Loss of Depalmitoylation Exaggerates Synaptic Upscaling and Leads to Neuroinflammation in a Lysosomal Storage Disease

Palmitoylation and depalmitoylation are the dichotomic processes of lipid modification regulating protein trafficking, recycling, and degradation, thereby controlling proteostasis. Despite our understanding of palmitoylation, depalmitoylation is far less studied. Here, we study a lysosomal depalmitoylating enzyme, palmitoyl-protein thioesterase 1 (PPT1), associated with the devastating neurodegenerative condition CLN1 disease and show that dark-rearing Ppt1-/- mice, which induces synaptic upscaling in vivo, worsen the symptoms. In Ppt1-/- cortical neurons, upscaling induction triggers exaggerated responses of synaptic calcium-permeable AMPA receptors composed of palmitoylated GluA1 subunits. Consequently, Ppt1-/- visual cortex exhibits hypersynchrony in vivo. Remarkably, we also find an overload of palmitoylated A-kinase anchor protein 5 (Akap5) in Ppt1-/- mouse brains, leading to microglial activation through NFAT. These findings indicate Ppt1 acts as a gatekeeper of homeostatic plasticity by regulating the proteostasis of palmitoylated synaptic proteins. Moreover, our results suggest that perturbed depalmitoylation results in neuroinflammation, which is common to neurodegenerative diseases.

How Antimalarials and Antineoplastic Drugs can Interact in Combination Therapies: a Perspective on the Role of PPT1 Enzyme

: Antimalarial drugs from different classes have demonstrated anticancer effects in different types of cancer cells, but their complete mode of action in cancer remains unknown. Recently, several studies reported the important role of palmitoyl-protein thioesterase 1 (PPT1), a lysosomal enzyme, as the molecular target of chloroquine and its derivates in cancer. It was also found that PPT1 is overexpressed in different types of cancer, such as breast, colon, etc. Our group has found a synergistic interaction between antimalarial drugs, such as mefloquine, artesunate and chloroquine and antineoplastic drugs in breast cancer cells, but the mechanism of action was not determined. Here, we describe the importance of autophagy and lysosomal inhibitors in tumorigenesis and hypothesize that other antimalarial agents besides chloroquine could also interact with PPT1 and inhibit the mechanistic target of rapamycin (mTOR) signalling, an important pathway in cancer progression. We believe that PPT1 inhibition results in changes in the lysosomal metabolism that result in less accumulation of antineoplastic drugs in lysosomes, which increases the bioavailability of the antineoplastic agents. Taken together, these mechanisms help to explain the synergism of antimalarial and antineoplastic agents in cancer cells.

PPT1 Deficiency-Induced GABAAR Hyperpalmitoylation Impairs Synaptic Transmission And Memory Formation

Background: Palmitoylation is a reversible and dynamic process involving addition of palmitic acid to cysteine residues of proteins. Studies have indicated that a variety of neuronal receptors, including glutamate receptors such as AMPAR, NMDAR, and GABAAR, are palmitoylated, which contributes to the dynamic modulation of synaptic strength in response to neuronal activity. However, little is known about the depalmitoylation of these receptors. Methods: A mouse model with a lost function mutation knock-in of palmitoyl protein thioesterase 1 (PPT1), an important enzyme for depalmitoylation, was employed to mimic human disease of infantile neuronal ceroid lipofuscinosis (INCLs). Immunofluorescent staining, Western blotting, biochemical assays, electrophysiological recording and behavioural tests were used to measure the effects of PPT1 deficiency.Results: We identified for the first time that the GABAARα1 subunit rather than AMPAR is the substrate of PPT1. In PPT1-deficient mice, excessive palmitoylation and extended membrane location of GABAAR were detected. Simultaneously, spatial learning and memory deficits with dysregulation of neuronal network γ oscillation and impairment of long-term plasticity were shown in the mice at as early as 2-month-old. Application of N-tert-butylhydroxylamine hydrochloride, a thioesterase mimetic, attenuated PPT1 mutation-induced GABAAR hyper-palmitoylation and its membrane accumulation with improved neuronal transmission and memory functions in the mice. Conclusions: These data provide new insights into the mechanisms of neuronal disorder caused by depalmitoylation deficiency and offer a clue for further intervention for INCLs and other neurodegenerative diseases.

