Introduction

The brain consumes 20% of the body’s ATP at rest, although it accounts for only 2% of body mass [1]. The high-energy requirements of the brain support neurotransmission, action potential firing, synapse development, maintenance of brain cells, neuronal plasticity, and cellular activities required for learning and memory [2, 3]. In neurons, most of the energy is consumed for synaptic transmission. Action potential signaling represents the second-largest metabolic need, and it is estimated that ~ 400–800 million ATP molecules are used to reestablish the electrochemical gradient (Na+ out, K+ in, at the plasma membrane) after production of the single action potential [4]. The energetic demand of neurons results in a substantial dependence on mitochondria for ATP production through oxidative phosphorylation (OxPhos) [4]. Any dysfunction in mitochondria can lessen the energetic capacity of OxPhos and may elicit a metabolic switch from OxPhos to glycolysis (Warburg-like effect) as a compensatory attempt to maintain cellular ATP in the context of neurodegenerative stress [5, 6]. However, a long-term OxPhos-to-glycolysis shift can result in a bioenergetic crisis and make neurons more vulnerable to oxidative stress and neuronal cell death [7, 8].

Neurodegenerative diseases (NDDs) are characterized by numerous cellular features, including the loss of neurons, neuronal dysfunction in specific brain regions, aggregation of distinct protein(s), impaired protein clearance, mitochondrial dysfunction, oxidative stress, neuroinflammation, axonal transport defects and cell death. The myriad of cellular pathologies suggest that there are common/central molecular mechanisms driving NDDs [9, 10]. In addition to ATP production, the mitochondrion is an epicenter of many metabolic pathways and important cellular functions, including the fine-tuning of intracellular calcium (iCa2+) signaling, regulation of cell death, lipid synthesis, ROS signaling, and cellular quality control [11]. Disruption in mitochondrial function and metabolism appears to underlie several NDDs such as Alzheimer’s disease (AD), Parkinson’s disease (PD), Huntington’s disease (HD), and others [12, 13]. At present, most therapies for NDDs provide only symptomatic relief, and there remain no drugs to inhibit neurodegeneration [14,15,16]. Mitochondrial alterations/impaired brain energetics are thought to present in the asymptomatic stage of disease prior to the onset of clinical symptoms [14, 17, 18]. This supports the notion that mitochondrial metabolic defects may be drivers or even initiators of the neurodegenerative process. In addition, several therapeutics that improve mitochondrial function have been reported to be efficacious in NDD models [19,20,21].

Mitochondrial calcium (mCa2+) is a critical regulator of mitochondrial function. In the matrix, mCa2+ tightly regulates TCA cycle activity and augments metabolic output. However, an excess of mCa2+ can impair mitochondrial respiration, enhance reactive oxygen species (ROS) production and activate cell death [22]. Here, we hypothesize that dysfunction in mCa2+ is an early common cellular event that impairs mitochondrial metabolism and drives and exacerbates neuropathology. Defining the molecular basis of mitochondrial function and metabolism in NDDs will help define novel cellular events and pathways and their temporal occurrence in NDD progression to identify new therapeutic targets for various neurological conditions. Here, we review recent advancements in our understanding of the essential role of mitochondrial metabolism and discuss how impaired mCa2+ signaling may be causal and central in neurodegeneration.

Evidence for impaired mitochondrial metabolism in NDDs

Strategies to combat NDDs have generally been unsuccessful and are focused on reducing symptoms and disease modification. Both clinical and experimental studies suggest that impaired energy metabolism correlates with various neurological deficits, highlighting new therapeutic opportunities [14]. Here we outline various mitochondrial metabolic defects that are strongly linked to the progression of neurodegeneration.

Alzheimer’s disease (AD)

AD is the most common form of dementia and is characterized by irreversible memory loss due to neuronal dysfunction, dysconnectivity, and cell death. Familial AD (FAD) is caused by pathogenic mutations in amyloid precursor protein (APP) or presenilin (PS1 and PS2) that lead to overproduction, improper cleavage, and the accumulation of amyloid-beta (Aβ). Prognostic disease phenotypes are associated with the formation of Aβ plaques, neurofibrillary tangles (NFTs, consisting of the microtubule protein tau), synaptic failure, reduced synthesis of the neurotransmitter acetylcholine, and chronic inflammation [9]. Most therapeutic strategies have been focused on Aβ metabolism and clearance due to extensive preclinical and clinical data in support of a causal role in AD progression [23, 24]. According to the “amyloid cascade hypothesis,” Aβ aggregation can initiate a series of events, including tau pathology, oxidative stress, inflammation, neuronal calcium (Ca2+) dysregulation, and metabolic alterations, which culminate in neuronal cell loss and AD pathogenesis [25]. However, this hypothesis does not fully explain the etiology of sporadic forms of AD (SAD) that account for 90–95% of AD-associated dementia.

An alternative hypothesis is that the microtubule-associated protein tau becomes hyperphosphorylated, resulting in axonal transport defects of organelles (including mitochondria), synaptic dysfunction, and cell death [26]. In cortical brain tissue from AD patients and mouse models, tau is reported to interact with mitochondrial transporters and complexes, resulting in mitochondrial dysfunction and AD pathology [27, 28]. However, there appears to be a limited correlation between the severity of cognitive decline and amyloid or tau plaque formation [29, 30], suggesting Aβ/tau metabolism and processing may not be the cause, or at least the singular cause, of disease. Consistent with previous studies, RNA-sequencing data from AD patients also suggest that Aβ and tau accumulation may not be mediators of the disease [31, 32]. Also, clinical trials of therapies targeting Aβ/tau production, metabolism, and clearance have universally shown little efficacy making it likely that other proximal mechanisms of AD pathogenesis exist [33, 34].

