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Davidson JW, Jain R, Kizzar T, Geoghegan G, Nesbitt DJ, Cavanagh A, Abe A, Nyame K, Hunger A, Chao X, James I, Walesewicz H, Baldwin DA, Wade G, Michorowska S, Verma R, Schueler K, Hinkovska-Galcheva V, Shishkova E, Ding WX, Coon JJ, Shayman JA, Abu-Remaileh M, Simcox JA. Hepatic lipid remodeling in cold exposure uncovers direct regulation of bis(monoacylglycero)phosphate lipids by phospholipase A2 group XV. Cell Metab 2025:S1550-4131(25)00253-0. [PMID: 40373767 DOI: 10.1016/j.cmet.2025.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/13/2025] [Accepted: 04/21/2025] [Indexed: 05/17/2025]
Abstract
Cold exposure is a selective environmental stress that elicits a rapid metabolic shift to maintain energy homeostasis. In response to cold exposure, the liver rewires the metabolic state, shifting from glucose to lipid catabolism. By probing the liver lipids in cold exposure, we observed that the lysosomal bis(monoacylglycero)phosphate (BMP) lipids were rapidly increased during cold exposure. BMP lipid changes occurred independently of lysosomal abundance but were dependent on the lysosomal transcriptional regulator transcription factor EB (TFEB). Knockdown of Tfeb in hepatocytes decreased BMP lipid levels and led to cold intolerance in mice. We assessed TFEB-binding sites of lysosomal genes and determined that the phospholipase a2 group XV (PLA2G15) regulates BMP lipid catabolism. Decreasing Pla2g15 levels in mice increased BMP lipids, ablated the cold-induced rise in BMP lipids, and improved cold tolerance. Mutation of the catalytic site of PLA2G15 ablated the BMP lipid breakdown. Together, our studies uncover TFEB regulation of BMP lipids through PLA2G15 catabolism.
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Affiliation(s)
- Jessica W Davidson
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Raghav Jain
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Thomas Kizzar
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gisela Geoghegan
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Daniel J Nesbitt
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Amy Cavanagh
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Akira Abe
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, 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
| | - Andrea Hunger
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Xiaojuan Chao
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Isabella James
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Helaina Walesewicz
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Dominique A Baldwin
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Gina Wade
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sylwia Michorowska
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Drug Chemistry, Pharmaceutical and Biomedical Analysis, Faculty of Pharmacy, Medical University of Warsaw, Warsaw, Poland
| | - Rakesh Verma
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kathryn Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wen-Xing Ding
- Department of Pharmacology, Toxicology and Therapeutics, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Morgridge Institute for Research, Madison, WI 53715, USA
| | - James A Shayman
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, 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
| | - Judith A Simcox
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA; Howard Hughes Medical Institute, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Nyame K, Xiong J, Alsohybe HN, de Jong APH, Peña IV, de Miguel R, Brummelkamp TR, Hartmann G, Nijman SMB, Raaben M, Simcox JA, Blomen VA, Abu-Remaileh M. PLA2G15 is a BMP hydrolase and its targeting ameliorates lysosomal disease. Nature 2025:10.1038/s41586-025-08942-y. [PMID: 40335701 DOI: 10.1038/s41586-025-08942-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 03/25/2025] [Indexed: 05/09/2025]
Abstract
Lysosomes catabolize lipids and other biological molecules, maintaining cellular and organismal homeostasis. Bis(monoacylglycero)phosphate (BMP), a major lipid constituent of intralysosomal vesicles, stimulates lipid-degrading enzymes and is altered in various human conditions, including neurodegenerative diseases1,2. Although lysosomal BMP synthase was recently discovered3, the enzymes mediating BMP turnover remain elusive. Here we show that lysosomal phospholipase PLA2G15 is a physiological BMP hydrolase. We further demonstrate that the resistance of BMP to lysosomal hydrolysis arises from its unique sn2, sn2' esterification position and stereochemistry, as neither feature alone confers resistance. Purified PLA2G15 catabolizes most BMP species derived from cell and tissue lysosomes. Furthermore, PLA2G15 efficiently hydrolyses synthesized BMP stereoisomers with primary esters, challenging the long-held thought that BMP stereochemistry alone ensures resistance to acid phospholipases. Conversely, BMP with secondary esters and S,S stereoconfiguration is stable in vitro and requires acyl migration for hydrolysis in lysosomes. Consistent with our biochemical data, PLA2G15-deficient cells and tissues accumulate several BMP species, a phenotype reversible by supplementing wild-type PLA2G15 but not its inactive mutant. Targeting PLA2G15 reduces the cholesterol accumulation in fibroblasts of patients with Niemann-Pick disease type C1 and significantly ameliorates disease pathologies in Niemann-Pick disease type C1-deficient mice, leading to an extended lifespan. Our findings established the rules governing BMP stability in lysosomes and identified PLA2G15 as a lysosomal BMP hydrolase and a potential target for therapeutic intervention in neurodegenerative diseases.
