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Domingues N, Pires J, Milosevic I, Raimundo N. Role of lipids in interorganelle communication. Trends Cell Biol 2024:S0962-8924(24)00095-3. [PMID: 38866684 DOI: 10.1016/j.tcb.2024.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 06/14/2024]
Abstract
Cell homeostasis and function rely on well-orchestrated communication between different organelles. This communication is ensured by signaling pathways and membrane contact sites between organelles. Many players involved in organelle crosstalk have been identified, predominantly proteins and ions. The role of lipids in interorganelle communication remains poorly understood. With the development and broader availability of methods to quantify lipids, as well as improved spatiotemporal resolution in detecting different lipid species, the contribution of lipids to organelle interactions starts to be evident. However, the specific roles of various lipid molecules in intracellular communication remain to be studied systematically. We summarize new insights in the interorganelle communication field from the perspective of organelles and discuss the roles played by lipids in these complex processes.
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Affiliation(s)
- Neuza Domingues
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Joana Pires
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal
| | - Ira Milosevic
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nuno Raimundo
- Multidisciplinary Institute of Ageing, University of Coimbra, Coimbra, Portugal; Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA; Penn State Cancer Institute, Hershey, PA, USA.
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2
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Nyame K, Xiong J, de Jong AP, Alsohybe HN, Raaben M, Hartmann G, Simcox JA, Blomen VA, Abu-Remaileh M. PLA2G15 is a Lysosomal BMP Hydrolase with Ester Position Specificity and its Targeting Ameliorates Lysosomal Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597919. [PMID: 38895439 PMCID: PMC11185675 DOI: 10.1101/2024.06.07.597919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Lysosomes catabolize lipids and other biological molecules, a function essential for cellular and organismal homeostasis. Key to lipid catabolism in the lysosome is bis(monoacylglycero)phosphate (BMP), a major lipid constituent of intralysosomal vesicles (ILVs) and a stimulator of lipid-degrading enzymes. BMP levels are altered in a broad spectrum of human conditions, including neurodegenerative diseases. Although BMP synthase was recently discovered, it has long been thought that BMP's unique stereochemistry confers resistance to acid phospholipases, a requirement for its role in the lysosome. Here, we demonstrate that PLA2G15, a major lysosomal phospholipase, efficiently hydrolyzes BMP with primary esters regardless of stereochemistry. Interestingly, we discover that BMP's unique esterification position is what confers resistance to hydrolysis. Purified PLA2G15 catabolizes most BMP species derived from cell and tissue lysosomes under acidic conditions. Furthermore, PLA2G15 catalytic activity against synthesized BMP stereoisomers with primary esters was comparable to its canonical substrates. Conversely, BMP with secondary esters is intrinsically stable in vitro and requires acyl migration for hydrolysis in lysosomes. Consistent with our biochemical data, PLA2G15-deficient tissues and cells accumulate multiple BMP species, a phenotype reversible by supplementing wildtype PLA2G15 but not its catalytically dead mutant. Increasing BMP levels by targeting PLA2G15 reverses the cholesterol accumulation phenotype in Niemann Pick Disease Type C (NPC1) patient fibroblasts and significantly ameliorate disease pathologies in NPC1-deficient mice leading to extended lifespan. Our findings establish the rules that govern the stability of BMP in the lysosome and identify PLA2G15 as a lysosomal BMP hydrolase and as a potential target for modulating BMP levels for therapeutic intervention.
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3
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Domingues N, Calcagni' A, Pires J, Freire SR, Herz NJ, Huynh T, Wieciorek K, Moreno MJ, Outeiro TF, Girão H, Milosevic I, Ballabio A, Raimundo N. Loss of the lysosomal protein CLN3 modifies the lipid content of the nuclear envelope leading to DNA damage and activation of YAP1 pro-apoptotic signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.31.596474. [PMID: 38853929 PMCID: PMC11160784 DOI: 10.1101/2024.05.31.596474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Batten disease is characterized by early-onset blindness, juvenile dementia and death during the second decade of life. The most common genetic causes are mutations in the CLN3 gene encoding a lysosomal protein. There are currently no therapies targeting the progression of the disease, mostly due to the lack of knowledge about the disease mechanisms. To gain insight into the impact of CLN3 loss on cellular signaling and organelle function, we generated CLN3 knock-out cells in a human cell line (CLN3-KO), and performed RNA sequencing to obtain the cellular transcriptome. Following a multi-dimensional transcriptome analysis, we identified the transcriptional regulator YAP1 as a major driver of the transcriptional changes observed in CLN3-KO cells. We further observed that YAP1 pro-apoptotic signaling is hyperactive as a consequence of CLN3 functional loss in retinal pigment epithelia cells, and in the hippocampus and thalamus of CLN3 exΔ7/8 mice, an established model of Batten disease. Loss of CLN3 activates YAP1 by a cascade of events that starts with the inability of releasing glycerophosphodiesthers from CLN3-KO lysosomes, which leads to perturbations in the lipid content of the nuclear envelope and nuclear dysmorphism. This results in increased number of DNA lesions, activating the kinase c-Abl, which phosphorylates YAP1, stimulating its pro-apoptotic signaling. Altogether, our results highlight a novel organelle crosstalk paradigm in which lysosomal metabolites regulate nuclear envelope content, nuclear shape and DNA homeostasis. This novel molecular mechanism underlying the loss of CLN3 in mammalian cells and tissues may open new c-Abl-centric therapeutic strategies to target Batten disease.
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4
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Yin Q, Yang C. Exploring lysosomal biology: current approaches and methods. BIOPHYSICS REPORTS 2024; 10:111-120. [PMID: 38774350 PMCID: PMC11103719 DOI: 10.52601/bpr.2023.230028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 01/04/2024] [Indexed: 05/24/2024] Open
Abstract
Lysosomes are the degradation centers and signaling hubs in the cell. Lysosomes undergo adaptation to maintain cell homeostasis in response to a wide variety of cues. Dysfunction of lysosomes leads to aging and severe diseases including lysosomal storage diseases (LSDs), neurodegenerative disorders, and cancer. To understand the complexity of lysosome biology, many research approaches and tools have been developed to investigate lysosomal functions and regulatory mechanisms in diverse experimental systems. This review summarizes the current approaches and tools adopted for studying lysosomes, and aims to provide a methodological overview of lysosomal research and related fields.
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Affiliation(s)
- Qiuyuan Yin
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650091, China
| | - Chonglin Yang
- State Key Laboratory of Conservation and Utilization of Bio-resources in Yunnan and Center for Life Sciences, School of Life Sciences, Yunnan University, Kunming 650091, China
- Southwest United Graduate School, Kunming 650092, China
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5
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Nyame K, Hims A, Aburous A, Laqtom NN, Dong W, Medoh UN, Heiby JC, Xiong J, Ori A, Abu-Remaileh M. Glycerophosphodiesters inhibit lysosomal phospholipid catabolism in Batten disease. Mol Cell 2024; 84:1354-1364.e9. [PMID: 38447580 PMCID: PMC10999246 DOI: 10.1016/j.molcel.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/08/2023] [Accepted: 02/07/2024] [Indexed: 03/08/2024]
Abstract
Batten disease, the most prevalent form of neurodegeneration in children, is caused by mutations in the CLN3 gene, which encodes a lysosomal transmembrane protein. CLN3 loss leads to significant accumulation of glycerophosphodiesters (GPDs), the end products of glycerophospholipid catabolism in the lysosome. Despite GPD storage being robustly observed upon CLN3 loss, the role of GPDs in neuropathology remains unclear. Here, we demonstrate that GPDs act as potent inhibitors of glycerophospholipid catabolism in the lysosome using human cell lines and mouse models. Mechanistically, GPDs bind and competitively inhibit the lysosomal phospholipases PLA2G15 and PLBD2, which we establish to possess phospholipase B activity. GPDs effectively inhibit the rate-limiting lysophospholipase activity of these phospholipases. Consistently, lysosomes of CLN3-deficient cells and tissues accumulate toxic lysophospholipids. Our work establishes that the storage material in Batten disease directly disrupts lysosomal lipid homeostasis, suggesting GPD clearance as a potential therapeutic approach to this fatal disease.
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Affiliation(s)
- Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Andy Hims
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Aya Aburous
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Nouf N Laqtom
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Uche N Medoh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Julia C Heiby
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA; Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Jian Xiong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute, Jena, Germany
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA; The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA 94305, USA.