Mitochondrial dysfunction appears to be a primary occurrence in AD that precedes Aβ deposition, synaptic degeneration, and NFTs formation. In support of this concept, cytoplasmic hybrid cells (cybrids) generated from platelet mitochondria of SAD patients were reported to have a deficiency in complex I and complex IV of the electron transport chain (ETC), reduced mitochondrial membrane potential (Δψm), altered mitochondrial morphology, increased Aβ generation and tau oligomerization (reviewed in [35]). Transmission electron microscopy (TEM) showed smaller mitochondria with altered cristae structure and a decrease in mitochondrial content both in AD mice and patients [36,37,38]. Furthermore, fibroblasts derived from SAD patients also showed impaired mitochondrial dynamics, bioenergetics, and Ca2+ dysregulation [17, 39]. This change in mitochondria morphology in AD may be due to a shift in the mitochondrial fission/fusion balance and a decrease in biogenesis [40].

Importantly, experimental evidence suggests that bioenergetic alterations in AD precede the formation of Aβ plaques [41]. Data supporting metabolic deficits in AD were first published in the early 1980s from 2-[18F] fluoro-2-deoxy-D-glucose (FDG) positron emission tomography (PET) studies, which showed reduced glucose metabolism in the parietal, temporal and frontal cortex of AD patients [42,43,44]. Postmortem brain tissue isolated from AD patients displays reduced mitochondrial metabolic enzyme activity for pyruvate dehydrogenase (PDH) [45, 46], alpha-ketoglutarate dehydrogenase (α-KGDH) [46], isocitrate dehydrogenase (ICDH) [47], and complex IV or cytochrome-c-oxidase (COX) [48,49,50]. In addition, succinate dehydrogenase (SDH) and malate dehydrogenase (MDH) activity are increased in AD patient's brains [51]. Microarray data [52] and bioinformatics analysis of four transcriptome datasets [53] suggests a significant downregulation in nuclear-encoded OxPhos genes in the hippocampus of AD patients. More recent data confirm impaired ATP synthase activity due to loss of the oligomycin sensitive conferring protein subunit in the brain of FAD and SAD patients [54].

Diminished PDH function, as noted in AD, limits the shuttling of pyruvate into the TCA cycle, causing pyruvate accumulation and favoring anaerobic metabolism. Anaerobic metabolism leads to the production of lactic acid and further reduces acetyl-CoA availability, which subsequently decreases OxPhos. These observations suggest a metabolic shift from OxPhos to glycolysis may occur with AD progression. This shift is perhaps a compensatory response to enhance energy production through glycolysis, which is noteworthy in the context of mitochondrial dysfunction [5, 6]. Interestingly, PDH, α-KGDH, and ICDH activity are all reported to be calcium-controlled, suggesting a clear link between mCa2+ levels and AD pathogenesis, which will be discussed in the upcoming section. A recent study also indicates that reduced mitochondrial pyruvate uptake in FAD-PS2-expressing cells may elicit impairments in bioenergetics and mitochondrial ATP synthesis [13]. The mechanism for defective mitochondrial pyruvate flux is associated with the hyper-activation of glycogen-synthase-kinase-3β (GSK3β), which decreases hexokinase 1 association with mitochondria and destabilizes the mitochondrial pyruvate carrier complexes [13]. Similarly, α-KGDH is sensitive to oxidative stress, and its reduced activity in PS1 mutant (M146L) fibroblasts suggests a possible mechanism for ROS-dependent metabolic deficiencies [18, 55]. Oxidative stress, as seen in AD brains [56], is reported to increase the expression of SDHA (one of the four nuclear-encoded subunits of complex II, SDH) [57, 58], and the activity of MDH [59]. In summation, alterations in key metabolic enzymes may compromise the neurons’ ability to generate ATP via OxPhos and be an early driver of cellular stress in AD.

Beyond energetic compromise, diminished acetyl-CoA supply caused either by a reduction in glucose metabolism or by reduced PDH activity impairs the synthesis of the neurotransmitter acetylcholine (ACh). ACh is generated from choline and acetyl-CoA by choline acetyltransferase. After synthesis, ACh is transported via an ATP-consuming process and stored in synaptic vesicles [60]. The loss of ACh synthesis in AD results in defective cholinergic neurotransmission [61, 62]. This provides another tangible link between energetic compromise and neuronal dysfunction in AD.

