclic form

DOI:  https://doi.org/10.1128/mBio.00375-21
J Cell Sci. 2021 May 26. pii: jcs.253781. [Epub ahead of print]

Atg32 dependent mitophagy sustains spermidine and nitric oxide required for heat stress tolerance in S. cerevisiae.

Jasvinder Kaur, Juliet Goldsmith, Alexandra Tankka, Sofía Bustamante Eguiguren, Alfredo A Gimenez, Lance Vick, Jayanta Debnath, Ariadne Vlahakis.

  In Saccharomyces cerevisiae, the selective autophagic degradation of mitochondria, termed mitophagy, is critically regulated by the adapter protein, Atg32. Despite our knowledge about the molecular mechanisms by which Atg32 controls mitophagy, its physiological roles in yeast survival and fitness remains less clear. Here, we demonstrate a requirement for Atg32 in promoting spermidine production during respiratory growth and heat-induced mitochondrial stress. During respiratory growth, mitophagy-deficient yeast exhibit profound heat-stress induced defects in growth and viability due to impaired biosynthesis of spermidine and its biosynthetic precursor S-Adenosyl-Methionine (SAM). Moreover, spermidine production is crucial for the induction of cytoprotective nitric oxide (NO) during heat stress. Hence, the re-addition of spermidine to Atg32 mutant yeast is sufficient to both enhance NO production and restore respiratory growth during heat stress. Our findings uncover a previously unrecognized physiological role for yeast mitophagy in spermidine metabolism and illuminate new interconnections between mitophagy, polyamine biosynthesis and NO signaling.

Keywords:  ATG32; Autophagy; Mitophagy; Nitric Oxide; S-Adenosyl-Methionine; Spermidine

DOI:  https://doi.org/10.1242/jcs.253781
Nat Commun. 2021 May 28. 12(1): 3210

Mitochondrial targeted meganuclease as a platform to eliminate mutant mtDNA in vivo.

Ugne Zekonyte, Sandra R Bacman, Jeff Smith, Wendy Shoop, Claudia V Pereira, Ginger Tomberlin, James Stewart, Derek Jantz, Carlos T Moraes.

Diseases caused by heteroplasmic mitochondrial DNA mutations have no effective treatment or cure. In recent years, DNA editing enzymes were tested as tools to eliminate mutant mtDNA in heteroplasmic cells and tissues. Mitochondrial-targeted restriction endonucleases, ZFNs, and TALENs have been successful in shifting mtDNA heteroplasmy, but they all have drawbacks as gene therapy reagents, including: large size, heterodimeric nature, inability to distinguish single base changes, or low flexibility and effectiveness. Here we report the adaptation of a gene editing platform based on the I-CreI meganuclease known as ARCUS®. These mitochondrial-targeted meganucleases (mitoARCUS) have a relatively small size, are monomeric, and can recognize sequences differing by as little as one base pair. We show the development of a mitoARCUS specific for the mouse m.5024C>T mutation in the mt-tRNAAla gene and its delivery to mice intravenously using AAV9 as a vector. Liver and skeletal muscle show robust elimination of mutant mtDNA with concomitant restoration of mt-tRNAAla levels. We conclude that mitoARCUS is a potential powerful tool for the elimination of mutant mtDNA.

DOI: https://doi.org/10.1038/s41467-021-23561-7
Arch Biochem Biophys. 2021 May 24. pii: S0003-9861(21)00183-1. [Epub ahead of print] 108934

NADPH supply and the contribution of NAD(P)+ transhydrogenase (NNT) to H2O2 balance in skeletal muscle mitochondria.

Tiago R Figueira, Annelise Francisco, Juliana A Ronchi, Guilherme R R M Dos Santos, William Dos Santos, Jason R Treberg, Roger F Castilho.

  H2O2 is endogenously generated and its removal in the matrix of skeletal muscle mitochondria (SMM) is dependent on NADPH likely provided by NAD(P)+ transhydrogenase (NNT) and isocitrate dehydrogenase (IDH2). Importantly, NNT activity is linked to mitochondrial protonmotive force. Here, we demonstrate the presence of NNT function in detergent-solubilized and intact functional SMM isolated from rats and wild type (Nnt+/+) mice, but not in SMM from congenic mice carrying a mutated NNT gene (Nnt-/-). Further comparisons between SMM from both Nnt mouse genotypes revealed that the NADPH supplied by NNT supports up to 600 pmol/mg/min of H2O2 removal under selected conditions. Surprisingly, SMM from Nnt-/- mice removed exogenous H2O2 at wild-type levels and exhibited a maintained or even decreased net emission of endogenous H2O2 when substrates that support Krebs cycle reactions were present (e.g., pyruvate plus malate or palmitoylcarnitine plus malate). These results may be explained by a compensation for the lack of NNT, since the total activities of concurrent NADP+-reducing enzymes (IDH2, malic enzymes and glutamate dehydrogenase) were ∼70% elevated in Nnt-/- mice. Importantly, respiratory rates were similar between SMM from both Nnt genotypes despite differing NNT contributions to H2O2 removal and their implications for an evolving concept in the literature are discussed. We concluded that NNT is capable of meaningfully sustaining NADPH-dependent H2O2 removal in intact SMM. Nonetheless, if the available substrates favor non-NNT sources of NADPH, the H2O2 removal by SMM is maintained in Nnt-/- mice SMM.