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6
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Haney MS, Pálovics R, Munson CN, Long C, Johansson PK, Yip O, Dong W, Rawat E, West E, Schlachetzki JCM, Tsai A, Guldner IH, Lamichhane BS, Smith A, Schaum N, Calcuttawala K, Shin A, Wang YH, Wang C, Koutsodendris N, Serrano GE, Beach TG, Reiman EM, Glass CK, Abu-Remaileh M, Enejder A, Huang Y, Wyss-Coray T. APOE4/4 is linked to damaging lipid droplets in Alzheimer's disease microglia. Nature 2024; 628:154-161. [PMID: 38480892 PMCID: PMC10990924 DOI: 10.1038/s41586-024-07185-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/09/2024] [Indexed: 03/26/2024]
Abstract
Several genetic risk factors for Alzheimer's disease implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells1. However, the relationship between lipid metabolism in glia and Alzheimer's disease pathology remains poorly understood. Through single-nucleus RNA sequencing of brain tissue in Alzheimer's disease, we have identified a microglial state defined by the expression of the lipid droplet-associated enzyme ACSL1 with ACSL1-positive microglia being most abundant in patients with Alzheimer's disease having the APOE4/4 genotype. In human induced pluripotent stem cell-derived microglia, fibrillar Aβ induces ACSL1 expression, triglyceride synthesis and lipid droplet accumulation in an APOE-dependent manner. Additionally, conditioned media from lipid droplet-containing microglia lead to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for Alzheimer's disease with microglial lipid droplet accumulation and neurotoxic microglia-derived factors, potentially providing therapeutic strategies for Alzheimer's disease.
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Affiliation(s)
- Michael S Haney
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Róbert Pálovics
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Christy Nicole Munson
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Chris Long
- Department of Materials Science & Engineering Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Patrik K Johansson
- Department of Materials Science & Engineering Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Oscar Yip
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Wentao Dong
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Eshaan Rawat
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Elizabeth West
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Johannes C M Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San Diego, San Diego, CA, USA
| | - Andy Tsai
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Ian Hunter Guldner
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Bhawika S Lamichhane
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Amanda Smith
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Nicholas Schaum
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Kruti Calcuttawala
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Andrew Shin
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Yung-Hua Wang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Chengzhong Wang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
| | - Nicole Koutsodendris
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Geidy E Serrano
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ, USA
| | - Thomas G Beach
- Banner Alzheimer's Institute and Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Eric M Reiman
- Banner Alzheimer's Institute and Arizona Alzheimer's Consortium, Phoenix, AZ, USA
| | - Christopher K Glass
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, USA
| | - Monther Abu-Remaileh
- The Institute for Chemistry, Engineering & Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Annika Enejder
- Department of Materials Science & Engineering Department, Stanford University School of Medicine, Stanford, CA, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Development and Stem Cell Biology Graduate Program, University of California, San Francisco, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, CA, USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- The Phil and Penny Knight Initiative for Brain Resilience, Stanford University, Stanford, CA, USA.
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7
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Schulz A, Patel N, Brudvig JJ, Stehr F, Weimer JM, Augustine EF. The parent and family impact of CLN3 disease: an observational survey-based study. Orphanet J Rare Dis 2024; 19:125. [PMID: 38500130 PMCID: PMC10949783 DOI: 10.1186/s13023-024-03119-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/03/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND CLN3 disease (also known as CLN3 Batten disease or Juvenile Neuronal Ceroid Lipofuscinosis) is a rare pediatric neurodegenerative disorder caused by biallelic mutations in CLN3. While extensive efforts have been undertaken to understand CLN3 disease etiology, pathology, and clinical progression, little is known about the impact of CLN3 disease on parents and caregivers. Here, we investigated CLN3 disease progression, clinical care, and family experiences using semi-structured interviews with 39 parents of individuals with CLN3 disease. Analysis included response categorization by independent observers and quantitative methods. RESULTS Parents reported patterns of disease progression that aligned with previous reports. Insomnia and thought- and mood-related concerns were reported frequently. "Decline in visual acuity" was the first sign/symptom noticed by n = 28 parents (70%). A minority of parents reported "behavioral issues" (n = 5, 12.5%), "communication issues" (n = 3, 7.5%), "cognitive decline" (n = 1, 2.5%), or "seizures" (n = 1, 2.5%) as the first sign/symptom. The mean time from the first signs or symptoms to a diagnosis of CLN3 disease was 2.8 years (SD = 4.1). Misdiagnosis was common, being reported by n = 24 participants (55.8%). Diagnostic tests and treatments were closely aligned with observed symptoms. Desires for improved or stabilized vision (top therapeutic treatment concern for n = 14, 32.6%), cognition (n = 8, 18.6%), and mobility (n = 3, 7%) dominated parental concerns and wishes for therapeutic correction. Family impacts were common, with n = 34 (81%) of respondents reporting a financial impact on the family and n = 20 (46.5%) reporting marital strain related to the disease. CONCLUSIONS Collectively, responses demonstrated clear patterns of disease progression, a strong desire for therapies to treat symptoms related to vision and cognition, and a powerful family impact driven by the unrelenting nature of disease progression.
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Affiliation(s)
- Angela Schulz
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nita Patel
- Amicus Therapeutics, Princeton, NJ, USA.
| | - Jon J Brudvig
- Amicus Therapeutics, Princeton, NJ, USA
- Pediatrics & Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | | | - Jill M Weimer
- Amicus Therapeutics, Princeton, NJ, USA
- Pediatrics & Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
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8
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Zhou Y, Wang Q, Chanmungkalakul S, Wu X, Xiao H, Miao R, Liu X, Fang Y. Fluorogenic Rhodamine Probes with Pyrrole Substitution Enables STED and Lifetime Imaging of Lysosomes in Live Cells. Chemistry 2024; 30:e202303707. [PMID: 38221317 DOI: 10.1002/chem.202303707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 01/16/2024]
Abstract
Fluorogenic dyes with high brightness, large turn-on ratios, excellent photostability, favorable specificity, low cytotoxicity, and high membrane permeability are essential for high-resolution fluorescence imaging in live cells. In this study, we endowed these desirable properties to a rhodamine derivative by simply replacing the N, N-diethyl group with a pyrrole substituent. The resulting dye, Rh-NH, exhibited doubled Stokes shifts (54 nm) and a red-shift of more than 50 nm in fluorescence spectra compared to Rhodamine B. Rh-NH preferentially exists in a non-emissive but highly permeable spirolactone form. Upon binding to lysosomes, the collective effects of low pH, low polarity, and high viscosity endow Rh-NH with significant fluorescence turn-on, making it a suitable candidate for wash-free, high-contrast lysosome tracking. Consequently, Rh-NH enabled us to successfully explore stimulated emission depletion (STED) super-resolution imaging of lysosome dynamics, as well as fluorescence lifetime imaging of lysosomes in live cells.
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Affiliation(s)
- Ying Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Qiuping Wang
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Supphachok Chanmungkalakul
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Xia Wu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Hui Xiao
- Colledge of Life Science, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Rong Miao
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
| | - Xiaogang Liu
- Fluorescence Research Group, Singapore University of Technology and Design, 8 Somapah Road, Singapore, 487372, Singapore
| | - Yu Fang
- Key Laboratory of Applied Surface and Colloid Chemistry (Ministry of Education), School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, 710119, P. R. China
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9
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Ha HT, Liu S, Nguyen XT, Vo LK, Leong NC, Nguyen DT, Balamurugan S, Lim PY, Wu Y, Seong E, Nguyen TQ, Oh J, Wenk MR, Cazenave-Gassiot A, Yapici Z, Ong WY, Burmeister M, Nguyen LN. Lack of SPNS1 results in accumulation of lysolipids and lysosomal storage disease in mouse models. JCI Insight 2024; 9:e175462. [PMID: 38451736 PMCID: PMC11141868 DOI: 10.1172/jci.insight.175462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/05/2024] [Indexed: 03/09/2024] Open
Abstract
Accumulation of sphingolipids, especially sphingosines, in the lysosomes is a key driver of several lysosomal storage diseases. The transport mechanism for sphingolipids from the lysosome remains unclear. Here, we identified SPNS1, which shares the highest homology to SPNS2, a sphingosine-1-phosphate (S1P) transporter, functions as a transporter for lysolipids from the lysosome. We generated Spns1-KO cells and mice and employed lipidomic and metabolomic approaches to reveal SPNS1 ligand identity. Global KO of Spns1 caused embryonic lethality between E12.5 and E13.5 and an accumulation of sphingosine, lysophosphatidylcholines (LPC), and lysophosphatidylethanolamines (LPE) in the fetal livers. Similarly, metabolomic analysis of livers from postnatal Spns1-KO mice presented an accumulation of sphingosines and lysoglycerophospholipids including LPC and LPE. Subsequently, biochemical assays showed that SPNS1 is required for LPC and sphingosine release from lysosomes. The accumulation of these lysolipids in the lysosomes of Spns1-KO mice affected liver functions and altered the PI3K/AKT signaling pathway. Furthermore, we identified 3 human siblings with a homozygous variant in the SPNS1 gene. These patients suffer from developmental delay, neurological impairment, intellectual disability, and cerebellar hypoplasia. These results reveal a critical role of SPNS1 as a promiscuous lysolipid transporter in the lysosomes and link its physiological functions with lysosomal storage diseases.
