Palmitoylation in Aging and Diseases with Cognitive Decline

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1		Domnic Colvin	--	2762	2023-04-21 11:50:31	\|
2	format	Jason Zhu	Meta information modification	2762	2023-04-23 03:59:41	\|

This entry is adapted from the peer-reviewed paper 10.3390/cells12030387

Protein lipidation is a common post-translational modification of proteins that plays an important role in human physiology and pathology. One form of protein lipidation, S-palmitoylation, involves the addition of a 16-carbon fatty acid (palmitate) onto proteins. This reversible modification may affect the regulation of protein trafficking and stability in membranes. From multiple experimental studies, a picture emerges whereby protein S-palmitoylation is a ubiquitous yet discrete molecular switch enabling the expansion of protein functions and subcellular localization in minutes to hours. Neural tissue is particularly rich in proteins that are regulated by S-palmitoylation.

S-palmitoylation synaptic plasticity learning and memory

1. Introduction

Numerous studies link defects in protein palmitoylation and the aberrant activity of palmitoylating/depalmitoylating enzymes with human neurological disorders and neurodegenerative diseases. Several reviews provide great references on that matter ^[1]^[2]^[3]^[4]. Below it will be discussed to what extent protein palmitoylation may contribute to pathomechanism of selected brain diseases associated with impaired neuronal plasticity and cognitive functions. Moreover, the pathomechanism of several human diseases modeled in mammals whose symptoms entail cognitive impairment involves elements of the palmitoylation machinery.

2. Palmitoylation and Aging

Cognitive abilities decline with age in mice and humans; however, the underlying mechanism is complex and debated. Several brain regions coordinate memory acquisition, consolidation, and retrieval. The prefrontal cortex is primarily involved in executive functions, including short-term or working memory and cognitive flexibility (reviewed in ^[5]). In the mouse brain, total protein expression of NMDAR subunits was previously reported to decrease with age (reviewed in ^[6]), in contrast to palmitoylation levels of these receptors. In a study by Zamzow and coworkers, young and old mice were behaviorally characterized with the Morris water maze test, and following the test, their brain samples were analyzed for palmitoylation. It was found that aging did not alter the fatty acid transport proteins or the availability of palmitate or palmitoyl-CoA; however, there were increases in the levels of palmitoylation of GluN2B, GluN2A, and Fyn in the prefrontal cortex, which most likely resulted from a disturbed cellular palmitoylation cycle and had detrimental effects on reference memory. An increase in palmitoylation was associated with reduced performance in reference memory tests and executive functioning but did not account for cognitive differences between young and old mice. Interestingly, aging led to an increase in palmitoylation of APT1 in the prefrontal cortex, which could trap the protein on the Golgi apparatus and this way contribute to the observed deficits in reference memory ^[7].

3. Neurodegenerative Diseases

3.1. Neuronal Ceroid Lipofuscinoses

The neuronal ceroid lipofuscinoses (NCLs) (also known as Batten disease) are a class of inherited nervous system disorders associated with mutations in 13 genes (CLN1 to CLN14) that most often begin in childhood and interfere with a cell’s ability to recycle a cellular residue called lipofuscin ^[8]. NCL-associated proteins are localized to lysosomes, endoplasmic reticulum, and other cellular locations; but CLN gene mutations lead primarily to dysfunction in lysosomes. One class of diseases called infantile neuronal ceroid lipofuscinosis (CLN1 disease) is caused by a mutation in CLN1, which encodes palmitoyl-protein thioesterase 1 (PPT1) ^[3] and may have several phenotypes and types of symptom progressions ^[9]. In the infantile form, difficulties in acquiring skills such as standing, walking, and talking occur between 6–12 months, and may progress with age into vision loss, seizures, psychomotor deterioration, and premature death ^[10].