Keywords:  Antioxidant; C57BL/6J; Krebs cycle; Oxidative stress; Redox balance

DOI:  https://doi.org/10.1016/j.abb.2021.108934
FEBS J. 2021 May 25.

Cancer Cell Metabolism Connects Epigenetic Modifications to Transcriptional Regulation.

Ashby J Morrison.

  Adaptation of cellular function with the nutrient environment is essential for survival. Failure to adapt can lead to cell death and/or disease. Indeed, energy metabolism alterations are a major contributing factor for many pathologies, including cancer, cardiovascular disease, and diabetes. In particular, a primary characteristic of cancer cells is altered metabolism that promotes survival and proliferation even in the presence of limited nutrients. Interestingly, recent studies demonstrate that metabolic pathways produce intermediary metabolites that directly influence epigenetic modifications in the genome. Emerging evidence demonstrates that metabolic processes in cancer cells fuel malignant growth, in part, through epigenetic regulation of gene expression programs important for proliferation and adaptive survival. In this review, recent progress towards understanding the relationship of cancer cell metabolism, epigenetic modification, and transcriptional regulation will be discussed. Specifically, the need for adaptive cell metabolism and its modulation in cancer cells will be introduced. Current knowledge on the emerging field of metabolite production and epigenetic modification will also be reviewed. Alterations of DNA (de)methylation, histone modifications, such as (de)methylation and (de)acylation, as well as chromatin remodeling, will be discussed in the context of cancer cell metabolism. Finally, how these epigenetic alterations contribute to cancer cell phenotypes will summarized. Collectively, these studies reveal that both metabolic and epigenetic pathways in cancer cells are closely linked, representing multiple opportunities to therapeutically target the unique features of malignant growth.

Keywords:  DNA methylation; acetylation; acylation; cancer; glycolysis; histone; metabolism; methylation; oxidative phosphorylation

DOI:  https://doi.org/10.1111/febs.16032
Sci Adv. 2021 May;pii: eabe7548. [Epub ahead of print]7(22):

Elevated type I interferon responses potentiate metabolic dysfunction, inflammation, and accelerated aging in mtDNA mutator mice.

Yuanjiu Lei, Camila Guerra Martinez, Sylvia Torres-Odio, Samantha L Bell, Christine E Birdwell, Joshua D Bryant, Carl W Tong, Robert O Watson, Laura Ciaccia West, A Phillip West.

Mitochondrial dysfunction is a key driver of inflammatory responses in human disease. However, it remains unclear whether alterations in mitochondria-innate immune cross-talk contribute to the pathobiology of mitochondrial disorders and aging. Using the polymerase gamma (POLG) mutator model of mitochondrial DNA instability, we report that aberrant activation of the type I interferon (IFN-I) innate immune axis potentiates immunometabolic dysfunction, reduces health span, and accelerates aging in mutator mice. Mechanistically, elevated IFN-I signaling suppresses activation of nuclear factor erythroid 2-related factor 2 (NRF2), which increases oxidative stress, enhances proinflammatory cytokine responses, and accelerates metabolic dysfunction. Ablation of IFN-I signaling attenuates hyperinflammatory phenotypes by restoring NRF2 activity and reducing aerobic glycolysis, which combine to lessen cardiovascular and myeloid dysfunction in aged mutator mice. These findings further advance our knowledge of how mitochondrial dysfunction shapes innate immune responses and provide a framework for understanding mitochondria-driven immunopathology in POLG-related disorders and aging.

DOI: https://doi.org/10.1126/sciadv.abe7548
Nat Metab. 2021 May;3(5): 665-681

Mammary epithelial cells have lineage-rooted metabolic identities.