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Affiliation(s)
- Hoa T.T. Ha
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | - SiYi Liu
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | | | - Linh K. Vo
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | | | - Dat T. Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | | | - Pei Yen Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - YaJun Wu
- Department of Anatomy, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
| | - Eunju Seong
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
| | - Toan Q. Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine
| | - Jeongah Oh
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - Markus R. Wenk
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - Amaury Cazenave-Gassiot
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
| | - Zuhal Yapici
- Department of Neurology, Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Wei-Yi Ong
- Department of Anatomy, Yong Loo-Lin School of Medicine, National University of Singapore, Singapore
| | - Margit Burmeister
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, USA
- Departments of Computational Medicine and Biochemistry, Psychiatry, and Human Genetics, University of Michigan, Ann Arbor, USA
| | - Long N. Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, and
- Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine
- Immunology Program, Life Sciences Institute, and
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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10
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Settembre C, Perera RM. Lysosomes as coordinators of cellular catabolism, metabolic signalling and organ physiology. Nat Rev Mol Cell Biol 2024; 25:223-245. [PMID: 38001393 DOI: 10.1038/s41580-023-00676-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2023] [Indexed: 11/26/2023]
Abstract
Every cell must satisfy basic requirements for nutrient sensing, utilization and recycling through macromolecular breakdown to coordinate programmes for growth, repair and stress adaptation. The lysosome orchestrates these key functions through the synchronised interplay between hydrolytic enzymes, nutrient transporters and signalling factors, which together enable metabolic coordination with other organelles and regulation of specific gene expression programmes. In this Review, we discuss recent findings on lysosome-dependent signalling pathways, focusing on how the lysosome senses nutrient availability through its physical and functional association with mechanistic target of rapamycin complex 1 (mTORC1) and how, in response, the microphthalmia/transcription factor E (MiT/TFE) transcription factors exert feedback regulation on lysosome biogenesis. We also highlight the emerging interactions of lysosomes with other organelles, which contribute to cellular homeostasis. Lastly, we discuss how lysosome dysfunction contributes to diverse disease pathologies and how inherited mutations that compromise lysosomal hydrolysis, transport or signalling components lead to multi-organ disorders with severe metabolic and neurological impact. A deeper comprehension of lysosomal composition and function, at both the cellular and organismal level, may uncover fundamental insights into human physiology and disease.
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Affiliation(s)
- Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy.
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy.
| | - Rushika M Perera
- Department of Anatomy, University of California at San Francisco, San Francisco, CA, USA.
- Department of Pathology, University of California at San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA.
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11
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Heins-Marroquin U, Singh RR, Perathoner S, Gavotto F, Merino Ruiz C, Patraskaki M, Gomez-Giro G, Kleine Borgmann F, Meyer M, Carpentier A, Warmoes MO, Jäger C, Mittelbronn M, Schwamborn JC, Cordero-Maldonado ML, Crawford AD, Schymanski EL, Linster CL. CLN3 deficiency leads to neurological and metabolic perturbations during early development. Life Sci Alliance 2024; 7:e202302057. [PMID: 38195117 PMCID: PMC10776888 DOI: 10.26508/lsa.202302057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Juvenile neuronal ceroid lipofuscinosis (or Batten disease) is an autosomal recessive, rare neurodegenerative disorder that affects mainly children above the age of 5 yr and is most commonly caused by mutations in the highly conserved CLN3 gene. Here, we generated cln3 morphants and stable mutant lines in zebrafish. Although neither morphant nor mutant cln3 larvae showed any obvious developmental or morphological defects, behavioral phenotyping of the mutant larvae revealed hyposensitivity to abrupt light changes and hypersensitivity to pro-convulsive drugs. Importantly, in-depth metabolomics and lipidomics analyses revealed significant accumulation of several glycerophosphodiesters (GPDs) and cholesteryl esters, and a global decrease in bis(monoacylglycero)phosphate species, two of which (GPDs and bis(monoacylglycero)phosphates) were previously proposed as potential biomarkers for CLN3 disease based on independent studies in other organisms. We could also demonstrate GPD accumulation in human-induced pluripotent stem cell-derived cerebral organoids carrying a pathogenic variant for CLN3 Our models revealed that GPDs accumulate at very early stages of life in the absence of functional CLN3 and highlight glycerophosphoinositol and BMP as promising biomarker candidates for pre-symptomatic CLN3 disease.
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Affiliation(s)
- Ursula Heins-Marroquin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Randolph R Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- https://ror.org/00hj8s172 Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Simon Perathoner
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Floriane Gavotto
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carla Merino Ruiz
- Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
- Biosfer Teslab SL, Reus, Spain
| | - Myrto Patraskaki
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Gemma Gomez-Giro
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Felix Kleine Borgmann
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Melanie Meyer
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Anaïs Carpentier
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Marc O Warmoes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Science and Medicine (DLSM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Institute for Orphan Drug Discovery, Bremerhaven, Germany
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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12
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Furderer ML, Berhe B, Chen TC, Wincovitch S, Jiang X, Tayebi N, Sidransky E, Han TU. A Comparative Biochemical and Pathological Evaluation of Brain Samples from Knock-In Murine Models of Gaucher Disease. Int J Mol Sci 2024; 25:1827. [PMID: 38339105 PMCID: PMC10855869 DOI: 10.3390/ijms25031827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Gaucher disease (GD) is a lysosomal storage disorder stemming from biallelic mutations in GBA1, characterized by glucocerebrosidase dysfunction and glucocerebroside and glucosylsphingosine accumulation. Since phenotypes of murine models of GD often differ from those in patients, the careful characterization of Gba1 mutant mice is necessary to establish their ability to model GD. We performed side-by-side comparative biochemical and pathologic analyses of four murine Gba1 models with genotypes L444P/L444P (p.L483P/p.L483P), L444P/null, D409H/D409H (p.D448H/p.D448H) and D409H/null, along with matched wildtype mice, all with the same genetic background and cage conditions. All mutant mice exhibited significantly lower glucocerebrosidase activity (p < 0.0001) and higher glucosylsphingosine levels than wildtype, with the lowest glucocerebrosidase and the highest glucosylsphingosine levels in mice carrying a null allele. Although glucocerebrosidase activity in L444P and D409H mice was similar, D409H mice showed more lipid accumulation. No Gaucher or storage-like cells were detected in any of the Gba1 mutant mice. Quantification of neuroinflammation, dopaminergic neuronal loss, alpha-synuclein levels and motor behavior revealed no significant findings, even in aged animals. Thus, while the models may have utility for testing the effect of different therapies on enzymatic activity, they did not recapitulate the pathological phenotype of patients with GD, and better models are needed.
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Affiliation(s)
- Makaila L. Furderer
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Bahafta Berhe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Tiffany C. Chen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Stephen Wincovitch
- Advanced Imaging & Analysis Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Xuntian Jiang
- Washington University Metabolomics Facility, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Tae-Un Han
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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13
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Liu Q, Wang W, Xu L, Zhang Q, Wang H. The host mannose-6-phosphate pathway and viral infection. Front Cell Infect Microbiol 2024; 14:1349221. [PMID: 38357444 PMCID: PMC10865371 DOI: 10.3389/fcimb.2024.1349221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/11/2024] [Indexed: 02/16/2024] Open
Abstract
Viruses, despite their simple structural composition, engage in intricate and complex interactions with their hosts due to their parasitic nature. A notable demonstration of viral behavior lies in their exploitation of lysosomes, specialized organelles responsible for the breakdown of biomolecules and clearance of foreign substances, to bolster their own replication. The man-nose-6-phosphate (M6P) pathway, crucial for facilitating the proper transport of hydrolases into lysosomes and promoting lysosome maturation, is frequently exploited for viral manipulation in support of replication. Recently, the discovery of lysosomal enzyme trafficking factor (LYSET) as a pivotal regulator within the lysosomal M6P pathway has introduced a fresh perspective on the intricate interplay between viral entry and host factors. This groundbreaking revelation illuminates unexplored dimensions of these interactions. In this review, we endeavor to provide a thorough overview of the M6P pathway and its intricate interplay with viral factors during infection. By consolidating the current understanding in this field, our objective is to establish a valuable reference for the development of antiviral drugs that selectively target the M6P pathway.