First-in-human phase I, pharmacokinetic (PK), and pharmacodynamic (PD) study of oral GNS561, a palmitoyl-protein thioesterase 1 (PPT1) inhibitor, in patients with primary and secondary liver malignancies.

e16175 Background: GNS561 belongs to a novel generation of drug blocking cancer cell proliferation by inhibiting late-stage autophagy and dose-dependent accumulation of enlarged lysosomes by interacting with palmitoyl-protein thioesterase-1 (PPT1). Methods: This phase I, multicenter, open-label, dose-escalation trial (3+3 design) explored two dosing schedules: one single oral intake three times a week and twice daily (BID) continuous oral intake of GNS561 in patients with advanced primary and secondary liver cancers (NCT03316222). The primary objective was to determine recommended phase II dose (RP2D) and schedule for further clinical development. The secondary objectives included a preliminary evaluation of the safety, pharmacokinetic (PK), pharmacodynamics (PD), and antitumor activity of GNS561. Results: Nineteen treatment-refractory patients were enrolled and were evaluable for primary endpoint: intrahepatic cholangiocarcinoma (iCCA) (9), hepatocellular carcinoma (HCC) (7), pancreatic ductal adenocarcinoma (PDAC) (2) and colorectal cancer (CRC) (1). Median age was 60, 89% were male and 37% had received 3 or more lines as prior cancer therapies. Dose escalation ranged from 50 mg three times a week to 200 mg BID. No dose-limiting toxicity were observed. Treatment-related adverse events were grade 1-2 gastrointestinal toxicity, primarily nausea/vomiting, occurring in 8 patients (42%) and diarrhea in 4 patients (21%). Occurrence of nausea/vomiting despite antiemetic prophylaxis prevented increasing doses above 200 mg BID. GNS561 displayed favorable bioavailability with interpatient variability (CV%: 13 to 223% and 21 to 98.2% on plasma concentrations on cycle 1 day 1 and cycle 2 day 1 respectively), and dose proportional exposure in plasma. GNS561 concentrations accumulated after multiple administration (2.60 - 9.00-fold) and exhibited a long half-life. Plasma and liver concentrations at doses ranging 100-200 mg BID were comparable to therapeutic exposures in preclinical models. Five patients (3 HCC and 2 iCCA) experienced tumor stabilization according to RECIST 1.1 criteria, including a minor response (-23%). Conclusions: GNS561 RP2D single agent was set at 200 mg BID based on this favorable safety profile and plasma exposure, GNS561 will be next further evaluated in monotherapy and in combination with checkpoint inhibitors considering the autophagic activity restriction of major histocompatibility complex-1 promotion of immune invasion. Clinical trial information: NCT03316222.

GNS561, a clinical-stage PPT1 inhibitor, is efficient against hepatocellular carcinoma via modulation of lysosomal functions

Background & AimsHepatocellular carcinoma (HCC) is the most frequent primary liver cancer. Autophagy inhibitors have been extensively studied in cancer but, to date, none has reached efficacy in clinical trials.Approach & ResultsTo explore the antitumor effects of GNS561, a new autophagy inhibitor, we first achieved in vitro assays using various human cancer cell lines. Having demonstrated that GNS561 displayed high liver tropism using mass spectrometry imaging, the potency of GNS561 on tumor was evaluated in vivo in two HCC models (human orthotopic patient-derived xenograft mouse model and diethylnitrosanime-induced cirrhotic immunocompetent rat model). Oral administration of GNS561 was well tolerated and decreased tumor growth in these two models. GNS561 mechanism of action was assessed in an HCC cell line, HepG2. We showed that due to its lysosomotropic properties, GNS561 could reach and inhibited its enzyme target, palmitoyl-protein thioesterase 1, resulting in lysosomal unbound Zn2+ accumulation, impairment of cathepsin activity, blockage of autophagic flux, altered location of mTOR, lysosomal membrane permeabilization, caspase activation and cell death.ConclusionsGNS561, currently tested in a global Phase 1b/2a clinical trial against primary liver cancer, represents a promising new drug candidate and a hopeful therapeutic strategy in cancer treatment.With an estimated 782,000 deaths in 2018, hepatocellular carcinoma (HCC) stands as the most common primary liver cancer and constitutes the fourth leading cause of cancer-related death worldwide (1). The rising incidence of HCC, the high worldwide mortality rate, and limited therapeutic options at advanced stages, make HCC a significant unmet medical need.Autophagy-related lysosomal cell death, either alone or in connection with several other cell death pathways, has been recognized as a major target for cancer therapy (2). Dysregulated autophagic-lysosomal activity and mTOR signaling were shown to allow cancer cells to become resistant to the cellular stress induced by chemotherapy and targeted therapy (3). Recently, several lysosome-specific inhibitors were shown to target palmitoyl-protein thioesterase 1 (PPT1), resulting in the modulation of protein palmitoylation and autophagy, and antitumor activity in melanoma and colon cancer models (4, 5).Chloroquine (CQ) and hydroxychloroquine (HCQ) have been used for more than 50 years to prevent and treat malarial infections and autoimmune diseases. Based on the lysosomotropic properties and the capacity for autophagy inhibition, these molecules have been proposed as active drugs in cancer (6–9). Over 40 clinical trials have been reported to evaluate the activity of both CQ or HCQ as single agent or in combination with chemotherapy in several tumor types (6–8. However, the required drug concentrations to inhibit autophagy were not achieved in humans, leading to inconsistent results in cancer clinical trials (5, 10). This prompted research to identify novel compounds with potent inhibitory properties against autophagy for cancer therapy.We previously reported that GNS561 was efficient in intrahepatic cholangiocarcinoma (iCCA) by inhibiting late-stage autophagy (11). In this study, we investigated the mechanism of action of GNS561. We identified lysosomal PPT1 as a target of GNS561. Exposure to GNS561 induced lysosomal accumulation of unbound zinc ion (Zn2+), inhibition of PPT1 and cathepsin activity, blockage of autophagic flux and mTOR displacement. Interestingly, these effects resulted in lysosomal membrane permeabilization (LMP) and caspase activation that led to cancer cell death. This mechanism was associated with dose-dependent inhibition of cancer cell proliferation and tumor growth inhibition in two HCC in vivo models. These data establish PPT1 and lysosomes as major targets for cancer cells and led to the development of a clinical program investigating the effects of GNS561 in patients with advanced HCC.

