H OH metabolites OH Review Clinical Insights into Mitochondrial Neurodevelopmental and Neurodegenerative Disorders: Their Biosignatures from Mass Spectrometry-Based Metabolomics Haorong Li 1 , Martine Uittenbogaard 2, Ling Hao 1,* and Anne Chiaramello 2,* 1 Department of Chemistry, George Washington University, Science and Engineering Hall 4000, 800 22nd St., NW, Washington, DC 20052, USA; [email protected] 2 Department of Anatomy and Cell Biology, School of Medicine and Health Sciences, George Washington University, 2300 I Street N.W. Ross Hall 111, Washington, DC 20037, USA; [email protected] * Correspondence: [email protected] (L.H.); [email protected] (A.C.); Tel.: +202-994-4492 (L.H.) Abstract: Mitochondria are dynamic multitask organelles that function as hubs for many metabolic pathways. They produce most ATP via the oxidative phosphorylation pathway, a critical pathway that the brain relies on its energy need associated with its numerous functions, such as synaptic homeostasis and plasticity. Therefore, mitochondrial dysfunction is a prevalent pathological hallmark of many neurodevelopmental and neurodegenerative disorders resulting in altered neurometabolic coupling. With the advent of mass spectrometry (MS) technology, MS-based metabolomics provides an emerging mechanistic understanding of their global and dynamic metabolic signatures. In this review, we discuss the pathogenetic causes of mitochondrial metabolic disorders and the recent MS-based metabolomic advances on their metabolomic remodeling. We conclude by exploring the Citation: Li, H.; Uittenbogaard, M.; MS-based metabolomic functional insights into their biosignatures to improve diagnostic platforms, Hao, L.; Chiaramello, A. Clinical stratify patients, and design novel targeted therapeutic strategies. Insights into Mitochondrial Neurodevelopmental and Keywords: mitochondrial genetics; neurometabolic coupling; mitochondrial neurodevelopmental Neurodegenerative Disorders: Their disorders; secondary mitochondrial neurodegenerative diseases; mass spectrometry; metabolomics Biosignatures from Mass Spectrometry-Based Metabolomics. Metabolites 2021, 11, 233. https:// doi.org/10.3390/metabo11040233 1. Introduction Academic Editor: Amedeo Lonardo 1.1. Mitochondria Function as Metabolic Nodes Mitochondria are ubiquitous double membraned multitask organelles where energy is Received: 23 January 2021 generated through aerobic respiration. Mitochondria produce the majority of ATP required Accepted: 7 April 2021 for cellular functions via the oxidative phosphorylation (OXPHOS) pathway, a process Published: 10 April 2021 involving a flow of electrons through a series of multisubunit OXPHOS complexes, also known as the electron transfer chain (ETC) (Figure1). Publisher’s Note: MDPI stays neutral OXPHOS is interlinked with the tricarboxylic acid (TCA) cycle that produces the with regard to jurisdictional claims in reducing equivalents, NADH and FADH2, to feed electrons to complex I (NADH dehy- published maps and institutional affil- drogenase) and complex II (succinate dehydrogenase) of the ETC, respectively (Figure1 ). iations. Electrons are then transferred to complex III (ubiquinol cytochrome c oxidoreductase) via ubiquinone, the reduced form of coenzyme Q (CoQ), and subsequently to complex IV (cytochrome c oxidoreductase) via the electron carrier cytochrome c where O2 functions as an electron acceptor to produce water in the presence of hydrogen. The flow of electrons Copyright: © 2021 by the authors. through the ETC is coupled with the proton motor force formed by complexes I, III, and IV. Licensee MDPI, Basel, Switzerland. This gradient of protons is converted by complex V (ATP synthase) into chemical energy This article is an open access article for ATP synthesis using ADP and inorganic phosphate. Acetyl-CoA occupies a central distributed under the terms and and pivotal position as a key metabolic intermediate for mitochondrial energy metabolism. conditions of the Creative Commons It is generated by several pathways: (1) oxidation of pyruvate generated during glycol- Attribution (CC BY) license (https:// ysis; (2) fatty acid oxidation; and (3) oxidative degradation of the amino acids, leucine, creativecommons.org/licenses/by/ isoleucine, and tryptophan (Figure1)[ 1,2]. This convergence of pathways highlights the 4.0/). Metabolites 2021, 11, 233. https://doi.org/10.3390/metabo11040233 https://www.mdpi.com/journal/metabolites Metabolites 2021, 11, 233 2 of 24 concept of mitochondria operating as hubs for additional biochemical pathways, such as Metabolites 2021, 11, x heme biosynthesis, nucleotide biosynthesis (pyrimidines and purines), steroid hormone2 of 25 biosynthesis, calcium homeostasis, innate immunity, and cell death programming [3,4]. FigureFigure 