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Affiliation(s)
- Qincheng Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
| | - Weiqi Wang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
| | - Liwei Xu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
| | - Qisheng Zhang
- Shanghai Sino Organoid Lifesciences Co., Ltd., Shanghai, China
| | - Hongna Wang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Cell Homeostasis and Cancer Research of Guangdong Higher Education Institutes, Guangzhou, China
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14
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Yu Y, Gao SM, Guan Y, Hu PW, Zhang Q, Liu J, Jing B, Zhao Q, Sabatini DM, Abu-Remaileh M, Jung SY, Wang MC. Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity. eLife 2024; 13:e85214. [PMID: 38240316 PMCID: PMC10876212 DOI: 10.7554/elife.85214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 01/18/2024] [Indexed: 02/20/2024] Open
Abstract
Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins associated with the lysosome mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked to longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using deep proteomic profiling, we systemically profiled lysosome-associated proteins linked with four different longevity mechanisms. We discovered the lysosomal recruitment of AMP-activated protein kinase and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we further elucidated lysosomal heterogeneity across tissues as well as the increased enrichment of the Ragulator complex on Cystinosin-positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity across multiple scales and provides resources for understanding the contribution of lysosomal protein dynamics to signal transduction, organelle crosstalk, and organism longevity.
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Affiliation(s)
- Yong Yu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
| | - Shihong M Gao
- Developmental Biology Graduate Program, Baylor College of MedicineHoustonUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Youchen Guan
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
- Molecular and Cellular Biology Graduate Program, Baylor College of MedicineHoustonUnited States
| | - Pei-Wen Hu
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
| | - Qinghao Zhang
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
| | - Jiaming Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Bentian Jing
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen UniversityXiamenChina
| | - Qian Zhao
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - David M Sabatini
- Institute of Organic Chemistry and BiochemistryPragueCzech Republic
| | - Monther Abu-Remaileh
- Institute for Chemistry, Engineering and Medicine for Human Health (ChEM-H), Stanford UniversityStanfordUnited States
- Department of Chemical Engineering and Genetics, Stanford UniversityStanfordUnited States
| | - Sung Yun Jung
- Department of Molecular and Cellular Biology, Baylor College of MedicineHoustonUnited States
| | - Meng C Wang
- Huffington Center on Aging, Baylor College of MedicineHoustonUnited States
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
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15
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Chen J, Gao G, He Y, Zhang Y, Wu H, Dai P, Zheng Q, Huang H, Weng J, Zheng Y, Huang Y. Construction and validation of a novel lysosomal signature for hepatocellular carcinoma prognosis, diagnosis, and therapeutic decision-making. Sci Rep 2023; 13:22624. [PMID: 38114725 PMCID: PMC10730614 DOI: 10.1038/s41598-023-49985-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Lysosomes is a well-recognized oncogenic driver and chemoresistance across variable cancer types, and has been associated with tumor invasiveness, metastasis, and poor prognosis. However, the significance of lysosomes in hepatocellular carcinoma (HCC) is not well understood. Lysosomes-related genes (LRGs) were downloaded from Genome Enrichment Analysis (GSEA) databases. Lysosome-related risk score (LRRS), including eight LRGs, was constructed via expression difference analysis (DEGs), univariate and LASSO-penalized Cox regression algorithm based on the TCGA cohort, while the ICGC cohort was obtained for signature validation. Based on GSE149614 Single-cell RNA sequencing data, model gene expression and liver tumor niche were further analyzed. Moreover, the functional enrichments, tumor microenvironment (TME), and genomic variation landscape between LRRSlow/LRRShigh subgroup were systematically investigated. A total of 15 Lysosomes-related differentially expressed genes (DELRGs) in HCC were detected, and then 10 prognosis DELRGs were screened out. Finally, the 8 optimal DELRGs (CLN3, GBA, CTSA, BSG, APLN, SORT1, ANXA2, and LAPTM4B) were selected to construct the LRRS prognosis signature of HCC. LRRS was considered as an independent prognostic factor and was associated with advanced clinicopathological features. LRRS also proved to be a potential marker for HCC diagnosis, especially for early-stage HCC. Then, a nomogram integrating the LRRS and clinical parameters was set up displaying great prognostic predictive performance. Moreover, patients with high LRRS showed higher tumor stemness, higher heterogeneity, and higher genomic alteration status than those in the low LRRS group and enriched in metabolism-related pathways, suggesting its underlying role in the progression and development of liver cancer. Meanwhile, the LRRS can affect the proportion of immunosuppressive cell infiltration, making it a vital immunosuppressive factor in the tumor microenvironment. Additionally, HCC patients with low LRRS were more sensitive to immunotherapy, while patients in the high LRRS group responded better to chemotherapy. Upon single-cell RNA sequencing, CLN3, GBA, and LAPTM4B were found to be specially expressed in hepatocytes, where they promoted cell progression. Finally, RT-qPCR and external datasets confirmed the mRNA expression levels of model genes. This study provided a direct links between LRRS signature and clinical characteristics, tumor microenvironment, and clinical drug-response, highlighting the critical role of lysosome in the development and treatment resistance of liver cancer, providing valuable insights into the prognosis prediction and treatment response of HCC, thereby providing valuable insights into prognostic prediction, early diagnosis, and therapeutic response of HCC.
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Affiliation(s)
- Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
- Central Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Gan Gao
- Department of Clinical Laboratory, Liuzhou Hospital, Guangzhou Women and Children's Medical Center, Liuzhou, 545616, Guangxi, China
- Guangxi Clinical Research Center for Obstetrics and Gynecology, Liuzhou, 545616, Guangxi, China
| | - Yufang He
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
| | - Yi Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Haixia Wu
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
| | - Peng Dai
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Qingzhu Zheng
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Hengbin Huang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Jiamiao Weng
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Yue Zheng
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
- Central Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
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16
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Kagohashi Y, Sasaki M, May AI, Kawamata T, Ohsumi Y. The mechanism of Atg15-mediated membrane disruption in autophagy. J Cell Biol 2023; 222:e202306120. [PMID: 37917025 PMCID: PMC10622257 DOI: 10.1083/jcb.202306120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/25/2023] [Accepted: 10/03/2023] [Indexed: 11/03/2023] Open
Abstract
Autophagy is a lysosomal/vacuolar delivery system that degrades cytoplasmic material. During autophagy, autophagosomes deliver cellular components to the vacuole, resulting in the release of a cargo-containing autophagic body (AB) into the vacuole. AB membranes must be disrupted for degradation of cargo to occur. The lipase Atg15 and vacuolar proteases Pep4 and Prb1 are known to be necessary for this disruption and cargo degradation, but the mechanistic underpinnings remain unclear. In this study, we establish a system to detect lipase activity in the vacuole and show that Atg15 is the sole vacuolar phospholipase. Pep4 and Prb1 are required for the activation of Atg15 lipase function, which occurs following delivery of Atg15 to the vacuole by the MVB pathway. In vitro experiments reveal that Atg15 is a phospholipase B of broad substrate specificity that is likely implicated in the disruption of a range of membranes. Further, we use isolated ABs to demonstrate that Atg15 alone is able to disrupt AB membranes.
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Affiliation(s)
- Yoko Kagohashi
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- POLA Chemical Industries, Inc., Yokohama, Japan
| | - Michiko Sasaki
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Alexander I. May
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tomoko Kawamata
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yoshinori Ohsumi
- Research Center for Cell Biology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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17
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Hertz E, Glasstetter LM, Chen Y, Sidransky E. New tools can propel research in lysosomal storage diseases. Mol Genet Metab 2023; 140:107729. [PMID: 37951057 DOI: 10.1016/j.ymgme.2023.107729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/13/2023]
Abstract
Historically, the clinical manifestations of lysosomal storage diseases offered an early glimpse into the essential digestive functions of the lysosome. However, it was only recently that the more subtle role of this organelle in the dynamic regulation of multiple cellular processes was appreciated. With the need for precise interrogation of lysosomal interplay in health and disease comes the demand for more sophisticated functional tools. This demand has recently been met with 1) induced pluripotent stem cell-derived models that recapitulate the disease phenotype in vitro, 2) methods for lysosome affinity purification coupled with downstream omics analysis that provide a high-resolution snapshot of lysosomal alterations, and 3) gene editing and CRISPR/Cas9-based functional genomic strategies that enable screening for genetic modifiers of the disease phenotype. These emerging methods have garnered much interest in the field of neurodegeneration, and their use in the field of metabolic disorders is now also steadily gaining momentum. Looking forward, these robust tools should accelerate basic science efforts to understand lysosomal dysfunction distal to substrate accumulation and provide translational opportunities to identify disease-modifying therapies.