Comparative proteomic profiling reveals mechanisms for early spinal cord vulnerability in CLN1 disease

CLN1 disease is a fatal inherited neurodegenerative lysosomal storage disease of early childhood, caused by mutations in the CLN1 gene, which encodes the enzyme Palmitoyl protein thioesterase-1 (PPT-1). We recently found significant spinal pathology in Ppt1-deficient (Ppt1−/−) mice and human CLN1 disease that contributes to clinical outcome and precedes the onset of brain pathology. Here, we quantified this spinal pathology at 3 and 7 months of age revealing significant and progressive glial activation and vulnerability of spinal interneurons. Tandem mass tagged proteomic analysis of the spinal cord of Ppt1−/−and control mice at these timepoints revealed a significant neuroimmune response and changes in mitochondrial function, cell-signalling pathways and developmental processes. Comparing proteomic changes in the spinal cord and cortex at 3 months revealed many similarly affected processes, except the inflammatory response. These proteomic and pathological data from this largely unexplored region of the CNS may help explain the limited success of previous brain-directed therapies. These data also fundamentally change our understanding of the progressive, site-specific nature of CLN1 disease pathogenesis, and highlight the importance of the neuroimmune response. This should greatly impact our approach to the timing and targeting of future therapeutic trials for this and similar disorders.

Identification of palmitoyl protein thioesterase 1 substrates defines roles for synaptic depalmitoylation

SUMMARYWe report here the identification of substrates of the depalmitoylating enzyme PPT1 by quantitative mass spectrometry. We first used a stringent Acyl Resin-Assisted Capture (Acyl RAC) screen in which PPT1 knockout (KO) mouse brain proteins showing increased in vivo palmitoylation are identified as putative PPT1 substrates. We then validated hits by directly depalmitoylating with PPT1 to confirm bona fide substrates. This novel two-step screen identified >100 substrates not previously known to be depalmitoylated by PPT1, including a wide range of channels/transporters, G-proteins, endo/exocytic components, synaptic adhesion molecules, and mitochondrial proteins. Interestingly, many sites of depalmitoylation on transmembrane proteins were located in extracellular domains facing the synaptic cleft. For this group of substrates, depalmitoylation appears to facilitate disulfide bond formation. Collectively, these diverse substrates may explain the many facets of CLN1 disease caused by the loss of PPT1 function.Highlights10% of palmitoylated proteins are palmitoyl protein thioesterase 1 (PPT1) substratesUnbiased proteomic approaches identify 9 broad classes of substrates, including synaptic adhesion molecules and endocytic proteinsPPT1 depalmitoylates several transmembrane proteins in their extracellular domainsDepalmitoylation allows for disulfide bond formation in some PPT1 substratesProtein degradation does not require depalmitoylation by PPT1Other palmitoylated Neuronal Ceroid Lipofuscinosis proteins are impacted by deficiency of PPT1, indicating a common disease pathway

Mice deficient in the lysosomal enzyme palmitoyl-protein thioesterase 1 (PPT1) display a complex retinal phenotype

Neuronal ceroid lipofuscinosis (NCL) type 1 (CLN1) is a neurodegenerative storage disorder caused by mutations in the gene encoding the lysosomal enzyme palmitoyl-protein thioesterase 1 (PPT1). CLN1 patients suffer from brain atrophy, mental and motor retardation, seizures, and retinal degeneration ultimately resulting in blindness. Here, we performed an in-depth analysis of the retinal phenotype of a PPT1-deficient mouse, an animal model of this condition. Reactive astrogliosis and microgliosis were evident in mutant retinas prior to the onset of retinal cell loss. Progressive accumulation of storage material, a pronounced dysregulation of various lysosomal proteins, and accumulation of sequestosome/p62-positive aggregates in the inner nuclear layer also preceded retinal degeneration. At advanced stages of the disease, the mutant retina was characterized by a significant loss of ganglion cells, rod and cone photoreceptor cells, and rod and cone bipolar cells. Results demonstrate that PPT1 dysfunction results in early-onset pathological alterations in the mutant retina, followed by a progressive degeneration of various retinal cell types at relatively late stages of the disease. Data will serve as a reference for future work aimed at developing therapeutic strategies for the treatment of retinal degeneration in CLN1 disease.