Several of the mitochondrial dehydrogenases mentioned above (PDH, α-KGDH, and ICDH) are known to be regulated by the Ca2+ concentration within the mitochondrial matrix [63,64,65]. The reactions catalyzed by the Ca2+-regulated mitochondrial dehydrogenases are rate-limiting steps in the TCA cycle, and therefore free-Ca2+ content in the mitochondrial matrix is a major regulator of metabolic output. PDH activity increases upon dephosphorylation of its E1α subunit, which is mediated by the Ca2+-sensitive phosphatase (PDP1) [64]. In neurons, Ca2+ influx through voltage-dependent Ca2+ channels is required for the fusion of synaptic vesicles with the plasma membrane and release of neurotransmitters at the synaptic cleft [66, 67]. Neuronal communication through synaptic transmission is an energy-demanding process, and mitochondria have a critical role in this process by providing ATP (via OxPhos) and by buffering synaptic Ca2+/iCa2+ to modulate neurotransmitter release [68]. The efficient regulation and buffering of iCa2+ is critical to prevent neuronal excitotoxicity. Mitochondria and the endoplasmic reticulum (ER) both are significant modulators of iCa2+ signaling and the role of ER in neuronal iCa2+ buffering is well known [69, 70]. However, our understanding of mCa2+ buffering in neurons is limited and evolving. Ca2+ enters the mitochondrial matrix through the mitochondrial calcium uniporter channel (mtCU) [71, 72] and is extruded via the mitochondrial Na+/Ca2+ exchanger (NCLX) [73, 74]. Any dysfunction in mCa2+ exchange or matrix buffering capacity can lead to impairments in mitochondrial Ca2+ homeostasis resulting in mCa2+ overload, oxidative stress, metabolic dysfunction, and cell death that can cause or precede AD-pathology [75,76,77,78]. We and others have reported that mitochondrial and metabolic dysfunction is a primary contributor to AD pathogenesis, with dysfunction observable before the appearance of Aβ aggregates and NFTs [18, 77, 79, 80]. We found alterations in the expression of mCa2+ handling genes in samples isolated from the brains of SAD patients post-mortem and in the triple transgenic mouse model of AD (3xTg-AD) prior to observable AD pathology [77]. Our observations suggest mCa2+ overload caused by an age-dependent remodeling of mCa2+ exchange machinery contributes to the progression of AD by promoting metabolic and mitochondrial dysfunction. We also found a decrease in OxPhos capacity in APPswe cell lines (K670N, M671L Swedish mutation), providing further evidence of impaired mitochondrial metabolism in AD [77]. Importantly, the genetic rescue of neuronal mCa2+ efflux capacity by expression of NCLX in 3xTg-AD mice was sufficient to block age-dependent AD-like pathology [77]. Employing quantitative comparative proteomics strategies in AD mice, other groups have reported significant alterations in the mitochondrial proteome, including the citric acid cycle, OxPhos, pyruvate metabolism, glycolysis, oxidative stress, ion transport, apoptosis, and mitochondrial protein synthesis well before the onset of the AD phenotype [79,80,81]. Further evidence of mCa2+ dysregulation is from metabolomics in an Aβ-transgenic C. elegans model (GRU102), wherein the authors showed a reduction in TCA cycle flux before the appearance of significant Aβ deposition, with the greatest reduction observed in α-KGDH activity. Knockdown of α-KGDH in control worms elicited reductions in both basal and maximal respiration like that observed in the AD worm model [18]. These observations suggest that reduced α-KGDH activity alone is sufficient to recapitulate the metabolic deficits observed in AD and is in line with a study by Yao et al. [46] wherein 3-month old 3xTg-AD mice were found to have reduced mitochondrial respiration and PDH activity, coupled with increased ROS generation [46]. Altogether, these data indicate that mCa2+ dysregulation is likely an early event in AD.

Mitochondria are highly dynamic, and exhibit cell type-specific metabolism in the brain [37, 82]. Axonal mitochondria appear small and sparse whereas dendritic mitochondria are elongated and more densely packed [82]. To ensure appropriate energy supply, especially in distal regions of the axons, mitochondria must be properly positioned. Indeed, mitochondria undergo bi-directional axonal transport including anterograde transport (from cell body to axon) and retrograde transport (from axon to cell body) [83, 84]. Axonal transport is mediated by ATP‐hydrolyzing motor proteins (kinesin‐I for anterograde and dynein for retrograde) to move cargo along microtubule tracks [85] and defects in transport seem to present before evident AD hallmarks [86, 87]. Defects in anterograde transport result in an insufficient supply of ATP at the synapse, resulting in synaptic starvation and dysfunction, an early pathological feature of AD [36]. Similarly, defective retrograde transport can lead to the accumulation of damaged mitochondria, which can compromise mitochondrial quality control mechanisms, which is also noted to occur in AD [88]. Recently, data from the APP-PS1 mouse model showed a reduction in neuronal mitochondria density around amyloid plaques, suggesting impaired mitochondrial transport and/or quality control in AD [37]. Further, several studies indicate that axonal transport of AD-associated proteins becomes defective early in disease progression, resulting in the accumulation of toxic cargo which can elicit protein aggregation, axonal swellings, and neuronal dysfunction [36, 87]. The mechanisms regulating axonal transport are not completely understood but some studies suggest that it is mediated by the interaction of kinesin motor protein with the mitochondrial adaptor proteins, Miro and Milton (known as trafficking kinesin protein (TRAK) family) [89]. Miro is a GTPase with two Ca2+ binding EF-hand domains and is localized to the outer mitochondrial membrane (OMM) and has an essential role in Ca2+-dependent regulation of mitochondrial transport. Intriguingly, Miro1 may also serve as a cytoplasmic Ca2+ sensor and may increase mCa2+ uptake via interaction with MCU’s N-terminal domain [90, 91]. An increase in mCa2+ has been shown to inhibit mitochondrial axonal transport and blocking mCa2+ influx into mitochondria by direct MCU inhibition enhances mitochondrial trafficking in axons [90].

While multiple molecular mechanisms likely contribute to AD pathogenesis, the data suggest that neuronal mCa2+ overload is a primary mediator of AD progression, causing impaired mitochondrial metabolism and ATP production, mitochondrial transport, and increased mitochondrial permeability transition pore (mPTP) opening (Fig. 1). This in turn results in loss of synaptic function, amyloid deposition, tau pathology, and cell death.