Mathepan Jeya Mahendralingam, Hyeyeon Kim, Curtis William McCloskey, Kazeera Aliar, Alison Elisabeth Casey, Pirashaanthy Tharmapalan, Davide Pellacani, Vladimir Ignatchenko, Mar Garcia-Valero, Luis Palomero, Ankit Sinha, Jennifer Cruickshank, Ronak Shetty, Ravi N Vellanki, Marianne Koritzinsky, Vid Stambolic, Mina Alam, Aaron David Schimmer, Hal Kenneth Berman, Connie J Eaves, Miquel Angel Pujana, Thomas Kislinger, Rama Khokha.

Cancer metabolism adapts the metabolic network of its tissue of origin. However, breast cancer is not a disease of a single origin. Multiple epithelial populations serve as the culprit cell of origin for specific breast cancer subtypes, yet our knowledge of the metabolic network of normal mammary epithelial cells is limited. Using a multi-omic approach, here we identify the diverse metabolic programmes operating in normal mammary populations. The proteomes of basal, luminal progenitor and mature luminal cell populations revealed enrichment of glycolysis in basal cells and of oxidative phosphorylation in luminal progenitors. Single-cell transcriptomes corroborated lineage-specific metabolic identities and additional intra-lineage heterogeneity. Mitochondrial form and function differed across lineages, with clonogenicity correlating with mitochondrial activity. Targeting oxidative phosphorylation and glycolysis with inhibitors exposed lineage-rooted metabolic vulnerabilities of mammary progenitors. Bioinformatics indicated breast cancer subtypes retain metabolic features of their putative cell of origin. Thus, lineage-rooted metabolic identities of normal mammary cells may underlie breast cancer metabolic heterogeneity and targeting these vulnerabilities could advance breast cancer therapy.

DOI: https://doi.org/10.1038/s42255-021-00388-6
Annu Rev Genomics Hum Genet. 2021 May 26.

Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline.

Swathi P Jeedigunta, Anastasia V Minenkova, Jonathan M Palozzi, Thomas R Hurd.

Mitochondria are unusual organelles in that they contain their own genomes, which are kept apart from the rest of the DNA in the cell. While mitochondrial DNA (mtDNA) is essential for respiration and most multicellular life, maintaining a genome outside the nucleus brings with it a number of challenges. Chief among these is preserving mtDNA genomic integrity from one generation to the next. In this review, we discuss what is known about negative (purifying) selection mechanisms that prevent deleterious mutations from accumulating in mtDNA in the germline. Throughout, we focus on the female germline, as it is the tissue through which mtDNA is inherited in most organisms and, therefore, the tissue that most profoundly shapes the genome. We discuss recent progress in uncovering the mechanisms of germline mtDNA selection, from humans to invertebrates. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 22 is August 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

DOI: https://doi.org/10.1146/annurev-genom-121420-081805
Methods Mol Biol. 2021 ;2322 81-92

Monitoring PINK1-Parkin Signaling Using Dopaminergic Neurons from iPS Cells.

Kahori Shiba-Fukushima, Yuzuru Imai.

  The physiological importance of mitochondrial quality control has been uncovered by the finding that genes for early onset Parkinson's disease (PD), PINK1 and Parkin, regulate mitochondrial autophagy, called mitophagy, and motility. Dopaminergic neurons derived from human-induced pluripotent stem (iPS) cells are a useful tool for analyzing the pathogenesis caused by defects in mitochondrial quality control and for screening candidate drugs for PD. Moreover, dopaminergic neurons could provide new findings not obtained in other cells. In this chapter, we will describe our method for monitoring PINK1-Parkin signaling using iPS cell-derived dopaminergic neurons.

Keywords:  Autophagy; Dopaminergic neuron; Immunocytochemistry; Mitochondria; PINK1; Parkin; Ubiquitin; Western blot; iPS cells

DOI:  https://doi.org/10.1007/978-1-0716-1495-2_9
Front Endocrinol (Lausanne). 2021 ;12 668517

Astrocyte-Neuron Metabolic Crosstalk in Neurodegeneration: A Mitochondrial Perspective.

Patrycja Mulica, Anne Grünewald, Sandro L Pereira.

  Converging evidence made clear that declining brain energetics contribute to aging and are implicated in the initiation and progression of neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Indeed, both pathologies involve instances of hypometabolism of glucose and oxygen in the brain causing mitochondrial dysfunction, energetic failure and oxidative stress. Importantly, recent evidence suggests that astrocytes, which play a key role in supporting neuronal function and metabolism, might contribute to the development of neurodegenerative diseases. Therefore, exploring how the neuro-supportive role of astrocytes may be impaired in the context of these disorders has great therapeutic potential. In the following, we will discuss some of the so far identified features underlining the astrocyte-neuron metabolic crosstalk. Thereby, special focus will be given to the role of mitochondria. Furthermore, we will report on recent advancements concerning iPSC-derived models used to unravel the metabolic contribution of astrocytes to neuronal demise. Finally, we discuss how mitochondrial dysfunction in astrocytes could contribute to inflammatory signaling in neurodegenerative diseases.