The molecular mechanism explaining how PPT1-deficiency may affect cell physiology was studied in various systems. In Drosophila, loss of PPT1 causes defects in endocytic trafficking ^[11] and exocytosis and endocytosis of synaptic vesicles ^[12]. In mice, PPT1 knockout resulted in reduced expression of presynaptic proteins (e.g., SNAP25), a smaller number of synaptic vesicles, and abnormal expression of NMDAR, contributing to excitotoxicity ^[3]. PPT1 deficiency caused persistent membrane anchorage of the palmitoylated SV proteins, which hindered the recycling of the vesicle components that normally fuse with the presynaptic plasma membrane during SV exocytosis both in postmortem brain tissues from patients and in brain tissues from PPT1 knockout mice ^[13]. Altogether, loss of PPT1 in infantile ceroid lipofuscinosis may result in degeneration of excitatory and inhibitory cells and impaired synaptic transmission ^[3]^[14]. Recent developments in targeted therapies against neuronal ceroid lipofuscinoses have been reviewed ^[10]^[15].

3.2. Huntington’s Disease

Huntington’s disease (HD) is an adult-onset autosomal-dominant neurodegenerative pathology characterized by progressive cognitive decline and other psychiatric disturbances, and motor dysfunction ^[16]. Huntingtin (HTT) acts as a scaffold protein and interacts with a great number of proteins (over 350) involved in diverse cellular processes, including transcription, trafficking, cytoskeleton dynamics, and autophagy ^[17]. Mutation in the gene for HTT leads to an abnormal protein with expanded polyglutamine in its N-terminal domain and impaired protein-protein interactions.

HD is recognized as a disease of altered palmitoylation for several reasons ^[1]^[4]^[18]. Firstly, HTT is palmitoylated at C214 by ZDHHC17 and its paralog, ZDHHC13, also known as huntingtin-interacting protein (HIP14) and HIP14-like, respectively. The palmitoylation of HTT is affected by the HD mutation. In the YAC128 transgenic mouse model expressing human mutant HTT, the mutant protein was shown to be less palmitoylated compared to the WT protein ^[19]. Secondly, transgenic mice lacking ZDHHC17 or ZDHHC13 mimic the pathophysiology of HD, and the mutant HTT negatively regulates the ZDHHCs, making them less active ^[20]^[21]^[22]. Consequently, the substrates of ZDHHC17 and ZDHHC13, such as postsynaptic density protein PSD-95 and presynaptic protein SNAP25, are less palmitoylated, leading to perturbed synaptic function.

Recently, several articles advanced the understanding of the palmitoylation in the pathogenesis of HD. In YAC128 mice, there’s increased striatal neuronal NMDAR-mediated current and excitotoxicity due to changes in membrane trafficking of the protein including enhanced extrasynaptic GluN2B-type NMDAR (NMDAR2B) surface expression, which is thought to promote a shift towards activation of cell death-signaling pathways underlying HD pathology. NMDAR2B surface expression is modulated by palmitoylation at two cystine clusters in the C-terminal domain of GluN2B. Palmitoylation at the cysteine cluster II is mediated by ZDHHC13 and when reduced leads to an increase in plasma-membrane incorporation of NMDAR2B at the extrasynaptic sites. Taken together, the perturbed function of huntingtin-associated PAT, ZDHHC13, in YAC128 mice, promotes NMDA toxicity in the striatal neurons, thereby increasing their susceptibility to apoptosis and contributing to HD pathology ^[23].

Mutant HTT-induced neurotoxicity was shown to be significantly reduced by increasing the HTT palmitoylation level by inhibition of depalmitoylating APTs (acyl-protein thioesterases) with palmostatin B in YAC128 neuronal cultures ^[22]. More precisely, it is the function of APT1 rather than APT2 that seems to be involved in the HD pathology. APT1 activity was found to be elevated in CAG140 mice (an alternative transgenic HD mouse model), and the APT1-selective inhibitor ML348 was shown to rescue trafficking, synapse number, and neuronal function in CAG140 neuronal cultures and ameliorate the behavioral phenotype and neuropathology in CAG140 mice ^[24]. Importantly, damaged corticostriatal circuitry, a hallmark of HD, is mainly due to impaired transport of the brain-derived neurotrophic factor (BDNF) ^[25]^[26] and ML348 restored trafficking of BDNF in CAG140 neurons and cortical neurons derived from iPSCs of a HD patient ^[24].