Fig. 1
figure 1

Hypothetical mechanisms of mCa2+ overload-induced cellular dysfunction in AD progression. Loss of NCLX and remodeling of the mtCU causes mCa2+ overload that leads to mPTP opening, loss of ATP, and interrupted axonal transport, resulting in AD progression

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Parkinson’s disease (PD)

PD is the second most common NDD afflicing ~ 1% of the population above 60 years of age [92]. It is clinically characterized by both motor dysfunction such as tremor (involuntary shaking), bradykinesia (slowness of movements), rigidity (resistance to movement), and akinesia, as well as non-motor disturbances such as depression, anxiety, fatigue, and dementia. These symptoms are caused by a diminishment of the neurotransmitter dopamine due to degeneration of dopaminergic neurons in the pars compacta of the substantia nigra in the midbrain and the deposition of intraneuronal proteinaceous inclusions known as Lewy bodies that are mainly composed of α-synuclein [93]. Most PD cases are sporadic with no known singular cause. Familial PD is associated with mutations in many genes including: SNCA (α-synuclein) [94], PRKN (parkin) [95], PARK7 (DJ-1) [96], LRRK2 (leucine-rich repeat kinase 2) [97], and PINK1 (phosphatase and tensin homologue (PTEN)-induced kinase 1) [98]. Studies suggest that homozygous mutations in Parkin are the most common cause of juvenile PD, but their role in idiopathic PD is unclear. Mutations in Parkin are not reliably associated with Lewy body pathology. Post-mortem examination of patients with Parkin mutations shows a clinical phenotype of dopaminergic neuronal loss and gliosis but lacking Lewy body pathology. However, this remains controversial as a few case reports demonstrate the presence of Lewy pathology in patients with Parkin mutations. Further studies are needed to define if parkin and Lewy body pathology are in linear pathways (reviewed in [99]).

Drug therapy for PD is limited and is primarily focused on enhancing dopamine levels via administration of l-3,4-dihydroxyphenylalanine (L-DOPA or Levodopa), which is metabolized to dopamine after crossing the blood–brain barrier [100, 101]. However, this therapy is only effective in the early stages of disease, and provides symptomatic relief with many adverse side effects, and is insufficient to block the progression of PD [15, 102], suggest a crucial need for new, effective therapies [103, 104]. Although the exact mechanisms of PD pathogenesis are not clear, many possible molecular events have been proposed to contribute to this process.

Mitochondrial dysfunction and impaired cellular bioenergetics have emerged as likely mechanisms driving PD pathogenesis in several studies [105, 106]. Dopaminergic neurons consume ~ 20-times more energy as compared to other neurons because of their anatomical structure (extensive long and branched axons), greater number of transmitter release sites, and their pacemaking activity [107]. The high-energetic demand of dopaminergic neurons makes them more susceptible to mitochondrial dysfunction and eventually to cell death in comparison to other neuronal cells [108, 109]. Defects in mitochondrial respiration are supported by findings of reduced glucose utilization in PD patients [110], as well as reduced pyruvate oxidation in fibroblasts derived from PD patients [111], which suggest reduced acetyl-CoA entry into the TCA cycle. The first study showing that defects in mitochondrial respiration may be causal in PD came in the early 1980s. In this study, experimental inhibition of complex I (NADH-ubiquinone reductase) of the ETC was sufficient to cause parkinsonism [112, 113]. This is consistently supported by observations of a profound reduction in ETC activity, mostly complex I, in the substantia nigra, platelets, and skeletal muscle of PD patients [114]. Furthermore, inhibitors of complex I, such as MPP+ (1-methyl-4-phenylpyridinium), 6-hydroxydopamine, rotenone and annonacin all elicit PD-like phenotypes, suggesting that mitochondrial dysfunction is sufficient to promote neuronal dysfunction in PD [115,116,117]. Complex I is a key entry point for electrons into the respiratory chain and is responsible for ~ 40% of mitochondrial ATP production [118, 119]. In addition to complex I, a reduction in complex II and III activity and the mitochondrial DNA (mtDNA) transcription factor, TFAM, has also been reported in PD patients [120,121,122]. Reduced ETC capacity in PD may cause a significant reduction in ATP [123] resulting in a cellular energy crisis that can impact various processes including: (1) ATP-dependent proton pumps that drive vesicular accumulation of dopamine [124, 125]; (2) axonal transport of cargo [126]; (3) mitochondrial dynamics (fusion, fission, turnover, biogenesis and transport) [127, 128]; and (4) ATP-dependent protein degradation systems (e.g. ubiquitin–proteasome and autophagy) [129, 130]. In addition, complex I and III deficiency in PD is linked with increased production of free radicals that further impair mitochondria function, drive protein aggregation and culminate in cell death [131,132,133]. Dopamine is very unstable and sequestered inside synaptic vesicles via the ATP-dependent vesicular monoamine transporter. If not sequestered, it is metabolized by monoamine oxidase to the toxic dopamine metabolite 3,4 dihydroxyphenylacetaldehyde, which contributes to oxidative stress, mPTP opening, and dopaminergic neuronal cell death [134]. Over the past decades, many PD-associated genetic mutations have been found to elicit changes in mitochondrial function and metabolism, supporting the notion that mitochondrial dysfunction is implicated in neuronal cell loss associated with familial PD and vice versa [98]. Mutant α-synuclein localizes to the inner mitochondrial membrane [135] and inhibits complex I activity, and promotes oxidative stress [136]. The interaction of α-synuclein with mitochondria can result in cytochrome c release, increased mCa2+ levels, changes in mitochondrial morphology, and a decline in mitochondrial respiration. α-synuclein-mitochondrial interplay may also inhibit autophagic clearance and increase its aggregation propensity (reviewed in [137]).