Keywords:  Alzheimer’s disease; Parkinson’s disease; astrocytes; metabolism; neurodegeneration; neurons

DOI:  https://doi.org/10.3389/fendo.2021.668517
FASEB J. 2021 Jun;35(6): e21620

Mitochondrial fusion and fission: The fine-tune balance for cellular homeostasis.

Mary Adebayo, Seema Singh, Ajay Pratap Singh, Santanu Dasgupta.

  Mitochondria are highly dynamic, maternally inherited cytoplasmic organelles, which fulfill cellular energy demand through the oxidative phosphorylation system. Besides, they play an active role in calcium and damage-associated molecular patterns signaling, amino acid, and lipid metabolism, and apoptosis. Thus, the maintenance of mitochondrial integrity and homeostasis is extremely critical, which is achieved through continual fusion and fission. Mitochondrial fusion allows the transfer of gene products between mitochondria for optimal functioning, especially under metabolic and environmental stress. On the other hand, fission is crucial for mitochondrial division and quality control. The imbalance between these two processes is associated with various ailments such as cancer, neurodegenerative and cardiovascular diseases. This review discusses the molecular mechanisms that control mitochondrial fusion and fission and how the disruption of mitochondrial dynamics manifests into various disease conditions.

Keywords:  diseases; dynamics; fission; fusion; mitochondria

DOI:  https://doi.org/10.1096/fj.202100067R
Nat Metab. 2021 May;3(5): 588-589

Mitochondrial ROS signals prevent excessive immune response.

Kim Zarse, Michael Ristow.

DOI: https://doi.org/10.1038/s42255-021-00387-7
Cell. 2021 May 22. pii: S0092-8674(21)00572-9. [Epub ahead of print]

Lipolysis drives expression of the constitutively active receptor GPR3 to induce adipose thermogenesis.

Olivia Sveidahl Johansen, Tao Ma, Jakob Bondo Hansen, Lasse Kruse Markussen, Renate Schreiber, Laia Reverte-Salisa, Hua Dong, Dan Ploug Christensen, Wenfei Sun, Thorsten Gnad, Iuliia Karavaeva, Thomas Svava Nielsen, Sander Kooijman, Cheryl Cero, Oksana Dmytriyeva, Yachen Shen, Maria Razzoli, Shannon L O'Brien, Eline N Kuipers, Carsten Haagen Nielsen, William Orchard, Nienke Willemsen, Naja Zenius Jespersen, Morten Lundh, Elahu Gosney Sustarsic, Cecilie Mørch Hallgren, Mikkel Frost, Seth McGonigle, Marie Sophie Isidor, Christa Broholm, Oluf Pedersen, Jacob Bo Hansen, Niels Grarup, Torben Hansen, Andreas Kjær, James G Granneman, M Madan Babu, Davide Calebiro, Søren Nielsen, Mikael Rydén, Raymond Soccio, Patrick C N Rensen, Jonas Thue Treebak, Thue Walter Schwartz, Brice Emanuelli, Alessandro Bartolomucci, Alexander Pfeifer, Rudolf Zechner, Camilla Scheele, Susanne Mandrup, Zachary Gerhart-Hines.

  Thermogenic adipocytes possess a therapeutically appealing, energy-expending capacity, which is canonically cold-induced by ligand-dependent activation of β-adrenergic G protein-coupled receptors (GPCRs). Here, we uncover an alternate paradigm of GPCR-mediated adipose thermogenesis through the constitutively active receptor, GPR3. We show that the N terminus of GPR3 confers intrinsic signaling activity, resulting in continuous Gs-coupling and cAMP production without an exogenous ligand. Thus, transcriptional induction of Gpr3 represents the regulatory parallel to ligand-binding of conventional GPCRs. Consequently, increasing Gpr3 expression in thermogenic adipocytes is alone sufficient to drive energy expenditure and counteract metabolic disease in mice. Gpr3 transcription is cold-stimulated by a lipolytic signal, and dietary fat potentiates GPR3-dependent thermogenesis to amplify the response to caloric excess. Moreover, we find GPR3 to be an essential, adrenergic-independent regulator of human brown adipocytes. Taken together, our findings reveal a noncanonical mechanism of GPCR control and thermogenic activation through the lipolysis-induced expression of constitutively active GPR3.