Caspase-6 (CASP6), a cysteine protease, plays a key role in axonal degeneration in HD ^[27]. HTT is a substrate of CASP6, and the cleavage of mutant HTT by CASP6 results in the generation of a toxic N-terminal HTT fragment. Impaired palmitoylation contributes to CASP6-related pathogenesis in HD. CASP6 is palmitoylated at two cysteines by ZDHHC17, and palmitoylation negatively affects CASP6 activity, and therefore, its ability to generate the toxic HTT fragments. CASP6 palmitoylation was found to be decreased in brains of YAC128 mice ^[28], which can be explained by the diminished activity of ZDHHC17 in HD.

3.3. Alzheimer’s Disease

Alzheimer’s disease is a neurodegenerative brain disorder characterized by the presence of abnormal clumps (called amyloid/neuritic plaques) and neurofibrillary tangles. There is no preventive drug or cure currently available (reviewed in ^[29]^[30]). Since the damage takes place initially in the parts of the brain which are involved in memory, the symptoms include the decline in cognitive functions such as memory, processing speed, reasoning, and problem-solving; and altered behavior, including paranoia, delusions, and loss of social appropriateness. The proteolytic processing of amyloid precursor β-protein (APP) by a β-Site APP cleaving enzyme-1 (BACE1), a trans-membrane aspartyl protease, results in the formation of β-amyloid peptides (Aβ). These Aβ are known to be axonally transported in neurons and accumulate in dystrophic neurites near cerebral amyloid deposits, leading to the pathogenesis of Alzheimer’s disease.

Several proteins implicated in the development of Alzheimer’s disease are regulated by palmitoylation, and the role of palmitoylation in the pathomechanism of Alzheimer’s diseases has been reported ^[2]. The APP trafficking is regulated by a protein alcadein containing an Asp–His–His–Cys (DHHC) domain and APP interacting DHHC protein (AID)/DHHC-12. An AID/DHHC-12 mutant of which the enzyme activity was impaired by replacing the DHHC sequence with Ala–Ala–His–Ser (AAHS) showed increased non-amyloidogenic α-cleavage of APP, suggesting that protein palmitoylation was involved in the regulation of non-amyloidogenic α-secretase activity ^[31]. APP was also reported to undergo palmitoylation itself at two cysteine residues, C186 and C187, and DHHC7 and DHHC21 overexpression increased Aβ production and APP palmitoylation ^[32]^[33]. In addition, BACE1 is a substrate for ZDHHC3, ZDHHC4, ZDHHC7, ZDHHC15, and ZDHHC20 and may be palmitoylated at four cysteine residues: C474, C478, C482, and C485 ^[34]. However, the role of BACE1 palmitoylation in APP processing is debated ^[2]. Since APP palmitoylation enhances amyloidogenic processing by targeting APP to lipid rafts and enhancing its BACE1-mediated cleavage ^[32], inhibition of palmitoylation of APP formation by specific palmitoylation inhibitors was proposed as a strategy for the prevention and/or treatment of Alzheimer’s disease ^[32]. An increase in palmitoylated APP levels was also found to increase APP dimerization in cells, along with an increase in Aβ generation ^[33]. Overall, studies of APP imply that APP palmitoylation, APP dimerization, and aging contribute to the development of Alzheimer’s disease.