A recent study suggested that mitochondrial impairments occur with Lewy body formation [138]. Furthermore, loss of function mutations in DJ-1 caused impairments in OxPhos, and complex I assembly resulting in decreased ATP production, oxidative stress, and increased glycolysis [139, 140]. These findings raise the possibility that mitochondrial dysfunction is causal in maladaptive protein aggregation. Furthermore, Parkin, as an E3 ubiquitin ligase, is directly involved in the proteasomal degradation of protein aggregates. It localizes to mitochondria and prevents cytochrome c release, mitochondrial swelling, and the accumulation of α-synuclein, which may protect dopaminergic neurons from mitochondrial and neuronal dysfunction [141,142,143].

Parkin and PINK1 are required for mitochondrial quality control [144, 145]; thus, loss of Parkin/PINK1 function is hypothesized to cause the accumulation of dysfunctional mitochondria that impair neuronal function. Previous work revealed that PINK1 deficient neurons display reduced NCLX-dependent mCa2+ efflux resulting in matrix Ca2+ overload and subsequent mPTP opening, mitochondrial oxidative stress, lower Δψm, and diminished OxPhos [146]. Furthermore, fibroblasts derived from patients with PINK1 mutations also exhibited impaired mitochondrial metabolism, low Δψm, and low respiration, which was linked to reduced substrate availability [147]. In addition, the activation of NCLX via protein kinase A (PKA)-dependent phosphorylation of serine 258, a putative NCLX regulatory site, increases mCa2+ efflux and protects PINK-1 deficient neurons from mitochondrial dysfunction and cell death [148]. This paradigm fits with previous reports where mCa2+ overload caused by increased mCa2+ uptake (via ERK1/2-dependent upregulation of MCU) caused dendritic degeneration in a late-onset familial PD model (mutation in Leucine-Rich Repeat Kinase 2) [149], and a report of MCU overexpression eliciting excitotoxic cell death [78]. Along the same line, inhibition of MCU is protective in zebrafish models of PD [150, 151]. These findings suggest mCa2+ overload is a contributor to PD progression.

In summary, increasing evidence supports the centrality of impaired mitochondrial function and metabolism in both sporadic and familial PD, resulting in oxidative stress, ETC dysfunction, defective mitochondrial quality control, protein aggregation, progressive cellular dysfunction, and neurodegeneration.

Huntington's disease (HD)

HD is an autosomal-dominant neurodegenerative disease resulting from an expansion of cytosine–adenine–guanine (CAG) repeats (> 35 bp) within the coding sequence of the huntingtin gene (HTT). Mutant huntingtin protein (mHtt) is prone to proteolytic cleavage, misfolding, and aggregation. Clinically, HD is characterized by progressive motor, cognitive, and behavioral dysfunction largely due to the loss of γ-aminobutyric acid (GABAergic) medium spiny neurons in the striatum [152]. The energy impairment hypothesis of HD was first proposed in the early 1980s from clinical observations, which revealed deficits in brain glucose utilization and weight loss in HD patients [153, 154]. Consistently, compelling evidence from PET studies suggests decreased glucose utilization in HD brains [155, 156], suggesting a defect in metabolism. In addition, compared to a control population, pre-symptomatic HD children, with no manifest symptoms, revealed a lower body mass index suggesting energy dysregulation and impairments in anabolic growth [157].

In HD patients, many key enzymes of the TCA cycle and ETC display reduced expression, including PDH, SDH, complex II, III, and IV [158]. In addition, HD patients increase lactate production in the pre-symptomatic phase of HD, indicating a possible reduction in oxidative mitochondrial metabolism and metabolic shift from OxPhos to glycolysis [159,160,161,162]. Irreversible inhibition of SDH by chronic administration of 3-nitropropionic acid in both rodents and non-human primates elicited regional lesions in the striatum accompanied by HD-like pathology [163,164,165]. These results suggest that defects in key TCA cycle enzymes are sufficient to drive HD-pathology. Furthermore, treatment of an HD mouse model with coenzyme Q and creatine for energy supplementation resulted in increased longevity and improved motor function [166, 167], suggesting that improving mitochondrial function and cellular bioenergetics is a viable therapeutic approach to treat HD.

Various other changes in mitochondrial function have been reported in HD. Recently, an examination of HD patient-derived induced pluripotent stem cells (iPSCs) and differentiated neural stem cells revealed altered mitochondria morphology (round and fragmented structure), lower mitochondrial respiration, decreased ATP levels and complex III activity, activation of apoptosis, and increased glycolysis [168]. Proteomic analysis in undifferentiated human HD embryonic stem cells found a decrease in key proteins involved in the ETC before observable differences in huntingtin protein [169]. These studies suggest that mitochondrial function is impaired early in HD pathogenesis. Also, mitochondrial dysfunction is linked with glutamate-mediated excitotoxicity in HD, and this is linked to defects in mCa2+ homeostasis. Studies indicate early abnormalities in mCa2+ that contribute to HD pathology [170]. For example, mitochondria from HD patients have an increased probability of mPTP opening, mitochondrial swelling, oxidative stress, and mCa2+ overload [170, 171]. As in other NDDs, impaired axonal transport is also reported in HD [172] and may be caused by mitochondrial dysfunction and impaired ATP production. Overall, these findings support a prominent role for mitochondrial and metabolic defects in HD pathogenesis.