1.1.The The mitochondrialmitochondrial oxidativeoxidative phosphorylationphosphorylation (OXPHOS)(OXPHOS) enzymaticenzymatic machinerymachinery andand keykey metabolic pathways. The mitochondrion is illustrated with its outer mitochondrial membrane, inner metabolic pathways. The mitochondrion is illustrated with its outer mitochondrial membrane, inner mitochondrial membrane, and mitochondrial matrix (yellow) along with the tricarboxylic acid mitochondrial membrane, and mitochondrial matrix (yellow) along with the tricarboxylic acid (TCA) (TCA) cycle and the fatty acid beta-oxidation with their functional link via acetyl-CoA. The reducing cycleagents, and NADH the fatty and acid FADH2, beta-oxidation produced with by their the functionaltricarboxylic link acid via acetyl-CoA.(TCA) cycle Theand reducing fatty acid agents, beta- NADHoxidation, and are FADH2, indicated produced along by thewith tricarboxylic their two acidpoints (TCA) of cycleentryand in fattythe acidOXPHOS beta-oxidation, pathway. areMagnification indicated along of the with OXPHOS their two enzymatic points of machinery entry in the with OXPHOS electrons pathway. transfer Magnification via the two-electron of the OXPHOScarriers, coenzyme enzymatic Q10 machinery (Q) and with cytochrome electrons c transfer(c), is shown via the below. two-electron The electron carriers, donor, coenzyme succinate, Q10 a (Q)product and cytochrome of the TCA c (c),cycle, is shown is also below. indicated The electronacting donor,at the succinate,level of complex a product II. ofFinally, the TCA protons cycle, istranslocated also indicated from acting complexes at the level I, III, of and complex IV into II. the Finally, intermembrane protons translocated space (orange) from are complexes shown along I, III, andwith IV protons into the being intermembrane transferred spaceback into (orange) the mitochondrial are shown along matrix with via protons complex being V, transferredresulting in back ATP synthesis from ADP and inorganic phosphate (Pi). into the mitochondrial matrix via complex V, resulting in ATP synthesis from ADP and inorganic phosphate (Pi). OXPHOS is interlinked with the tricarboxylic acid (TCA) cycle that produces the 1.2.reducing Mitochondrial equivalents, Inheritance NADH and FADH2, to feed electrons to complex I (NADH dehydrogenase)Mitochondria and originate complex from II a(succinate symbiotic dehydrogenase) event during which of the an ETC, archaebacterium respectively engulfed(Figure a1). proteobacterium Electrons are resemblingthen transferred a modern-day to complex rod-negative III (ubiquinol bacterium cytochrome with aerobic c metabolismoxidoreductase) capacity via viaubiquinone, an ETC encoded the reduced by its own form genome. of coenzyme This event Q occurred (CoQ), onceand 1.5subsequently billion years to ago complex and led toIV the (cytochrome modern-day c eukaryotic oxidoreductase) cells with via mitochondria the electron retaining carrier theircytochrome own circular c where genome O2 functions of limited as an size electron (about acceptor 16,569 bp)to produce and coding water capacity, in the presence after a phenomenonof hydrogen. calledThe flow reductive of electrons evolution. through The the mitochondrial ETC is coupled genome with contains the proton 37 genesmotor encodingforce formed 2 mitochondrial by complexesribosomal I, III, and IV. RNAs This (mt-rRNAs),gradient of protons 22 mitochondrial is converted tRNAs by complex (mt- tRNAs)V (ATP and synthase) 13 proteins, into allchemical of them energy required for subunits ATP synthesis of the OXPHOS using ADP complexes and inorganic I, III, IV, andphosphate. V. Thus, theAcetyl-CoA nuclear genome occupies is a a required central major and contributorpivotal position to mitochondrial as a key functionsmetabolic viaintermediate 1158 nuclear-encoded for mitochondrial proteins energy [5–7]. metabolism. It is generated by several pathways: 1) oxidationThe human of mitochondrialpyruvate generated genome during has an glycolysis; overall uniparental 2) fatty acid inheritance, oxidation; with and the 3) maternaloxidative genome degradation being of the the only amino one acids, passed leuc onine, to progeny isoleucine, [8]. and However, tryptophan several (Figure species, 1) such[1,2]. asThis Drosophila, convergence mouse of pathways and sheep, highlight exhibits the leakage concept of of the mitochondria paternal mitochondrial operating as genomehubs for [9 –additional12]. Following biochemical fertilization pathways, of the human such oocyte,as heme the biosynthesis, paternal mitochondrial nucleotide genomebiosynthesis is eliminated (pyrimidines via elusive and mechanisms. purines), Recentsteroid studies hormone have providedbiosynthesis, several calcium break- throughshomeostasis, in