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Affiliation(s)
- Kwamina Nyame
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
- Department of Biochemistry, Stanford University, Stanford, CA, USA
| | - Jian Xiong
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
| | - Hisham N Alsohybe
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
| | | | - Isabelle V Peña
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
- Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA
| | | | - Thijn R Brummelkamp
- Scenic Biotech, Science Park 301, Amsterdam, The Netherlands
- Oncode Institute, Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Guido Hartmann
- Scenic Biotech, Science Park 301, Amsterdam, The Netherlands
| | | | - Matthijs Raaben
- Scenic Biotech, Science Park 301, Amsterdam, The Netherlands
| | - Judith A Simcox
- Howard Hughes Medical Institute, Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Monther Abu-Remaileh
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA.
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Institute for Chemistry, Engineering and Medicine for Human Health (Sarafan ChEM-H), Stanford University, Stanford, CA, USA.
- The Phil & Penny Knight Initiative for Brain Resilience at the Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
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Davidson JW, Jain R, Kizzar T, Geoghegan G, Nesbitt DJ, Cavanagh A, Abe A, Nyame K, Hunger A, Chao X, James I, Von Bank H, Baldwin DA, Wade G, Michorowska S, Verma R, Scheuler K, Hinkovska-Galcheva V, Shishkova E, Ding WX, Coon JJ, Shayman JA, Abu-Remaileh M, Simcox JA. Modulation of hepatic transcription factor EB activity during cold exposure uncovers direct regulation of bis(monoacylglycero)phosphate lipids by Pla2g15. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2023.11.03.565498. [PMID: 37986778 PMCID: PMC10659384 DOI: 10.1101/2023.11.03.565498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Cold exposure is a selective environmental stress that elicits a rapid metabolic shift to maintain energy homeostasis. In response to cold exposure, the liver rewires the metabolic state shifting from glucose to lipid catabolism. By probing the liver lipids in cold exposure, we observed that the lysosomal bis(monoacylglycero)phosphate (BMP) lipids were rapidly increased during cold exposure. BMP lipid changes occurred independently of lysosomal abundance but were dependent on the lysosomal transcriptional regulator transcription factor EB (TFEB). Knockdown of TFEB in hepatocytes decreased BMP lipid levels and led to cold intolerance in mice. We assessed TFEB binding sites of lysosomal genes and determined that the phospholipase Pla2g15 regulates BMP lipid catabolism. Knockdown of Pla2g15 in mice increased BMP lipid levels, ablated the cold-induced rise, and improved cold tolerance. Knockout of Pla2g15 in mice and hepatocytes led to increased BMP lipid levels, that were decreased with re-expression of Pla2g15. Mutation of the catalytic site of Pla2g15 ablated the BMP lipid breakdown. Together, our studies uncover TFEB regulation of BMP lipids through Pla2g15 catabolism.