Altogether, numerous studies support that mitochondrial dysfunction and energy impairments occur before overt pathological symptoms and appear to be central in driving the progression of various NDDs. We hypothesize that metabolic and mitochondrial dysfunction is a result of iCa2+ dysfunction and remodeling of the mCa2+ exchange machinery, which, although initially meant to be compensatory, causes a series of events that culminate in neurodegeneration (Fig. 2).

Fig. 2
figure 2

Mitochondrial and metabolic dysfunction in neurodegeneration. Mitochondrial dysfunction and energy impairments are central events in neurodegeneration

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Molecular mechanisms of altered metabolism in NDDs

Above we outlined experimental evidence linking impaired energy metabolism to the initiation or progression of NDDs. This has led to the hypothesis that defects in mitochondrial energy production initiate a cascade of events that causes the neuronal cell death observed in NDDs [173]. However, additional work has raised the possibility that primary defects in other cellular processes may secondarily impair mitochondrial bioenergetics and contribute to NDD pathogenesis [10, 174]. Potential mechanisms that may alter metabolism in NDDs (Fig. 3), and the significance of such altered metabolism for NDDs etiology, are discussed below.

Fig. 3
figure 3

Calcium-centric view of impaired mitochondrial metabolism in NDDs. (1–2) An increase in intracellular calcium by different Ca2+ transport systems in the plasma membrane and the endoplasmic reticulum promotes its entry into the mitochondrial matrix via the mtCU. (3) mCa2+ enhances the activity of key TCA enzymes, leading to elevated OxPhos and ATP generation. On the other side, insufficient or excessive mCa2+ content can impair mitochondrial metabolism in NDDs. The ER plays a crucial role in regulating cellular energetics via the regulated release of Ca2+ near sites of ER-mitochondrial contact to support ATP production. (4) The changes in mitochondrial dynamics alter respiratory complex assembly and affect the coupling between respiration and ATP synthesis. (5–8) The production of ROS and activation of AMPK signaling by Ca2+ and insulin signaling also constitute the diverse array of signaling pathways that elicit transcription regulation of energy metabolism genes

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Calcium signaling

Calcium signaling is required for neuronal function and regulates a range of processes, including neuronal excitability, neurotransmitter release, mitochondrial metabolism, and cell death. Tight control over iCa2+ flux is therefore essential for coordinated activity and neuronal homeostasis. As discussed above, altered Ca2+ homeostasis has been reported in NDDs and may contribute to neuronal dysfunction and death (reviewed in [175]). This section discusses the impact of altered Ca2+ handling in various subcellular compartments and its impact on metabolism.

Intracellular calcium

Perturbation of global iCa2+ homeostasis alters Ca2+ content in compartments, including the ER and mitochondria. Both organelles are implicated in the pathophysiology of NDDs, thus altered iCa2+ levels may contribute to NDD progression. Indeed, iCa2+ overload is a widely accepted feature of NDDs and is a likely cause of dysfunction and death of the neuronal populations affected by these diseases [176].

Elevated iCa2+ content is a common feature of AD and is especially pronounced in neurons containing NFTs [177]. Elevated iCa2+ in AD can exert detrimental effects by altering Ca2+-dependent signaling. Two examples of Ca2+-dependent proteins in neurons are the phosphatase calcineurin and Ca2+/calmodulin-dependent protein kinase II (CaMKII). Altered calcineurin and CaMKII signaling have been linked to memory impairment, synaptic loss, and neurodegeneration, all features of AD progression [178]. Such findings have inspired the “Ca2+ hypothesis of AD,” which proposes that cellular Ca2+ dysregulation is a central driver of disease progression [179, 180].

While Ca2+ dysregulation likely precedes neurodegeneration, several reports describe mechanisms by which Aβ directly elevates iCa2+ content, suggesting a vicious positive feedback loop that reinforces Ca2+ overload. First, Aβ can promote ROS production and subsequent oxidation of membrane lipids that can disrupt cellular ion transport [181]. Second, Aβ peptides may form Ca2+-permeable pores in the plasma membrane, allowing for direct influx of Ca2+ into the neuron [182]. This idea is supported by the observation that neurites with more Aβ have greater levels of iCa2+ [183]. Aβ is also proposed to stimulate Ca2+ uptake through L-type voltage-gated Ca2+ channels [184], but this notion is still debated [185]. Finally, Aβ may hyperactivate the NMDA receptor, leading to cellular Ca2+ overload [186]. Dysregulated Ca2+ handling is also implicated in the pathophysiology of PD [187]. Neurons with α-synuclein mutations have increased plasma membrane ion permeability, possibly due to the formation of pores by mutant α-synuclein [188]. Pharmacologic inhibition of Cav1.3 L-type Ca2+ channels is protective in animal models of PD [189], suggesting that increased ion channel activity contributes to excess iCa2+ entry. Store-operated calcium entry is also impaired in PD and leads to the depletion of ER Ca2+ content [175]. Likewise, neuronal Ca2+ dysregulation is a common feature of HD [190]. mHtt can stimulate NMDA receptors in medium spiny striatal neurons, potentially leading to excess iCa2+ [176]. Also, mHtt binds to and potentiates IP3 receptor signaling, enhancing Ca2+ release from the ER [191]. These combined effects all tend to deplete the ER of Ca2+ and can ultimately enhance store-operated Ca2+ entry [192], setting up a continuous cycle that promotes increased iCa2+ load.