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Affiliation(s)
- Ellen Hertz
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Logan M Glasstetter
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yu Chen
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ellen Sidransky
- Molecular Neurogenetics Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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18
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Tan JX, Finkel T. Lysosomes in senescence and aging. EMBO Rep 2023; 24:e57265. [PMID: 37811693 PMCID: PMC10626421 DOI: 10.15252/embr.202357265] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/08/2023] [Accepted: 09/21/2023] [Indexed: 10/10/2023] Open
Abstract
Dysfunction of lysosomes, the primary hydrolytic organelles in animal cells, is frequently associated with aging and age-related diseases. At the cellular level, lysosomal dysfunction is strongly linked to cellular senescence or the induction of cell death pathways. However, the precise mechanisms by which lysosomal dysfunction participates in these various cellular or organismal phenotypes have remained elusive. The ability of lysosomes to degrade diverse macromolecules including damaged proteins and organelles puts lysosomes at the center of multiple cellular stress responses. Lysosomal activity is tightly regulated by many coordinated cellular processes including pathways that function inside and outside of the organelle. Here, we collectively classify these coordinated pathways as the lysosomal processing and adaptation system (LYPAS). We review evidence that the LYPAS is upregulated by diverse cellular stresses, its adaptability regulates senescence and cell death decisions, and it can form the basis for therapeutic manipulation for a wide range of age-related diseases and potentially for aging itself.
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Affiliation(s)
- Jay Xiaojun Tan
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPAUSA
- Department of Cell BiologyUniversity of Pittsburgh School of MedicinePittsburghPAUSA
| | - Toren Finkel
- Aging InstituteUniversity of Pittsburgh School of Medicine/University of Pittsburgh Medical CenterPittsburghPAUSA
- Department of MedicineUniversity of Pittsburgh School of MedicinePittsburghPAUSA
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19
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Affiliation(s)
- Nouf N Laqtom
- Chemical Engineering, Stanford University, Stanford, CA, USA.
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20
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de Castro RJA, Marina CL, Sturny-Leclère A, Hoffmann C, Bürgel PH, Wong SSW, Aimanianda V, Varet H, Agrawal R, Bocca AL, Alanio A. Kicking sleepers out of bed: Macrophages promote reactivation of dormant Cryptococcus neoformans by extracellular vesicle release and non-lytic exocytosis. PLoS Pathog 2023; 19:e1011841. [PMID: 38033163 PMCID: PMC10715671 DOI: 10.1371/journal.ppat.1011841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/12/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
Macrophages play a key role in disseminated cryptococcosis, a deadly fungal disease caused by Cryptococcus neoformans. This opportunistic infection can arise following the reactivation of a poorly characterized latent infection attributed to dormant C. neoformans. Here, we investigated the mechanisms underlying reactivation of dormant C. neoformans using an in vitro co-culture model of viable but non-culturable (VBNC; equivalent of dormant) yeast cells with bone marrow-derived murine macrophages (BMDMs). Comparative transcriptome analysis of BMDMs incubated with log, stationary phase or VBNC cells of C. neoformans showed that VBNC cells elicited a reduced transcriptional modification of the macrophage but retaining the ability to regulate genes important for immune response, such as NLRP3 inflammasome-related genes. We further confirmed the maintenance of the low immunostimulatory capacity of VBNC cells using multiplex cytokine profiling, and analysis of cell wall composition and dectin-1 ligands exposure. In addition, we evaluated the effects of classic (M1) or alternative (M2) macrophage polarization on VBNC cells. We observed that intracellular residence sustained dormancy, regardless of the polarization state of macrophages and despite indirect detection of pantothenic acid (or its derivatives), a known reactivator for VBNC cells, in the C. neoformans-containing phagolysosome. Notably, M0 and M2, but not M1 macrophages, induced extracellular reactivation of VBNC cells by the secretion of extracellular vesicles and non-lytic exocytosis. Our results indicate that VBNC cells retain the low immunostimulatory profile required for persistence of C. neoformans in the host. We also describe a pro-pathogen role of macrophage-derived extracellular vesicles in C. neoformans infection and reinforce the impact of non-lytic exocytosis and the macrophage profile on the pathophysiology of cryptococcosis.
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Affiliation(s)
- Raffael Júnio Araújo de Castro
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Clara Luna Marina
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Aude Sturny-Leclère
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Christian Hoffmann
- Food Research Center, Department of Food Sciences and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Pedro Henrique Bürgel
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Sarah Sze Wah Wong
- Immunobiology of Aspergillus, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vishukumar Aimanianda
- Immunobiology of Aspergillus, Institut Pasteur, Université Paris Cité, Paris, France
| | - Hugo Varet
- Plate-forme Technologique Biomics, Institut Pasteur, Université Paris Cité, Paris, France
| | - Ruchi Agrawal
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anamélia Lorenzetti Bocca
- Laboratory of Applied Immunology, Department of Cell Biology, Institute of Biological Sciences, University of Brasilia, Brasília, Distrito Federal, Brazil
| | - Alexandre Alanio
- Translational Mycology Research Group, National Reference Center for Invasive Mycoses and Antifungals, Mycology Department, Institut Pasteur, Université Paris Cité, Paris, France
- Laboratoire de parasitologie-mycologie, AP-HP, Hôpital Saint-Louis, Paris, France
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21
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Mancini MC, Noland RC, Collier JJ, Burke SJ, Stadler K, Heden TD. Lysosomal glucose sensing and glycophagy in metabolism. Trends Endocrinol Metab 2023; 34:764-777. [PMID: 37633800 PMCID: PMC10592240 DOI: 10.1016/j.tem.2023.07.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/28/2023]
Abstract
Lysosomes are cellular organelles that function to catabolize both extra- and intracellular cargo, act as a platform for nutrient sensing, and represent a core signaling node integrating bioenergetic cues to changes in cellular metabolism. Although lysosomal amino acid and lipid sensing in metabolism has been well characterized, lysosomal glucose sensing and the role of lysosomes in glucose metabolism is unrefined. This review will highlight the role of the lysosome in glucose metabolism with a focus on lysosomal glucose and glycogen sensing, glycophagy, and lysosomal glucose transport and how these processes impact autophagy and energy metabolism. Additionally, the role of lysosomal glucose metabolism in genetic and metabolic diseases will be briefly discussed.
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Affiliation(s)
- Melina C Mancini
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Robert C Noland
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - J Jason Collier
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | - Susan J Burke
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA
| | | | - Timothy D Heden
- Pennington Biomedical Research Center, Baton Rouge, LA 70808, USA.
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22
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Leppert HG, Anderson JT, Timm KJ, Davoli C, Pratt MA, Booth CD, White KA, Rechtzigel MJ, Meyerink BL, Johnson TB, Brudvig JJ, Weimer JM. Sortilin inhibition treats multiple neurodegenerative lysosomal storage disorders. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559064. [PMID: 37790379 PMCID: PMC10543011 DOI: 10.1101/2023.09.22.559064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Lysosomal storage disorders (LSDs) are a genetically and clinically diverse group of diseases characterized by lysosomal dysfunction. Batten disease is a family of severe LSDs primarily impacting the central nervous system. Here we show that AF38469, a small molecule inhibitor of sortilin, improves lysosomal and glial pathology across multiple LSD models. Live-cell imaging and comparative transcriptomics demonstrates that the transcription factor EB (TFEB), an upstream regulator of lysosomal biogenesis, is activated upon treatment with AF38469. Utilizing CLN2 and CLN3 Batten disease mouse models, we performed a short-term efficacy study and show that treatment with AF38469 prevents the accumulation of lysosomal storage material and the development of neuroinflammation, key disease associated pathologies. Tremor phenotypes, an early behavioral phenotype in the CLN2 disease model, were also completely rescued. These findings reveal sortilin inhibition as a novel and highly efficacious therapeutic modality for the treatment of multiple forms of Batten disease.
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Affiliation(s)
- Hannah G. Leppert
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
| | | | - Kaylie J. Timm
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
| | - Cristina Davoli
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
| | - Melissa A. Pratt
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
| | - Clarissa D. Booth
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
| | | | | | | | - Tyler B. Johnson
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
| | - Jon J. Brudvig
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - Jill M. Weimer
- Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
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23
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Medoh UN, Hims A, Chen JY, Ghoochani A, Nyame K, Dong W, Abu-Remaileh M. The Batten disease gene product CLN5 is the lysosomal bis(monoacylglycero)phosphate synthase. Science 2023; 381:1182-1189. [PMID: 37708259 DOI: 10.1126/science.adg9288] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
Lysosomes critically rely on bis(monoacylglycero)phosphate (BMP) to stimulate lipid catabolism, cholesterol homeostasis, and lysosomal function. Alterations in BMP levels in monogenic and complex neurodegeneration suggest an essential function in human health. However, the site and mechanism responsible for BMP synthesis have been subject to debate for decades. Here, we report that the Batten disease gene product CLN5 is the elusive BMP synthase (BMPS). BMPS-deficient cells exhibited a massive accumulation of the BMP synthesis precursor lysophosphatidylglycerol (LPG), depletion of BMP species, and dysfunctional lipid metabolism. Mechanistically, we found that BMPS mediated synthesis through an energy-independent base exchange reaction between two LPG molecules with increased activity on BMP-laden vesicles. Our study elucidates BMP biosynthesis and reveals an anabolic function of late endosomes/lysosomes.