Keywords:  G protein-coupled receptor; GPCR; GPR3; adrenergic receptor; brown adipose tissue; constitutively active; energy expenditure; lipolysis; thermogenesis; transcription

DOI:  https://doi.org/10.1016/j.cell.2021.04.037
Diabetes. 2021 May 26. pii: db210037. [Epub ahead of print]

Mitochondrial efflux of citrate and isocitrate is fully dispensable for glucose-stimulated insulin secretion and pancreatic islet β-cell function.

Casey J Bauchle, Kristen E Rohli, Cierra K Boyer, Vidhant Pal, Jonathan V Rocheleau, Siming Liu, Yumi Imai, Eric B Taylor, Samuel B Stephens.

The defining feature of pancreatic islet β-cell function is the precise coordination of changes in blood glucose levels with insulin secretion to regulate systemic glucose homeostasis. While ATP has long been heralded as a critical metabolic coupling factor to trigger insulin release, glucose-derived metabolites have been suggested to further amplify fuel-stimulated insulin secretion. The mitochondrial export of citrate and isocitrate through the citrate-isocitrate carrier (CIC) has been suggested to initiate a key pathway that amplifies glucose-stimulated insulin secretion, though the physiological significance of β-cell CIC to glucose homeostasis has not been established. Here, we generated constitutive and adult CIC β-cell knockout mice and demonstrate these animals have normal glucose tolerance, similar responses to diet-induced obesity, and identical insulin secretion responses to various fuel secretagogues. Glucose-stimulated NADPH production was impaired in β-cell CIC KO islets, whereas glutathione reduction was retained. Furthermore, suppression of the downstream enzyme, cytosolic isocitrate dehydrogenase, Idh1, inhibited insulin secretion in wild type islets, but failed to impact β-cell function in β-cell CIC KO islets. Our data demonstrate that the mitochondrial citrate-isocitrate carrier is not required for glucose-stimulated insulin secretion, and that additional complexities exist for the role of Idh1 and NADPH in the regulation of β-cell function.

DOI: https://doi.org/10.2337/db21-0037
Nat Metab. 2021 May;3(5): 593-594

Endothelial metabolism going single.

Abhishek Subramanian, Lisa M Becker, Peter Carmeliet.

DOI: https://doi.org/10.1038/s42255-021-00399-3
Trends Cell Biol. 2021 May 22. pii: S0962-8924(21)00097-0. [Epub ahead of print]

Hunger Brings Down the Tumor Fort.

Anastasia-Maria Zavitsanou, Thales Papagiannakopoulos.

  In a recent article published in Molecular Cell, Dai et al. demonstrate that energy stress induced by a ketogenic diet or fasting can enhance checkpoint blockade therapy. Energy stress promotes lysosome-mediated degradation of the immunoinhibitory ligand programmed death-ligand 1 (PDL1) and upregulation of tumor interferon (IFN) responses.

Keywords:  AMPK; PDL1; immunotherapy; ketogenic diet

DOI:  https://doi.org/10.1016/j.tcb.2021.05.005
FEBS J. 2021 May 24.

Energy metabolism in brown adipose tissue.

Zhichao Wang, Qiong A Wang, Yong Liu, Lei Jiang.

  Brown adipose tissue (BAT) is well known to burn calories through uncoupled respiration, producing heat to maintain body temperature. This 'calorie wasting' feature makes BAT a special tissue, which can function as an 'energy sink' in mammals. While a combination of high energy intake and low energy expenditure is the leading cause of overweight and obesity in modern society, activating a safe 'energy sink' has been proposed as a promising obesity treatment strategy. Metabolically, lipids and glucose have been viewed as the major energy substrates in BAT, while succinate, lactate, branched-chain amino acids, and other metabolites can also serve as energy substrates for thermogenesis. Since the cataplerotic and anaplerotic reactions of these metabolites interconnect with each other, BAT relies on its dynamic, flexible, and complex metabolism to support its special function. In this review, we summarize how BAT orchestrates the metabolic utilization of various nutrients to support thermogenesis and contributes to whole-body metabolic homeostasis.

Keywords:  brown adipose tissue; glucose metabolism; metabolic flux; obesity; thermogenesis

DOI:  https://doi.org/10.1111/febs.16015
Methods Mol Biol. 2021 ;2304 315-337

Developing Analysis Protocols for Monitoring Intracellular Oxygenation Using Fluorescence Lifetime Imaging of Myoglobin-mCherry.