ER calcium

Alterations in iCa2 handling in NDDs can cause secondary changes in ER Ca2+ load. The ER plays a critical role in regulating cellular energetics via the regulated release of Ca2+ near sites of ER-mitochondrial contact. In brief, these discrete sites of ER-mitochondrial apposition (examined further below under “MAMs” or mitochondrial associated membranes) create a microdomain where Ca2+ concentration can rise to levels as much as 20 × greater than in the bulk cytosol [193, 194]. This localized, high Ca2+ concentration is required for the activation of the mCa2+ uptake machinery (gating of the mtCU) and efficient ER-to-mitochondria Ca2+ transfer [195]. Inter-organelle Ca2+ transport is especially important in regulating iCa2+ homeostasis in neurons and is implicated not only in energetic homeostasis but also vesicle trafficking and neurotransmitter release [196, 197]. Thus, any structural disruption in ER-mitochondrial contact sites in NDDs and subsequent perturbation in ER-mitochondrial Ca2+ transfer has the potential to exacerbate iCa2+ stress and accelerate disease progression. Moreover, altered ER Ca2+ content and ER Ca2+ release will affect mCa2+ content. As discussed in the next section, either insufficient or excessive mCa2+ content can impair mitochondrial metabolism and signaling, thus underlying the significance of altered ER Ca2+ handling for cellular bioenergetics in NDDs.

Mitochondrial calcium

Given the central role of mCa2+ in regulating cellular metabolism and survival, it is not surprising that altered mCa2+ handling is reported in cellular NDD models. NDDs are universally associated with mCa2+ overload, which can impair cellular metabolism by inducing oxidative stress, which itself can impair OxPhos; and by inducing mPTP, which compromises ATP production by collapsing Δψm [198, 199].

In AD, mCa2+ overload can result from excessive ER-to-mitochondrial Ca2+ transfer induced by Aβ oligomers [200]. There are also reports that Aβ accumulates in mitochondria and interacts with the matrix mPTP regulator cyclophilin D, thus increasing permeability transition [201, 202] and impairing mitochondrial energetics in a Ca2+-independent manner. More recent results from our laboratory indicate that mCa2+ efflux is compromised in AD, due to downregulation of NCLX, which further promotes mCa2+ overload [77].

Signs of mCa2+ overload are observed in cellular models of PD induced by expression of mutant α-synuclein. These include loss of Δψm, cristae structure, and ATP content, features that are exacerbated by simultaneous expression of mutant PINK1 and rescued by pharmacologic blockade of mCa2+ uptake [203]. α-synuclein can accumulate within mitochondria and increases mCa2+ content, leading to increased ROS production [204]. However, conflicting reports [205] suggest that the effects of α-synuclein on mCa2+ homeostasis may be more nuanced. In some cases, α-synuclein may be beneficial by promoting ER-mitochondrial contacts to enhance ER-to-mitochondrial Ca2+ transfer and support mitochondrial bioenergetics [206]. Altered mCa2+ handling has been suggested in HD, but existing reports have yielded disparate conclusions on this point. The reader is referred to a recent review by Cali et al. [198] for a more detailed discussion.

Mitochondrial-associated membranes

Mitochondrial-associated membranes (MAMs) are regions where the ER is in close proximation with the outer mitochondrial membrane to allow crosstalk between these organelles. MAMs are particularly important for the exchange of Ca2+ and phospholipids, both of which impact ER/mitochondrial function and thus have profound effects on cellular metabolism and overall homeostasis (reviewed in [207]). MAMs are required for the synthesis of lipids such as phosphatidylcholine [208], with the mitochondrion serving as the site of phosphatidylethanolamine (PE) generation, an intermediate in phosphatidylcholine production. In turn, PE is crucial for overall mitochondrial morphology and function [209]. MAMs are also enriched for proteins involved in mitochondrial fission and fusion [210, 211], and so can influence mitochondrial dynamics, morphology, and biogenesis. Likewise, MAMs are important sites for the regulation of mitophagy and the clearance of defective mitochondria [212].

MAMs are often found at synapses, where they may modulate synaptic activity [213]. Efficient ER-to-mitochondria Ca2+ transfer is necessary for ATP production and may be especially important for meeting the high energetic demands of synaptic transmission [214] and/or serve as an important mechanism to buffer synaptic Ca2+. The ER and mitochondrial membranes are held in apposition at MAMs via a network of tether proteins [215, 216], some of which have been implicated in NDDs.

ER-mitochondrial tethers include the ER-mitochondria encounter structure (ERMES), which was identified in yeast [217]. Mammalian counterparts to the ERMES complex are still being validated, but may include the IP3 receptor, phosphofurin acidic cluster sorting protein-2 (PACS-2), B-cell receptor associated protein 31 (Bap31), PDZD8 in the ER, the mitochondrial fission protein Fis1, and the outer mitochondrial membrane protein VDAC [218]. PDZD8 is required for ER-mitochondria tethering, and loss of PDZD8 is sufficient to impact ER-mitochondrial Ca2+ dynamics in mammalian neurons [219]. Mitofusin 2 has also been proposed as a MAM tether [220], but this idea remains controversial [221, 222]. Additional proposed tethers include the oxysterol binding-related proteins ORP5 and ORP8, which can interact with mitochondrial protein tyrosine phosphatase interacting protein 51 (PTPIP51) [223]. The OMM protein synaptojanin 2 binding protein (SYNJ2BP) and the ER protein ribosome-binding protein 1 (RRBP1) are proposed to mediate specific interactions between the rough ER and mitochondria [224]. Finally, a tethering complex that may have particular importance in NDDs is comprised of the ER vesicle-associated membrane proteins-associated protein B (VAPB) and mitochondrial PTPIP51 [225, 226].