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Affiliation(s)
- Uche N Medoh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andy Hims
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Julie Y Chen
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Ali Ghoochani
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering & Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
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24
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Colella P, Sayana R, Suarez-Nieto MV, Sarno J, Nyame K, Xiong J, Vera LNP, Basurto JA, Corbo M, Limaye A, Davis KL, Abu-Remaileh M, Gomez-Ospina N. CNS Repopulation by Hematopoietic-Derived Microglia-Like Cells Corrects Progranulin deficiency. RESEARCH SQUARE 2023:rs.3.rs-3263412. [PMID: 37790525 PMCID: PMC10543302 DOI: 10.21203/rs.3.rs-3263412/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Hematopoietic stem cell transplantation can deliver therapeutic proteins to the CNS through donor-derived hematopoietic cells that become microglia-like cells. However, using standard conditioning approaches, hematopoietic stem cell transplantation is currently limited by low and slow engraftment of microglia-like cells. We report an efficient conditioning regimen based on Busulfan and a six-day course of microglia depletion using the colony-stimulating factor receptor 1 inhibitor PLX3397. Combining Busulfan-myeloablation and transient microglia depletion results in robust, rapid, and persistent microglia replacement by bone marrow-derived microglia-like cells throughout the CNS. Adding PLX3397 does not affect neurobehavior or has adverse effects on hematopoietic reconstitution. Through single-cell RNA sequencing and high-dimensional CyTOF mass cytometry, we show that microglia-like cells are a heterogeneous population and describe six distinct subpopulations. Though most bone-marrow-derived microglia-like cells can be classified as homeostatic microglia, their gene signature is a hybrid of homeostatic/embryonic microglia and border associated-macrophages. Busulfan-myeloablation and transient microglia depletion induce specific cytokines in the brain, ultimately combining myeloid proliferative and chemo-attractive signals that act locally to repopulate microglia from outside the niche. Importantly, this conditioning approach demonstrates therapeutic efficacy in a mouse model of GRN deficiency. Transplanting wild-type bone marrow into Grn-/- mice conditioned with Busulfan plus PLX3397 results in high engraftment of microglia-like cells in the brain and retina, restoring GRN levels and normalizing lipid metabolism.
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Affiliation(s)
- Pasqualina Colella
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305
| | - Ruhi Sayana
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305
| | | | - Jolanda Sarno
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, 94305
| | - Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Jian Xiong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
| | | | | | - Marco Corbo
- MedGenome, Inc, 348 Hatch Dr, Foster City, CA 94404
| | - Anay Limaye
- MedGenome, Inc, 348 Hatch Dr, Foster City, CA 94404
| | - Kara Lynn Davis
- Hematology, Oncology, Stem Cell Transplant, and Regenerative Medicine, Department of Pediatrics, Stanford University, Stanford, CA, 94305
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305
- Department of Genetics, Stanford University, Stanford, CA 94305
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305
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25
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Dang Do AN, Sleat DE, Campbell K, Johnson NL, Zheng H, Wassif CA, Dale RK, Porter FD. Cerebrospinal Fluid Protein Biomarker Discovery in CLN3. J Proteome Res 2023; 22:2493-2508. [PMID: 37338096 PMCID: PMC11095826 DOI: 10.1021/acs.jproteome.3c00199] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Syndromic CLN3-Batten is a fatal, pediatric, neurodegenerative disease caused by variants in CLN3, which encodes the endolysosomal transmembrane CLN3 protein. No approved treatment for CLN3 is currently available. The protracted and asynchronous disease presentation complicates the evaluation of potential therapies using clinical disease progression parameters. Biomarkers as surrogates to measure the progression and effect of potential therapeutics are needed. We performed proteomic discovery studies using cerebrospinal fluid (CSF) samples from 28 CLN3-affected and 32 age-similar non-CLN3 individuals. Proximal extension assay (PEA) of 1467 proteins and untargeted data-dependent mass spectrometry [MS; MassIVE FTP server (ftp://MSV000090147@massive.ucsd.edu)] were used to generate orthogonal lists of protein marker candidates. At an adjusted p-value of <0.1 and threshold CLN3/non-CLN3 fold-change ratio of 1.5, PEA identified 54 and MS identified 233 candidate biomarkers. Some of these (NEFL, CHIT1) have been previously linked with other neurologic conditions. Others (CLPS, FAM217B, QRICH2, KRT16, ZNF333) appear to be novel. Both methods identified 25 candidate biomarkers, including CHIT1, NELL1, and ISLR2 which had absolute fold-change ratios >2. NELL1 and ISLR2 regulate axonal development in neurons and are intriguing new candidates for further investigation in CLN3. In addition to identifying candidate proteins for CLN3 research, this study provides a comparison of two large-scale proteomic discovery methods in CSF.
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Affiliation(s)
- An N. Dang Do
- Unit on Cellular Stress in Development and Diseases, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - David E. Sleat
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
- Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Kiersten Campbell
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nicholas L. Johnson
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Christopher A. Wassif
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Ryan K. Dale
- Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Forbes D. Porter
- Section on Molecular Dysmorphology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
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26
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Calcagni' A, Staiano L, Zampelli N, Minopoli N, Herz NJ, Di Tullio G, Huynh T, Monfregola J, Esposito A, Cirillo C, Bajic A, Zahabiyon M, Curnock R, Polishchuk E, Parkitny L, Medina DL, Pastore N, Cullen PJ, Parenti G, De Matteis MA, Grumati P, Ballabio A. Loss of the batten disease protein CLN3 leads to mis-trafficking of M6PR and defective autophagic-lysosomal reformation. Nat Commun 2023; 14:3911. [PMID: 37400440 DOI: 10.1038/s41467-023-39643-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/21/2023] [Indexed: 07/05/2023] Open
Abstract
Batten disease, one of the most devastating types of neurodegenerative lysosomal storage disorders, is caused by mutations in CLN3. Here, we show that CLN3 is a vesicular trafficking hub connecting the Golgi and lysosome compartments. Proteomic analysis reveals that CLN3 interacts with several endo-lysosomal trafficking proteins, including the cation-independent mannose 6 phosphate receptor (CI-M6PR), which coordinates the targeting of lysosomal enzymes to lysosomes. CLN3 depletion results in mis-trafficking of CI-M6PR, mis-sorting of lysosomal enzymes, and defective autophagic lysosomal reformation. Conversely, CLN3 overexpression promotes the formation of multiple lysosomal tubules, which are autophagy and CI-M6PR-dependent, generating newly formed proto-lysosomes. Together, our findings reveal that CLN3 functions as a link between the M6P-dependent trafficking of lysosomal enzymes and lysosomal reformation pathway, explaining the global impairment of lysosomal function in Batten disease.
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Affiliation(s)
- Alessia Calcagni'
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
| | - Leopoldo Staiano
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Institute for Genetic and Biomedical Research, National Research Council (CNR), Milan, Italy
| | | | - Nadia Minopoli
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Niculin J Herz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Tuong Huynh
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | | | - Alessandra Esposito
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- SSM School for Advanced Studies, Federico II University, Naples, Italy
| | - Carmine Cirillo
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Aleksandar Bajic
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Mahla Zahabiyon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Rachel Curnock
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Elena Polishchuk
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
| | - Luke Parkitny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA
| | - Diego Luis Medina
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Nunzia Pastore
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Peter J Cullen
- School of Biochemistry, Biomedical Sciences Building, University of Bristol, Bristol, BS8 1TD, UK
| | - Giancarlo Parenti
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy
| | - Maria Antonietta De Matteis
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, Naples, Italy
| | - Paolo Grumati
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy
- Department of Clinical Medicine and Surgery, Federico II University, Naples, Italy
| | - Andrea Ballabio
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.
- Telethon Institute of Genetics and Medicine (TIGEM), Naples, Italy.
- Department of Translational Medical Sciences, Federico II University, 80131, Naples, Italy.
- SSM School for Advanced Studies, Federico II University, Naples, Italy.