Greg Alspaugh, Branden Roarke, Alexandra Chand, Rozhin Penjweini, Alessio Andreoni, Jay R Knutson.

  Oxygen (O2) is a critical metabolite for cellular function as it fuels aerobic cellular metabolism; further, it is a known regulator of gene expression. Monitoring oxygenation within cells and organelles can provide valuable insights into how O2, or lack thereof, both influences and responds to cell processes. In recent years, fluorescence lifetime imaging microscopy (FLIM) has been used to track several probe concentration independent intracellular phenomena, such as pH, viscosity, and, in conjunction with Förster resonance energy transfer (FRET), protein-protein interactions. Here, we describe methods for synthesizing and expressing the novel FLIM-FRET intracellular O2 probe Myoglobin-mCherry (Myo-mCherry) in cultured cell lines, as well as acquiring FLIM images using a laser scanning confocal microscope configured for two-photon excitation and a time-correlated single photon counting (TCSPC) module. Finally, we provide step-by-step protocols for FLIM analysis of Myo-mCherry using the commercial software SPCImage and conversion of fluorescence lifetime values in each pixel to apparent intracellular oxygen partial pressures (pO2).

Keywords:  Förster resonance energy transfer; Hypoxia; Intracellular oxygenation; Myo-mCherry; Two-photon fluorescence lifetime imaging

DOI:  https://doi.org/10.1007/978-1-0716-1402-0_17
Trends Cancer. 2021 May 19. pii: S2405-8033(21)00099-6. [Epub ahead of print]

Metabolic Plasticity of Neutrophils: Relevance to Pathogen Responses and Cancer.

Thomas Rogers, Ralph J DeBerardinis.

  Neutrophils, the most abundant leukocyte population in humans, constantly patrol the body for foreign cells, including pathogens and cancer cells. Once neutrophils are activated, they engage distinct metabolic pathways to fulfill their specialized antipathogen functions. In this review, we examine current research on the metabolism of neutrophil differentiation and antipathogen responses. We also discuss how tumor-associated neutrophils (TANs) can be educated by cytokines and by the nutrient-restrictive milieu of the tumor microenvironment (TME) to suppress antitumor immunity, promote cancer progression, and contribute to biological heterogeneity among tumors. Last, we discuss the clinical implications of circulating neutrophils and infiltrating TANs and consider how targeting TAN metabolism may synergize with cancer immunotherapy.

Keywords:  immunotherapy; metabolism; metastasis; neutrophils; tumor microenvironment

DOI:  https://doi.org/10.1016/j.trecan.2021.04.007
Methods Mol Biol. 2021 ;2299 123-137

Methods for Studying Myofibroblast Apoptotic Pathways.

Yan Zhou, David Lagares.

  Evasion of apoptosis by myofibroblasts is a hallmark of fibrotic diseases, ultimately leading to persistent myofibroblast activation, extracellular matrix (ECM) deposition, and remodeling. Targeting myofibroblast apoptosis is emerging as a novel therapeutic strategy to reverse established fibrosis. We have recently discovered that in the process of fibroblast-to-myofibroblast transdifferentiation driven by matrix stiffness, the "mitochondrial priming" (readiness to undergo apoptosis) is dramatically increased in stiffness-activated myofibroblasts. Thus, myofibroblasts, traditionally viewed as apoptosis-resistant cells, appear poised to die when survival pathways are blocked, a cellular state we call "primed for death." This apoptosis-prone phenotype is driven by high levels of pro-apoptotic proteins loaded in myofibroblast's mitochondria, which require concomitant upregulation of pro-survival BCL-2 proteins to suppress mitochondrial apoptosis and ensure survival. Here, we describe a method called BH3 profiling which measures myo/fibroblast apoptotic priming as well as their antiapoptotic dependencies for survival. In addition, we describe how BH3 profiling can be used to predict myofibroblast responses to therapeutic agents targeting pro-survival BCL-2 proteins, also known as BH3 mimetic drugs. Finally, we describe methods to assess myofibroblast sensitivity to extrinsic apoptosis via Annexin V staining.

Keywords:  Annexin V; Apoptosis; BH3 mimetic drugs; BH3 profiling; Fibrosis; Myofibroblasts

DOI:  https://doi.org/10.1007/978-1-0716-1382-5_9
Nat Rev Genet. 2021 May 24.

Biparental inheritance of mitochondrial DNA revisited.

Alistair T Pagnamenta, Wei Wei, Shamima Rahman, Patrick F Chinnery.

DOI: https://doi.org/10.1038/s41576-021-00380-6
EMBO Mol Med. 2021 May 27. e14316

Machine learning algorithms reveal the secrets of mitochondrial dynamics.