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Nyame K, Xiong J, Alsohybe HN, de Jong AP, Peña IV, de Miguel R, Brummelkamp TR, Hartmann G, Nijman SMB, Raaben M, Simcox JA, Blomen VA, Abu-Remaileh M. PLA2G15 is a Lysosomal BMP Hydrolase and its Targeting Ameliorates Lysosomal Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.06.07.597919. [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 and a stimulator of lipid-degrading enzymes. BMP levels are altered in a broad spectrum of human conditions, including neurodegenerative diseases. While a lysosomal BMP synthase was recently discovered, the enzymes that mediate BMP turnover has remained elusive. Here we show that the lysosomal phospholipase PLA2G15 is a physiological BMP hydrolase. We further demonstrate that BMP's resistance to hydrolysis in the lysosome is conferred by the combination of its unique sn2, sn2' esterification position and stereochemistry, as neither feature alone is sufficient to provide this resistance. 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 challenging the long-held thought that BMP's unique stereochemistry is sufficient to confer resistance to acid phospholipases. Conversely, BMP with secondary esters and S,S stereoconfiguration is intrinsically stable in vitro and requires acyl migration for hydrolysis in lysosomes. Consistent with our biochemical data, PLA2G15-deficient cells and tissues accumulate multiple BMP species, a phenotype reversible by supplementing wildtype PLA2G15 but not its catalytically dead mutant. In addition, targeting PLA2G15 to increase BMP reverses the cholesterol phenotype in Niemann Pick Disease Type C (NPC1) patient fibroblasts and significantly ameliorates 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 a potential target for therapeutic intervention in neurodegenerative diseases.
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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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Liang S, Wang S, Meng Y, Sun C. Enzymatic preparation of glycerophosphatilcholine catalyzed by combinational phospholipases: a comparative study of concerted versus stepwise catalysis. RSC Adv 2020; 10:38727-38735. [PMID: 35518402 PMCID: PMC9057254 DOI: 10.1039/d0ra07012b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 10/13/2020] [Indexed: 12/16/2022] Open
Abstract
Glycerophosphatilcholine (GPC) is widely applied in medical, pharmaceutical, food and cosmetic industries. Due to the lack of natural resources, enzymatic preparation of GPC has been explored in recent years. This study aimed to investigate and compare the effects of different addition methods of combinational phospholipases (PLA1 and PLA2) and various process parameters (time, temperature, pH, substrate concentrate, enzyme load, and stirring rate) on the preparation of GPC. The results showed that compared with concerted catalysis, the catalytic efficiency of adding PLA2 and then PLA1 (PLA2 → A1) was higher, whereas that of adding PLA1 and then PLA2 was lower. The main reason might be that the method of PLA2 → A1 could reduce acyl migration and the competition between PLA1 and PLA2, which was beneficial to improve the GPC yield and shorten the reaction time. This paper could provide a novel approach for the future preparation of GPC catalyzed by combinational phospholipases. The addition methods of PLA1 and PLA2 had a vital influence on the preparation of GPC, and the method of PLA2 → A1 was the most effective.![]()
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Affiliation(s)
- Shaohua Liang
- College of Food Science and Engineering, Henan University of Technology Lianhua Road 100 Zhengzhou 450001 Henan Province P. R. China +86-371-67758022 +86-371-67758022
| | - Shukun Wang
- College of Food Science and Engineering, Henan University of Technology Lianhua Road 100 Zhengzhou 450001 Henan Province P. R. China +86-371-67758022 +86-371-67758022
| | - Yannan Meng
- College of Food Science and Engineering, Henan University of Technology Lianhua Road 100 Zhengzhou 450001 Henan Province P. R. China +86-371-67758022 +86-371-67758022
| | - Cong Sun
- College of Food Science and Engineering, Henan University of Technology Lianhua Road 100 Zhengzhou 450001 Henan Province P. R. China +86-371-67758022 +86-371-67758022
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