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27
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Chen J, Soni RK, Xu Y, Simoes S, Liang FX, DeFreitas L, Hwang R, Montesinos J, Lee JH, Area-Gomez E, Nandakumar R, Vardarajan B, Marquer C. Juvenile CLN3 disease is a lysosomal cholesterol storage disorder: similarities with Niemann-Pick type C disease. EBioMedicine 2023; 92:104628. [PMID: 37245481 PMCID: PMC10227369 DOI: 10.1016/j.ebiom.2023.104628] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/30/2023] [Accepted: 05/10/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND The most common form of neuronal ceroid lipofuscinosis (NCL) is juvenile CLN3 disease (JNCL), a currently incurable neurodegenerative disorder caused by mutations in the CLN3 gene. Based on our previous work and on the premise that CLN3 affects the trafficking of the cation-independent mannose-6 phosphate receptor and its ligand NPC2, we hypothesised that dysfunction of CLN3 leads to the aberrant accumulation of cholesterol in the late endosomes/lysosomes (LE/Lys) of JNCL patients' brains. METHODS An immunopurification strategy was used to isolate intact LE/Lys from frozen autopsy brain samples. LE/Lys isolated from samples of JNCL patients were compared with age-matched unaffected controls and Niemann-Pick Type C (NPC) disease patients. Indeed, mutations in NPC1 or NPC2 result in the accumulation of cholesterol in LE/Lys of NPC disease samples, thus providing a positive control. The lipid and protein content of LE/Lys was then analysed using lipidomics and proteomics, respectively. FINDINGS Lipid and protein profiles of LE/Lys isolated from JNCL patients were profoundly altered compared to controls. Importantly, cholesterol accumulated in LE/Lys of JNCL samples to a comparable extent than in NPC samples. Lipid profiles of LE/Lys were similar in JNCL and NPC patients, except for levels of bis(monoacylglycero)phosphate (BMP). Protein profiles detected in LE/Lys of JNCL and NPC patients appeared identical, except for levels of NPC1. INTERPRETATION Our results support that JNCL is a lysosomal cholesterol storage disorder. Our findings also support that JNCL and NPC disease share pathogenic pathways leading to aberrant lysosomal accumulation of lipids and proteins, and thus suggest that the treatments available for NPC disease may be beneficial to JNCL patients. This work opens new avenues for further mechanistic studies in model systems of JNCL and possible therapeutic interventions for this disorder. FUNDING San Francisco Foundation.
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Affiliation(s)
- Jacinda Chen
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, New York City, NY 10032, USA
| | - Yimeng Xu
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Sabrina Simoes
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Feng-Xia Liang
- Microscopy Core Laboratory of Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York City, NY 10016, USA
| | - Laura DeFreitas
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Robert Hwang
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Jorge Montesinos
- Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA; G. H. Sergievsky Center, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Epidemiology, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Estela Area-Gomez
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA; Institute of Human Nutrition, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Renu Nandakumar
- Biomarkers Core Laboratory, Irving Institute for Clinical and Translational Research, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Neurology, Columbia University Irving Medical Center, New York City, NY 10032, USA; G. H. Sergievsky Center, Columbia University Irving Medical Center, New York City, NY 10032, USA
| | - Catherine Marquer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York City, NY 10032, USA; Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York City, NY 10032, USA.
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Fasimoye R, Dong W, Nirujogi RS, Rawat ES, Iguchi M, Nyame K, Phung TK, Bagnoli E, Prescott AR, Alessi DR, Abu-Remaileh M. Golgi-IP, a tool for multimodal analysis of Golgi molecular content. Proc Natl Acad Sci U S A 2023; 120:e2219953120. [PMID: 37155866 PMCID: PMC10193996 DOI: 10.1073/pnas.2219953120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/05/2023] [Indexed: 05/10/2023] Open
Abstract
The Golgi is a membrane-bound organelle that is essential for protein and lipid biosynthesis. It represents a central trafficking hub that sorts proteins and lipids to various destinations or for secretion from the cell. The Golgi has emerged as a docking platform for cellular signaling pathways including LRRK2 kinase whose deregulation leads to Parkinson disease. Golgi dysfunction is associated with a broad spectrum of diseases including cancer, neurodegeneration, and cardiovascular diseases. To allow the study of the Golgi at high resolution, we report a rapid Golgi immunoprecipitation technique (Golgi-IP) to isolate intact Golgi mini-stacks for subsequent analysis of their content. By fusing the Golgi-resident protein TMEM115 to three tandem HA epitopes (GolgiTAG), we purified the Golgi using Golgi-IP with minimal contamination from other compartments. We then established an analysis pipeline using liquid chromatography coupled with mass spectrometry to characterize the human Golgi proteome, metabolome, and lipidome. Subcellular proteomics confirmed known Golgi proteins and identified proteins not previously associated with the Golgi. Metabolite profiling established the human Golgi metabolome and revealed the enrichment of uridine-diphosphate (UDP) sugars and their derivatives, which is consistent with their roles in protein and lipid glycosylation. Furthermore, targeted metabolomics validated SLC35A2 as the subcellular transporter for UDP-hexose. Finally, lipidomics analysis showed that phospholipids including phosphatidylcholine, phosphatidylinositol, and phosphatidylserine are the most abundant Golgi lipids and that glycosphingolipids are enriched in this compartment. Altogether, our work establishes a comprehensive molecular map of the human Golgi and provides a powerful method to study the Golgi with high precision in health and disease.
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Affiliation(s)
- Rotimi Fasimoye
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Wentao Dong
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Raja S. Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Eshaan S. Rawat
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Miharu Iguchi
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
| | - Kwamina Nyame
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA94305
| | - Toan K. Phung
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Enrico Bagnoli
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
| | - Dario R. Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, DundeeDD1 5EH, United Kingdom
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
| | - Monther Abu-Remaileh
- Aligning Science Across Parkinson’s Collaborative Research Network, Chevy Chase, MD20815
- Department of Chemical Engineering, Stanford University, Stanford, CA94305
- Department of Genetics, Stanford University, Stanford, CA94305
- The Institute for Chemistry, Engineering & Medicine for Human Health, Stanford University, Stanford, CA94305
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Scharenberg SG, Dong W, Ghoochani A, Nyame K, Levin-Konigsberg R, Krishnan AR, Rawat ES, Spees K, Bassik MC, Abu-Remaileh M. An SPNS1-dependent lysosomal lipid transport pathway that enables cell survival under choline limitation. SCIENCE ADVANCES 2023; 9:eadf8966. [PMID: 37075117 PMCID: PMC10115416 DOI: 10.1126/sciadv.adf8966] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
Lysosomes degrade macromolecules and recycle their nutrient content to support cell function and survival. However, the machineries involved in lysosomal recycling of many nutrients remain to be discovered, with a notable example being choline, an essential metabolite liberated via lipid degradation. Here, we engineered metabolic dependency on lysosome-derived choline in pancreatic cancer cells to perform an endolysosome-focused CRISPR-Cas9 screen for genes mediating lysosomal choline recycling. We identified the orphan lysosomal transmembrane protein SPNS1 as critical for cell survival under choline limitation. SPNS1 loss leads to intralysosomal accumulation of lysophosphatidylcholine (LPC) and lysophosphatidylethanolamine (LPE). Mechanistically, we reveal that SPNS1 is a proton gradient-dependent transporter of LPC species from the lysosome for their re-esterification into phosphatidylcholine in the cytosol. Last, we establish that LPC efflux by SPNS1 is required for cell survival under choline limitation. Collectively, our work defines a lysosomal phospholipid salvage pathway that is essential under nutrient limitation and, more broadly, provides a robust platform to deorphan lysosomal gene function.
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Affiliation(s)
- Samantha G. Scharenberg
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University, Stanford, CA 94305, USA
- Stanford Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Wentao Dong
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Ali Ghoochani
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Aswini R. Krishnan
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
- Stanford Medical Scientist Training Program, Stanford University, Stanford, CA 94305, USA
| | - Eshaan S. Rawat
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
| | - Kaitlyn Spees
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Michael C. Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- The Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA 94305, USA
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Vaughen JP, Theisen E, Clandinin TR. From seconds to days: Neural plasticity viewed through a lipid lens. Curr Opin Neurobiol 2023; 80:102702. [PMID: 36965206 DOI: 10.1016/j.conb.2023.102702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/31/2023] [Accepted: 02/16/2023] [Indexed: 03/27/2023]
Abstract
Many adult neurons are dynamically remodeled across timescales ranging from the rapid addition and removal of specific synaptic connections, to largescale structural plasticity events that reconfigure circuits over hours, days, and months. Membrane lipids, including brain-enriched sphingolipids, play crucial roles in these processes. In this review, we summarize progress at the intersection of neuronal activity, lipids, and structural remodeling. We highlight how brain activity modulates lipid metabolism to enable adaptive structural plasticity, and showcase glia as key players in membrane remodeling. These studies reveal that lipids act as critical signaling molecules that instruct the dynamic architecture of the brain.