Postsynaptic density protein (PSD-95) levels are known to normally get diminished in aging and neurodegenerative disorders. α/β-Hydrolase-domain-containing protein 17 (ABHD17) in neurons selectively reduces PSD-95 palmitoylation and synaptic clustering of PSD-95. ABHD17 inhibition was shown to increase the level of PSD-95 by selectively blocking its depalmitoylation and reversing the Aβ effects on synapses ^[35]. Interestingly, increasing PSD-95 by epigenetic editing in aged or Alzheimer’s disease model mice has been shown to enhance cognitive function ^[36]. Therefore, selectively blocking PSD-95 depalmitoylation may serve as a viable therapeutic option for developing a treatment for Alzheimer’s disease. Most recently, to address this issue, Dore et al. performed experiments in organotypic hippocampal slices with an increased Aβ level. It was found that palmostatin B (an ABHD17 inhibitor) rescued Aβ-induced synaptic depression and Aβ-mediated effects on dendritic spines ^[37]. It was concluded that increasing PSD-95 synaptic content via palmitoylation may protect synapses from Aβ-induced synaptic deficits by reducing NMDA receptor metabotropic function.

4. Neuropsychiatric Disorders

4.1. Major Depressive Disorder

Clinical depression, or major depressive disorder (MDD), is a common mental disorder described with a spectrum of symptoms, such as pervasive low mood and vegetative symptoms, along with deficits in cognitive and psychomotor processes ^[38]. The underlying mechanism is extremely heterogeneous and complex, which hinders the development of treatments that are effective for all depressed individuals. Abnormalities in the neurotransmitter serotonin levels and efficacy of serotonergic neurotransmission are thought to play a crucial role in MDD (reviewed in ^[39]), and thus, the primary treatment involves the use of selective serotonin reuptake inhibitors (SSRIs). The role of serotonin receptors in the pathomechanism of depression has been discussed but remains debated (reviewed by ^[40]). Existing evidence links palmitoylation of serotonin receptors with MDD (reviewed by ^[1]). Most recently, it has been shown that serotonin 1A receptors (5-HT1AR) are implicated in MDD. In particular, palmitoylated 5-HT1AR has been shown in human and rodent brains and is a substrate for ZDHHC21. Depressive-like behavior in animals has been linked to reduced brain ZDHHC21 expression and attenuated 5-HT1AR palmitoylation. Furthermore, analysis of post-mortem brain samples of MDD patients who died by suicide were found to corroborate results from animals. This suggests that downregulation of 5-HT1AR palmitoylation is a mechanism involved in depression ^[41]. Altogether, MDD may be associated with reduced brain ZDHHC21 expression and attenuated 5-HT1AR palmitoylation.

Serotonin transporters are responsible for the clearance of serotonin from the extraneuronal space. Serotonin modulates mood, aggression, motivation, appetite, sleep, cognition, and sexual function. An SSRI, fluoxetine, which has been used to enhance serotonin efficacy, has been recently implicated in affecting cellular glucose uptake by palmitoylation of glucose transporters GLUT3 and GLUT1. This suggests that some actions of fluoxetine may be ascribed to palmitoylation of non-target proteins ^[42].

Another study introduced the relation of peripheral spared nerve injury (SNI)-induced interleukin 6 (IL-6) overexpression with depression-like behaviors. Astrocytes that serve as an important supporting cell in modulating glutamatergic synaptic transmission were demonstrated to release IL-6 in basolateral amygdala (BLA) as a result of SNI. This enhanced the abundance of ZDHHC2 in the synaptosome and ZDHHC3 in the Golgi apparatus, promoting PSD-95 palmitoylation to thereby increase the recruitment of GluR1 and GluN2B at the synapses. Suppression of IL-6 or PSD-95 palmitoylation attenuated the synaptic accumulation of GluR1 and GluN2B in BLA and improved depression-like behaviors that were induced by SNI ^[43].