Jack J Collier, Robert W Taylor.

Mitochondria exist as dynamic networks whose morphology is driven by the complex interplay between fission and fusion events. Failure to modulate these processes can be detrimental to human health as evidenced by dominantly inherited, pathogenic variants in OPA1, an effector enzyme of mitochondrial fusion, that lead to network fragmentation, cristae dysmorphology and impaired oxidative respiration, manifesting typically as isolated optic atrophy. However, a significant number of patients develop more severe, systemic phenotypes, although no genetic modifiers of OPA1-related disease have been identified to date. In this issue of EMBO Molecular Medicine, supervised machine learning algorithms underlie a novel tool that enables automated, high throughput and unbiased screening of changes in mitochondrial morphology measured using confocal microscopy. By coupling this approach with a bespoke siRNA library targeting the entire mitochondrial proteome, the work described by Cretin and colleagues yielded significant insight into mitochondrial biology, discovering 91 candidate genes whose endogenous depletion can remedy impaired mitochondrial dynamics caused by OPA1 deficiency.

DOI: https://doi.org/10.15252/emmm.202114316
Nat Commun. 2021 May 28. 12(1): 3204

Pareto optimality between growth-rate and lag-time couples metabolic noise to phenotypic heterogeneity in Escherichia coli.

Diego Antonio Fernandez Fuentes, Pablo Manfredi, Urs Jenal, Mattia Zampieri.

Despite mounting evidence that in clonal bacterial populations, phenotypic variability originates from stochasticity in gene expression, little is known about noise-shaping evolutionary forces and how expression noise translates to phenotypic differences. Here we developed a high-throughput assay that uses a redox-sensitive dye to couple growth of thousands of bacterial colonies to their respiratory activity and show that in Escherichia coli, noisy regulation of lower glycolysis and citric acid cycle is responsible for large variations in respiratory metabolism. We found that these variations are Pareto optimal to maximization of growth rate and minimization of lag time, two objectives competing between fermentative and respiratory metabolism. Metabolome-based analysis revealed the role of respiratory metabolism in preventing the accumulation of toxic intermediates of branched chain amino acid biosynthesis, thereby supporting early onset of cell growth after carbon starvation. We propose that optimal metabolic tradeoffs play a key role in shaping and preserving phenotypic heterogeneity and adaptation to fluctuating environments.

DOI: https://doi.org/10.1038/s41467-021-23522-0
Nat Commun. 2021 May 24. 12(1): 3039

Evolution of core archetypal phenotypes in progressive high grade serous ovarian cancer.

Aritro Nath, Patrick A Cosgrove, Hoda Mirsafian, Elizabeth L Christie, Lance Pflieger, Benjamin Copeland, Sumana Majumdar, Mihaela C Cristea, Ernest S Han, Stephen J Lee, Edward W Wang, Sian Fereday, Nadia Traficante, Ravi Salgia, Theresa Werner, Adam L Cohen, Philip Moos, Jeffrey T Chang, David D L Bowtell, Andrea H Bild.

The evolution of resistance in high-grade serous ovarian cancer (HGSOC) cells following chemotherapy is only partially understood. To understand the selection of factors driving heterogeneity before and through adaptation to treatment, we profile single-cell RNA-sequencing (scRNA-seq) transcriptomes of HGSOC tumors collected longitudinally during therapy. We analyze scRNA-seq data from two independent patient cohorts to reveal that HGSOC is driven by three archetypal phenotypes, defined as oncogenic states that describe the majority of the transcriptome variation. Using a multi-task learning approach to identify the biological tasks of each archetype, we identify metabolism and proliferation, cellular defense response, and DNA repair signaling as consistent cell states found across patients. Our analysis demonstrates a shift in favor of the metabolism and proliferation archetype versus cellular defense response archetype in cancer cells that received multiple lines of treatment. While archetypes are not consistently associated with specific whole-genome driver mutations, they are closely associated with subclonal populations at the single-cell level, indicating that subclones within a tumor often specialize in unique biological tasks. Our study reveals the core archetypes found in progressive HGSOC and shows consistent enrichment of subclones with the metabolism and proliferation archetype as resistance is acquired to multiple lines of therapy.

DOI: https://doi.org/10.1038/s41467-021-23171-3
Cancer Res. 2021 May 28. pii: canres.0436.2021. [Epub ahead of print]

Epigenetic induction of mitochondrial fission is required for maintenance of liver cancer initiating cells.