Altered ER-mitochondrial contacts in NDDs may contribute to disease pathology [227, 228]. Loss of MAM tethers can disrupt ER-mitochondrial Ca2+ transfer and so impair mitochondrial metabolism, leading to cellular energy depletion and the activation of autophagy [229, 230]. MAM disruption in NDDs could also lead to energetic compromise by impairing the synthesis of phospholipids important for mitochondrial membranes, such as cardiolipin [208, 231, 232]. This species is enriched in the mitochondrial inner membrane and is critical for proper ETC and ATP synthase function [233,234,235,236]. Finally, ER-mitochondrial associations regulate a number of processes that are commonly disrupted in NDDs such as Ca2+ handling, inflammation, axonal transport, and mitochondrial function [237]. These observations support the hypothesis that altered ER-mitochondrial communication is a common mechanism underlying NDDs.

The AD-related proteins APP and γ-secretase are all enriched at MAMs [238]. Observations of altered lipid metabolism and Ca2+ handling in both FAD and SAD suggest that these proteins may be associated with MAM dysfunction [228, 239]. Altered iCa2+ handling in AD could result from enhanced ER-mitochondrial Ca2+ transfer. The finding that ER Ca2+ concentration is increased in AD supports this view. Finally, altered lipid homeostasis resulting from dysfunctional ER/mitochondrial tethering may also impair mitochondrial energetics in AD. The MAMs of AD brain tissue and cells exhibit increased sphingomyelin hydrolysis by sphingomyelinase, which leads to increased ceramide content [240]. Increased ceramide content in AD appears sufficient to impair mitochondrial respiration [241, 242], as pharmacologic reduction of ceramide levels in AD models can rescue mitochondrial respiration [240]. Specific mechanisms by which elevated ceramide content in mitochondrial membranes may impair respiratory function and cellular bioenergetics have been detailed elsewhere [173].

Furthermore, altered ER-mitochondrial contacts and signaling are reported in PD, leading some to propose that disrupted MAMs are a significant contributor to PD pathogenesis [228, 237]. Proteins that are implicated in familial PD such as α-synuclein, PINK1, and Parkin all alter ER-mitochondrial signaling [243,244,245]. However, the specific consequences of these alterations on PD pathology are still the subject of active investigation [207].

The protein α-synuclein localizes to MAMs [245] and is thought to influence Ca2+ signaling [205, 206] and lipid metabolism [246], ultimately leading to defective ER and mitochondrial function [206]. Whereas wild-type α-synuclein promotes ER-mitochondrial contacts [206], the association of familial PD mutant α-synuclein with MAMs is disrupted. This change may represent one mechanism for compromised MAM structure and function in PD [246]. However, conflicting data suggest that overexpression of either wild-type or mutant α-synuclein can disrupt ER-mitochondrial contacts by binding to VAPB on the ER membrane and interfering with VAPB-PTPIP51 interactions [245]. Disruption of this tether complex can impair mitochondrial energetics because it compromises Ca2+ exchange between the two organelles [245]. Similar mechanisms may explain how DJ-1 mutations contribute to early-onset PD [247]. DJ-1 is normally localized to MAMs where it promotes ER-mitochondrial association and facilitates mCa2+ uptake [248]. Mutant DJ-1, as seen in PD, may disrupt MAM structure, ER-mitochondrial contacts, mCa2+ uptake, and mitochondrial bioenergetics [249]. In addition, mutations in Parkin and PINK1 may initiate PD pathogenesis via effects at MAMs. PINK and Parkin are recruited to sites of contact between ER and defective mitochondria to coordinate their autophagic clearance [244, 250]. Thus, defective PINK or Parkin may disrupt mitochondrial quality control mechanisms that rely on MAM interactions. Over time, this could impair cellular metabolism and contribute to PD pathology due to the accumulation of dysfunctional mitochondria.

Mitochondrial structural defects

Mitochondrial structure is determined by a precise balance between mitochondrial fusion and fission and membrane dynamics that are mediated by several proteins including mitofusin 1 (MFN1), mitofusin 2 (MFN2), optic atrophy 1 (OPA1), dynamin-related protein 1 (DRP1), mitochondrial fission factor (MFF), and fission 1 protein [251]. During fasting or starvation mitochondria tend to fuse [252] due to inhibition of Drp1 by PKA and AMPK [253, 254]. These changes in mitochondrial structure alter respiratory complex assembly and affect the coupling between respiration and ATP synthesis [252], thereby increasing ATP production efficiency when fuel is scarce.

Defective mitochondrial fission and fusion have been implicated in NDDs [251], and abnormal mitochondrial structure and morphology are reported in AD, PD, and HD [319]. Variants in insulin signaling pathway genes, such as AKT [1), and determining the precise temporal order of pathological cellular events is of paramount importance to development of novel therapeutic targets to combat NDDs.