4.2. Schizophrenia

Schizophrenia is a chronic mental disorder interfering with the ability to think clearly, management of emotions, and decision making. Various PTMs, particularly palmitoylation, have been found to be differentially expressed in several pathways that are hypothesized to be dysregulated in schizophrenia ^[2]. For example, membrane association and transport of phosphodiesterase 10A (PDE10A) throughout dendritic processes in primary mouse striatal neuron cultures require palmitoylation at C11 of PDE10A2, likely by the palmitoyl acyltransferases ZDHHC7/19 ^[44]. Many reports also suggest that the abnormalities of neurotransmitter receptor trafficking, targeting, dendritic localization, recycling, and degradation in the brain during schizophrenia are due to dysregulation of protein palmitoylation. A mass spectrometry study which identified 219 palmitoylated proteins in a normal human frontal cortex showed significant reductions in the levels of vesicular glutamate transporter 1 (VGLUT1), myelin basic protein (MBP), and Ras family proteins when palmitoylation was assayed and compared in the dorsolateral prefrontal cortices from 16 schizophrenia patients and their pair-matched comparison subjects ^[45]. In addition, rats chronically treated with haloperidol showed the same pattern and unchanged extent of palmitoylation. These two results suggest that there is a 20% reduction in the palmitoylation level of many proteins in the frontal cortex in schizophrenia, which is not due to chronic antipsychotic treatment ^[45].

Similarly, a cohort study of approximately 36 individuals was performed to substantiate a bivariate correlation analysis of PPT1 enzymatic activity in first-episode psychosis (FEP) patients with a psychiatric assessment score. It established that the higher enzymatic PPT1 activity in FEP schizophrenia patients is associated with increased positive and negative syndrome scaling values, indicating more serious rates of developing psychosis ^[46]. Interestingly, there are also some genetic deletions disturbing regular palmitoylation processes that are associated with the risk of developing schizophrenia. The deletion of ZDHHC8, which codes for PAT, contributed to the development of schizophrenic symptoms, including alterations in cellular, anatomical, and behavioral levels. Basically, a ZDHHC8 knockout mice demonstrated reduced palmitoylation of Cdc42 and Ras-related C3 botulinum toxin substrate 1 (Rac1), altering neuron polarity and showing some deficits in the connectivity between the hippocampus and the medial prefrontal cortex, eventually contributing to impaired working memory performance ^[47]. To better understand the genetic basis of schizophrenia, a large-scale integrative analysis of genome-wide association study (GWAS) and expression quantitative trait loci (eQTLs) data detected ZDHHC18 and ZDHHC5 as two of the five significant genes associated with schizophrenia ^[48].

5. Neurological Disorders

Chromosome X-Linked Intellectual Disability

Intellectual disability is a neurodevelopmental disorder occurring in 1–3% of the general population ^[49]. Several clinical signs/symptoms have been associated with X-linked intellectual disability, including developmental delay with severe speech delay, dysmorphic features, epilepsy, or abnormal brain visualized with magnetic resonance imaging. However, the most prevalent features are the deficits in intellectual functions, such as learning and problem solving, and in adaptive functions, such as practical and social skills ^[50]^[51]. In humans, X-chromosome-linked intellectual disability has been linked to over 100 gene mutations, including ZDHHC9 and ZDHHC15 genes ^[52]^[53]^[54]. Mutations in ZDHHC9 are more prevalent in males ^[55] and may impair ZDHHC9 enzyme activity by affecting its auto-S-fatty acylation levels ^[56]. Interestingly, ZDHHC9 knockout male mice exhibited neurological impairments observed in humans, such as hypotonia and impaired performance in a spatial learning task ^[57]. In addition, ZDHHC9 knockout mice exhibited reduced corpus callosum volume, similar to that seen in humans with a ZDHHC9 mutation ^[58]. This proves that ZDHHC9 activity may be crucial for maintaining some of the higher brain functions, including cognitive abilities. At the current state, the molecular substrates for ZDHHC9 in these processes remain unknown. Finally, the ZDHHC9 mutant mouse line could provide a model system to better understand the mechanism of pathological neurodevelopmental changes that lead to intellectual disabilities associated with X-chromosome mutations.

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