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Affiliation(s)
- John P Vaughen
- Department of Neurobiology, Stanford University, Stanford, CA, 94305, United States; Department of Developmental Biology, Stanford University, Stanford, CA, 94305, United States. https://twitter.com/gliaful
| | - Emma Theisen
- Department of Neurobiology, Stanford University, Stanford, CA, 94305, United States. https://twitter.com/emmaktheisen
| | - Thomas R Clandinin
- Department of Neurobiology, Stanford University, Stanford, CA, 94305, United States.
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Remtulla AAN, Huber RJ. The conserved cellular roles of CLN proteins: Novel insights from Dictyostelium discoideum. Eur J Cell Biol 2023; 102:151305. [PMID: 36917916 DOI: 10.1016/j.ejcb.2023.151305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/15/2023] [Accepted: 03/07/2023] [Indexed: 03/14/2023] Open
Abstract
The neuronal ceroid lipofuscinoses (NCLs), collectively referred to as Batten disease, are a group of fatal neurodegenerative disorders that primarily affect children. The etiology of Batten disease is linked to mutations in 13 genes that encode distinct CLN proteins, whose functions have yet to be fully elucidated. The social amoeba Dictyostelium discoideum has been adopted as an efficient and powerful model system for studying the diverse cellular roles of CLN proteins. The genome of D. discoideum encodes several homologs of human CLN proteins, and a growing body of literature supports the conserved roles and networking of CLN proteins in D. discoideum and humans. In humans, CLN proteins have diverse cellular roles related to autophagy, signal transduction, lipid homeostasis, lysosomal ion homeostasis, and intracellular trafficking. Recent work also indicates that CLN proteins play an important role in protein secretion. Remarkably, many of these findings have found parallels in studies with D. discoideum. Accordingly, this review will highlight the translatable value of novel work with D. discoideum in the field of NCL research and propose further avenues of research using this biomedical model organism for studying the NCLs.
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Affiliation(s)
- Adam A N Remtulla
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada
| | - Robert J Huber
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario, Canada; Department of Biology, Trent University, Peterborough, Ontario, Canada.
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Pardridge WM. Physiologically Based Pharmacokinetic Model of Brain Delivery of Plasma Protein Bound Drugs. Pharm Res 2023; 40:661-674. [PMID: 36829100 PMCID: PMC10036418 DOI: 10.1007/s11095-023-03484-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/10/2023] [Indexed: 02/26/2023]
Abstract
INTRODUCTION A physiologically based pharmacokinetic (PBPK) model is developed that focuses on the kinetic parameters of drug association and dissociation with albumin, alpha-1 acid glycoprotein (AGP), and brain tissue proteins, as well as drug permeability at the blood-brain barrier, drug metabolism, and brain blood flow. GOAL The model evaluates the extent to which plasma protein-mediated uptake (PMU) of drugs by brain influences the concentration of free drug both within the brain capillary compartment in vivo and the brain compartment. The model also studies the effect of drug binding to brain tissue proteins on the concentration of free drug in brain. METHODS The steady state and non-steady state PBPK models are comprised of 11-12 variables, and 18-23 parameters, respectively. Two model drugs are analyzed: propranolol, which undergoes modest PMU from the AGP-bound pool, and imipramine, which undergoes a high degree of PMU from both the albumin-bound and AGP-bound pools in plasma. RESULTS The free propranolol concentration in brain is under-estimated 2- to fourfold by in vitro measurements of free plasma propranolol, and the free imipramine concentration in brain is under-estimated by 18- to 31-fold by in vitro measurements of free imipramine in plasma. The free drug concentration in brain in vivo is independent of drug binding to brain tissue proteins. CONCLUSIONS In vitro measurement of free drug concentration in plasma under-estimates the free drug in brain in vivo if PMU in vivo from either the albumin and/or the AGP pools in plasma takes place at the BBB surface.
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Pfrieger FW. The Niemann-Pick type diseases – A synopsis of inborn errors in sphingolipid and cholesterol metabolism. Prog Lipid Res 2023; 90:101225. [PMID: 37003582 DOI: 10.1016/j.plipres.2023.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
Disturbances of lipid homeostasis in cells provoke human diseases. The elucidation of the underlying mechanisms and the development of efficient therapies represent formidable challenges for biomedical research. Exemplary cases are two rare, autosomal recessive, and ultimately fatal lysosomal diseases historically named "Niemann-Pick" honoring the physicians, whose pioneering observations led to their discovery. Acid sphingomyelinase deficiency (ASMD) and Niemann-Pick type C disease (NPCD) are caused by specific variants of the sphingomyelin phosphodiesterase 1 (SMPD1) and NPC intracellular cholesterol transporter 1 (NPC1) or NPC intracellular cholesterol transporter 2 (NPC2) genes that perturb homeostasis of two key membrane components, sphingomyelin and cholesterol, respectively. Patients with severe forms of these diseases present visceral and neurologic symptoms and succumb to premature death. This synopsis traces the tortuous discovery of the Niemann-Pick diseases, highlights important advances with respect to genetic culprits and cellular mechanisms, and exposes efforts to improve diagnosis and to explore new therapeutic approaches.
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Shaimardanova AA, Solovyeva VV, Issa SS, Rizvanov AA. Gene Therapy of Sphingolipid Metabolic Disorders. Int J Mol Sci 2023; 24:ijms24043627. [PMID: 36835039 PMCID: PMC9964151 DOI: 10.3390/ijms24043627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023] Open
Abstract
Sphingolipidoses are defined as a group of rare hereditary diseases resulting from mutations in the genes encoding lysosomal enzymes. This group of lysosomal storage diseases includes more than 10 genetic disorders, including GM1-gangliosidosis, Tay-Sachs disease, Sandhoff disease, the AB variant of GM2-gangliosidosis, Fabry disease, Gaucher disease, metachromatic leukodystrophy, Krabbe disease, Niemann-Pick disease, Farber disease, etc. Enzyme deficiency results in accumulation of sphingolipids in various cell types, and the nervous system is also usually affected. There are currently no known effective methods for the treatment of sphingolipidoses; however, gene therapy seems to be a promising therapeutic variant for this group of diseases. In this review, we discuss gene therapy approaches for sphingolipidoses that are currently being investigated in clinical trials, among which adeno-associated viral vector-based approaches and transplantation of hematopoietic stem cells genetically modified with lentiviral vectors seem to be the most effective.
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Affiliation(s)
- Alisa A. Shaimardanova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Valeriya V. Solovyeva
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Shaza S. Issa
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Albert A. Rizvanov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Correspondence: ; Tel.: +7-(905)-316-7599
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Chear S, Perry S, Wilson R, Bindoff A, Talbot J, Ware TL, Grubman A, Vickers JC, Pébay A, Ruddle JB, King AE, Hewitt AW, Cook AL. Lysosomal alterations and decreased electrophysiological activity in CLN3 disease patient-derived cortical neurons. Dis Model Mech 2022; 15:dmm049651. [PMID: 36453132 PMCID: PMC10655821 DOI: 10.1242/dmm.049651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 11/17/2022] [Indexed: 12/02/2022] Open
Abstract
CLN3 disease is a lysosomal storage disorder associated with fatal neurodegeneration that is caused by mutations in CLN3, with most affected individuals carrying at least one allele with a 966 bp deletion. Using CRISPR/Cas9, we corrected the 966 bp deletion mutation in human induced pluripotent stem cells (iPSCs) of a compound heterozygous patient (CLN3 Δ 966 bp and E295K). We differentiated these isogenic iPSCs, and iPSCs from an unrelated healthy control donor, to neurons and identified disease-related changes relating to protein synthesis, trafficking and degradation, and in neuronal activity, which were not apparent in CLN3-corrected or healthy control neurons. CLN3 neurons showed numerous membrane-bound vacuoles containing diverse storage material and hyperglycosylation of the lysosomal LAMP1 protein. Proteomic analysis showed increase in lysosomal-related proteins and many ribosomal subunit proteins in CLN3 neurons, accompanied by downregulation of proteins related to axon guidance and endocytosis. CLN3 neurons also had lower electrophysical activity as recorded using microelectrode arrays. These data implicate inter-related pathways in protein homeostasis and neurite arborization as contributing to CLN3 disease, and which could be potential targets for therapy.
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Affiliation(s)
- Sueanne Chear
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Sharn Perry
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia
| | - Aidan Bindoff
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Jana Talbot
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Tyson L. Ware
- Department of Paediatrics, Royal Hobart Hospital, Hobart, TAS 7000, Australia
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Clayton, VIC 3800, Australia
| | - James C. Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Alice Pébay
- Department of Anatomy and Physiology, University of Melbourne, Parkville, VIC 3010, Australia
- Department of Surgery, Royal Melbourne Hospital, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jonathan B. Ruddle
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, VIC 3002, Australia
| | - Anna E. King
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
| | - Alex W. Hewitt
- Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7001, Australia
| | - Anthony L. Cook
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7001, Australia
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