Miaoling Tang, Meisongzhu Yang, Geyan Wu, Shuang Mo, Xingui Wu, Shuxia Zhang, Ruyuan Yu, Yameng Hu, Yingru Xu, Ziwen Li, Xinyi Liao, Jun Li, Libing Song.

Mitochondrial dynamics play vital roles in the tumorigenicity and malignancy of various types of cancers by promoting the tumor-initiating potential of cancer cells, suggesting that targeting crucial factors that drive mitochondrial dynamics may lead to promising anticancer therapies. In the current study, we report that overexpression of mitochondrial fission factor (MFF), which is upregulated significantly in liver cancer initiating cells (LCIC), promotes mitochondrial fission and enhances stemness and tumor-initiating capability in non-LCICs. MFF-induced mitochondrial fission evoked mitophagy and asymmetric stem cell division and promoted a metabolic shift from oxidative phosphorylation to glycolysis that decreased mitochondrial reactive oxygen species (ROS) production, which prevented ROS-mediated degradation of the pluripotency transcription factor OCT4. CRISPR affinity purification in situ of regulatory elements (CAPTURE) showed that T-Box transcription factor 19 (TBX19), which is overexpressed uniquely in LCICs compared to non-LCICs and liver progenitor cells, forms a complex with PRMT1 on the MFF promoter in LCICs, eliciting epigenetic histone H4R3me2a/H3K9ac-mediated transactivation of MFF. Targeting PRMT1 using furamidine, a selective pharmacological inhibitor, suppressed TBX19-induced mitochondrial fission, leading to a profound loss of self-renewal potential and tumor-initiating capacity of LCICs. These findings unveil a novel mechanism underlying mitochondrial fission-mediated cancer stemness and suggest that regulation of mitochondrial fission via inhibition of PRMT1 may be an attractive therapeutic option for liver cancer treatment.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-0436
EMBO Rep. 2021 May 27. e53232

Lysosome positioning and mTOR activity in Lowe syndrome.

Cansu Karabiyik, Sung Min Son, David C Rubinsztein.

Lowe syndrome is a rare, developmental disorder caused by mutations in the phosphatase, OCRL. A study in this issue of EMBO Reports shows that OCRL is required for microtubule nucleation and that mutations in this protein lead to an inability to activate mTORC1 signaling and consequent cell proliferation in the presence of nutrients. These defects are the result of impaired microtubule-dependent lysosomal trafficking to the cell periphery and are independent of OCRL phosphatase activity.

DOI: https://doi.org/10.15252/embr.202153232
Nat Metab. 2021 May;3(5): 590-592

Breast cancer has a new metabolic Achilles' heel.

Tatiana Alfonso-Pérez, Gabriel Baonza, Fernando Martin-Belmonte.

DOI: https://doi.org/10.1038/s42255-021-00394-8
Nat Metab. 2021 May;3(5): 587

The cellular-resolution revolution.

DOI: https://doi.org/10.1038/s42255-021-00401-y
Am J Respir Cell Mol Biol. 2021 May 24.

Mitochondrial Succinate Dehydrogenase in COPD: Is Complex II too Complex?

Paul T Schumacker.

DOI: https://doi.org/10.1165/rcmb.2021-0200ED
Trends Cancer. 2021 May 21. pii: S2405-8033(21)00101-1. [Epub ahead of print]

Co-occurrence and mutual exclusivity: what cross-cancer mutation patterns can tell us.

Geniver El Tekle, Tiziano Bernasocchi, Arun M Unni, Francesco Bertoni, Davide Rossi, Mark A Rubin, Jean-Philippe Theurillat.

  Cancer is the dysregulated proliferation of cells caused by acquired mutations in key driver genes. The most frequently mutated driver genes promote tumorigenesis in various organisms, cell types, and genetic backgrounds. However, recent cancer genomics studies also point to the existence of context-dependent driver gene functions, where specific mutations occur predominately or even exclusively in certain tumor types or genetic backgrounds. Here, we review examples of co-occurring and mutually exclusive driver gene mutation patterns across cancer genomes and discuss their underlying biology. While co-occurring driver genes typically activate collaborating oncogenic pathways, we identify two distinct biological categories of incompatibilities among the mutually exclusive driver genes depending on whether the mutated drivers trigger the same or divergent tumorigenic pathways. Finally, we discuss possible therapeutic avenues emerging from the study of incompatible driver gene mutations.

Keywords:  cancer driver mutations; co-occurrence; driver genes antagonism; genomic patterns; mutual exclusivity; pathway redundancy and divergence; synergy; synthetic essentiality; synthetic lethality

DOI:  https://doi.org/10.1016/j.trecan.2021.04.009